title: DC3 RSG

status: Public on Sep 19 2006

city: Debrecen

first: Istvan

last: Szatmari

address: Egyetem tér 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description: Monocytes (98% CD14+) were obtained from Buffy coats by Ficoll gradient centrifugation and magnetic cell separation using anti-CD14-conjugated microbeads (VarioMACS; Miltenyi Biotec).

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix GCOS 1.4, statistical (MAS5) algorithm

source_name: Monocyte derived dendritic cells

label_protocol: cRNA was generated from 5 ug of total RNA by using the SuperScript Choice kit (Invitrogen) and the High Yield RNA transcription labeling kit.

growth_protocol: Monocytes were resuspended into six-well culture dishes at a density of 1.5x106 cells/ml and cultured in RPMI 1640 (Sigma) supplemented with 10% Fetal bovine serum (FBS) (Invitrogen), containing 800 U/ml GM-CSF (Peprotech) and 500 U/ml IL-4 (Peprotech).

extract_protocol: Total RNA was isolated using Trizol Reagent (Invitrogen) and further purified by using the RNeasy kit (Quiagen).

treatment_protocol: Cells were treated with 2.5 uM rosiglitazone (RSG). Ligands or vehicle were added to the cell culture starting from the first day.

tag: tissue

value: freshly isolated human monocyte

tag: gender:male; age

value: 41 yr; weight:92 kg


title: DC2 AM

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens

treatment_protocol: Cells were treated with 100 nM AM580 (AM). Ligands or vehicle were added to the cell culture starting from the first day.

value: 47 yr; weight:80 kg


title: DC3 AM


title: DC2 RSG AGN

treatment_protocol: Cells were treated with 2.5 uM rosiglitazone (RSG) along with 1 uM AGN193109 (AGN). Ligands or vehicle were added to the cell culture starting from the first day. AGN193109 administration was repeated at day 3.


title: DC3 RSG AGN


title: DC1 RSG

description: Monocytes (98% CD14+) were obtained from Buffy coats by Ficoll gradient centrifugation and magnetic cell separation using anti-CD14-conjugated microbeads (VarioMACS; Miltenyi Biotec)

label: biotine

label_protocol: cRNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).

tag: gender:female; age

value: 19 yr; weight:65 kg


title: Cell line MCF-7_control_expt3

status: Public on Sep 28 2006

city: VILLEJUIF

first: David

last: CAPPELLEN

address: 39, rue Camille Desmoulins

department: UMR 8126 CNRS

country: France

institute: Institut Gustave Roussy

description: Analysis of human cancer cell lines depleted of c-MYC via RNA interference (RNAi), or the corresponding control

data_processing: The displayed array hybridization values were obtained using the Affymetrix MAS 4.0 software

source_name: carcinoma

tag: carcinoma


title: DC1

growth_protocol: Monocytes were cultured for 5 days with 500 U/ml IL-4 and 800 U/ml GM-CSF, cytokine treatment was repeated at day 3.

treatment_protocol: Cells were treated with vehicle (DMSO/ethanol). Ligands or vehicle were added to the cell culture starting from the first day.


title: DC3


title: DC1 AM

label_protocol: cRNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen) and the High Yield RNA transcription labeling kit.


title: DC2


title: DC2 RSG


title: Endometrium in trophoblast conditioned medium for 12 hours TCM-12

status: Public on Sep 18 2006

city: San Francisco

first: Said

last: Talbi

state: CA

address: 500 Parnassus

country: USA

institute: UCSF

description: Trophoblast conditioned medium endometrium  12 hours TCM-12

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG 133 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 HR3000.

data_processing: The data were analyzed with Gene Chip Operating System GCOS version 1.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: uterus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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: E2P4 to decidualization (14 days) + Trophoblast conditionned medium for 12 hrs


title: Endometrium in trophoblast conditioned medium for 3 hours TCM-8

description: Trophoblast conditioned medium endometrium  3 hours TCM-8

treatment_protocol: E2P4 to decidualization (14 days) + Trophoblast conditionned medium for 3hrs


title: Endometrium in control conditioned medium for 12 hours TCM-15

description: Control conditioned medium endometrium  12 hours TCM-15

treatment_protocol: E2P4 to decidualization (14 days) + control conditionned medium for 12 hrs


title: Endometrium in control conditioned medium for 12 hours TCM-9

description: Control conditioned medium endometrium  12 hours TCM-9


title: Endometrium in control conditioned medium for 12 hours TCM-11

description: Control conditioned medium endometrium  12 hours TCM-11


title: Endometrium in control conditioned medium for 3 hours TCM-7

description: Control conditioned medium endometrium  3 hours TCM-7

treatment_protocol: E2P4 to decidualization (14 days) + control conditionned medium for 3 hrs


title: Endometrium in trophoblast conditioned medium for 12 hours TCM-17

description: Trophoblast conditioned medium endometrium  12 hours TCM-17


title: Endometrium in trophoblast conditioned medium for 3 hours TCM-16

description: Trophoblast conditioned medium endometrium  3 hours TCM-16


title: Endometrium in control conditioned medium for 3 hours TCM-14

description: Control conditioned medium endometrium  3 hours TCM-14


title: Endometrium control 0 hours TCM-3

description: Control endometrium  0 hours TCM-3

treatment_protocol: E2P4 to decidualization (14 days)

tag: Control endometrium  0 hours TCM-3


title: Endometrium in trophoblast conditioned medium for 3 hours TCM-6

description: Trophoblast conditioned medium endometrium  3 hours TCM-6


title: Endometrium control 0 hours TCM-13

description: Control endometrium  0 hours TCM-13

tag: Control endometrium  0 hours TCM-13


title: Endometrium control 0 hours TCM-4

description: Control endometrium  0 hours TCM-4

tag: Control endometrium  0 hours TCM-4


title: Endometrium in control conditioned medium for 3 hours TCM-5

description: Control conditioned medium endometrium  3 hours TCM-5

treatment_protocol: E2P4 to decidualization (14 days)+ control conditionned medium for 3 hrs


title: brain, cortex: Sample20_e1_le1

status: Public on Sep 12 2006

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description:
gfp pos. sorted cells from 3 disected e14.5 cortecies
Treatment, type=wait

organism: Mus musculus

source_name: brain, cortex


title: brain, cortex: Sample19_e1_le1


title: brain, cortex: Sample18_e1_le1


title: brain, cortex: Sample14_e1_le1

description:
gfp pos. sorted cells from 3 disected e14.5 ganglionic eminences
Treatment, type=wait


title: brain, cortex: Sample16_e1_le1

description:
gfp neg. sorted cells from 3 disected e14.5 cortecies
Treatment, type=wait


title: brain, cortex: Sample21_e1_le1


title: brain, cortex: Sample15_e1_le1


title: brain, cortex: Sample12_e1_le1


title: brain, cortex: Sample10_e1_le1


title: brain, cortex: Sample13_e1_le1


title: brain, cortex: Sample5_e1_le1


title: brain, cortex: Sample7_e1_le1


title: brain, cortex: Sample11_e1_le1


title: brain, cortex: Sample9_e1_le1


title: brain, cortex: Sample6_e1_le1


title: brain, cortex: Sample17_e1_le1


title: brain, cortex: Sample8_e1_le1


title: brain, cortex: Sample4_e1_le1


title: brain, cortex: Sample3_e1_le1


title: dStr, biological rep3

status: Public on Sep 10 2006

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description: Gene expression data from  dorsal striatum of mouse

hyb_protocol: Labeled cRNA was purified, and 20 ?g of cRNA was fragmented to a range of 35 to 200 bases in length. Samples were hybridized at 450C for 16 h to Affymetrix mouse430_2 chips GeneChips were washed and stained in the Affymetrix Fluidic

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with dChip softwareusing invariant-set normalization method.

source_name: dorsal striatum

label_protocol: Starting with 10 ng of total RNA, cRNA targets were generated using the two-cycle target labeling method.

extract_protocol: Stat-60 (Tel-Test) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were briefly anesthetized with isoflurane then rapidly decapitated.  Brains were submerged in oxygenated (95% O2-5% CO2) ice-cold sucrose-artificial cerebrospinal fluid solution (in mM: 194 sucrose, 20 NaCl, 4.4 KCl, 2 CaCl2, 1 MgCl2, 1.2 NaH2PO4, 10.0 glucose, and 26.0 NaHCO3) and coronal brain slices (300 um) were made using a vibratome (Leica).  Slices were transferred onto a glass Petri dish with a transfer pipette and excess fluid was drained from the area surrounding the tissue.  The Petri dish was placed on top of a chilled aluminum block and tissue was brought to a semi-frozen state before punches were taken.

tag: Male C57Bl/6J mouse

tag: 12 weeks old at the time of sacrifice


title: brain, cortex: Affy labeling kit


title: NAc, biological rep3

description: Gene expression data from  nucleus accumbens of mouse

source_name: nucleus accumbens


title: dStr, biological rep1

description: Gene expression data from dorsal striatum of mouse


title: NAc, biological rep1


title: brain, cortex: Sample2_e1_le1


title: BNST, biological rep2

description: Gene expression data from bed nucleus of the stria terminalis of mouse

source_name: bed nucleus of the stria terminalis


title: BNST, biological rep1


title: BNST, biological rep3


title: dStr, biological rep2


title: NAc, biological rep2


title: Col-0_5day_+lincomycin_rep2

status: Public on Sep 09 2006

city: La Jolla

first: Joanne

last: Chory

address: 10010 N. Torrey Pines Road.

department: Plant Biology Laboratory

institute: The Salk Institute for Biological Studies

description: Purpose of the experimen is to study the difference in genomic response to lincomycin in three genotypes (Col-0, abi4, gun1).

hyb_protocol: Affymetrix protocol.

data_processing: All 12 arrays were pre-processed using RMA mehtod provided by bioconductor

organism: Arabidopsis thaliana

source_name: 5 day old, light grown, whole seedlings+ 200 microgram/ml lincomycin

label_protocol: Affymetrix protocol.

growth_protocol: Seedlings were grown at 21o C, under light/dark cycles of 20 µmol/m-2/sec-1.

extract_protocol: RNA was extracted with the RNeasy kit (Qiagen; Hilden, Germany)

treatment_protocol: Seeds were surface sterilized and plated on 1/2 Murashige Skoog (MS) medium  containing 1% sucrose with 220 µg/ml lincomycin.

tag: Ecotype

tag: genotype

value: wild type

tag: Age

value: 5 days

tag: Tissue

value: whole seedling


title: abi4-102_5day_+lincomycin_rep2


title: gun1-1_5day_-lincomycin_rep2

source_name: 5 day old, light grown, whole seedlings

treatment_protocol: Seeds were surface sterilized and plated on 1/2 Murashige Skoog (MS) medium  containing 1% sucrose without 220 µg/ml lincomycin.

value: wild type, gun1-1, abi4-102


title: gun1-1_5day_+lincomycin_rep1


title: Col-0_5day_+lincomycin_rep1


title: Col-0_5day_-lincomycin_rep2


title: abi4-102_5day_-lincomycin_rep1


title: gun1-1_5day_+lincomycin_rep2


title: gun1-1_5day_-lincomycin_rep1


title: Col-0_5day_-lincomycin_rep1


title: MAQC_AFX_2_N5

status: Public on Sep 08 2006

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

description: Colorectal adenocarcinomas and matched normal colonic RNA sample were purchased from Oncomatrix, Inc., San Diego, CA.  The RNA from each biological sample was distributed to and processed in two laboratories at Stanford University.

