title: PPAR in Rat  Liver_d03_ Wy-14;643_100.0mkd_#1203

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ Wy-14;643_100.0mkd_#1203


title: Replicate2_Voxel B6

status: Public on Jul 12 2007

type: RNA

city: Los Angeles

first: Mark

middle: H.

last: Chin

state: CA

address: 650 Charles E. Young Dr

department: Human Genetics

country: USA

institute: UCLA

description: Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3.

hyb_protocol: Dried-down targets were then resuspended in 50ul of MWG Hyb Buffer (Ocimum Biosolutions, cat#1180-200000) and 1 ug of Poly A RNA (Sigma, P9403) was added to each target. The targets were heat denatured and then hybridized 16 hours at 42C on a Maui Hyb Station (BioMicro Systems, Inc., 4 chamber model).  Immediately prior to hybridization, the microarrays were first vigorously dunked in a 0.2% SDS solution at room temp followed by  prehybridization in a solution of 5x SSC, 1% SDS, and 1% BSA at 55o C for 60 minutes.  Following prehybridization, the arrays were vigorously washed in 9 exchanges of ddH2O to remove all traces of the prehybridization solution, rinsed in isopropanol, and dried at room temperature.  The target samples were denatured at 95oC for three minutes and placed on the prehybridized arrays, covered with specialized hybridization chambers from BioMicro Inc (Salt Lake City, UT).  Arrays were hybridized using the MAUI hybridization system (BioMicro) for 16 hours at 42o C using the manufacturer's mixing protocol.  After hybridization, the arrays were washed in 2X SSC/0.1% SDS at 55o C with agitation for 5 minutes then washed with two successive 5 minute washes with 1x SSC and 0.1xSSC at RT.  The washed arrays were dried by centrifugation at 50xg for 5 minutes and immediately scanned using a GenePix 4000B microarray scanner [Axon Instruments, Union City, CA].

scan_protocol: Microarrays were scanned using a GenePix 4000B microarray scanner and GenePix Pro version 6 [Axon Instruments, Union City, CA].

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. GeneSpring (Agilent) software was used.

molecule: total RNA

organism: Mus musculus

source_name: Total RNA from pooled mouse brain voxels P56, labeled with Cyanine-5 (red).

label_protocol: Briefly, 5-10 mg of total RNA from each sample were reverse transcribed using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA).  Generated cDNA targets were purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA). The purified cDNA targets were dried to completion and then differentially coupled to ester-linked Cy3 (controls) or Cy5 (LiCl-treated) dye (Amersham, Piscataway, NJ). After quenching of unbound dye with 4M Hydroxylamine, Cy3- and Cy5-labeled cDNA target pairs were combined and cleaned up over QIAquick columns (Qiagen, Valencia, CA).

growth_protocol: Mice were housed in a vivarium with littermates according to DLAM housing protocols.  Rooms were maintained with a 12 hour day/night light schedule and cage bedding was changed weekly.  Mice were anesthetized using isoflourane and the brain was immediately removed.

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

tag: Tissue

value: Brain Voxel

tag: Age

tag: Strain

tag: Gender

value: Male

source_name: Total RNA from whole mouse brain P56, labeled with Cyanine-3 (green).

value: Whole Brain


title: PPAR in Rat  Liver_d03_ Wy-14;643_100.0mkd_#1201

city: Rahway

first: Olivia

last: Fong

state: NJ

department: Molecular Profiling

institute: Merck & Co.

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ Wy-14;643_100.0mkd_#1201

hyb_protocol: All treated individual samples were hybridized against a pool of RNA from time-matched (concurrent) control animals (e.g., animals treated for 3 days were hybridized against a pool of animals dosed for 3 days with vehicle). The ratio of individual animal expression to control pool expression was used for all data analysis. All hybridizations (Hughes et al., 2001, PMID: 11283592) were performed in duplicate, with fluor reversal (Cy3 or Cy5) in the second hybridization.

scan_protocol: Arrays were scanned using a DNA microarray scanner (Model G2565AA; Agilent Technologies), and feature intensities (background subtracted) were determined using feature extraction software developed at Rosetta.

data_processing: Local background correction

organism: Rattus norvegicus

source_name: Liver

label_protocol: Cy3- or Cy5-labeled cRNA was created from total RNA using reverse transcription followed by in vitro transcription and a two-step label incorporation method (Hughes et al., 2001, PMID: 11283592).

extract_protocol: tissues were collected for RNA extraction (snap frozen in liquid nitrogen). RNA was extracted from tissues using a combination of TRIzol RNA extraction (Invitrogen Life Technologies, Carlsbad, CA) with the RNeasy RNA extraction kit (Qiagen, Valencia, CA). Briefly, tissue was incubated in TRIzol reagent (1 ml/100 mg tissue) for 15 s at room temperature and homogenized with a Polytron homogenizer followed by an ~ 5-min room temperature incubation. After the addition of 100 µl chloroform, 500 µl of homogenate was mixed by shaking for 15 s, incubated at room temperature for 2–3 min, and centrifuged at 10,000 x g for 10 min at 2–8°C. The supernatant was used as the input material for the RNeasy RNA extraction kit and RNA isolated according to the manufacturer's protocol. Following isolation, RNA quantity, purity, and quality were determined using a SpectraMax Plus384 (Molecular Devices, Sunnyvale, CA) spectrophotometer and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: Sprague Dawley CD, Approximately 8 wks at the onset of dosing, Vehicle Treated, Liver

label_protocol: same as for channel_1

extract_protocol: same as for channel_1

tag: Sprague Dawley CD, Approximately 8 wks at the onset of dosing, Fenofibrate; Wy-14,643; bezafibrate; rosiglitazone; all trans retinoic acid, Liver


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1032

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1032


title: PPAR in Rat  Liver_d03_Bezafibrate_250.0mkd_#1257

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_Bezafibrate_250.0mkd_#1257


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1028

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1028


title: PPAR in Rat  Liver_d03_ Wy-14;643_100.0mkd_#1202

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ Wy-14;643_100.0mkd_#1202


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1030

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1030


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1027

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1027


title: Replicate2_Voxel B3


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1029

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1029


title: Replicate2_Voxel A6


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1026

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1026


title: Replicate2_Voxel A8


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1025

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1025


title: Replicate2_Voxel A5


title: Replicate2_Voxel A7


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1020

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1020


title: Replicate2_Voxel A3


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1024

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1024


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1022

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1022


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1021

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1021


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1018

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1018


title: Replicate1_Voxel G7

description: Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5.

source_name: Total RNA from whole mouse brain P56, labeled with Cyanine-5 (red).

source_name: Total RNA from pooled mouse brain voxels P56, labeled with Cyanine-3 (green).


title: Replicate1_Voxel G8


title: ORF K080D Hrp1-D H3 cter slideX

type: genomic

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description: Chip on CHIP

hyb_protocol: Robyr et al Methods 31 (2003)

scan_protocol: Chip Reader

data_processing: GeneSpring

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: CHIP Input Hrp1-D H3 cter

label_protocol: Robyr et al Methods 31 (2003)

extract_protocol: Robyr et al Methods 31 (2003)

tag: CHIP Input Hrp1-D H3 cter

source_name: CHIP IP Hrp1-D H3 cter

tag: CHIP IP Hrp1-D H3 cter


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1017

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1017


title: Replicate2_Voxel A4

description: Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3.


title: Replicate1_Voxel G5


title: Replicate2_Voxel A10


title: ORF K080D Hrp1-D H3 cter slide20

description: Chip on CHIP


title: IGR K080D Hrp1-D H3 cter slideX

description: Chip on CHIP

scan_protocol: Chip reader


title: Replicate1_Voxel G9


title: PPAR in Rat  Liver_d03_ vehicle control_000.0mkd_#1019

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_ vehicle control_000.0mkd_#1019


title: Replicate1_Voxel G6


title: Replicate1_Voxel G4


title: PPAR in Rat  Liver_d02_Rosiglitazone_100.0mkd_#1367

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_Rosiglitazone_100.0mkd_#1367


title: IGR K080D Hrp1-D H3 cter slide20

description: Chip on CHIP


title: Replicate1_Voxel G3


title: Replicate1_Voxel G2


title: Replicate1_Voxel F9


title: PPAR in Rat  Liver_d02_Rosiglitazone_100.0mkd_#1366

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_Rosiglitazone_100.0mkd_#1366


title: PPAR in Rat  Liver_d02_Rosiglitazone_100.0mkd_#1365

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_Rosiglitazone_100.0mkd_#1365


title: Replicate1_Voxel F6


title: Replicate1_Voxel F4


title: Replicate1_Voxel F3


title: Replicate1_Voxel F7


title: Replicate1_Voxel F5


title: PPAR in Rat  Liver_d02_Retinoic acid_025.0mkd_#1309

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_Retinoic acid_025.0mkd_#1309


title: PPAR in Rat  Liver_d02_Retinoic acid_025.0mkd_#1311

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_Retinoic acid_025.0mkd_#1311


title: V608

city: Brussels

first: Vincent

last: Detours

address: 808 Route de Lennik

department: School of Medicine

country: Belgium

institute: Free University of Brussels

description: Papillary thyroid carcinoma

data_processing: Intensity- and space-based 2D LOESS, average of dye swap replicates, see companion paper.

organism: Homo sapiens

source_name: Tumor

tag: Origin

value: CTB; Sex:F; Age in 1986:15; Age at operation 32; BRAF-; RETPTC+

source_name: Patient-matched nontumor control


title: S425

description: Papillary thyroid carcinoma

value: CTB; Sex:M; Age in 1986:3; Age at operation 19; BRAF-; RETPTC+


title: Replicate1_Voxel F8


title: S423

description: Papillary thyroid carcinoma

value: CTB; Sex:F; Age in 1986:5; Age at operation 22; BRAF+; RETPTC-


title: PPAR in Rat  Liver_d02_Fenofibrate_400.0mkd_#1143

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_Fenofibrate_400.0mkd_#1143


title: Replicate1_Voxel E8


title: V519

description: Papillary thyroid carcinoma

value: CTB; Sex:F; Age in 1986:2; Age at operation 18; BRAF-; RETPTC+


title: Replicate1_Voxel E9


title: Replicate1_Voxel E7


title: S422

description: Papillary thyroid carcinoma

value: CTB; Sex:M; Age in 1986:15; Age at operation 31; BRAF+; RETPTC-


title: Replicate1_Voxel E6


title: PPAR in Rat  Liver_d02_Fenofibrate_400.0mkd_#1141

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_Fenofibrate_400.0mkd_#1141


title: Replicate1_Voxel F10


title: S420

description: Papillary thyroid carcinoma

value: CTB; Sex:F; Age in 1986:12; Age at operation 28; BRAF-; RETPTC-


title: Replicate1_Voxel F2


title: PPAR in Rat  Liver_d02_Fenofibrate_400.0mkd_#1142

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_Fenofibrate_400.0mkd_#1142


title: Replicate1_Voxel E4


title: S415

description: Papillary thyroid carcinoma

value: CTB; Sex:M; Age in 1986:12; Age at operation 28; BRAF+; RETPTC-


title: Replicate1_Voxel E5


title: Replicate1_Voxel E2


title: Replicate1_Voxel D9


title: Replicate1_Voxel E1


title: Replicate1_Voxel E11


title: PPAR in Rat  Liver_d02_Bezafibrate_250.0mkd_#1253

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_Bezafibrate_250.0mkd_#1253


title: Replicate1_Voxel D8


title: PPAR in Rat  Liver_d02_Bezafibrate_250.0mkd_#1255

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_Bezafibrate_250.0mkd_#1255


title: Replicate1_Voxel D6


title: PPAR in Rat  Liver_d02_ Wy-14;643_100.0mkd_#1198

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ Wy-14;643_100.0mkd_#1198


title: PPAR in Rat  Liver_d02_ Wy-14;643_100.0mkd_#1200

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ Wy-14;643_100.0mkd_#1200


title: Replicate1_Voxel E10


title: S414

description: Papillary thyroid carcinoma

value: CTB; Sex:F; Age in 1986:16; Age at operation 33; BRAF-; RETPTC+


title: PPAR in Rat  Liver_d02_Bezafibrate_250.0mkd_#1256

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_Bezafibrate_250.0mkd_#1256


title: S409

description: Papillary thyroid carcinoma

value: CTB; Sex:F; Age in 1986:11; Age at operation 28; BRAF+; RETPTC-


title: Replicate1_Voxel D4

description: Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5.


title: Replicate1_Voxel D5


title: Replicate1_Voxel D7


title: Replicate1_Voxel D3


title: S418

description: Papillary thyroid carcinoma

value: CTB; Sex:M; Age in 1986:10; Age at operation 27; BRAF+; RETPTC-


title: Replicate1_Voxel D2


title: S405

description: Papillary thyroid carcinoma

value: CTB; Sex:F; Age in 1986:1; Age at operation 16; BRAF-; RETPTC+


title: S404

description: Papillary thyroid carcinoma

value: CTB; Sex:F; Age in 1986:1; Age at operation 16; BRAF-; RETPTC-


title: Replicate1_Voxel D10


title: PTC8

description: Papillary thyroid carcinoma

value: France; Sex:M; Age in 1986:22; Age at operation 36; BRAF-; RETPTC+


title: PTC9

description: Papillary thyroid carcinoma

value: France; Sex:F; Age in 1986:24; Age at operation 38; BRAF+; RETPTC-


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1015

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1015


title: Replicate1_Voxel D1

value: Brain Voxel


title: PPAR in Rat  Liver_d02_ Wy-14;643_100.0mkd_#1197

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ Wy-14;643_100.0mkd_#1197


title: Replicate1_Voxel D11

value: Male


title: PTC7

description: Papillary thyroid carcinoma

value: France; Sex:F; Age in 1986:13; Age at operation 29; BRAF+; RETPTC-


title: Replicate1_Voxel C9

value: Whole Brain


title: Replicate1_Voxel C6


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1011

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1011


title: Replicate1_Voxel C8


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1012

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1012


title: PTC6

description: Papillary thyroid carcinoma

value: France; Sex:M; Age in 1986:24; Age at operation 37; BRAF-; RETPTC-


title: PTC26

description: Papillary thyroid carcinoma

value: France; Sex:F; Age in 1986:36; Age at operation 47; BRAF+; RETPTC-


title: Replicate1_Voxel C5


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1013

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1013


title: Replicate1_Voxel C2


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1008

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1008


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1010

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1010


title: Replicate1_Voxel C3


title: Replicate1_Voxel C4


title: Replicate1_Voxel C11


title: PTC20

description: Papillary thyroid carcinoma

value: France; Sex:F; Age in 1986:54; Age at operation 68; BRAF+; RETPTC-


title: Replicate1_Voxel C10


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1009

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1009


title: Replicate1_Voxel B8


title: PTC22

description: Papillary thyroid carcinoma

value: France; Sex:F; Age in 1986:44; Age at operation 60; BRAF-; RETPTC-


title: PTC25

description: Papillary thyroid carcinoma

value: France; Sex:F; Age in 1986:49; Age at operation 60; BRAF-; RETPTC-


title: PTC23

description: Papillary thyroid carcinoma

value: France; Sex:M; Age in 1986:17; Age at operation 33; BRAF-; RETPTC-


title: Replicate1_Voxel B6


title: Replicate1_Voxel C1


title: Replicate1_Voxel B11


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1006

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1006


title: PTC21

description: Papillary thyroid carcinoma

value: France; Sex:F; Age in 1986:39; Age at operation 54; BRAF-; RETPTC+


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1007

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1007


title: Replicate1_Voxel B7


title: Replicate1_Voxel A9


title: PTC19

description: Papillary thyroid carcinona

value: France; Sex:M; Age in 1986:54; Age at operation 68; BRAF-; RETPTC+


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1003

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1003


title: Replicate1_Voxel B10


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1005

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1005


title: Replicate2_Voxel A9

description: Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3.


title: PTC14

description: Papillary thyroid carcinoma

value: France; Sex:N; Age in 1986:17; Age at operation 32; BRAF-; RETPTC-

value: France; Sex:M; Age in 1986:17; Age at operation 32


title: Replicate1_Voxel A5


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1004

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1004


title: Replicate1_Voxel A6


title: Replicate1_Voxel A4


title: PTC18

description: Papillary thyroid carcinoma

value: France; Sex:F; Age in 1986:NA; Age at operation 59; BRAF+; RETPTC-


title: Replicate1_Voxel A7


title: Replicate1_Voxel A3


title: ORF A260E Hrp1-D H3 cter slide1

description: Chip on CHIP


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1001

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1001


title: PPAR in Rat  Liver_d02_ vehicle control_000.0mkd_#1002

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_ vehicle control_000.0mkd_#1002


title: ZAS3-null vs wild-type mouse thymus #4

status: Public on Jul 11 2007

city: Houston

first: Carl

last: Allen

state: TX

address: 6621 Fannin St

department: Pediatrics

institute: Texas Children's Cancer Center/Baylor College of Medicine

description: No additional data.

hyb_protocol: After purification, cDNA samples from ZAS3-null or control mouse thymus were labeled with Cy3 or Cy5, respectively, and hybridized to the Agilent Whole Mouse Genome Oligo Microarray (G4121A) for 14 hours at 48oC.

scan_protocol: Slide images was acquired using an Affymetrix 428 scanner with gain settings set so that 95% of spots were below saturation to hyield the maximum dynamic range within an experiment.

data_processing: Images were converted into ".gpr" files using GenePix software (Axon, Union City, CA).  Data were analyzed using GeneTraffic 2.6 software (Ibion, La Jolla, CA).  Lowess-global normalization was applied to all experiments.  Flagging parameters were set as spot intensity lower than intensity of local spot background, spot intensity lower than average background, and raw spot intensity less than 100.  Flagged spots were not included in normalization or aggregate calculations.

source_name: ZAS3-null mouse whole thymus #4

label_protocol: Five independent microarray hybridizations were performed with total RNA isolated from whole thymus from sex- and age-matched ZAS3-null and wild-type littermates at 6-8 weeks of age.  Probe labeling and hybridization were performed by the Microarray Core Facility (Columbus Children's Research Institute).  Briefly, cDNA probes were synthesized with Superscript III, oligo-dT primers and dNTPs supplemented with amino-allyl-UTP to improve hybridization characteristics and stability.

extract_protocol: Whole thymus was dissected and immediately placed in Trizol and total RNA was isolated according to manufactuere's protocol (Invitrogen, Carlsbad, CA).  Total RNA was purified with the RNEAsy Kit (Qiagen Inc, Valencia, CA).

tag: Whole thymus isolated from 6 week old female with homozygous deletion of ZAS3/schnurri3.  Mice were back-crossed to C57BL/6 background to minimize differences influenced by genetic background.  Mice used in this experiment were sex- and age-matched littermates.

source_name: Wild-type mouse whole thymus #4

tag: Whole thymus isolated from 6 week old control female mouse.  Mice were back-crossed to C57BL/6 background to minimize differences influenced by genetic background.  Mice used in this experiment were sex- and age-matched littermates.


title: PTC11

description: Papillary thyroid carcinoma

data_processing: Intensity- and 2D space-based LOESS, average of dye swap replicates, see companion paper.

value: France; Sex:F; Age in 1986:22; Age at operation 37; BRAF-; RETPTC-

value: CTB; Sex:F; Age in 1986:22; Age at operation 37;


title: ZAS3-null vs wild-type mouse thymus #1

description: No additional data.

source_name: ZAS3-null mouse whole thymus #1

tag: Whole thymus isolated from 7 week old male with homozygous deletion of ZAS3/schnurri3.  Mice were back-crossed to C57BL/6 background to minimize differences influenced by genetic background.  Mice used in this experiment were sex- and age-matched littermates

source_name: Wild-type mouse whole thymus #1

tag: Whole thymus isolated from 7 week old wild-type male.  Mice were back-crossed to C57BL/6 background to minimize differences influenced by genetic background.  Mouse pairs were sex- and age-matched littermates.


title: ZAS3-null vs wild-type mouse thymus #5

description: No additional data.

source_name: ZAS3-null whole thymus #5

tag: Whole thymus isolated from 6 week old male with homozygous deletion of ZAS3/schnurri3.  Mice were back-crossed to C57BL/6 background to minimize differences influenced by genetic background.  Mice used in this experiment were sex- and age-matched littermates.

source_name: Wild-type mouse whole thymus #5

tag: Whole thymus isolated from 6 week old wild-type male.  Mice were back-crossed to C57BL/6 background to minimize differences influenced by genetic background.  Mice used in this experiment were sex- and age-matched littermates.


title: ZAS3-null vs wild-type mouse thymus #3

description: No additional data.

source_name: ZAS3-null whole thymus #3

tag: Whole thymus isolated from 8 week old male with homozygous deletion of ZAS3/schnurri3.  Mice were back-crossed to C57BL/6 background to minimize differences influenced by genetic background.  Mice used in this experiment were sex- and age-matched littermates.

source_name: Wild-type mouse whole thymus #3

tag: Whole thymus isolated from 8 week old wild-type male.  Mice were back-crossed to C57BL/6 background to minimize differences influenced by genetic background.  Mice used in this experiment were sex- and age-matched littermates.


title: H295R forskolin 3H_B

status: Public on Jul 09 2007

city: Jackson

first: Damian

middle: G.

last: Romero

state: MS

address: 2500 N. State St.