scan_protocol: GeneChips were scanned using the Affymetrix scanner.

data_processing: The CEL file data were analyzed with BioConductor to generate probeset level data using the justPlier() function.  Probe-level data were quantile normalized before PLIER summarization per test site (10 arrays).  An offset value of 16 was then added to each probeset-level data point.

source_name: Sample type N (Normal, matched normal colon tissue)

label_protocol: 5 µg of total RNA was used to synthesize cRNA for each sample. !Sample_hyb_protocol = 20 µg of cRNA was hybridized to each individual microarray (HG-U133-Plus-2.0). The microarrays were hybridized for 16 hours at 45°C, stained, and washed according to an Affymetrix protocol (EukGE-WS2v4) using an Affymetrix fluidics station.

tag: MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.


title: MAQC_AFX_2_T1

source_name: Sample type T (Tumor, colon adenocarcinoma)


title: abi4-102_5day_+lincomycin_rep1


title: MAQC_AFX_2_T4


title: MAQC_AFX_2_T5


title: abi4-102_5day_-lincomycin_rep2


title: MAQC_AFX_2_N3


title: MAQC_AFX_2_T3


title: MAQC_AFX_2_T2


title: MAQC_AFX_2_N4


title: MAQC_AFX_1_T2


title: MAQC_AFX_2_N1


title: MAQC_AFX_1_T5


title: MAQC_AFX_1_N3


title: MAQC_AFX_1_T3


title: MAQC_AFX_1_N5


title: MAQC_AFX_1_T4


title: MAQC_AFX_2_N2


title: MAQC_AFX_1_N4


title: MAQC_AFX_1_N2


title: MAQC_AFX_1_T1


title: MAQC_AFX_1_N1


title: MAQC_AFX_5_D5

hyb_protocol: Affymetrix GeneChip Operating Software (GCOS) is used to automate the control of GeneChip Fluidics Stations and Scanners.

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

data_processing: The CEL file data were analyzed with BioConductor to generate probeset level data using the justPlier() function.  Probe-level data were quantile normalized before PLIER summarization per test site (20 arrays).  An offset value of 16 was then added to each probeset-level data point.

source_name: MAQC sample D, i.e., MAQC samples A and B mixed at 25%:75% ratio (A:B).

label_protocol: MAQC samples were processed following Affymetrix one-cycle sample preparation protocol with 5 ug of total RNA (Please refer to GeneChip Expression Analysis Technical Manual for details) and hybridized to Human Genome U133 Plus 2.0 array (catalog #900470, #900466 or #900467).


title: MAQC_AFX_6_A1

source_name: MAQC sample A, i.e., Stratagene Universal Human Reference RNA (UHRR, Catalog #740000)


title: MAQC_AFX_6_D1


title: MAQC_AFX_6_C3

source_name: MAQC sample C, i.e., MAQC samples A and B mixed at 75%:25% ratio (A:B).


title: MAQC_AFX_5_D1


title: MAQC_AFX_6_C2


title: MAQC_AFX_6_D2


title: MAQC_AFX_6_A5


title: MAQC_AFX_5_C5


title: MAQC_AFX_6_C1


title: MAQC_AFX_6_B1

source_name: MAQC sample B, i.e., Ambion Human Brain Reference RNA (HBRR, Catalog #6050)


title: MAQC_AFX_5_D4


title: MAQC_AFX_6_D4


title: MAQC_AFX_6_C5


title: MAQC_AFX_6_A4


title: MAQC_AFX_6_A3


title: MAQC_AFX_5_D3


title: MAQC_AFX_6_D5


title: MAQC_AFX_5_C3


title: MAQC_AFX_6_A2


title: MAQC_AFX_5_D2


title: MAQC_AFX_6_D3


title: MAQC_AFX_6_B4


title: MAQC_AFX_5_C4


title: MAQC_AFX_6_B5


title: MAQC_AFX_5_C2


title: MAQC_AFX_6_B2


title: MAQC_AFX_5_C1


title: MAQC_AFX_6_B3


title: MAQC_AFX_5_B5


title: MAQC_AFX_5_B3


title: MAQC_AFX_5_A5


title: MAQC_AFX_4_D2


title: MAQC_AFX_4_C4


title: MAQC_AFX_4_C2


title: MAQC_AFX_4_B5


title: MAQC_AFX_4_B2


title: MAQC_AFX_5_B1


title: MAQC_AFX_4_D3


title: MAQC_AFX_4_D1


title: MAQC_AFX_4_D4


title: MAQC_AFX_4_C5


title: MAQC_AFX_4_A4


title: MAQC_AFX_5_A2


title: MAQC_AFX_4_B1


title: MAQC_AFX_4_C3


title: MAQC_AFX_4_B4


title: MAQC_AFX_5_B4


title: MAQC_AFX_4_A5


title: MAQC_AFX_5_B2


title: MAQC_AFX_5_A3


title: MAQC_AFX_4_B3


title: MAQC_AFX_4_C1


title: MAQC_AFX_4_A3


title: MAQC_AFX_4_D5


title: MAQC_AFX_4_A2


title: MAQC_AFX_5_A4


title: MAQC_AFX_4_A1


title: MAQC_AFX_5_A1


title: MAQC_AFX_3_D4


title: MAQC_AFX_3_D5


title: MAQC_AFX_3_D3


title: MAQC_AFX_6_C4


title: MAQC_AFX_3_C5


title: MAQC_AFX_3_B4


title: MAQC_AFX_3_C2


title: MAQC_AFX_3_B2


title: MAQC_AFX_3_D1


title: MAQC_AFX_3_D2


title: MAQC_AFX_3_A4


title: MAQC_AFX_2_D4


title: MAQC_AFX_3_A1


title: MAQC_AFX_3_C1


title: MAQC_AFX_3_A2


title: MAQC_AFX_3_B1


title: MAQC_AFX_2_D1


title: MAQC_AFX_2_C1


title: MAQC_AFX_2_C2


title: MAQC_AFX_2_C3


title: MAQC_AFX_2_D2


title: MAQC_AFX_2_B3


title: MAQC_AFX_2_C4


title: MAQC_AFX_2_B4


title: MAQC_AFX_3_C3


title: MAQC_AFX_3_A3


title: MAQC_AFX_3_B3


title: MAQC_AFX_2_D3


title: MAQC_AFX_3_A5


title: MAQC_AFX_2_D5


title: MAQC_AFX_3_B5


title: MAQC_AFX_1_D5


title: MAQC_AFX_2_A4


title: MAQC_AFX_3_C4


title: MAQC_AFX_2_A5


title: MAQC_AFX_1_D2


title: MAQC_AFX_1_C5


title: MAQC_AFX_1_D4


title: MAQC_AFX_2_A2


title: MAQC_AFX_2_B5


title: MAQC_AFX_2_B1


title: MAQC_AFX_2_A1


title: MAQC_AFX_1_D3


title: MAQC_AFX_2_C5


title: MAQC_AFX_1_D1


title: MAQC_AFX_2_A3


title: MAQC_AFX_1_C4


title: MAQC_AFX_1_C3


title: MAQC_AFX_1_C2


title: MAQC_AFX_1_B4


title: MAQC_AFX_1_B5


title: MAQC_AFX_1_A5


title: MAQC_AFX_1_A2


title: MAQC_AFX_1_A3


title: MAQC_AFX_1_B3


title: Col-0_4day_red illumination_+lincomycin_rep1

status: Public on Sep 06 2006

description: Arabidopsis thaliana seeds were obtained from the Arabidopsis Biological Resource Centre (ABRC) at Ohio State University (Columbus, OH). . Seeds were surface sterilized and plated on 1/2 Murashige Skoog (MS) medium (Caisson laboratories; Rexburg, ID) containing 1% sucrose with or without 5 µM  norflurazon (Sandoz Pharmaceuticals; Vienna, Austria) or 220 µg/ml lincomycin (Sigma; St Luis, MO).

data_processing: 8 array were normalized using RMA method hosted by Bioconductor

label: biotin.

source_name: 4 day old, dark grown + 30 min red light, whole seedlings+ 200 microgram/ml

label_protocol: Affymetrix protocol

growth_protocol: Seedlings were grown at 21C, in darkness and tissue was collected after a 30 min red light treatment

treatment_protocol: Seeds were surface sterilized and plated on 1/2 Murashige Skoog (MS) medium containing 1% sucrose  with 220 µg/ml lincomycin.

value: 4 days


title: MAQC_AFX_1_A4


title: MAQC_AFX_1_C1


title: MAQC_AFX_2_B2


title: Col-0_4day_red illumination _+lincomycin_rep2

source_name: 4 day old, dark grown + 30 min red light, whole seedlings+ 200 microgram/ml lincomycin


title: Col-0_4day_dark_-lincomycin_rep2

source_name: 4 day old, dark grown, whole seedlings

growth_protocol: Seedlings were grown at 21C, in darkness and tissue was collected before a 30 min red light treatment

treatment_protocol: Seeds were surface sterilized and plated on 1/2 Murashige Skoog (MS) medium containing 1% sucrose  without 220 µg/ml lincomycin.


title: MAQC_AFX_1_B1


title: MAQC_AFX_1_B2


title: MAQC_AFX_1_A1


title: Col-0_4day_dark_+lincomycin_rep1

source_name: 4 day old, dark grown, whole seedlings+ 200 microgram/ml lincomycin


title: Col-0_4day_red illumination_-lincomycin_rep2

source_name: day old, dark grown + 30 min red light, whole seedlings


title: Col-0_4day_dark_-lincomycin_rep1


title: MII-stage oocytes

status: Public on Sep 05 2006

city: Bar Harbor

first: You-Qiang

last: Su

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Mature MII-stage oocytes isolated from 22-24d old eCG(44-46h)/hCG(14h)- treated mice.

hyb_protocol: Standard AffyMetrix procedures

scan_protocol: Standard AffyMetrix

data_processing: Probe level data were imported into the R software environment and expression values were summarized using the RMA (Robust MultiChip Average) function (Irizarry et al., 2003) in the R/affy package with rma2 background adjustment, no inter-array normalization, and median polish summarization of perfect match values (Gautier et al., 2004). To account for the difference in starting RNA amount obtained from the same number of GV and MII oocytes, and based on the fact that there is no new transcriptional activity in the fully grown oocytes (De La Fuente, 2006), a normalization was performed on a sample of non-differentially expressed genes which were estimated and sampled using EM algorithm for a normal mixture model (Gautier et al., 2004; McLachlan and Krishnan, 1997)

label: Biotin

source_name: oocyte

label_protocol: Total RNA was extracted from oocytes using the PicoPure RNA Isolation Kit according to the manufacturer?s instruction. The RNA quality and yield of each sample were determined using the Bioanalyzer 2100 and RNA 6000 Pico LabChip assay (Agilent Technologies Inc, Palo Alto, CA) in combination with Quant-iTTM RiboGreen Reagent according to supplied protocols (Invitrogen, Carlsbad, CA).  Ten nanograms of total RNA from each sample was employed in the two-round cDNA synthesis and subsequent in vitro-transcription according to the Two-Cycle Eukaryotic Target Labeling Assay (Affymetrix Expression Analysis Technical Manual: ? Section 2: Eukaryotic Sample and Array Processing? (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)) with the following modifications.  For the first and second cycle of cDNA synthesis steps, Full Spectrum? MultiStart Primers for in vitro transcription (SystemBiosciences, Mountain View, CA) were used, instead of Affymetrix?s standard T7-Oligo(dT) primer or random hexamers.