department: Biochemistry

institute: University of Mississippi Medical Center

description: H295R CELLS FORSKOLIN (10 UM) 3 H

data_processing: GCOS 1.2

label: BIOTIN

source_name: H295R CELLS - FORSKOLIN - 3H

tag: H295R HUMAN ADRENOCORTICAL CELLS


title: H295R control 3H_1_B

description: H295R CELLS CONTROL 3 H

source_name: H295R CELLS - CONTROL - 3H

tag: H295R HUMAN ADRENOCORTICAL CELL LINE


title: H295R control 3H_2_B

description: H295R CELLS CONTROL 3 H

source_name: H295R CELL - CONTROL - 3H


title: Hepatopancreas of intermolt males_ref1 vs. intermolted males_ref3

status: Public on Jul 10 2007

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

country: Israel

institute: Israel Oceanographic and Limnological Research

description: Evaluated Gene expression ratio between hepatopncreas tissues of two pooled intermolt male populations was part of a broader experiment which includes males in five experimental conditions. Individual variability was integrated into the hybridization design, by using RNA populations of 3 individual crayfish males for each of four experimental conditions: injected-premolted, injected-postmolted, extirpated-premolted and extirpated-postmolted males. Three pools of reference intermolt individuals were used: Ref pool 1 contained RNA from 6 individuals whereas each of Ref pools 2 and 3 contained 3 individuals. The hybridization experiments of the treated males are described in samples: GSM160067-70; GSM160083-86 of this series (GSE6947). In addition, for examining the variability among the reference intermolt male populations, a second hybridization was performed among the three reference pools, comparing ref_1 to ref_2 (this sample, and to ref_3. The hybridization was loop-designed, namely, each labeled cDNA population was hybridized to the other two population, totaling three dual labeled slides.

hyb_protocol: Microarray slides were incubated with pre-hybridization solution (1% BSA; 5x SSC; 0.1% SDS, 25% formamide) for 2h at 42oC to block non-specific DNA interactions, reducing background fluorescence, followed by two short rinses in water, one in ethanol and drying by mild centrifugation of vertical slides. Dual-labeled solutions, aimed at binary comparisons between two experimental conditions, were prepared by mixing the two compared labeled cDNA populations, followed by 1:1 dilution with hybridization solution containing 200 µg/ml salmon sperm DNA, 10x SSC, 0.2% SDS, 50% formamide. The heat denatured hybridization mixture (3' at 95oC) was layered onto the microarray, covered (Lifterslip, Erie Scientific; #25x60-2-4789) and incubated over night at 42°C in humidified hybridization chamber (Corning). Following incubation, slides were washed as follows: 5’ at 42°C in x2 SSC - 0.1% SDS, mild shaking for 10’ at room temperature in x0.1 SSC - 0.1% SDS; mild shaking 4x for 5’ at room temperature in x0.1 SSC, ending by two quick dips, one in water and one in ethanol. The slides were dried by centrifugation.

scan_protocol: The slides were scanned by Axon 4000B laser scanner in two wavelengths, corresponding to the Cy3 and Cy5 emissions. The TIF imaged dual fluorescence was quantified by the GENEPIX software (Axon), which provided also weight index of the quality for each hybridized spot.

data_processing: Data analysis was conducted under the R/BioConductor environment (Gentleman et al., 2005). Calculation and statistical analysis of log2 expression ratios (VALUE column of the sample data table) of each unique spot across a binary comparison was carried out using the LIMMA package (Linear Models for Microarray data Analysis; Smyth, 2004). GENEPIX quantified image files were imported into LIMMA, spots with quality flags < -49 were marked as unreliable, and the Cy5 and Cy3 intensities within each slide were normalized using the print-tip Loess method. No background correction was applied. LIMMA calculated for each spot on an individual slide an M-value [M=log2(Cy5)/Cy3); Cy5 / Cy3 are the normalized emission intensities of the spot] and an emission intensity A-value [A=(log2(Cy5)*Cy3))/2]. Subsequently, LIMMA fitted a linear model to the expression data followed by Empirical Bayes smoothing. Inter-duplicate correlation method was used at the linear modeling step. A meanA value, which is the average spot emission intensity across the analyzed experiment, was calculated for each unique spot and only spots with meanA > 8.5 were included in the analysis, avoiding faint emissions. The LIMMA summary statistics of each unique spot included an estimated average M-value across each binary comparison associated to two statistical parameters: B statistic, the log-odds that the spot is differentially expressed and p-value, derived from a moderated t-statistic after multiple testing correction according to Benjamini and Hochberg (1995). All these parameters are found in the sample data table.

label: Cy3 and Cy5 alternatively in different slides (see Description below)

molecule: polyA RNA

organism: Cherax quadricarinatus

source_name: Hepatopancreas from intermolt males_ref1

label_protocol: Messenger RNA was labeled by the fluorescent dyes Cy3 and Cy5, using the amino allyl indirect cDNA labeling method, as follows: 200-400 ng mRNA of the transcript population was incubated for 10’ at 70oC with 100 µg dT primer (T15VN) and was immediately chilled on ice. The resulting RNA-dT primer hybrid was reverse transcribed in a total volume of 30 µl for 1h at 42oC, in a solution containing: reverse transcriptase (ImProm II, Promega #A3802; 1.5 µl/reaction), 32 units of RNase inhibitor, 3.5 mM of MgCl2 solution and 0.5 mM dNTP mix in which the dTTP was replaced by Amino Allyl-dUTP / dTTP mixture (4:1). The reverse transcription was followed by mRNA hydrolysis for 15’ at 65oC in alkaline pH (0.2 M NaOH (fresh), and 0.1 M of EDTA). The alkaline solution was neutralized by 0.35 M HEPES (pH 7.0) followed by buffer replacement and cDNA concentration, accomplished by wash x3 of the solution by 450 µl of water through Microcon YM-30 filter (Amicon, #42410) ending with a volume of 50-100 µl. The cDNAs were coupled to an aliquot of the fluorescent dyes Cy3 or Cy5 mono-reactive succinimidyl ester-derivetized NHS-ester through the reactive Amino Allyl groups. Raw dye solution was prepared from a tube of dry dye (Amersham PA23001 / PA25001 for Cy3 and Cy5, respectively) dissolved in 72 µl DMSO, divided into 8 single labeling aliquots. The reaction was carried out for 1h at room temperature in 9 µl of 0.1M fresh Na-Bicarbonate Buffer pH 9.0. Hydroxylamine was added to the solution at a final concentration of 1.33M and was incubated for 15’ at room temperature. Finally the solution was neutralized by sodium acetate, pH=5.2 to a final concentration of 72 mM and purified by affinity column-based kit (Qiaquick, Qiagen). Labeling level was evaluated by spectrophotometry at both 260 nm for cDNA estimation and 550 nm (Cy3) and 650 nm (Cy5) for labeling intensity measurement.

growth_protocol: C. quadricarinatus males were maintained in captivity, before and during the experiment at 28oC, with a photoperiod of 14L:10D

extract_protocol: EZ-RNA II Kit (Biological Industries, Israel) was used for total RNA extraction. PolyTtract kit (Promega) was used for mRNA extraction from total RNA solutions

treatment_protocol: Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph. 6 intermolt males were sacrificed and their hepatopancreas was dissected and immediately frozen in liquid nitrogen. Total RNA and mRNA were purified later starting from the frozen tissue and pooled into one mRNA population named ref_1.

tag: Hepatopancreas of intact intermolt C. quadricarinatus males were dissected and snap frozen in liquid nitrogen.

source_name: Hepatopancreas from intermolt males_ref3

treatment_protocol: Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph. 3 intermolt males were sacrificed and their hepatopancreas was dissected and immediately frozen in liquid nitrogen. Total RNA and mRNA were purified later starting from the frozen tissue and pooled into one mRNA population named ref_2.


title: Hepatopancreas of intermolt males_ref1 vs. intermolted males_ref2

source_name: Hepatopancreas from intermolt males_ref2


title: ZAS3-null vs wild-type mouse thymus #2

description: No additional data.

source_name: ZAS3-null mouse whole thymus #2

tag: Whole thymus isolated from 7 week old female with homozygous deletion of ZAS3/schnurri3.  Mice were back-crossed to C57BL/6 background to minimize differences influenced by genetic background.  Mice used in this experiment were sex- and age-matched littermates.

source_name: Wild-type mouse whole thymus #2

tag: Whole thymus isolated from 7 week old wild-type female.  Mice were back-crossed to C57BL/6 background to minimize differences influenced by genetic background.  Mouse pairs were sex- and age-matched littermates.


title: DR7d(3)

city: Amsterdam

first: Floor

middle: J

last: Stam

address: de Boelelaan 1087

department: Institute for Neurosciences

country: Netherlands

institute: Vrije Universiteit

description: gene expression data of regenerating Dorsal Root Ganglia

hyb_protocol: according to manufacturers instructions

scan_protocol: Agilent scanner

data_processing: The data were analyzed with the limma package for R/bioconductor. Dual color microarray median spot intensities were background subtracted, Ratios were loess normalized within slide, normalized between slides using the A quantile method. The thus obtained M and A values were used to calculate the normalized red and green signal intensities shown in the VALUE column.

source_name: L4, L5 and L6 DRG, pool of 3 animals

label_protocol: Agilent labelling kit, according to manufacturers' protocol

extract_protocol: GTC method

tag: Dorsal Root Ganglion 7d after dorsal root crush, replicate 3


title: DR14d(1)

tag: Dorsal Root Ganglion 14d after dorsal root crush, replicate 1


title: DR14d(2)

tag: Dorsal Root Ganglion 14d after dorsal root crush, replicate 2


title: DR7d(2)

tag: Dorsal Root Ganglion 7d after dorsal root crush, replicate 2


title: OA 1

city: London

first: Tom

last: Appleton

state: ON

address: Rm 0061 DSB The University of Western Ontario

department: Physiology & Pharmacology

country: Canada

institute: The University of Western Ontario

description: Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit.

hyb_protocol: See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Fluidics Station 450.

scan_protocol: See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Scanner 3000 with Workstation.

data_processing: Raw data gene expression files from Affymetrix GeneChips were imported into GeneSpring, version 7.2, software (Silicon Genetics, Redwood City, CA). GC-robust multichip analysis preprocessing was performed. Raw data transformation set values <0.01 at 0.01, per-chip normalization was set at the 50th percentile, and per-gene normalization was set to the median and to values in control/sham samples. Data sets from sham-operated samples were assigned to the normal treatment group, and thus defined baseline expression for each probe. The remaining data sets (samples from contralateral and ipsilateral joints) were assigned to diseased treatment groups, averaged, and used in subsequent analysis. All data were interpreted using the log-ratio setting. From the starting list of 31,099 probes, 17,597 probes were determined to have a reliable signal, using the GeneSpring 7.2 SG1a-1 signal intensity quality control script. The script was adjusted to require signal intensity above a threshold of 50 in 2 of the 3 conditions. The data were then passed through a parametric Welch one-way analysis of variance (ANOVA) script, with P values less than 0.05 considered significant, which reduced the list to 3,877 probes. Post hoc Bonferroni multiple comparison testing was performed to identify statistically significant changes in expression between sham-operated samples and contralateral samples, and between sham-operated samples and ipsilateral samples, with P values less than 0.05 considered significant.

label: Affymetrix Hyb/Wash/Stain Kit

source_name: Knee articular cartilage, 4 weeks following OA surgery

extract_protocol: Tissue dissection and immediate immersion/homogenization in TRIzol.  Aqueous phase transferred to QIAgen RNeasy Mini column for RNA prep.

treatment_protocol: OA Surgery: ACL transection and partial medial meniscectomy; Exercise protocol: 30 minutes walking on rotating cylinder 3x per week

tag: Strain

value: Sprague-Dawley, Gender:male, Weight:350 g


title: DR7d(1)

tag: Dorsal Root Ganglion 7d after dorsal root crush, replicate 1


title: DR72h(3)

tag: Dorsal Root Ganglion 72h after dorsal root crush, replicate 3


title: DR72h(2)

tag: Dorsal Root Ganglion 72h after dorsal root crush, replicate 2


title: H295R AII 3H_B

description: H295R CELLS Angiotensin II (100 nM) 3 H

source_name: H295R CELLS - AII - 3H


title: Contralateral 1

source_name: Contralateral knee articular cartilage, 4 weeks following OA surgery

label_protocol: See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Fluidics Station 450.

extract_protocol: Tissue dissection and immediate immersion/homogenization in TRIzol. Aqueous phase transferred to QIAgen RNeasy Mini column for RNA prep.


title: H295R potassium B

description: H295R CELLS POTASSIUM (16 mM) 3 H

source_name: H295R CELLS - POTASSIUM - 3H


title: DR72h(1)

tag: Dorsal Root Ganglion 72h after dorsal root crush, replicate 1


title: DR14d(3)

tag: Dorsal Root Ganglion 14d after dorsal root crush, replicate 3


title: DR48h(4)

tag: Dorsal Root Ganglion 48h after dorsal root crush, replicate 4


title: DR48h(3)

tag: Dorsal Root Ganglion 48h after dorsal root crush, replicate 3


title: DR24h(2)

tag: Dorsal Root Ganglion 24h after dorsal root crush, replicate 2


title: DR48h(1)

tag: Dorsal Root Ganglion 48h after dorsal root crush, replicate 1


title: PPAR in Rat  Liver_d03_Bezafibrate_250.0mkd_#1260

description: Liver_d03_ vehicle control pool_000.0mkd_n=15 vs. Liver_d03_Bezafibrate_250.0mkd_#1260

source_name: Liver

tag: Sprague Dawley CD, Approximately 8 wks at the onset of dosing, Vehicle Treated, Liver

tag: Sprague Dawley CD, Approximately 8 wks at the onset of dosing, Fenofibrate; Wy-14,643; bezafibrate; rosiglitazone; all trans retinoic acid, Liver


title: DR24h(3)

tag: Dorsal Root Ganglion 24h after dorsal root crush, replicate 3


title: DR48h(2)

tag: Dorsal Root Ganglion 48h after dorsal root crush, replicate 2


title: DR12h(4)

tag: Dorsal Root Ganglion 12h after dorsal root crush, replicate 4


title: DR12h(3)

tag: Dorsal Root Ganglion 12h after dorsal root crush, replicate 3


title: DR12h(1)

tag: Dorsal Root Ganglion 12h after dorsal root crush, replicate 1


title: DR12h(5)

tag: Dorsal Root Ganglion 12h after dorsal root crush, replicate 5


title: DR6h(3)

tag: Dorsal Root Ganglion 6h after dorsal root crush, replicate 3


title: DR24h(1)

tag: Dorsal Root Ganglion 24h after dorsal root crush, replicate 1


title: DR6h(4)

tag: Dorsal Root Ganglion 6h after dorsal root crush, replicate 4


title: 100ng pAc-Clk

city: Jerusalem

first: Sebastian

last: Kadener

address: Alexander Silberman Inst. of Life Sciences, Edmund Safra Givat Ram Campus

department: Biological Chemistry

institute: Hebrew University

description: 100ng pAc-Clk

hyb_protocol: AFFYMETRIX

scan_protocol: AFFYMETRIX

data_processing: gcrma

organism: Drosophila melanogaster

source_name: S2 cells

label_protocol: AFFYMETRIX

extract_protocol: TRIZOL

tag: S2 cells transfected with 100ng pAc-Clk


title: PPAR in Rat  Liver_d02_Retinoic acid_025.0mkd_#1312

description: Liver_d02_ vehicle control pool_000.0mkd_n=14 vs. Liver_d02_Retinoic acid_025.0mkd_#1312


title: Control Transfection (1)

description: AFFYMETRIX

tag: S2 cells control transfection


title: Control ZT23

description: Control ZT23

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

label: Biotin

source_name: Fly Head

label_protocol: Affymetrix

extract_protocol: Trizol

tag: Fly Head yw strain


title: Control ZT19

description: Control ZT19


title: 30ng pAc-Clk

description: 30ng pAc-Clk

tag: S2 cells transfected with 30ng pAc-Clk


title: 10ng pAc-Clk (1)

description: 10ng pAc-Clk (1)

tag: S2 cells transfected with 10ng pAc-Clk


title: DR12h(2)

tag: Dorsal Root Ganglion 12h after dorsal root crush, replicate 2


title: Control Transfection (2)

description: Control Transfection (2)


title: DR6h(2)

tag: Dorsal Root Ganglion 6h after dorsal root crush, replicate 2


title: 10ng pAc-Clk (2)

description: 10ng pAc-Clk (2)


title: Control ZT15(1)

description: Control ZT15(1)


title: Control ZT15(2)

description: Control ZT15(2)


title: Control ZT15(3)

description: Control ZT15(3)


title: SN14d(3)

tag: Dorsal Root Ganglion 14d after  Sciatic-Nerve crush replicate 3


title: CON(DR)(1)

tag: Dorsal Root Ganglion of uninjured control animal, control (t0) belonging to the Dorsal Root crush time-course, replicate 1


title: Control ZT11

description: Control ZT11


title: SN14d(1)

tag: Dorsal Root Ganglion 14d after  Sciatic-Nerve crush replicate 1


title: Control ZT3(3)

description: Control ZT3(3)


title: CON(DR)(3)

tag: Dorsal Root Ganglion of uninjured control animal, control (t0) belonging to the Dorsal Root crush time-course, replicate 3


title: SN7d(3)

tag: Dorsal Root Ganglion 7d after  Sciatic-Nerve crush replicate 3


title: SN7d(2)

tag: Dorsal Root Ganglion 7d after  Sciatic-Nerve crush replicate 2


title: SN72h(3)

tag: Dorsal Root Ganglion 72h after  Sciatic-Nerve crush replicate 3


title: Control ZT3(1)

description: Control ZT3(1)


title: DR6h(1)

tag: Dorsal Root Ganglion 6h after dorsal root crush, replicate 1


title: CON(DR)(2)

tag: Dorsal Root Ganglion of uninjured control animal, control (t0) belonging to the Dorsal Root crush time-course, replicate 2


title: SN7d(1)

tag: Dorsal Root Ganglion 7d after  Sciatic-Nerve crush replicate 1


title: 5073 ZT23

description: 5073 ZT23

hyb_protocol: affymetrix

scan_protocol: affymetrix

label: biotin

label_protocol: affymetrix

extract_protocol: trizol

tag: Fly Head 5073 strain


title: SN72h(2)

tag: Dorsal Root Ganglion 72h after  Sciatic-Nerve crush replicate 2


title: SN72h(1)

tag: Dorsal Root Ganglion 72h after  Sciatic-Nerve crush replicate 1


title: SN48h(3)

tag: Dorsal Root Ganglion 48h after  Sciatic-Nerve crush replicate 3


title: SN48h(2)

tag: Dorsal Root Ganglion 48h after  Sciatic-Nerve crush replicate 2


title: SN48h(1)

tag: Dorsal Root Ganglion 48h after  Sciatic-Nerve crush replicate 1


title: SN24h(3)

tag: Dorsal Root Ganglion 24h after  Sciatic-Nerve crush replicate 3


title: 5073 ZT11

description: 5073 ZT11


title: 5073 ZT19

description: 5073 ZT19


title: 5073 ZT15(2)

description: 5073 ZT15(2)


title: Control ZT3(2)

description: Control ZT3(2)

tag: Fly Head yw strain


title: 5073 ZT3(3)

description: 5073 ZT3(3)


title: SN24h(1)

tag: Dorsal Root Ganglion 24h after  Sciatic-Nerve crush replicate 1


title: 5073 ZT15(1)

description: 5073 ZT15(1)


title: 5073 ZT3(2)

description: 5073 ZT3(2)


title: 5073 ZT7

description: 5073 ZT7


title: SN12h(3)

tag: Dorsal Root Ganglion 12h after  Sciatic-Nerve crush replicate 6


title: 5073 ZT3(1)

description: 5073 ZT3(1)


title: CLKGR fly heads ZT16 DEX +CHX (2)

description: CLKGR fly heads ZT16 DEX +CHX (2)

source_name: CLKGR fly heads

tag: tim-gal4; UAS-CLKGR fly heads


title: CLKGR fly heads ZT16 V+CHX (2)

description: CLKGR fly heads ZT16 V+CHX (2)


title: SN12h(2)

tag: Dorsal Root Ganglion 12h after  Sciatic-Nerve crush replicate 5


title: CLKGR fly heads ZT16 V+CHX (1)

description: CLKGR fly heads ZT16 V+CHX (1)


title: SN24h(2)

tag: Dorsal Root Ganglion 24h after  Sciatic-Nerve crush replicate 2


title: E coli O157:H7 w/t LB-Glu with 500uM Indole 7 hr biofilm cells

city: College Station

first: Tarun

last: Bansal

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A & M University

description: RNA extracted from biofilm cells of E coli O157H7 w/t after 7 hours of growth in LB-glu-IND with glass wool