growth_protocol: MII oocytes were washed thoroughly in the collection medium to ensure that no cumulus cells were present.  Medium used for oocyte collection was the same as for collection of GV-oocytes

extract_protocol: Total RNA was extracted from 300 oocytes using the Picopure RNA isolation Kit (Arcturus, Mountain View, CA).

treatment_protocol: Ovarian follicular development was stimulated by intraperitoneal injection of 5 IU of eCG (EMD Biosciences, Inc., Calbiochem, La Jolla, CA).  Mice were then injected with hCG (5IU/mouse), and the oviducts were removed 14 h post hCG injection.  Ovulated OCCs were released by gently teasing apart the ampulla of oviducts.  Denuded oocytes were obtained by incubating the mass of OCCs in medium containing 1 mg/ml of hyaluronidase for about 3-5 min at 37 ºC.  Mature oocytes with a visible first polar body (hereafter termed MII oocytes) and no apparent sign of degeneration were collected.  Both GV and MII oocytes were washed thoroughly in the collection medium to ensure that no cumulus cells were present.

tag: Mature MII-oocytes isolated from eCG(44-46h)/hCG (14h) treated 22-24 days old female (C57BL/6JxSJL)F1 mice


title: Col-0_4day_red illumination_-lincomycin_rep1

source_name: 4 day old, dark grown + 30 min red light, whole seedlings


title: Mature MII-oocyte sample #2

treatment_protocol: Ovarian follicular development was stimulated by intraperitoneal injection of 5 IU of eCG (EMD Biosciences, Inc., Calbiochem, La Jolla, CA).  Mice were then injected with hCG (5IU/mouse), and the oviducts were removed 14 h post hCG injection.  Ovulated OCCs were released by gently teasing apart the ampulla of oviducts.  Denuded oocytes were obtained by incubating the mass of OCCs in medium containing 1 mg/ml of hyaluronidase for about 3-5 min at 37 ?C.  Mature oocytes with a visible first polar body (hereafter termed MII oocytes) and no apparent sign of degeneration were collected.  Both GV and MII oocytes were washed thoroughly in the collection medium to ensure that no cumulus cells were present.

tag: Mature MII-oocyte isolated eCG944-46h)/hCG(14h)-treated female 22-24 days old (C57BL/6JxSJL)F1 mice


title: OX-LDL-treatment, biological rep2

status: Public on Sep 01 2006

city: Baltimore

first: Yanqin

last: Yang

state: MD

address: 600 N. Wolfe Street

institute: The Johns Hopkins University

description: human APRE cell line APRE-19 cells with OX-LDL treatment.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix G3000 GeneArray Scanner

data_processing: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.1.1 (GCOS) software from Affymetrix, using the standard default settings.The details of data nalysis are described in paper.

source_name: APRE-19 cells with OX-LDL treatment

treatment_protocol: ARPE-19 cells were seeded at 100,000/cm2 in T-75 cm2 flasks containing Dulbecco’s Modified Eagle medium with 15 mM Hepes buffer (DMEM; Invitrogen-Gibco BRL, Gaithersberg, MD) and 10% fetal bovine serum (FBS; Invitrogen-Gibco BRL) and 2 mM L-glutamine solution, (Invitrogen-Gibco BRL) at 37oC for 1 week, and serum withdrawn in DMEM+1% bovine serum albumin (BSA) for 3 days to make ARPE-19 cells quiescent11.OX-LDL (Intracel, Frederick, MD was added to the medium for 24 hours.

tag: nonimmortalized human RPE cell line ARPE-19


title: OX-LDL-treatment, biological rep3


title: Col-0_4day_dark_+lincomycin_rep2


title: LDL-treatment, biological rep3

description: human APRE cell line APRE-19 cells with LDL treatment.

source_name: APRE-19 cells with LDL treatment

treatment_protocol: ARPE-19 cells were seeded at 100,000/cm2 in T-75 cm2 flasks containing Dulbecco’s Modified Eagle medium with 15 mM Hepes buffer (DMEM; Invitrogen-Gibco BRL, Gaithersberg, MD) and 10% fetal bovine serum (FBS; Invitrogen-Gibco BRL) and 2 mM L-glutamine solution, (Invitrogen-Gibco BRL) at 37oC for 1 week, and serum withdrawn in DMEM+1% bovine serum albumin (BSA) for 3 days to make ARPE-19 cells quiescent11.LDL (Intracel, Frederick, MD was added to the medium for 24 hours.


title: OX-LDL-treatment, biological rep1


title: Fully grown GV-stage oocyte sample #3

description: Fully grown GV-stage oocytes isolated from 22-24d old eCG-primed mice.

growth_protocol: Released oocyte-cumulus cell complexes (OCCs) were collected and cumulus cells surrounding the oocyte were removed completely by passing OCCs several times through a hand-drawn small fine glass pipette with an inner diameter slightly narrower than the oocyte.  Only those oocytes with an intact GV and no apparent sign of degeneration were collected.   Both GV and MII oocytes were washed thoroughly in the collection medium to ensure that no cumulus cells were present.  Medium used for oocyte collection was MEM-α (Invitrogen Corporation, Grand Island, NY) supplemented with 3 mg/ml of crystallized lyophilized bovine serum albumin (Sigma, St. Louis, MO), 75 mg/liter of penicillin G (Sigma) and 50 mg/liter streptomycin sulfate (Sigma). Milrinone (Sigma), a selective inhibitor of oocyte-specific phosphodiesterase (PDE3), was added into the medium at the concentration of 5 ?M to prevent the GV-stage oocytes from undergoing maturation.

treatment_protocol: Ovarian follicular development was stimulated by intraperitoneal injection of 5 IU of eCG (EMD Biosciences, Inc., Calbiochem, La Jolla, CA).  Immature GV-stage oocytes were collected at 44-46 h post eCG priming by puncturing large antral follicles on ovarian surface with a pair of 26 gauge needles.

tag: GV-stage oocytes isolated from eCG-primed (44-46h) 22-24 days old female (C57BL/6JxSJL)F1 mice


title: LDL-treatment, biological rep1


title: non-treatment, biological rep2

description: human APRE cell line APRE-19 cells without any treatment.

source_name: APRE-19 cells without any treatment

treatment_protocol: ARPE-19 cells were seeded at 100,000/cm2 in T-75 cm2 flasks containing Dulbecco’s Modified Eagle medium with 15 mM Hepes buffer (DMEM; Invitrogen-Gibco BRL, Gaithersberg, MD) and 10% fetal bovine serum (FBS; Invitrogen-Gibco BRL) and 2 mM L-glutamine solution, (Invitrogen-Gibco BRL) at 37oC for 1 week, and serum withdrawn in DMEM+1% bovine serum albumin (BSA) for 3 days to make ARPE-19 cells quiescent11.


title: LDL-treatment, biological rep2


title: non-treatment, biological rep3


title: Mature MII-oocytes Sample #3

tag: Mature MII-stage oocytes isolated eCG(44-46h)/hCG(14h)-treated female 22-24 days old (C57BL/6JxSJL)F1 mice


title: non-treatment, biological rep1


title: Fully grown GV-stage oocytes sample #2


title: Fully grown GV-stage oocytes

label_protocol: Total RNA was extracted from oocytes using the PicoPure RNA Isolation Kit according to the manufacturer’s instruction. The RNA quality and yield of each sample were determined using the Bioanalyzer 2100 and RNA 6000 Pico LabChip assay (Agilent Technologies Inc, Palo Alto, CA) in combination with Quant-iTTM RiboGreen Reagent according to supplied protocols (Invitrogen, Carlsbad, CA).  Ten nanograms of total RNA from each sample was employed in the two-round cDNA synthesis and subsequent in vitro-transcription according to the Two-Cycle Eukaryotic Target Labeling Assay (Affymetrix Expression Analysis Technical Manual: “ Section 2: Eukaryotic Sample and Array Processing” (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)) with the following modifications.  For the first and second cycle of cDNA synthesis steps, Full Spectrum™ MultiStart Primers for in vitro transcription (SystemBiosciences, Mountain View, CA) were used, instead of Affymetrix’s standard T7-Oligo(dT) primer or random hexamers.

growth_protocol: Released oocyte-cumulus cell complexes (OCCs) were collected and cumulus cells surrounding the oocyte were removed completely by passing OCCs several times through a hand-drawn small fine glass pipette with an inner diameter slightly narrower than the oocyte.  Only those oocytes with an intact GV and no apparent sign of degeneration were collected.   Both GV and MII oocytes were washed thoroughly in the collection medium to ensure that no cumulus cells were present.  Medium used for oocyte collection was MEM-α (Invitrogen Corporation, Grand Island, NY) supplemented with 3 mg/ml of crystallized lyophilized bovine serum albumin (Sigma, St. Louis, MO), 75 mg/liter of penicillin G (Sigma) and 50 mg/liter streptomycin sulfate (Sigma). Milrinone (Sigma), a selective inhibitor of oocyte-specific phosphodiesterase (PDE3), was added into the medium at the concentration of 5 µM to prevent the GV-stage oocytes from undergoing maturation.

tag: GV-stage oocytes isolated from eCG primed (44-46h) 22-24d-old female (C57BL/6JxSJL)F1 mice


title: LungTissue_FeedTreatment_Pentachloronitrobenzene_Animal20

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

description: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, pentachloronitrobenzene, 8187 ppm

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: affylmGUI, The Walter and Eliza Hall Institute of Medical Research

source_name: Sample Type: tissue, Tissue: Lung, Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen Rneasy

treatment_protocol: in vivo Treatment: Pentachloronitrobenzene, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Route of Exposure: Diet, Dose or Concentration: 8187, Units of Dose or Concentration: ppm

tag: Array Type

value: Affymetrix Mouse 430_2

tag: Amount to Core

tag: Units of Amount

value: ug

tag: Ratio

tag: RNA Integrity Number

tag: Bioanalyzer Results

value: Good

tag: Sample Preservation

value: RNA later

tag: Strain or Line

tag: NCBI Taxonomy ID

tag: Individual

tag: Developmental State

value: Adult

tag: Sacrifice Method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: Sex

value: Female

tag: Units of Age

value: weeks


title: LiverTissue_GavageTreatment_2,3-Benzofuran_Animal8

description: liver tissue, gavage treatment, 13 weeks, 5 days per week, 2,3-benzofuran, 240 mg per kg

source_name: Sample Type: tissue, Tissue: Liver, Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade

treatment_protocol: in vivo Treatment: 2,3-Benzofuran, Treatment Repeat: 1, Units of Treatment Repeat: day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 240, Units of Dose or Concentration: mg/kg

tag: Dilution

value: Excellent

tag: Age


title: LungTissue_FeedTreatment_Pentachloronitrobenzene_Animal18


title: LiverTissue_FeedTreatment_N-(1-naphthyl)ethylenediamineDihydrochloride_Animal14

description: liver tissue, feed treatment, 13 weeks, 7 days per week, N-1-naphthyl)ethylenediamine dihydrochloride, 2000 ppm

treatment_protocol: in vivo Treatment: N-(1-naphthyl)ethylenediamine dihydrochloride, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Route of Exposure: Diet, Dose or Concentration: 2000, Units of Dose or Concentration: ppm


title: LiverTissue_FeedTreatment_1,5-Naphthalenediamine_Animal4

description: liver tissue, feed treatment, 13 weeks, 7 days per week, 1,5-naphthalenediamine, 2000 ppm

treatment_protocol: in vivo Treatment: 1,5-Naphthalenediamine, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Route of Exposure: Diet, Dose or Concentration: 2000, Units of Dose or Concentration: ppm


title: LiverTissue_GavageTreatment_2,3-Benzofuran_Animal6


title: LungTissue_FeedTreatment_1,5-Naphthalenediamine_Animal2

description: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, 1,5-naphthalenediamine, 2000 ppm


title: LiverTissue_FeedTreatment_1,5-Naphthalenediamine_Animal5


title: LiverTissue_FeedTreatment_Rodent Chow_Control_Animal29

description: liver tissue, feed treatment, 13 weeks, 7 days per week, rodent chow control

treatment_protocol: in vivo Treatment: Rodent Chow, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Route of Exposure: Diet


title: LiverTissue_GavageTreatment_2,3-Benzofuran_Animal10


title: LungTissue_GavageTreatment_2,3-Benzofuran_Animal10

description: lung tissue, right lobe, gavage treatment, 13 weeks, 5 days per week, 2,3-benzofuran, 240 mg per kg


title: LiverTissue_FeedTreatment_Rodent Chow_Control_Animal27


title: LiverTissue_FeedTreatment_Pentachloronitrobenzene_Animal18

description: liver tissue, feed treatment, 13 weeks, 7 days per week, pentachloronitrobenzene, 8187 ppm


title: LiverTissue_FeedTreatment_1,5-Naphthalenediamine_Animal2


title: LiverTissue_FeedTreatment_Rodent Chow_Control_Animal28


title: LiverTissue_FeedTreatment_N-(1-naphthyl)ethylenediamineDihydrochloride_Animal15


title: LiverTissue_GavageTreatment_CornOil_Control_Animal24

description: liver tissue, gavage treatment, 13 weeks, 5 days per week, corn oil vehicle control

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Route of Exposure: Gavage, Dose or Concentration: 5, Units of Dose or Concentration: ml/kg

value: Okay


title: LungTissue_FeedTreatment_1,5-Naphthalenediamine_Animal4


title: LiverTissue_GavageTreatment_CornOil_Control_Animal25


title: LiverTissue_FeedTreatment_Pentachloronitrobenzene_Animal20


title: LungTissue_GavageTreatment_2,3-Benzofuran_Animal6


title: LiverTissue_GavageTreatment_CornOil_Control_Animal22


title: LungTissue_FeedTreatment_Pentachloronitrobenzene_Animal16


title: LiverTissue_FeedTreatment_N-(1-naphthyl)ethylenediamineDihydrochloride_Animal12


title: LiverTissue_FeedTreatment_Pentachloronitrobenzene_Animal16


title: LungTissue_FeedTreatment_N-(1-naphthyl)ethylenediamineDihydrochloride_Animal15

description: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, N-1-naphthyl)ethylenediamine dihydrochloride, 2000 ppm


title: LungTissue_FeedTreatment_N-(1-naphthyl)ethylenediamineDihydrochloride_Animal14


title: LungTissue_FeedTreatment_1,5-Naphthalenediamine_Animal5


title: LungTissue_GavageTreatment_2,3-Benzofuran_Animal8


title: LungTissue_GavageTreatment_CornOil_Control_Animal24

description: lung tissue, right lobe, gavage treatment, 13 weeks, 5 days per week, corn oil vehicle control


title: High Group, Line 2, Replicate 2, female

status: Public on Aug 30 2006

city: Raleigh

first: Alexis

last: Edwards

address: Campus Box 7614

department: Genetics

institute: North Carolina State University

description: Gene expression data from adult female flies of the high group of an artificial selection experiment for aggression.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Drosophila melanogaster

source_name: female Drosophila adults, age 3-7 days

tag: artificially selected, wild-derived lines


title: LungTissue_FeedTreatment_Rodent Chow_Control_Animal28

description: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, rodent chow control

tag: Array Type


title: LungTissue_FeedTreatment_Rodent Chow_Control_Animal27

tag: Amount to Core


title: LungTissue_FeedTreatment_N-(1-naphthyl)ethylenediamineDihydrochloride_Animal12

tag: Units of Amount


title: LungTissue_FeedTreatment_Rodent Chow_Control_Animal29

tag: Ratio


title: LungTissue_GavageTreatment_CornOil_Control_Animal25

tag: RNA Integrity Number


title: High Group, Line 2, Replicate 2, Male

description: Gene expression data from adult male flies of the high group of an artificial selection experiment for aggression.

source_name: Male Drosophila adults, age 3-7 days


title: Control Group, Line 2, Replicate 2, Male

description: Gene expression data from adult male flies of the control group of an artificial selection experiment for aggression.


title: Control Group, Line 1, Replicate 2, Male


title: Low Group, Line 2, Replicate 2, Male

description: Gene expression data from adult male flies of the low group of an artificial selection experiment for aggression.


title: High Group, Line 2, Replicate 1, female


title: Low Group, Line 2, Replicate 2, female

description: Gene expression data from adult female flies of the low group of an artificial selection experiment for aggression.


title: Low Group, Line 1, Replicate 2, Male


title: Control Group, Line 2, Replicate 2, Female

description: Gene expression data from adult female flies of the control group of an artificial selection experiment for aggression.

source_name: Female Drosophila adults, age 3-7 days


title: Control Group, Line 1, Replicate 2, Female


title: LungTissue_GavageTreatment_CornOil_Control_Animal22

tag: Bioanalyzer Results


title: Low Group, Line 2, Replicate 1, Male


title: Control Group, Line 2, Replicate 1, Male


title: High Group, Line 1, Replicate 2, female


title: Control Group, Line 2, Replicate 1, Female


title: High Group, Line 1, Replicate 1, female


title: High Group, Line 1, Replicate 1, Male


title: High Group, Line 1, Replicate 2, Male


title: Low Group, Line 1, Replicate 2, female


title: Low Group, Line 2, Replicate 1, female


title: Control Group, Line 1, Replicate 1, Female


title: Low Group, Line 1, Replicate 1, female


title: Low Group, Line 1, Replicate 1, Male


title: High Group 2, Line 1, Replicate 1, Male


title: Hoxb1-IRES-tauGFP E10.5, rep 1

status: Public on Aug 28 2006

city: Salt Lake City

first: Petr

last: Tvrdik

state: UT

department: Human Genetics

institute: University of Utah

description: Comparison of gene expression profiles in rhombomere 4 of E10.5 mouse embryos expressing either normal endogenous Hox-B1 protein or the paralogous Hox-A1 protein from the Hoxb1 locus.

data_processing: Bioconductor affy package

source_name: Hoxb1-IRES-tauGFP mouse embryos, rhombomere 4

tag: FACS-sorted GFP-positive cells from hindbrains of E10.5 mouse embryos with normal Hoxb1 gene co-expressing tauGFP through the IRES element.


title: Hoxb1-IRES-tauGFP E10.5, rep 2


title: Hoxb1>A1-IRES-tauGFP E10.5, rep 3

source_name: Hoxb1>A1-IRES-tauGFP mouse embryos, rhombomere 4

tag: FACS-sorted GFP-positive cells from hindbrains of gene-swapped E10.5 mouse embryos expressing the Hox-A1 protein from the Hoxb1 locus and co-expressing tauGFP through the IRES element.


title: Hoxb1-IRES-tauGFP E10.5, rep 3


title: Control Group, Line 1, Replicate 1, Male


title: Hoxb1>A1-IRES-tauGFP E10.5, rep 2


title: FACS-purified B cells_129SV/EV_non-infected_rep4

status: Public on Aug 26 2006

first: Michael

middle: E.

last: Salazar

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

description:
B cells from control mice (uninfected wild type)
Array 18 - 18.N.B._482.CEL

hyb_protocol: Hybridized washed and stained with streptavidin-PE per the manufacturer's protocol (Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 253

data_processing: The dataset was preprocessed using the following procedures: (1) background correction; (2) normalization using the quantile method (Bolstad et al. 2003); (3) summarization of probe set values using the RMA (Robust Multi-array Analysis) method, which fits a specified robust linear model to the probe level data. The abovementioned procedures were performed using the Bioconductor package “affyPLM”.

source_name: B cells - wildtype mice - not infected

label_protocol: Bioarray (Enzo)

growth_protocol: Mice were bred and held under conventional housing conditions in filtertop cages

extract_protocol: RNAeasy kit (Qiagen)

tag: Strain

tag: Gender

tag: Tissue

value: Lymph node B cell

tag: Noninfected


title: Hoxb1>A1-IRES-tauGFP E10.5, rep 1


title: FACS-purified B cells_IFNAR1-/-_influenza-infected_rep1

description:
B cells from flu-infected mice (IFNR knockout)
Array 22 - 22.N.B._561.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 258

source_name: B cells - IFNAR1-/-mice - influenza-infected

treatment_protocol: Infected with influenza A/Mem71 virus for 2 days

value: Mediastinal lymph node B cell

tag: Influenza A/Mem71 48h


title: FACS-purified B cells_wildtype_influenza-infected_rep1

description:
B cells from flu-infected mice (wild type)
Array 19 - 19.N.B._493.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 254

source_name: B cells -  wildtype mice - influenza-infected


title: FACS-purified B cells_129SV/EV_IFN-b-stimulated_rep1

description:
B cells from wild type mice treated with IFN-b
Array 23 - 23.N.B._565.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 262

source_name: B cells -  wildtype mice - IFN-b stimulated

treatment_protocol: In vitro exposure to IFN-b (17 hours, 2000U/ml)

tag: 17h treatment IFN-beta (2000U/ml)


title: FACS-purified B cells_IFNAR1-/-_influenza-infected_rep4

description:
B cells from flu-infected mice (IFNR knockout)
Array 32 - 32.N.B._630.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 261

value: 129SV/EV IFNAR1-/-


title: FACS-purified B cells_129SV/EV_influenza-infected_rep4

description:
B cells from flu-infected mice (wild type)
Array 33 - 33.N.B._633.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 257


title: FACS-purified B cells_IFNAR1-/-_influenza-infected_rep3

description:
B cells from flu-infected mice (IFNR knockout)
Array 27 - 27.N.B._620.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 260


title: FACS-purified B cells_IFNAR1-/-_influenza-infected_rep2

description:
B cells from flu-infected mice (IFNR knockout)
Array 24 - 24.N.B._566.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 259


title: FACS-purified B cells_129SV/EV_IFN-b-stimulated_rep4

description:
B cells from wild type mice treated with IFN-b
Array 34 - 34.N.B._638.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 265


title: FACS-purified B cells_129SV/EV_IFN-b-stimulated_rep2

description:
B cells from wild type mice treated with IFN-b
Array 25 - 25.N.B._569.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 263


title: FACS-purified B cells_129SV/EV_influenza-infected_rep3

description:
B cells from flu-infected mice (wild type)
Array 21 - 21.N.B._528.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 256


title: FACS-purified B cells_129SV/EV_IFN-b-stimulated_rep3

description:
B cells from wild type mice treated with IFN-b
Array 26 - 26.N.B._581_1.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 264


title: Wild type 1 Thymus, Whole thymus: Amplified mRNA_le1 1

status: Public on Aug 24 2006

description:
Flow cytometry sorted double negative thymocytes from wild type animal #1.
Treatment, type=fractionate

source_name: Thymus, Whole thymus


title: FACS-purified B cells_129SV/EV_influenza-infected_rep2

description:
B cells from flu-infected mice (wild type)
Array 20 - 20.N.B._494.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 255


title: Wild type 3 Thymus, Whole thymus: Amplified mRNA_le1

description:
Flow cytometry sorted double negative thymocytes from wild type animal #3.
Treatment, type=fractionate


title: FACS-purified B cells_wildtype_non-infected_rep2

description:
B cells from control mice (uninfected wild type)
Array 16 - 16.N.B._473.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 251


title: FACS-purified B cells_wildtype_non-infected_rep1

description:
B cells from control mice (uninfected wild type)
Array 15 - 15.N.B._467.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 250


title: Double KO 2 Thymus, Whole thymus: Amplified mRNA_le1

description:
Flow cytometry sorted double negative thymocytes from Egr1/Egr3 double knockout animal #2.
Treatment, type=fractionate


title: Double KO 3 Thymus, Whole thymus: Amplified mRNA_le1

description:
Flow cytometry sorted double negative thymocytes from Egr1/Egr3 double knockout animal #3.
Treatment, type=fractionate


title: Double KO 1 Thymus, Whole thymus: Amplified mRNA_le1

description:
Flow cytometry sorted double negative thymocytes from Egr1/Egr3 double knockout animal #1.
Treatment, type=fractionate


title: Wild type 2 Thymus, Whole thymus: Amplified mRNA_le1

description:
Flow cytometry sorted double negative thymocytes from wild type animal #2.
Treatment, type=fractionate


title: Mittler_1-5_MBF1c_Rep2_ATH1

status: Public on Aug 15 2006

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: Growth conditions: Arabidopsis thaliana plants (cv. Columbia) were grown in peat pellets (Jiffy-7, Shippagan, Canada), under controlled conditions: 21oC, 14 h light cycle, 100 micro mol m-2 s-1 and a relative humidity of 70% (E-30, AR-66; Percival Scientific, Perry, IA).