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: EHEC biofilm 7 hrs Lb-glu-IND


title: E coli O157:H7 w/t LB-Glu with 50uM norepinephrine 7 hr biofilm cells

description: RNA extracted from biofilm cells of E coli O157H7 w/t after 7 hours of growth in LB-glu-NE with glass wool

source_name: EHEC biofilm 7 hrs Lb-glu-NE


title: CLKGR fly heads ZT4 DEX+CHX (2)

description: CLKGR fly heads ZT4 DEX+CHX (2)

source_name: CLKGR fly head


title: CLKGR fly heads DEX+CHX (2)

description: CLKGR fly heads DEX+CHX (2)


title: SN12h(1)

tag: Dorsal Root Ganglion 12h after  Sciatic-Nerve crush replicate 4


title: SN6h(3)

tag: Dorsal Root Ganglion 6h after  Sciatic-Nerve crush replicate 3


title: CLKGR fly heads DEX+CHX (1)

description: CLKGR fly heads DEX+CHX (1)


title: CLKGR fly heads ZT4 DEX+CHX (1)

description: CLKGR fly heads ZT4 DEX+CHX (1)


title: E coli O157:H7 w/t LB-Glu with 0.1%DMF 7 hr biofilm cells

description: RNA extracted from biofilm cells of E coli O157H7 w/t after 7 hours of growth in LB-glu with glass wool

source_name: EHEC biofilm 7 hrs Lb-glu


title: E coli O157:H7 w/t LB-Glu with 50uM Epinephrine 7 hr biofilm cells

description: RNA extracted from biofilm cells of E coli O157H7 w/t after 7 hours of growth in LB-glu-EPI with glass wool

source_name: EHEC biofilm 7 hrs Lb-glu-epi


title: CLKGR fly heads V+CHX(2)

description: CLKGR fly heads V+CHX(2)

source_name: fly heads of CLKGR flies


title: CON(SN)(3)

tag: Dorsal Root Ganglion of uninjured control animal, control (t0) belonging to the Sciatic-Nerve crush time-course, replicate 3


title: SN6h(1)

tag: Dorsal Root Ganglion 6h after  Sciatic-Nerve crush replicate 1


title: CLKGR fly heads ZT16 DEX +CHX (1)

description: CLKGR fly heads ZT16 DEX +CHX (1)


title: SN6h(2)

tag: Dorsal Root Ganglion 6h after  Sciatic-Nerve crush replicate 2


title: CLKGR fly heads V+CHX (1)

description: CLKGR fly heads V+CHX (1)


title: CLKGR fly heads V+CHX

description: CLKGR fly heads V+CHX

source_name: fly heads of CLKGR expressing flies


title: S2 cells CLKGR DEX+CHX (2)

description: S2 cells CLKGR DEX+CHX (2)

tag: S2 cells CLKGR stable


title: H295R forskolin 3H_A

description: H295R CELLS FORSKOLIN (10 uM) 3 H

source_name: H295R CELLS - FORSKOLIN - 3H

tag: H295R HUMAN ADRENOCORTICAL CELL LINE


title: CLKGR fly heads ZT4 V+CHX (2)

description: CLKGR fly heads ZT4 V+CHX (2


title: CON(SN)(2)

source_name: L4, L5 and L6 DRG, pool of 3 animals

tag: Dorsal Root Ganglion of uninjured control animal, control (t0) belonging to the Sciatic-Nerve crush time-course, replicate 2


title: H295R potassium 3H_A

description: H295R CELLS POTASSIUM (16 mM) 3 H

source_name: H295R - POTASSIUM - 3H


title: S2 cells CLKGR DEX+CHX(1)

description: S2 cells CLKGR DEX+CHX(1)

source_name: S2 cells CLKGR DEX+CHX(1)

tag: S2 cells CLKGR


title: S2 cells CLKGR DEX+CHX(2)

description: S2 cells CLKGR DEX+CHX(2)


title: CON(SN)(1)

tag: Dorsal Root Ganglion of uninjured control animal, control (t0) belonging to the Sciatic-Nerve crush time-course, replicate 1


title: S2 cells CLKGR V+CHX(2)

description: S2 cells CLKGR V+CHX(2)

source_name: S2 cells CLKGR V+CHX(2)


title: H295R AII 3H_A

description: H295R CELLS ANGIOTENSIN II (100 nM) 3 H

source_name: H295R CELLS - ANG II - 3H


title: S2 cells CLKGR Dex+CHX (1)

description: S2 cells CLKGR DEX+CHX(1)

tag: S2 cells stably transfected with CLKGR


title: H295R control 3H_2_A

description: H295R CELLS CONTROL 3 H

source_name: H295 CELLS - CONTROL - 3H


title: S2 cells CLKGR V+CHX

description: S2 cells CLKGR V+CHX

source_name: S2 cells


title: H295R control  3H_1_A

description: H295R CELLS CONTROL 3 H

source_name: H295R CELLS - CONTROL - 3H


title: total_eIF4E purified_rep4

status: Public on Jul 07 2007

type: mixed

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

description: The array hybridization was performed to compare transcripts abundance in total and GST-eIF4E purified RNA from P. falciparum parasites.

hyb_protocol: Microarrays were hybridized to the Cy3/Cy5 mix overnight at 42°C. After hybridization, the microarrays were washed according to the Pronto!Universal Hybridization Kit instructions (Corning).

scan_protocol: Arrays were scanned using a ScanArray 4000 (Packard BioScience). Spot images were processed and quantified using ScanAlyze software (Eisen, available from: http://rana.lbl.gov/EisenSoftware.htm)

data_processing: Bad spots were flagged by visual inspection of the spot images and cutoff filtering using fraction of pixels in the spot > 1.5 times the background (CH1GTB2 and CH2GTB2 > 0.55). Flagged spots were not considered for further analysis. The processed data were normalized within each array by the scaled print-tip method, and between arrays, using the Aroma package run in R project environment

organism: Plasmodium falciparum

source_name: total RNA K1 strain parasites

label_protocol: 20 µg of total P. falciparum RNA was denatured with 2.5µg of oligo-dT(21) by incubating 5 min at 70°C and then placed on ice, after which cDNA was synthesized by the addition of: dATP, dCTP, dGTP (0.5mM each); dTTP, 0.2 mM; amino allyl-dUTP (Sigma), 0.3 mM; MgCl2, 3 mM; ImpromII reverse-transcriptase 2.5 µl (Promega) . After 2 hour incubation at 37°C, RNA was hydrolysed by adding EDTA to 100 mM and NaOH to 200 mM and incubating at 65°C for 15 min, then neutralized with 25 µl of 1 M HEPES (pH 7.4). cDNA sample was desalted on Microcon 30 column (Millipore), and then coupled to 1 pmol monoreactive Cy5 dye (GE Healthcare), in 0.1 M sodium bicarbonate buffer (pH 9.0) for 1 hour at room temperature in the dark. Unincorporated dyes were removed by purification with QIAquick PCR purification columns (Qiagen). Labeled cDNAs were quantified by Nanodrop ND1000 (Nanodrop Technologies) and dried down with a vacuum centrifuge. The labeled cDNA was resuspended in Pronto! Long Oligo/cDNA hybridization solution (Corning) to give 1pmol/µl Cy5.

growth_protocol: asynchronous parasites cultured at 37°C under 3% CO2 in RPMI 1640 medium supplemented with 25 mM HEPES, pH 7.4, 0.2% NaHCO3, 40 µg/ml gentamicin, 10% human serum and human erythrocytes in standard parasite culture conditions (Trager and Jensen 1976: Science vol 193:673-5).

extract_protocol: Parasites were liberated from host cells by saponin-lysis. Total parasite RNA was obtained using Trizol (Invitrogen) as recommended by the manufacturer

treatment_protocol: No treatments were used

tag: strain K1 asynchronous parasites

molecule: other

source_name: GST-PfeIF4E purified RNA

label_protocol: 2 µg of GST-PfeIF4E purified RNA was denatured with 2.5µg of oligo-dT(21) by incubating 5 min at 70°C and then placed on ice, after which cDNA was synthesized by the addition of: dATP, dCTP, dGTP (0.5mM each); dTTP, 0.2 mM; amino allyl-dUTP (Sigma), 0.3 mM; MgCl2, 3 mM; ImpromII reverse-transcriptase 2.5 µl (Promega) . After 2 hour incubation at 37°C, RNA was hydrolysed by adding EDTA to 100 mM and NaOH to 200 mM and incubating at 65°C for 15 min, then neutralized with 25 µl of 1 M HEPES (pH 7.4). cDNA sample was desalted on Microcon 30 columns (Millipore), and then coupled to 1 pmol monoreactive Cy3 dye (GE Healthcare) in 0.1 M sodium bicarbonate buffer (pH 9.0) for 1 hour at room temperature in the dark. Unincorporated dyes were removed by purification with QIAquick PCR purification column (Qiagen). Labeled cDNAs were quantified by Nanodrop ND1000 (Nanodrop Technologies) and dried down with a vacuum centrifuge. The labeled cDNAs were resuspended in Pronto! Long Oligo/cDNA hybridization solution (Corning) to give 0.25 pmol/µl Cy3.

growth_protocol: not applicable

extract_protocol: Capped mRNA was purified from total RNA as follows: SP-sepharose purified extract containing GST-PfeIF4E (approx. 1-3 mg) was bound to 0.4 ml of glutathione sepharose 4B beads (GE Healthcare) equilibrated in PBS. Beads were washed four times in 10 ml of PBS and then 100 µg of total P. falciparum RNA were incubated with the bead-bound GST-PfeIF4E in 1 ml of PBS containing 1 mM GTP. After 10 min incubation on ice, the beads were washed four times in 10 ml PBS. mRNA and GST-Pf IF4E were eluted from the washed beads using 1 ml of 0.3 M sodium acetate pH5.5 containing 1% SDS. Eluate was phenol-chloroform extracted, isopropanol precipitated and resuspended in diethylpyrocabonate-treated water

treatment_protocol: not applicable

tag: mRNA purified from total RNA using RNA binding protein


title: E- diet, tn treatment vs. E+ diet, tn treatment (26 cy3 ----12 Cy 5)

city: Columbia

first: Raja

middle: S

last: Settivari

state: MO

address: 920 E Campus Drive

department: ASRC

institute: University of Missouri

description: Rats (n=24) were fed ad libitum diets containing either ground endophyte-free (E-) seed or endophyte–infected (E+) seed for five days at thermoneutrality (21°C) followed by a 3 day heat stress. Rats (n=24) with intraperitonial transmitters were used with core temperature (Tc) and general activity measured every 5 minutes during the study. At treatment end, the liver was removed, weighed and frozen in liquid nitrogen.  RNA was extracted from liver samples, converted to cDNA, and hybridized with the printed oligonucleotide slides.