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

source_name: Columbia:At3g24500 overexpression

tag: Developmental stage

value: 3-week-old non-bolting plants

value: whole plant

tag: Genetic background

value: Columbia

tag: Genetic variation

value: At3g24500 overexpression


title: Crx-Nr2e3-Nrl-ko-Gfp4W-4

status: Public on Aug 18 2006

city: Ann Arbor

first: Swaroop

last: Anand

state: MI

address: 1000 Wall St.

department: Ophthalmology & Visual Sciences

institute: University of Michigan

description:
The transgenic Crx-Nr2e3-Nrl-ko-Gfp samples were compared to Nrl-ko-Gfp
at 4weeks. The Nrl-ko-Gfp data has already been submitted to GEO with series entry GSE4051

hyb_protocol: Affymetrix Standard Protocol

scan_protocol: Affymetrix

data_processing: RMA normalization method was used to obtain expression scores

source_name: Gfp purified photoreceptors

label_protocol: Nugene Kit

extract_protocol: Trizol

value: Mix 129X1/SvJ and C57BL/6J and Sjl

value: Mix

tag: Age

value: retina


title: Mittler_1-3_control_Rep3_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)

source_name: Columbia


title: Mittler_1-4_MBF1c_Rep1_ATH1


title: Crx-Nr2e3-Nrl-ko-Gfp4W-3


title: Mukhtar_1-4_WK27-XVE-ETL_Rep1_ATH1

description:
Growth protocol: Plants were grown on soil (Metro Mix 200) at 22°C under a 10 -- 14 h light -- dark cycle
Location: Growth Chamber
Growth substrate: commercial soil
Average daily humidity (%): 65
Average daily temperature (°C): 22

treatment_protocol: Plant were treated for 6 hours with 10mM beta-oestradiol after which RNA was immediately isolated.

value: gene knock out - enhancer trap


title: Zarka_3-3_MT-E24B_Rep1_ATH1

description:
growth media substrate: phytagar   (0.80%)
light intensity: 100 umol m-2 s-1
light regime: continuous light
light source: fluorescence
nutrients: Gamborg's B5 salts 1X
stratification: cold  (4oC)   for 4 days
average daily temperature: 24C  (10 days)
vitamins: Gamborg's B5 salts

treatment_protocol: Four plates, each containing approximately 100 35S::CBF2 (E2) plants, were individually harvested after 10 d of growth.

value: 10 day old

value: whole plants

value: CBF2 overexpressor under 35S promoter


title: Mittler_1-6_MBF1c_Rep3_ATH1


title: Crx-Nr2e3-Nrl-ko-Gfp4W-2


title: Zarka_2-8_MT-7DCB(SOIL)_Rep2_ATH1

description:
temperature: cold  (4oC)   for 7 days
growth media substrate: soils  (Bacto mix)
light intensity: 100 umol m-2 s-1
light regime: continuous light
light source: fluorescence
stratification: cold  (4oC)   for 4 days
average daily temperature: 22C for 10 days

treatment_protocol: Flats containing the plants were transferred to 4 degree celsius under continuous light (~25 umol m-2 s-1) and tissue samples were harvested after 7 days at 4 degree celsius

tag: Stock Code

value: 18 days old

value: whole plants, above ground (not roots)


title: Mukhtar_1-2_XVE-ETL_Rep1_ATH1

value: gene knock out - enhancer trap. Genes modified - At5g52830


title: Zarka_3-1_MT-WSA_Rep1_ATH1

treatment_protocol: Four plates, each containing approximately 100 wild type plants, were invidually harvested after 10 d of growth.


title: Crx-Nr2e3-Nrl-ko-Gfp4W-1


title: Mukhtar_1-3_WK27-XVE-SALK_Rep1_ATH1

source_name: XVE-SALK


title: Zarka_2-4_MT-1HCB(SOIL)_Rep2_ATH1

description:
temperature: cold  (4oC)   for 1 hour
growth media substrate: soils  (Bacto mix)
light intensity: 100 umol m-2 s-1
light regime: continuous light
light source: fluorescence
stratification: cold  (4oC)   for 4 days
average daily temperature: 22C for 10 days

treatment_protocol: Flats containing the plants were transferred to 4 degree celsius under continuous light (~25 umol m-2 s-1) and tissue samples were harvested after 1 hour at 4 degree celsius


title: Mittler_1-1_control_Rep1_ATH1


title: Mukhtar_1-1_XVE-SALK_Rep1_ATH1


title: Mittler_1-2_control_Rep2_ATH1


title: Zarka_2-3_MT-1HCA(SOIL)_Rep1_ATH1


title: Zarka_2-1_MT-0HCA(SOIL)_Rep1_ATH1

description:
temperature: cold  (4oC)   for 0 hours
growth media substrate: soils  (Bacto mix)
light intensity: 100 umol m-2 s-1
light regime: continuous light
light source: fluorescence
stratification: cold  (4oC)   for 4 days
average daily temperature: 22C for 10 days

treatment_protocol: This was a control sample and was harvested under the biosample growth conditions.


title: Zarka_2-7_MT-7DCA(SOIL)_Rep1_ATH1


title: Zarka_3-4_MT-E2A_Rep1_ATH1


title: Zarka_2-2_MT-0HCB(SOIL)_Rep2_ATH1


title: Zarka_2-5_MT-24HCA(SOIL)_Rep1_ATH1

description:
temperature: cold  (4oC)   for 24 hours
growth media substrate: soils  (Bacto mix)
light intensity: 100 umol m-2 s-1
light regime: continuous light
light source: fluorescence
stratification: cold  (4oC)   for 4 days
average daily temperature: 22C for 10 days

treatment_protocol: Flats containing the plants were transferred to 4 degree celsius under continuous light (~25 umol m-2 s-1) and tissue samples were harvested after 24 hours at 4 degree celsius


title: Zarka_1-8_MT-WT7DB_Rep2_ATH1

description:
temperature: 4C   for 7 days
growth media substrate: phytagar  0.80%
light intensity : 100 umol m-2 s-1
light regime: continuous light
light source: fluorescence
nutrients: Gamborg's B5 salts  1X
stratification: 4C  for 4 days
average daily temperature: 24C  for 10 days

treatment_protocol: Plates containing the plants were transferred to 4 degree celsius under continuous light (~25 umol m-2 s-1) and tissue samples were harvested after 7 days at 4 degree celsius.


title: Zarka_3-2_MT-WSB_Rep2_ATH1


title: Zarka_2-6_MT-24HCB(SOIL)_Rep2_ATH1


title: Zarka_1-7_MT-WT7DA_Rep1_ATH1


title: Zarka_1-6_MT-WT24HB_Rep2_ATH1

description:
temperature: 4C   for 24 hours
growth media substrate: phytagar  0.80%
light intensity : 100 umol m-2 s-1
light regime: continuous light
light source: fluorescence
nutrients: Gamborg's B5 salts  1X
stratification: 4C  for 4 days
average daily temperature: 24C  for 10 days

treatment_protocol: Plates containing the plants were transferred to 4 degree celsius under continuous light (~25 umol m-2 s-1) and tissue samples were harvested after 24 hour at 4 degree celsius.


title: Zarka_1-1_MT-WT0HA_Rep1_ATH1

description:
temperature: 4C   for 0 hours
growth media substrate: phytagar  0.80%
light intensity : 100 umol m-2 s-1
light regime: continuous light
light source: fluorescence
nutrients: Gamborg's B5 salts  1X
stratification: 4C  for 4 days
average daily temperature: 24C  for 10 days


title: Zarka_1-5_MT-WT24HA_Rep1_ATH1


title: Zarka_1-2_MT-WT0HB_Rep2_ATH1


title: Zarka_1-4_MT-WT1HB_Rep2_ATH1

description:
temperature: 4C   for1 hours
growth media substrate: phytagar  0.80%
light intensity : 100 umol m-2 s-1
light regime: continuous light
light source: fluorescence
nutrients: Gamborg's B5 salts  1X
stratification: 4C  for 4 days
average daily temperature: 24C  for 10 days

treatment_protocol: Plates containing the plants were transferred to 4 degree celsius under continuous light (~25 umol m-2 s-1) and tissue samples were harvested after 1 hour at 4 degree celsius.


title: Somerville_1-11_stem-GH8_Rep2_ATH1

description:
growth space: controlled system
light intensity: 125 umol m-2s-1
light source: fluorescence
light regime: long day
photoperiod: 16 hr
day temperature: 25 C
night temperature: 20 C

value: 29 days after germination

value: Upper 2" of the stem minus siliques and pedicels


title: Somerville_1-10_stem-GH7_Rep1_ATH1


title: Somerville_1-1_leaf-GC2_Rep1_ATH1

value: 15 days after germination

value: rosette leaf


title: Somerville_1-7_flower-GH6_Rep2_ATH1

value: Developed flowers and unopened buds


title: Somerville_1-4_flower-GC5_Rep1_ATH1


title: Somerville_1-3_leaf-GH2_Rep2_ATH1

description:
growth space: greenhouse
light intensity: 125 umol m-2s-1
light source: fluorescence
light regime: long day
photoperiod: 16 hr
day temperature: 25 C
night temperature: 20 C


title: Zarka_1-3_MT-WT1HA_Rep1_ATH1

description:
temperature: 4C   for 1 hours
growth media substrate: phytagar  0.80%
light intensity : 100 umol m-2 s-1
light regime: continuous light
light source: fluorescence
nutrients: Gamborg's B5 salts  1X
stratification: 4C  for 4 days
average daily temperature: 24C  for 10 days

treatment_protocol: Plates containing the plants were transferred to 4 degree celsius under continuous light (~25 umol m-2 s-1) and tissue samples were harvested after 1 hour at 4 degree celsius..

value: whole plant


title: Mittler_2-9_Zat12_Rep3_ATH1

description: Growth conditions: Hydrogen peroxide treatment was performed by applying 20 mM hydrogen peroxide for 1 hour. All seedlings were grown in liquid culture (MS) and sampled at the same time as described by Davletova et al., 2005

value: 5-day old seedlings

value: seedlings

value: Columbia

value: transgenic Arabidopsis constitutively expressing the zinc-finger protein Zat12 (At5g59820) under the control of the 35S-CaMV promoter


title: Mittler_2-11_Zat12+H2O2_Rep2_ATH1

treatment_protocol: 20 mM hydrogen peroxide for 1 hour


title: Eulgem_1-1_Col-0-untreated_Rep1_AG

description:
na
na

value: 2 week old plants

value: Leaves


title: Mittler_2-5_wildtype+H2O2_Rep2_ATH1


title: Mittler_2-10_Zat12+H2O2_Rep1_ATH1


title: Somerville_1-5_flower-GC6_Rep2_ATH1


title: Somerville_1-9_stem-GC8_Rep2_ATH1


title: Mittler_2-7_Zat12_Rep1_ATH1


title: Mittler_2-6_wildtype+H2O2_Rep3_ATH1


title: Mittler_2-12_Zat12+H2O2_Rep3_ATH1


title: Mittler_2-8_Zat12_Rep2_ATH1


title: Eulgem_1-3_Col-0-MKK2-w.t.4_Rep1_AG


title: Somerville_1-2_leaf-GH1_Rep1_ATH1


title: Mittler_2-4_wildtype+H2O2_Rep1_ATH1


title: Somerville_1-6_flower-GH5_Rep1_ATH1


title: Mittler_2-3_wildtype_Rep3_ATH1


title: Mittler_2-2_wildtype_Rep2_ATH1


title: De Veylder_1-7_E2Fa-Dpa_Rep3_ATH1

description:
Seed sterilisation: Seeds were surface sterilized with 15% sodium hypochloride for 10 min
Growth protocol: Plants were grown on 1x Murashige and Skoog medium (Duchefa, Haarlem, The Netherlands) and 0.6% plant tissue culture agar (LabM, Bury, UK) at 22°C and 65 ?E?m 2?s 1 radiation in a 16 h light/8 h dark photoperiod.
Location: Growth chamber
Growth substrate: Agar
Growth medium: 1x Murashige and Skoog basal salt mixture
Sample description: Total seedlings were harvested 6 days after germiantion (8 days after sowing)


title: Edwards_3-2_fri-flc1_Rep1_ATH1

description:
Location: growth chamber
growthsubstrate: Agar
Temperature: 22oC
Medium: Murashige and Skoog basal salt mixture
Seed stratification: Stratified in darkness at 4degC for 4-5 days in liquid (0.15%) Agar.
Seed sterilisation: Seed were surface sterilized in 70% ethanol for 2 min, immediately followed by 8 min in 50% bleach, and then were rinsed twice in sterile distilled water.
Growth protocol: Seedlings were plated on Murashige-Skoog 1.5% agar medium containing 3% sucrose and grown for 6 days under constant light of  55-60 micro mol m-2sec-1 cool white fluorescent light. They were then entrained for 4 days at 22°C under (12 hr/12 hr) light/dark cycles of 75 micro mol m-2sec-1 cool white fluorescent light. At dawn on the 4th day of entrainment seedlings were transferred to constant 25 micro mol m-2sec-1 cool white fluorescent light at 27°C.

treatment_protocol: The seedlings were placed into constant light at 27degC following entrainment to 12h/12h light dark cycles at 22degC. Four samples were taken at 6h intervals starting 24h after transfer to the 27degC constant light conditions at times 24, 30, 36 and 42h. Equal amounts of total RNA were pooled from each timepoint to produce one sample averaged over one circadian cycle.

value: At5g10140  gene_knock_out


title: De Veylder_1-3_wildtype_Rep3_ATH1


title: Somerville_1-8_stem-GC7_Rep1_ATH1


title: De Veylder_1-5_E2Fa-Dpa_Rep1_ATH1


title: De Veylder_1-1_wildtype_Rep1_ATH1


title: Hennig_1-4_flower-buds-CK_021114_1_B_Rep2_ATH1

description: Experimental Design: Plants (Arabidopsis L. Heynh., accession Landsberg erecta) were grown in growth chambers at 70% humidity and daily cycles of 16 h light at 21°C and 8 h darkness at 21°C. Plant material used for the experiments was pooled from 12 plants. Samples contained complete flower buds. About 10% of the tissues for each sample were cleared and analyzed by microscopy to ensure that homogenous developmental stages were harvested. The entire experiment was performed twice providing independent biological replicates.

source_name: Landsberg erecta

value: 6 weeks

value: closed flower buds shortly before pollination


title: De Veylder_1-6_E2Fa-Dpa_Rep2_ATH1


title: Pieterse_1-11_Foccidentalis-24h_Rep1_ATH1

description: Growth protocol: Seeds were sown in quartz sand for two weeks. Two-week-old seedlings were transferred to 60-mL pots containing a sand - potting soil mixture that was autoclaved twice for 20 min. Plants were cultivated in a growth chamber with a 8-h day (200 uEm-2.sec-1 at 24oC) and 16-h night (20oC) cycle at 70percent  relative humidity for another 3 weeks. Plants were watered every other day and received half-strength Hoagland nutrient solution containing 10 uM Sequestreen once a week.

treatment_protocol: The population of the Western flower thrips Frankliniella occidentalis originated from a greenhouse infestation on chrysanthemum. This virus-free population was reared on Phaseolus vulgaris cv. Prelude pods, supplied with Pinus pollen, in glass jars that were placed at 25°C in a growth chamber with a 16-h day and 8-h night cycle as described (Kindt et al., 2003). Thrips infestations were performed by transferring 20 larvae of F. occidentalis to each Arabidopsis Col-0 plant.


title: Hennig_1-3_siliques-CK_021114_3_A_Rep1_ATH1

description: Experimental Design: Plants (Arabidopsis L. Heynh., accession Landsberg erecta) were grown in growth chambers at 70% humidity and daily cycles of 16 h light at 21°C and 8 h darkness at 21°C. Plant material used for the experiments was pooled from 12 plants. Samples only siliques without withering flower organs were harvested. About 10% of the tissues for each sample were cleared and analyzed by microscopy to ensure that homogenous developmental stages were harvested. The entire experiment was performed twice providing independent biological replicates.

value: siliques 2 d after pollination


title: Edwards_3-4_fri-flc2_Rep2_ATH1

description:
Location: growth chamber
growthsubstrate: Agar
Temperature: 22oC
Medium: Murashige and  Skoog basal salt mixture
Seed stratification: Stratified in darkness at 4degC for 4-5 days in liquid (0.15%) Agar.
Seed sterilisation: Seed were surface sterilized in 70% ethanol for 2 min, immediately followed by 8 min in 50% bleach, and then were rinsed twice in sterile distilled water.
Growth protocol: Seedlings were plated on Murashige-Skoog 1.5% agar medium containing 3% sucrose and grown for 6 days under constant light of  55-60 micro mol m-2sec-1 cool white fluorescent light. They were then entrained for 4 days at 22°C under (12 hr/12 hr) light/dark cycles of 75 micro mol m-2sec-1 cool white fluorescent light. At dawn on the 4th day of entrainment seedlings were transferred to constant 25 micro mol m-2sec-1 cool white fluorescent light at 27°C.


title: Hennig_1-2_flowers-CK_021114_2_A_Rep1_ATH1

description: Experimental Design: Plants (Arabidopsis L. Heynh., accession Landsberg erecta) were grown in growth chambers at 70% humidity and daily cycles of 16 h light at 21°C and 8 h darkness at 21°C. Plant material used for the experiments was pooled from 12 plants. Samples contained complete flowers. About 10% of the tissues for each sample were cleared and analyzed by microscopy to ensure that homogenous developmental stages were harvested. The entire experiment was performed twice providing independent biological replicates.

value: open pollinated flowers


title: Pieterse_1-10_Prapae-24h_Rep1_ATH1

treatment_protocol: Tissue-chewing larvae of the small cabbage white butterfly Pieris rapae were reared on Brussels sprout plants (Brassica oleracea gemmifera cv. Cyrus) in a growth chamber with a 16-h day and 8-h night cycle (21°C; 50-70% relative humidity), as described previously (Van Poecke et al., 2001). Infestation of Arabidopsis Col-0 plants was carried out by transferring five first-instar larvae of P. rapae to each plant using a fine paintbrush.


title: Hennig_1-6_siliques-CK_021114_3_B_Rep2_ATH1


title: Edwards_3-1_FRI-FLC-wt1_Rep1_ATH1

source_name: FRI; FLC


title: De Veylder_1-8_E2Fa-Dpa_Rep4_ATH1


title: Pieterse_1-14_Mpersicae-72h_Rep1_ATH1

treatment_protocol: Phloem-feeding green peach aphids (Myzus persicae) were maintained on Brassica chinensis L. cv. Granaat under greenhouse conditions (25°C; 50-70% relative humidity). The 16-h light period prevented sexual reproduction, keeping the population clonal. Arabidopsis Col-0 plants were infested with M. persicae by transferring 40 nymphs and apterous adults to each plant (Van Poecke et al., 2003).


title: De Veylder_1-2_wildtype_Rep2_ATH1


title: De Veylder_1-4_wildtype_Rep4_ATH1


title: Pieterse_1-8_Abrassicicola-48h_Rep1_ATH1

treatment_protocol: Bioassays with the fungal leaf pathogen Alternaria brassicicola strain MUCL 20297 were carried out as described by Ton et al. (MPMI, 2002). Briefly, A. brassicicola was grown on potato dextrose agar plates for 2 weeks at 22°C. Subsequently, conidia were collected as described by Broekaert et al. (1990). Five-week-old susceptible pad3-1 plants were challenge inoculated by applying 3-µL drops of 10 mM MgSO4 containing 106 spores per mL onto all fully expanded leaves of 5-week-old plants.


title: Edwards_3-3_FRI-FLC-wt2_Rep2_ATH1


title: Mittler_2-1_wildtype_Rep1_ATH1


title: Pieterse_1-7_Abrassicicola-24h_Rep1_ATH1


title: Pieterse_1-12_Foccidentalis-48h_Rep1_ATH1


title: Hennig_1-1_flower-buds-CK_021114_1_A_Rep1_ATH1


title: FACS-purified B cells_129SV/EV_non-infected_rep3

description:
B cells from control mice (uninfected wild type)
Array 17 - 17.N.B._478.CEL

scan_protocol: Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 252

value: Female

value: Lymph node B cell


title: Pieterse_1-9_Prapae-12h_Rep1_ATH1


title: Pieterse_1-6_avrPstDC3000-24h_Rep1_ATH1

treatment_protocol: P. syringae pv. tomato DC3000 with the plasmid pV288 carrying avirulence gene avrRpt2 (Kunkel et al., 1993) was cultured overnight at 28°C in liquid King's medium B, supplemented with 25 mg.L-1  kanamycin to select for the plasmid. Subsequently, bacterial cells were collected by centrifugation and resuspended in 10 mM MgSO4 to a final density of 107 cfu.mL-1. Wild-type Col-0 plants were inoculated by pressure infiltrating a suspension of P. syringae pv. tomato DC3000(avrRpt2) at 107 cfu.mL-1 into all fully expanded leaves of 5-week-old plants.