hyb_protocol: custom protocol

scan_protocol: Genepix 6

data_processing: Data was analyzed using Genepix, JMAANOVA softwares

label_protocol: cy5 dye protocol

extract_protocol: Qiagen RNA extraction protocol

tag: MALE RAT LIVER TISSUE, E+ DIET, TN TREATMENT

label_protocol: Cy3 dye kit protocol (Amersham)

extract_protocol: qiagenkit protocol

tag: MALE RAT LIVER TISSUE, E- DIET, TN TREATMENT


title: E+ diet, tn treatment vs. E- diet, tn treatment (30 cy3 ----9 Cy 5)


title: S2 cells CLKGR EtOH+CHX(2)

description: S2 cells CLKGR EtOH+CHX(2)

source_name: S2 cells stable transfected with CLKGR

tag: S2 cells


title: total_eIF4E purified_rep2


title: total_eIF4E purified_rep3


title: total_eIF4E purified_rep1

label_protocol: 20 µg of total P. falciparum RNA was denatured with 2.5µg of oligo-dT(21) by incubating 5 min at 70°C and then placed on ice, after which cDNA was synthesized by the addition of: dATP, dCTP, dGTP (0.5mM each); dTTP, 0.2 mM; amino allyl-dUTP (Sigma), 0.3 mM; MgCl2, 3 mM; ImpromII reverse-transcriptase 2.5 µl (Promega) . After 2 hour incubation at 37°C, RNA was hydrolysed by adding EDTA to 100 mM and NaOH to 200 mM and incubating at 65°C for 15 min, then neutralized with 25 µl of 1 M HEPES (pH 7.4). cDNA sample was desalted on Microcon 30 column (Millipore), and then coupled to 1 pmol monoreactive Cy5 dye (GE Healthcare), in 0.1 M sodium bicarbonate buffer (pH 9.0)  for 1 hour at room temperature in the dark. Unincorporated dyes were removed by purification with QIAquick PCR purification columns (Qiagen). Labeled cDNAs were quantified by Nanodrop ND1000 (Nanodrop Technologies) and dried down with a vacuum centrifuge. The labeled cDNA was resuspended in Pronto! Long Oligo/cDNA hybridization solution (Corning) to give 1pmol/µl Cy5.

label_protocol: 2 µg of GST-PfeIF4E purified RNA was denatured with 2.5µg of oligo-dT(21) by incubating 5 min at 70°C and then placed on ice, after which cDNA was synthesized by the addition of: dATP, dCTP, dGTP (0.5mM each); dTTP, 0.2 mM; amino allyl-dUTP (Sigma), 0.3 mM; MgCl2, 3 mM; ImpromII reverse-transcriptase 2.5 µl (Promega) . After 2 hour incubation at 37°C, RNA was hydrolysed by adding EDTA to 100 mM and NaOH to 200 mM and incubating at 65°C for 15 min, then neutralized with 25 µl of 1 M HEPES (pH 7.4). cDNA sample was desalted on Microcon 30 columns (Millipore), and then coupled to 1 pmol monoreactive Cy3 dye (GE Healthcare) in 0.1 M sodium bicarbonate buffer (pH 9.0)  for 1 hour at room temperature in the dark. Unincorporated dyes were removed by purification with QIAquick PCR purification column (Qiagen). Labeled cDNAs were quantified by Nanodrop ND1000 (Nanodrop Technologies) and dried down with a vacuum centrifuge. The labeled cDNAs were resuspended in Pronto! Long Oligo/cDNA hybridization solution (Corning) to give 0.25 pmol/µl Cy3.


title: S2 cells CLKGR EtOH+CHX

description: S2 cells CLKGR EtOH+CHX

tag: S2 cells stable for CLKGR transgene


title: E- diet, HS treatment vs. E+ diet, HS treatment (6 cy3 ----14 Cy 5)

tag: MALE RAT LIVER TISSUE, E+ DIET, HS TREATMENT

tag: MALE RAT LIVER TISSUE,  E- DIET, HS TREATMENT


title: E- diet, tn treatment vs. E+ diet, tn treatment (17 cy3 ----18 Cy 5)


title: E- diet, HS treatment vs. E+ diet, HS treatment (5 cy3 ----13 Cy 5)

tag: MALE RAT LIVER TISSUE, E- DIET, HS TREATMENT


title: E- diet, tn treatment vs. E+ diet, tn treatment (20 cy3 ----22 Cy 5)


title: E- diet, tn treatment vs. E+ diet, HS treatment (16 cy3 ----8 Cy 5)


title: E+ diet, tn treatment vs. E- diet, HS treatment (12 cy3 ----29 Cy 5)


title: E- diet, tn treatment vs. E+ diet, tn treatment (6 cy3 ----15 Cy 5)


title: E+ diet, HS treatment vs. E- diet, tn treatment  (8 cy3 ----9 Cy 5)

tag: MALE RAT LIVER, E- DIET, TN TREATMENT


title: E- diet, tn treatment vs. E+ diet, HS treatment (16 cy3 ----30 Cy 5)


title: E- diet, tn treatment vs. E+ diet, tn treatment (9 cy3 ----21 Cy 5)

tag: male rat liver tissue, E+ DIET, TN TREATMENT

tag: male rat liver tissue, E- DIET, TN TREATMENT


title: E- diet, tn treatment vs. E+ diet, HS treatment (20 cy3 ----13 Cy 5)


title: E+ diet, tn treatment vs. E- diet, HS treatment (22 cy3 ----5 Cy 5)


title: SN14d(2)

tag: Dorsal Root Ganglion 14d after  Sciatic-Nerve crush replicate 2


title: E+ diet, HS treatment vs. E- diet, tn treatment (14 cy3 ----26 Cy 5)

tag: male rat liver, E- DIET, TN TREATMENT

tag: male rat liver tissue, E+ DIET, HS TREATMENT


title: E+ diet, HS treatment vs. E- diet, tn treatment (10 cy3 ----17 Cy 5 )


title: E+ diet, tn treatment vs. E- diet, HS treatment (30 cy3 ----27 Cy 5)


title: E+ diet, tn treatment vs. E- diet, tn treatment (15 cy3 ----26 Cy 5)


title: E- diet, HS treatment vs. E+ diet, HS treatment (4 cy3 ----10 Cy 5)


title: SN:1011115;Fetal Cartilage, U133B validation

status: Public on Jul 06 2007

middle: Anthony

last: Funari

address: 8700 Beverly Drive

department: Medical Genetics

institute: Cedars Sinai

description: Normal human fetal cartilage from 18-22 weeks.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed using R 2.2.1 and RMA as normalization method with PM model.

source_name: RNA isolated Fetal Cartilage 18-22 weeks - U133B

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

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

treatment_protocol: Distal fetal cartilage from femur of Homo sapiens at 18-22 weeks was dissected from non cartilage tissue using a dissecting scope. RNA was isolated from Cartilage using the Trizol solution (GibcoBRL).

tag: Normal Fetal Cartilage from Distal Femur


title: E+ diet, HS treatment vs. E- diet, HS treatment (3 cy3 ----5 Cy 5)

hyb_protocol: Custom protocol

label_protocol: Cy5 dye protocol

extract_protocol: Qiagen kit protocol


title: E- diet, HS treatment vs. E+ diet, th treatment (4 cy3 ----18 Cy 5)

tag: MALE RAT LIVER TISSUE, E+ DIET, TH TREATMENT


title: SN:1011116;Fetal Cartilage, U133B validation


title: intestine_wildtype_24hfasted_rep3

status: Public on Jul 04 2007

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description: small intestine PPARa knockout mice, fasted for 24 hours

hyb_protocol: Detailed methods for the labeling and subsequent hybridizations to the arrays are described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual, Revision 3, from Affymetrix (Santa Clara, CA).

data_processing: GCRMA version 2.20, emperical Bayes

extract_protocol: Total RNA was isolated from small intestinal samples using TRIzol reagent (Invitrogen, Breda, the Netherlands) according to the manufacturer’s instructions. RNA was treated with DNAse and purified using the SV total RNA isolation system (Promega, Leiden, the Netherlands).

tag: Strain

value: (129S1/SvImJ) (wildtype)

tag: Gender

value: male

tag: Age

value: 14 weeks

tag: Tissue

value: small intestine


title: E- diet, HS treatment vs. E+ diet, HS treatment (29 cy3 ----3 Cy 5)


title: Brain control cy5 vs Brain Macs cy3_2

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute for Molecular Bioscience, Uni of Qld

description: Pairwise comparison of Total Brain RNA vs Brain Macrophage RNA

hyb_protocol: Followed protocol described in: PMID: 15998744

data_processing: Imagene5.0, Lowess Normalisation (R)

source_name: Total Brain Extract

label_protocol: Indirect aRNA Ambion

extract_protocol: RNAAmplification Ambion

tag: RNA extract of pooled total brain tissue

source_name: Brain Macrophage Extract

tag: RNA extract of Isolation of EGFP positive brain macrophages


title: SN:1011109;Fetal Cartilage, U133A validation

source_name: RNA isolated Fetal Cartilage 18-22 weeks - U133A


title: E+ diet, tn treatment vs. E- diet, HS treatment (18 cy3 ----11 Cy 5)

tag: Male rat liver tissue, E- DIET, HS TREATMENT

tag: MALE RAT LIVER TISSUE, E+ DIET, TN TREATMENT


title: E+ diet, tn treatment vs. E- diet, HS treatment (15 cy3 ----1 Cy 5)

tag: MALE RAT LIVER TISSUE, E- DIET, HS TREATMENT


title: intestine_PPARa_kockout_24hfasted_rep1

scan_protocol: Detailed methods for the labeling and subsequent hybridizations to the arrays are described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual, Revision 3, from Affymetrix (Santa Clara, CA).

value: (129S4/SvJae) (PPARalpha knockout)


title: E+ diet, HS treatment vs. E- diet, HS treatment (10 cy3 ----11 Cy 5)

tag: male rat liver tissue E- DIET, HS TREATMENT


title: intestine_wildtype_24hfasted_rep1

label_protocol: Detailed methods for the labeling and subsequent hybridizations to the arrays are described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual, Revision 3, from Affymetrix (Santa Clara, CA).


title: intestine_PPARa_kockout_24hfasted_rep2


title: intestine_PPARa_kockout_24hfasted_rep3


title: SN:1011113;Fetal Cartilage, U133A validation


title: Brain Macs cy5 vs Brain control cy3_3

description: Pairwise comparison of Total Brain RNA vs Brain Macrophage RNA (dye swap)

scan_protocol: Followed protocol described in: PMID: 15998744


title: intestine_wildtype_24hfasted_rep2


title: E- diet, HS treatment vs. E+ diet, tn treatment (27 cy3 ----21 Cy 5)


title: E- diet, HS treatment vs. E+ diet, HS treatment (1 cy3 ----14 Cy 5)

tag: E+ DIET, HS TREATMENT

tag: E- DIET, HS TREATMENT


title: E- diet, HS treatment vs. E+ diet, HS treatment (11 cy3 ----28 Cy 5)


title: E- diet, HS treatment vs. E+ diet, tn treatment (1 cy3 ----12 Cy 5)

source_name: RAT 12

tag: Male rat liver tissue, E+ DIET, TN TREATMENT

source_name: RAT 1

tag: male rat liver tissue, E- DIET, HS TREATMENT


title: E- diet, HS treatment vs. E+ diet, HS treatment (27 cy3 ----8 Cy 5)

tag: MALE RAT LIVER TISSUE, E+ DIET, HS TREATMENT


title: Brain control cy5 vs Brain Macs cy3_1


title: intestine_PPARa-knockout_control_rep3

description: small intestine PPARalpha knockout mice, control diet.