title: Pieterse_1-13_Mpersicae-48h_Rep1_ATH1


title: Hennig_1-5_flowers-CK_021114_2_B_Rep2_ATH1


title: Pieterse_1-5_avrPstDC3000-12h_Rep1_ATH1

description: Growth protocol: Seeds were sown in quartz sand for two weeks. Two-week-old seedlings were transferred to 60-mL pots containing a sand - potting soil mixture that was autoclaved twice for 20 min. Plants were cultivated in a growth chamber with a 8-h day (200 uEm-2.sec-1 at 24oC) and 16-h night (20oC) cycle at 70% relative humidity for another 3 weeks. Plants were watered every other day and received half-strength Hoagland nutrient solution containing 10 uM Sequestreen once a week.


title: Pieterse_1-2_Control-24h_Rep1_ATH1


title: Thorlby_1-2_3h-post-freeze_REP3_ATH1

description:
stratification: 2 days at 4°C
Growth protocol: Plants were grown in Levington?s Plant Protection compost in a growth room with a 9/15 day/night cycle at 20°C until they reached growth stage 1.14. For Cold acclimation plants were then transferred to a growth room at 4°C with the same day/night cycle.
Location: Growth Room
Sample description: Samples were either from a cold acclimated plant or such a plant that had been frozen and allowed to recover at 20°C in the dark for either 3 hours or 24 hours.

treatment_protocol: For cold acclimation plants were transferred to a growth room at 4°C with a 9/15 hour day/night cycle. Material was harvested after 11 days of growth at hour 5 of the light cycle (cold acclimated control). At the end of the light cycle plants were frozen at 6.0°C for 20 hours, then placed at 20°C in the dark for 3 hours, at which time a sample was collected. Plants were left in the dark at 20°C for a total of 24 hours at which time a second sample was collected.

value: all aerial parts


title: Shirras_3-1_LabCalcicole-1mM-CaCl2_Rep1_ATH1

description:
location: Growth Room
Atmosphere: Normal
Humidity: 55%
Temperature: 22C
Lighting: 10 hour days
Medium: sterile sand
Nutrients: 0.5X Long Ashton solution
Water: daily

treatment_protocol: 1 mM CaCl2

value: Whole plant


title: Thorlby_1-3_24h-post-freeze_REP3_ATH1


title: Shirras_3-5_WildEcotype-low-soil-pH-1mM-CaCl2_Rep1_ATH1

treatment_protocol: 1mM CaCl2


title: Pieterse_1-4_Control-72h_Rep1_ATH1


title: Heinekamp_1-11_cs-shoot_Rep3_ATH1

value: shoot


title: Shirras_3-7_WildEcotype-low-soil-pH-12.5mM-CaCl2_Rep1_ATH1

treatment_protocol: 12.5 mM CaCl2


title: Shirras_3-6_WildEcotype-high-soil-pH-1mM-CaCl2_Rep1_ATH1


title: Heinekamp_1-9_control-shoot_Rep3_ATH1


title: Shirras_3-3_LabCalcicole-12.5mM-CaCl2_Rep1_ATH1


title: Shirras_3-4_LabCalcifuge-12.5mM-CaCl2_Rep1_ATH1


title: Heinekamp_1-7_cs-shoot_Rep2_ATH1


title: Heinekamp_1-3_cs-shoot_Rep1_ATH1


title: Heinekamp_1-2_control-root_Rep1_ATH1

value: root


title: Heinekamp_1-6_control-root_Rep2_ATH1


title: Pieterse_1-1_Control-12h_Rep1_ATH1


title: Heinekamp_1-4_cs-root_Rep1_ATH1


title: Helenius_1-3_ERD15-oex-non-treated_Rep1_ATH1

description:
Stratification: The sterilized seeds were kept in the dark at +4ºC for 2-4 days before plating
Storage conditions: The seeds were stored at +4ºC.
Growth protocol: The seeds were germinated on ½ x MS media (0,7% agar, 2% sucrose, 0,1% MES, pH 5,7) containing 50 µg/ml kanamycin. After 5-7 days the seedlings were transferred to pots containing a mixture of peat and vermiculite (1:1). The plants were grown in a growth room with a temperature of 22ºC and a relative humidity of 70%. The photoperiod was 12 h of light and 12 h of dark.
Location: Growth Room
Growth substrate: peat-vermiculite (1:1) mixture

source_name: ERD15 oex 52

treatment_protocol: oex-non-treated: The plants were sprayed with distilled water containing 0,07% EtOH (=control for ABA treatment). The samples were collected after 90 min. Rosette leaves from three plants were pooled.

value: 3 week old soil-grown plant

value: rosette leaves


title: Heinekamp_1-8_cs-root_Rep2_ATH1


title: Helenius_1-2_control-ABA-treated_Rep1_ATH1

treatment_protocol: ABA-treated: The plants were sprayed with 100 microM ABA (diluted in distilled water, stock solution of ABA in 70%EtOH, so the final concentration of EtHO is 0,07%). The samples were collected after 90 min. Rosette leaves from three plants were pooled.


title: Helenius_1-4_ERD15 oex-ABA-treated_Rep1_ATH1

treatment_protocol: oex-ABA-treated: The plants were sprayed with 100 microM ABA (diluted in distilled water, stock solution of ABA in 70%EtOH, so the final concentration of EtOH is 0,07%). The samples were collected after 90 min. Rosette leaves from three plants were pooled.


title: Heinekamp_1-10_control-root_Rep3_ATH1


title: Shirras_3-8_WildEcotype-high-soil-pH-12.5mM-CaCl2_Rep1_ATH1


title: Heinekamp_1-5_control-shoot_Rep2_ATH1


title: Shirras_3-2_LabCalcifuge-1mM-CaCl2_Rep1_ATH1


title: Heinekamp_1-12_cs-root_Rep3_ATH1


title: Thorlby_1-1_cold-acclimated_REP3_ATH1

description:
stratification: 2 days at 4°C
Growth protocol: Plants were grown in Levington?s Plant Protection compost in a growth room with a 9/15 day/night cycle at 20°C until they reached growth stage 1.14. For Cold acclimation plants were then transferred to a growth room at 4°C with the same day/night cycle
Location: Growth Room
Sample description: Samples were either from a cold acclimated plant or such a plant that had been frozen and allowed to recover at 20°C in the dark for either 3 hours or 24 hours.


title: Heinekamp_1-1_control-shoot_Rep1_ATH1


title: Underwood_1-38_E.coli-TUV86-2-fliC-10e8-7h_Rep1_ATH1

description:
stratification: Stratified 3 days at 4degC
growth protocol: Arabidopsis thaliana accession Col-0 plants were grown in soil in growth chambers with a day/night cycle of 12 h/12 h, a light intensity of 100 µE, and a constant temperature of 20°C. Four- to 5-week-old plants were used for experiments.
Location: Growth chamber
Growth  substrate: Commercial soil
Watering: flats were watered every 2-3 days

treatment_protocol: Plants were inoculated by vacuum infiltration with a suspension of E. coli TUV86-2 fliC mutant bacteria at a concentration of 10e8 cfu/ml. Inoculated leaf tissue from at least 15 plants was collected 7 hours after inoculation for RNA isolation.


title: Underwood_1-39_E.coli-TUV86-2-fliC-10e8-7h_Rep2_ATH1


title: Underwood_1-40_E.coli-TUV86-2-fliC-10e8-7h_Rep3_ATH1


title: Underwood_1-36_E.coli-0157-H7-10e8-7h_Rep2_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with a suspension of E. coli O157:H7 bacteria at a concentration of 10e8 cfu/ml. Inoculated leaf tissue from at least 15 plants was collected 7 hours after inoculation for RNA isolation.


title: Underwood_1-34_Mock-Inoculum-7h_Rep4_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with a mock inoculum of distilled/deionized water. Inoculated leaf tissue from at least 15 plants was collected 7 hours after inoculation for RNA isolation.


title: Underwood_1-35_E.coli-0157-H7-10e8-7h_Rep1_ATH1


title: Helenius_1-1_control-non-treated_Rep1_ATH1

description:
Stratification: The sterilized seeds were kept in the dark at +4ºC for 2-4 days before plating.
Storage: The seeds were stored at +4ºC
Growth Protocol: The seeds were germinated on ½ x MS media (0,7% agar, 2% sucrose, 0,1% MES, pH 5,7) containing 50 µg/ml kanamycin. After 5-7 days the seedlings were transferred to pots containing a mixture of peat and vermiculite (1:1). The plants were grown in a growth room with a temperature of 22ºC and a relative humidity of 70%. The photoperiod was 12 h of light and 12 h of dark
Location: Growth Room
Growth Substrate: peat-vermiculite (1:1) mixture

treatment_protocol: The plants were sprayed with distilled water containing 0,07% EtOH (=control for ABA treatment). The samples were collected after 90 min


title: Underwood_1-33_Mock-Inoculum-7h_Rep3_ATH1


title: Underwood_1-32_Mock-Inoculum-7h_Rep2_ATH1


title: Pieterse_1-3_Control-48h_Rep1_ATH1


title: Underwood_1-31_Mock-Inoculum-7h_Rep1_ATH1


title: Underwood_1-27_hrpA-10e8-7h_Rep3_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with a suspension of Pseudomonas syringae pv. tomato DC3000 hrpA mutant bacteria at 10e8 cfu/ml. Inoculated leaf tissue from at least 15 plants was collected 7 hours after inoculation for RNA isolation.


title: Underwood_1-30_DC3000-10e8-7h_Rep3_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with a suspension of Pseudomonas syringae pv. tomato DC3000 bacteria at 10e8 cfu/ml. Inoculated leaf tissue from at least 15 plants was collected 7 hours after inoculation for RNA isolation.


title: Underwood_1-25_hrpA-10e8-7h_Rep1_ATH1


title: Underwood_1-26_hrpA-10e8-7h_Rep2_ATH1


title: Underwood_1-19_Mock-Inoculum-10h_Rep1_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with a mock inoculum of distilled/deionized water. Inoculated leaf tissue from at least 15 plants was collected 10 hours after inoculation for RNA isolation.


title: Underwood_1-29_DC3000-10e8-7h_Rep2_ATH1


title: Underwood_1-23_hrpAfliC-10e8-7h_Rep2_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with a suspension of Pseudomonas syringae pv. tomato DC3000 hrpAfliC double mutant bacteria at 10e8 cfu/ml. Inoculated leaf tissue from at least 15 plants was collected 7 hours after inoculation for RNA isolation.


title: Underwood_1-22_hrpAfliC-10e8-7h_Rep1_ATH1


title: Underwood_1-14_Cor-5x10e7-10h_Rep2_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with a suspension of Pseudomonas syringae pv. tomato DC3118 Coronatine- bacteria at a concentration of 5x10e7 cfu/ml. Inoculated leaf tissue from at least 15 plants was collected for RNA isolation.


title: Underwood_1-37_E.coli-0157-H7-10e8-7h_Rep3_ATH1


title: Underwood_1-20_Mock-Inoculum-10h_Rep2_ATH1


title: Underwood_1-18_Cor-hrpS-5x10e7-10h_Rep3_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with a suspension of Pseudomonas syringae pv. tomato DC3118 COR-hrpS double mutant bacteria at a concentration of 5x10e7 cfu/ml. Inoculated leaf tissue from at least 15 plants was collected for RNA isolation.


title: Underwood_1-13_Cor-5x10e7-10h_Rep1_ATH1


title: Underwood_1-17_Cor-hrpS-5x10e7-10h_Rep2_ATH1


title: Underwood_1-16_Cor-hrpS-5x10e7-10h_Rep1_ATH1


title: Underwood_1-12_Mock-Inoculum-24h_Rep3_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with a mock inoculum of distilled/deionized water. Inoculated leaf tissue from at least 15 plants was collected for RNA isolation.