value: 129Sv (PPARalpha knockout)


title: GLUR6_Sample_V:1

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

description: Array CGH analysis of a proband with GLUR6 deletion

hyb_protocol: Hybridisation was done overnight at 42C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned using an Agilent scanner . PMT settings:100/100%

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalised by subgrid LOWESS. Aberrant ratios involving three or more neighbouring clones were considered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Mar. 2007)

source_name: DNA isolated from EBV-transformed cell line

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: DNA was extracted from EBV-transformed lymphoblastoid cell line using standard phenol-chloroform extraction procedures

tag: male proband with GLUR6 deletion

tag: DNA isolated from EBV-transformed lymphoblastoid cell line from a healthy male donor


title: E15.5_total_kidney_vs_E15.5_renal_macrophage2

description: Pairwise comparison of Total Kidney RNA vs Renal Macrophage RNA

source_name: Total Kidney Extract E15.5

tag: RNA extract of pooled E15.5 total kidney

source_name: E15.5 renal macrophage

tag: RNA extract of Isolation of EGFP positive renal macrophages


title: E15.5_total_kidney_vs_E15.5_renal_macrophage1


title: GLUR6_Sample_V:5

tag: female proband with GLUR6 deletion

tag: DNA isolated from EBV-transformed lymphoblastoid cell line from a healthy female donor


title: intestine_wildtype_control_rep3

description: small intestine wild type mice, control conditions

tag: Strain

value: 129Sv (wildtype)

tag: Gender

tag: Age

tag: Tissue


title: E15.5_renal_macrophage_vs_E15.5_total_kidney3

description: Pairwise comparison of Total Kidney RNA vs Renal Macrophage RNA (dye swap)


title: Lung control cy5 vs Lung Macs cy3_2

description: Pairwise comparison of Total Lung RNA vs Lung Macrophage RNA

source_name: Total Lung Extract

tag: RNA extract of pooled total lung tissue

source_name: Lung Macrophage Extract

tag: RNA extract of Isolation of EGFP positive lung macrophages


title: GLUR6_Sample_V:12


title: intestine_wildtype_control_rep2


title: intestine_PPARa-knockout_control_rep1


title: GLUR6_Sample_V:6

extract_protocol: DNA was extracted blood using standard phenol-chloroform extraction procedures


title: Lung control cy5 vs Lung Macs cy3_1


title: Lung macs cy5 vs Lung control cy3_3

description: Pairwise comparison of Total Lung RNA vs Lung Macrophage RNA (dye swap)


title: Arabidopsis_Water-30M_rep2

status: Public on Jul 03 2007

first: Gary

last: Stacey

address: 1201 Rollins Road

department: Plant Sciences

institute: University of Missouri-Columbia

description: Gene expression data from 14-day-old Arabidopsis seedlings treated with water.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Arabidopsis Genome Array ATH1. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were normalized and analyzed with DNA-Chip Analyzer (dChip; Version Release, April 1, 2005) using the default settings.

organism: Arabidopsis thaliana

source_name: Arabidopsis 2-week-old seedlings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seedlings (~ 30 seeds at the beginning) were grown hydroponically in a 50-ml falcon tube containing 10 ml of liquid medium (1X Murashige and  skoog basal salt mixture + 2% dextrose, pH 5.8). The tube was incubated with gentle shaking in a growth chamber  with the following settings: constant light at 125 umol m-2 s-1 at a temperature of 23 C. After 14 days, 20 ul of ddH2O was added to the mdieum containing the seedlings. Whole seedlings were collected 30 minutes after treatment, immediately frozen in liquid nitrogen and stored at -80 C for later use..

treatment_protocol: 2-week-old seedlings were treated with 20 ul ddH2O for 30 minutes, with gentle shaking.

tag: Ecotype

value: Col 0


title: GLUR6_Sample_V:11


title: Arabidopsis_Chitooctaose-30M_rep3

growth_protocol: Seedlings (~ 30 seeds at the beginning) were grown hydroponically in a 50-ml falcon tube containing 10 ml of liquid medium (1X Murashige and  skoog basal salt mixture + 2% dextrose, pH 5.8). The tube was incubated with gentle shaking in a growth chamber  with the following settings: constant light at 125 umol m-2 s-1 at a temperature of 23 C. After 14 days, 20 ul of chitooctaose was added to the mdieum containing the seedlings to achieve a final concentration of 1 uM. Whole seedlings were collected 30 minutes after treatment, immediately frozen in liquid nitrogen and stored at -80 C for later use..

treatment_protocol: 2-week-old seedlings were treated with 20 ul 0.5 mM chitooctaose (with a final concentration of 1 uM) for 30 minutes, with gentle shaking.


title: intestine_PPARa-knockout_control_rep2


title: intestine_wildtype_control_rep1


title: Arabidopsis_Water-30M_rep3


title: Arabidopsis_Chitooctaose-30M_rep1


title: Arabidopsis_Water-30M_rep1


title: Arabidopsis_Chitooctaose-30M_rep2


title: Geobacter Ben-Ac slide K

city: Knoxville

first: Qiang

last: He

state: TN

address: 57A Perkins Hall

department: Civil and Environmental Engineering

institute: The University of Tennessee

description: The objective of the experiment is to compare the gene expression profiles of Geobacter metallireducens given different electron donors, i.e. benzoate and acetate, under iron-reducing growth conditions.

hyb_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.

organism: Geobacter metallireducens GS-15

source_name: Geobacter metallireducens with benzoate as electron donor

growth_protocol: Esteve-Nunez, A., Rothermich, M. M., Sharma, M., Lovley, D. R. 2005. Growth of Geobacter sufurreducens under nutrient-limiting conditions in continuous culture. Environ. Microbiol. 7(5):641-648.

treatment_protocol: Benzoate as the electron donor

tag: Geobacter metallireducens GS-15 chemostat cultures were grown

tag: at 30 degree C with a dilution rate of 0.05 h-1 and with 55 mM ferric citrate as the electron acceptor. The electron donor was limiting, and was 1.25 mM benzoate.

source_name: Geobacter metallireducens with acetate as electron donor

treatment_protocol: Acetate as the electron donor

tag: at 30 degree C with a dilution rate of 0.05 h-1 and with 55 mM ferric citrate as the electron acceptor. The electron donor was limiting, and was 5 mM acetate.


title: Geobacter Ben-Ac slide L

scan_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.


title: Geobacter Ben-Ac slide H

data_processing: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.


title: Geobacter Ben-Ac slide B

label_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.


title: Geobacter Ben-Ac slide I

extract_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.


title: Geobacter Ben-Ac slide F


title: Geobacter Ben-Ac slide G


title: Geobacter Ben-Ac slide E


title: Geobacter Ben-Ac slide J


title: Geobacter Ben-Ac slide D


title: Geobacter Ben-Ac slide A


title: Geobacter Ben-Ac slide C

tag: at 30°C with a dilution rate of 0.05 h-1 and with 55 mM ferric citrate as the electron acceptor.  The electron donor was limiting, and was 1.25 mM benzoate.

tag: at 30°C with a dilution rate of 0.05 h-1 and with 55 mM ferric citrate as the electron acceptor.  The electron donor was limiting, and was 5 mM acetate.


title: Control ZT7

description: Control ZT7

source_name: Fly Head

tag: Fly Head yw strain


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E18, replicate 4)

status: Public on Jul 02 2007

city: New Haven

first: Lawrence

last: Rizzolo

state: CT

address: 333 Cedar St

department: Dept of Surgery

institute: Yale University

description: E18, replicate 4

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: signal value generated from global scaling

label: biotin-UTP

organism: Gallus gallus

source_name: Retinal Pigment Epithelium

label_protocol: affymetrix 3'-amplification ivt

extract_protocol: RNeasy Protect kit (Qiagen)

tag: Isolated from chicken embryos on embryoinic day 18 (E18)


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E18, replicate 2)

description: E18, replicate 2


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E14, replicate 2)

description: E14, replicate 2

tag: Isolated from chicken embryos on embryoinic day 14 (E14)


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E7, replicate 3)

description: E7, replicate 3

tag: Isolated from chicken embryos on embryoinic day 7 (E7)


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E18, replicate 3)

description: E18, replicate 3


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E7, replicate 4)

description: E7, replicate 4

tag: from chicken embryos on embryoinic day 7 (E7)


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E18, replicate 1)

description: E18, replicate 1


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E14, replicate 3)

description: E14, replicate 3


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E14, replicate 1)

description: E14, replicate 1


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E10, replicate 3)

description: E10, replicate 3

tag: Isolated from chicken embryos on embryoinic day 10 (E10)


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E10, replicate 2)

description: E10, replicate 2


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E10, replicate 1)

description: E10, replicate 1


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E7 replicate 2)

description: E7, replicate 2

tag: Isolated from chicken embryos on embryoinic day 7


title: Developmental regulation of the transcriptome of chicken retinal pigment epithelium (E7 replicate 1)

description: E7, replicate 1


title: E- diet, HS treatment vs. E+ diet, tn treatment (1 cy3 ----12 Cy 5 FF)

hyb_protocol: Protocol for reverse transcription and amino - allyl coupling of RNA 1.	RT Reaction: Clean the desk, pipettes and gloves with alcohol. Take two PCR tubes, label them as reference and sample. And add the following: 	Sample	Reference Oligo dT  (5μl/ μl)	1 μl	1 μl PdN6        (5 μl/ μl)	1 μl	1 μl RNA (15  μg)	15/Conc. of RNA	15/Conc. Of ref RNA Spike	10 μl	10 μl TOTAL VOL. Don’t add spike till last. Add spike first to sample and then to reference. 2.	Drying: Take 2 ml tube and keep the 	PCR tubes in that tube and keep in dryer. Turn it on an heat the RNA at 45C for 5-6 min. take out the tubes and measure the volume of the samples. It should be close to 15.5 μl. If it is more again keep dry it. If the volume is too low then add sufficient amount of nano water to bring the final volume to 15.5 μl. 3.	Annealing: Centrifuge the PCR tubes in PCR machine. (keep the tubes in PCR machine. Y !1. files!start!enter!M card!70C –10 min. press G to start. After it stops, press enter and exit and open.1!Y. Incubate the tubes on ice for 10 min. In the mean while prepare the master mix for c DNA synthesis. 4.	cDNA synthesis: Take a PCR tube and add the following: 	 X 2 (one for sample and one for reference) Water 	10 μl 10X buffer	6 μl DTT	6 μl 50X Dutp/Dntp	1.2 μl RT	6 μl TOTAL	29.2 μl Remove RT reagent from the freezer only just before adding the master mix to the samples. Immediately after adding the RT keep it back in –20. Take half the master mix (14.6 μl )and add in sample and the other half in the reference sample. Incubate the tube at 42 C for 2 hours in PCR machine. ( start, enter, 42C for 2 hours, enter.) 5.	Hydrolysis Add the following to the tubes: 	Sample	Reference 1N NaOH	10 μl	10 μl 0.5M EDTA	10 μl	10 μl Incubate at 65C for 15 min in PCR machine. Add 25 μl of 1M tris with pH of 7.4 (neutralization). Mix the contents many times by repeated pipetting. 6.	Clean up To continue with the amino allyl dye coupling procedure all Tris must be removed from the reaction to prevent the mono functional NHS ester Cy dyes from coupling to free amine groups in solution. Microcon Sample + nano water up to 450 μl. Spin at 12000RPM (10000 g for 8 min). Discard the flow through. Repeat the above step twice using water up to 450 μl. And again discard the flowthrough.  Turn the filter upside down and spin at 2000 RPM for 3 min. Go for nano drop. : DNA 50. Blank: nano water. The concentration of c DNA must be between 1-5% of total RNA conc. Dry aliquot in speed vac at 45C for 30 min or till it dried up completely. In between prepare the dyes (always keep the dyes in vacuum at 4C as the dyes are susceptible both for light and moisture). Preparation of dyes   Take fresh tube of Cy3 and Cy5. Add 10 μl of DMSO. Mix well. Aliquot 1.25 μl X8 tubes and immediately dry them in speed vac. And store the tubes at 4 C in vacuum. 7.	Coupling: Check the pH of 0.5 NaOH buffer (pH should be 9.0). Add 9 μl of 0.5N NaHCO3 to the RNA pellet. Keep it at room temperature for 10-15 min. Now take the dye tube from 4 C. and transfer cDNA and bicarbonate buffer to the aliquot of dye. Let it incubate for 1 hour at room temperature in dark. 8.	Labeling: We do 2 hybridizations for each sample. 	Hyb 1	Hyb 2 Sample	Cy3	Cy5 Reference	Cy5	Cy3 9.	Quenching: (to remove unincorporated or quenched Cy dyes). 	Sample	Reference Water	70 μl	70 μl Buffer PE	500 μl	500 μl Take 2 new tubes and fix qia quick filter column and add sample and reference to it. Spin at 12000RPM for 30-60 min. discard the flow through. Add 750 μl of buffer PE and spin for 30-60 sec . discard the flow through. Again add 750 μl of buffer PE and repeat the above step. Transfer the spin unit to a new tube and add 30 μl buffer EB to center of the filter. Let it sit at room temperature for 1 min. and then spin it at 13000rpm for 1 min. Again add 30 μl of buffer EB and incubate at room temperature for 1 min and repeat the above step. (We should get colored cDNA in the elution tube). Go for nano drop. : see in others. Blank: buffer EB/ water. Note down the conc, absorbance of the dyes, and the ratios. 10.	Hybridization preparation: Now combine the Cy3 andCy5 and dry down them for 1 hour at 45-60C. Cover dryer with paper to avoid the exposure of the sample to light. Bring the volume to 15 μl with water. Add : 3.0 μl of SSC.           1.5 μl of Poly A (10 mg/ml).            0.5 μl 1M HEPES pH 7.0

scan_protocol: scanned to have the ratio close to 1

data_processing: gene pix analysis

label: CY 5

source_name: Rat 12

label_protocol: CUSTOM

extract_protocol: QIAGEN

tag: E+ TN

tag: E- HS


title: E- diet, HS treatment vs. E+ diet, tn treatment (29 cy3 ----22 Cy 5)

tag: male rat liver tissue, E+ DIET, TN TREATMENT

tag: male rat liver tissue, E- DIET, HS TREATMENT


title: P3_AS_HeLaS3_RCyP+_C88_B1

status: Public on May 25 2007

city: Santa Clara

first: Thomas

middle: R

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

description: See publication for details

hyb_protocol: See publication for details

scan_protocol: See publication for details

data_processing: See publication for details

source_name: Total Cytoplasmic RNA from HeLa cell line

label_protocol: See publication for details

extract_protocol: Long RNA protocol - see publication for details

tag: See publication for details


title: P3_AS_HDF_RCyP+_C82_B1

description: See publication for details

source_name: Total RNA from HDF cell line


title: P3_AS_HDF_RCyP+_C76_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C82_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C87_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C75_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C68_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C77_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C83_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C64_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C72_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C85_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C73_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C83_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C88_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C90_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C87_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C86_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C86_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C71_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C74_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C78_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C66_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C63_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C70_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C91_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C90_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C85_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C59_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C69_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C62_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C53_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C39_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C65_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C54_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C57_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C52_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C56_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C46_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C55_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C60_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C67_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C84_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C48_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C84_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C47_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C91_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C58_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C61_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C50_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C51_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C45_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C37_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C43_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C38_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C44_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C36_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C23_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C31_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C42_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C22_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C21_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C27_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C32_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C40_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C35_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C49_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C29_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C29_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C34_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C30_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C30_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C31_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C21_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C23_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C28_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C28_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C27_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C25_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C22_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C25_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C26_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C33_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C20_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C26_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C14_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C16_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C16_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C14_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C18_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C12_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C20_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C13_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C24_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C18_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C17_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C09_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C12_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C19_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C06_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C19_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C09_B1

description: See publication for details


title: P3_AS_HeLaS3_RNuP+_C05_B1

description: See publication for details

source_name: Total Nuclear RNA from HeLa cell line


title: P3_AS_HeLaS3_RCyP+_C15_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C06_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C11_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C05_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C11_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C15_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C07_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C07_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C04_B1

description: See publication for details


title: P3_AS_HeLaS3_RNuP+_C04_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C81_B1

description: See publication for details


title: P3_AS_HeLaS3_RNuP+_C02_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C24_B1

description: See publication for details


title: 10T 1/2 Glis3 vs. 10T 1/2 Con (ExpID 2922)

status: Public on May 22 2007

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

data_processing: Total RNA was extracted from C3H10T1/2 cells infected with empty vector or Glis3 using Qiagen Rneasy Mini kit.  Each RNA sample was amplified and converted to fluorescently labeled cRNA, either with cyanine 3 (Cy3) or cyanine 5 (Cy5), using the Agilent Fluorescent Linear Amplification Kit. The fluorescently labeled cRNAs were mixed and hybridized simultaneously to Agilent mouse oligo arrays. Chips were scanned with an Agilent dual-laser scanner.  Gene expression data were generated using the Agilent feature extraction software (v7.5), with defaults for all parameters.


title: P3_AS_HeLaS3_RCyP+_C10_B1

description: See publication for details


title: P3_AS_HeLaS3_RNuP+_C03_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C13_B1

description: See publication for details


title: 10T 1/2 Con vs. 10T 1/2 Glis3 (ExpID 2922)

description: C3H10T1/2 cells infected with empty vector or Glis3


title: P3_AS_HDF_RCyP+_C02_B1

description: See publication for details


title: Pooled glp-1 C elegans old adults_rep1

status: Public on May 16 2007

description: Gene expression analysis was conducted using C. Elegans Genome Genechip® arrays (Affymetrix, Santa Clara, CA).  Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.  For each array, 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.  Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000.  Data was obtained using the Genechip® Operating Software (Version 1.2.0.037).

data_processing: Data were processed using the Rosetta Resolver® system (version 5.1), as described in Weng (2004).  Weng, L. (2004). Data processing and analysis methods in the Rosetta Resolver system, Rosetta Biosoftware Technical Note, http://www.rosettabio.com/tech/default.htm

organism: Caenorhabditis elegans

source_name: Pooled glp-1 C elegans 6-day-old adults.

growth_protocol: Eggs obtained from adults raised at 15ºC were hatched in M9 buffer overnight at 20ºC, transferred as L1s to OP50-seeded K agar plates, and raised at 25ºC (to prevent germ cell proliferation) until 6 days post-L4 stage. Worms were transferred to fresh plates every 2 days by washing off in K medium.

extract_protocol: 6-day-old adults were rinsed off plates with K medium and allowed to settle by gravity. They were washed twice with K medium over ~30 minutes, and after the final wash were resuspended in ~500ul K medium and dripped into liquid nitrogen using a glass pasteur pipette. The resulting pellets were ground in liquid nitrogen, and the powder dissolved in lysis buffer with proteinase K and RNase A from the RNEasy extraction kit (Qiagen); subsequent extraction was per the Qiagen protocol.

treatment_protocol: Normal culturing conditions.

tag: Pool of ~3000-5000 age-matched 6-day-old (“old”) adults, Strain

value: JK1107, Genotype:glp-1(q224) III


title: Pooled glp-1 C elegans old adults_rep2

hyb_protocol: 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000.  Data was obtained using the Genechip® Operating Software (Version 1.2.0.037).

label_protocol: Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.


title: Pooled glp-1 C elegans young adults_rep2

source_name: Pooled glp-1 C elegans 1-day-old adults.

growth_protocol: Eggs obtained from adults raised at 15ºC were hatched in M9 buffer overnight at 20ºC, transferred as L1s to OP50-seeded K agar plates, and raised at 25ºC (to prevent germ cell proliferation) until 24 hours post-L4 stage.

extract_protocol: Young adults were rinsed off plates with K medium and allowed to settle by gravity. They were washed twice with K medium over ~30 minutes, and after the final wash were resuspended in ~500ul K medium and dripped into liquid nitrogen using a glass pasteur pipette. The resulting pellets were ground in liquid nitrogen, and the powder dissolved in lysis buffer with proteinase K and RNase A from the RNEasy extraction kit (Qiagen); subsequent extraction was per the Qiagen protocol.

tag: Pool of ~3000-5000 age-matched 1-day-old (“young”) adults, Strain


title: Pooled glp-1 C elegans young adults_rep3


title: Pooled glp-1 C elegans young adults_rep1


title: Pooled glp-1 C elegans embryos_bleach NaOH prep_rep3

source_name: Pooled glp-1 C elegans embryos obtained by bleach sodium hydroxide treatment.

growth_protocol: Obtained from adults raised at 15ºC, grown on K agar plates with OP50 bacteria.

extract_protocol: After bleach-NaOH treatment and washing, eggs were resuspended in ~500uL K medium and dripped into liquid nitrogen using a glass pasteur pipette. The resulting pellets were ground in liquid nitrogen, and the powder dissolved in lysis buffer with proteinase K and RNase A from the RNEasy extraction kit (Qiagen); subsequent extraction was per the Qiagen protocol.

tag: Pool of ~5000 eggs at various developmental stages, Strain


title: P3_AS_HDF_RCyP+_C03_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C08_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C05_B1

description: See publication for details


title: Pooled glp-1 C elegans embryos_bleach NaOH prep_rep2


title: P3_AS_HDF_RCyP+_C04_B1

description: See publication for details