title: Underwood_1-15_Cor-5x10e7-10h_Rep3_ATH1


title: Underwood_1-10_Mock-Inoculum-24h_Rep1_ATH1


title: Underwood_1-3_Cor-10e6-24h_Rep3_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with Pseudomonas syringae DC3118 Coronatine- bacteria at a concentration of 10e6 cfu per ml. Inoculated leaf tissue from at least 15 plants was collected for RNA isolation.


title: Underwood_1-5_Cor-hrpS-10e6-24h_Rep2_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with Pseudomonas syringae DC3118 COR-hrpS double mutant bacteria at a concentration of 10e6 cfu/ml. Inoculated leaf tissue from at least 15 plants was collected for RNA isolation.


title: Underwood_1-7_DC3000-10e6-24h_Rep1_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with Pseudomonas syringae pv. tomato strain DC3000 bacteria at a concentration of 10e6 cfu/ml. Inoculated leaf tissue from at least 15 plants was collected for RNA isolation.


title: Underwood_1-8_DC3000-10e6-24h_Rep2_ATH1


title: Underwood_1-11_Mock-Inoculum-24h_Rep2_ATH1


title: Underwood_1-6_Cor-hrpS-10e6-24h_Rep3_ATH1


title: Underwood_1-24_hrpAfliC-10e8-7h_Rep3_ATH1


title: G4D_TAC_Rep5

status: Public on Aug 12 2006

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description:
An important event in the pathogenesis of heart failure is the development of pathological cardiac hypertrophy. In cultured cardiac cardiomyocytes, the transcription factor Gata4 is required for agonist-induced cardiomyocyte hypertrophy. We hypothesized that in the intact organism Gata4 is an important regulator of postnatal heart function and of the hypertrophic response of the heart to pathological stress. To test
this hypothesis, we studied mice heterozygous for deletion of the second exon of Gata4 (G4D). At baseline, G4D mice had mild systolic and diastolic dysfunction associated with reduced heart weight and decreased cardiomyocyte number. After transverse aortic constriction (TAC), G4D mice developed overt heart failure and eccentric cardiac
hypertrophy, associated with significantly increased fibrosis and cardiomyocyte apoptosis. Inhibition of apoptosis by overexpression of the insulin-like growth factor 1 receptor prevented TAC-induced heart failure in G4D mice. Unlike WT-TAC controls, G4D-TAC cardiomyocytes hypertrophied by increasing in length more than width. Gene expression profiling revealed upregulation of genes associated with apoptosis and
fibrosis, including members of the TGFβ pathway. Our data demonstrate that Gata4 is essential for cardiac function in the postnatal heart. After pressure overload, Gata4 regulates the pattern of cardiomyocyte hypertrophy and protects the heart from loadinduced failure.

data_processing: PLIER algorithm

source_name: Cardiacmyocyte

treatment_protocol: The ligature for aortic banding was sized by tying around a 27 gauge needle. The ligature was placed on the transverse aorta between the brachiocephalic trunk and the left common carotid artery. The identical procedure was used for sham operation, except that the aorta was not manipulated.

tag: This allele contains a deletion of the second coding exon of Gata4, including the start codon and the Nterminal 46% of the coding region. The mice used in this study were all male and on a uniform F1 genetic background resulting from the cross of Gata4WT/Δex2 (abbreviated

tag: G4D) mice, backcrossed for greater than 8 generations into C57BL6/J, to wild-type FVB/N mice. G4D progeny from this cross were present at weaning at the expected Mendelian ratio (104/218, 48%), survived normally to 18 months of age, and had no evidence of structural heart disease (0 out of 15 embryos examined histologically at E15.5-E18.5). Gata4WT/WT littermates (WT) from these crosses were used as controls.


title: Wildtype_TAC_Rep3


title: Wildtype_TAC_Rep6


title: Underwood_1-28_DC3000-10e8-7h_Rep1_ATH1


title: G4D_TAC_Rep4


title: G4D_Sham_Rep5


title: Wildtype_TAC_Rep5


title: G4D_Sham_Rep3


title: G4D_TAC_Rep3


title: Wildtype_Sham_Rep3


title: G4D_Sham_Rep4


title: G4D_Sham_Rep1


title: Wildtype_TAC_Rep1


title: G4D_Sham_Rep2


title: G4D_TAC_Rep6


title: Wildtype_Sham_Rep4


title: Wildtype_TAC_Rep2


title: Wildtype_Sham_Rep2


title: G4D_TAC_Rep1


title: G4D_TAC_Rep2


title: Wildtype_TAC_Rep4


title: SW480_Caff+Act/Caff

status: Public on Aug 11 2006

city: Buffalo

first: Ken

last: Lo

state: NY

address: Elm and Carlton Streets

department: Cancer Genetics

institute: Roswell Park Cancer Institute

hyb_protocol: As per Affymetrix Protocol

scan_protocol: As per Affymetrix Protocol

data_processing: RAW

source_name: SW480 cell line treated with Caffeine and Actinomycin D/Caffeine

label_protocol: As per Affymetrix Protocol

growth_protocol: DMEM with 10% FBS and antibiotics

extract_protocol: TRIZOL protocol

treatment_protocol:
10 mM Caffeine in media (treatment for 4 hours)
Wash 2X with PBS
2ug/mL actinomycin D and 10mM Caffeine in media (treatment for 4 hours)
RNA extraction

tag: Morphology

value: epithelial-like

tag: Species


title: SW480_Caff+Act

source_name: SW480 cell line treated with Caffeine and Actinomycin D

treatment_protocol:
10 mM Caffeine in media (treatment for 4 hours)
Wash 2X with PBS
2ug/mL actinomycin D in media (treatment for 4 hours)
RNA extraction


title: SW480_Em

source_name: SW480 cell line treated with emetine

treatment_protocol:
100ug/mL emetine in media (treatment for 8 hours)
wash 2X with PBS
RNA extraction


title: LS180_Caff+Act

source_name: LS180 cell line treated with Caffeine and Actinomycin D

value: Epithelial

tag: Human Caucasian colon adenocarcinoma


title: LS180_Con

source_name: LS180 cell line untreated

treatment_protocol: no treatment


title: LS180_Caff+Act/Caff

source_name: LS180 cell line treated with Caffeine and Actinomycin D/Caffeine


title: LS180_Em

source_name: LS180 cell line treated with emetine


title: caMCF, biological rep2

status: Public on Aug 10 2006

description: Gene expression data from the cell lines established from solid tumors in SCID mice after transplatation of bsMCF cells

hyb_protocol: Following fragmentation, 8 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

source_name: MCF-10F cells transformed by 17-beta-estradiol

treatment_protocol: bsMCF cells were subcutaneously injected into SCID mice. Solid tumors were grown after transplantation. Cells were derived from the tumor fragments by digestion in enzyme.

tag: Genotype

value: slightly aneuploid


title: SW480_Con

source_name: SW480 cell line untreated

treatment_protocol: untreated


title: bcMCF, biological rep2

description: Gene expression data from the bsMCF cell clone

treatment_protocol: bsMCF cells were cloned and expanded


title: trMCF, biological rep3

description: Gene expression data from estrogen transformed MCF-10F cells; the transformation phenotype was validated by conoly formation in agar-methocel and ductulogenesis in collagen matrix

treatment_protocol: MCF-10F cells were repeatedly treated by 70nM 17-beta-estradiol for 2 weeks


title: trMCF, biological rep2


title: bcMCF, biological rep1


title: caMCF, biological rep3


title: MCF-10F, biological rep2

description: Gene expression data from nontumorigenic ER(-) human breast epithelial cells

source_name: breast epithelial cells derived from fibroadenoma

treatment_protocol: Cells were grown in medium in normal condition without 17-beta-estradiol treatment


title: MCF-10F, biological rep1


title: Wildtype_Sham_Rep1


title: Seedling_wild-type_rep2

status: Public on Aug 09 2006

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

description: Arabidopsis 10-day-old wild-type seedlings grown under normal growth conditions were used for total RNA isolation. The high-quality total RNA (260/280 ratio between 1.9-2.1 and 260/230 ratio >2.0) was used for microarray analysis

data_processing: Signal intensity was calculated by GCOS1.4 under default parameters

source_name: 10-day-old light-grown Arabidopsis seedlings

growth_protocol: Seeds were surface sterilized with 2% sodium hypochlorite and 0.01% triton X-100 for 5 min followed by rinsing in sterile water for 5 times. Seeds were then suspended in 0.1% agar solution and dispensed on 0.8% agar-gelled MS medium containing 2% sucrose. Plates were sealed and shifted to cold room for 72 h to break dormancy and facilitate uniform germination and then transferred to culture room under continuous illumination.

extract_protocol: TRIzol reagent

tag: Ecotype

value: Columbia

value: light-grown seedlings

tag: Stage


title: Seedling_OETOP6B_rep1

description: Arabidopsis 10-day-old transgenic seedlings (overexpressing rice OsTOP6B cDNA) grown under normal growth conditions were used for total RNA isolation. The high-quality total RNA (260/280 ratio between 1.9-2.1 and 260/230 ratio >2.0) was used for microarray analysis

source_name: 10-day-old light-grown transgenic Arabidopsis seedlings

tag: Tissue

tag: Seedlings:from homozygous transgenic Arabidopsis plants overexpressing rice OsTOP6B (Oryza sativa topoisomerase 6 subunit B) cDNA


title: Seedling_OEA3L5_rep1

description: Arabidopsis 10-day-old transgenic seedlings (overexpressing rice OsTOP6A3 cDNA) grown under normal growth conditions were used for total RNA isolation. The high-quality total RNA (260/280 ratio between 1.9-2.1 and 260/230 ratio >2.0) was used for microarray analysis

tag: Seedlings:from homozygous transgenic Arabidopsis plants overexpressing rice OsTOP6A3 (Oryza sativa topoisomerase 6 subunit A3) cDNA


title: caMCF, biological rep1


title: MCF-10F, biological rep3


title: Seedling_OEA3L5_rep2


title: Seedling_OETOP6B_rep2


title: Seedling_wild-type_rep1


title: embryo at 8-10hour, unfractionated, biological rep2

status: Public on Aug 02 2006

city: Berkeley

first: Soyeon

last: Ahn

address: 367 Evans Hall #3860

institute: UC Berkeley

description: Gene expression data from embryos during first 10 hours after egg laying to see the global and transcript-specific translation profile

hyb_protocol: Following fragmentation, at least 10 microg of cRNA were hybridized on GeneChip Drosophila Genome 2.0 Array.

data_processing: Gene expression measures were computed using the Robust Multichip Average (RMA) method and implemented in the Bioconductor R package.

source_name: Drosophila embryos

extract_protocol: EDTA-treated embryos were lysed in an EDTA extaction buffer (20mM Tris, pH7.4, 140mM KCl, 15mM EDTA, 0.5mM DTT, 1% Triton X-100, 0.1mg/ml cycloheximide, 1mg/ml heparin, 50unit/ml RNasin) and sedimented through 20-50% gradients prepared with the same EDTA lysis buffer, but without Triton X-100.

treatment_protocol: embryos were collected in 2-hour intervals and aged to generate animals 0-2, 4-6 and 8-10 hour old.

tag: Canon S embryos


title: embryo at 8-10hour, unfractionated, biological rep1


title: embryo at 8-10hour, fraction 10-12,EDTA treated biological rep1


title: embryo at 8-10hour, fraction 1-5,EDTA treated biological rep1


title: embryo at 4-6hour, unfractionated, biological rep1


title: embryo at 0-2hour, unfractionated, biological rep2


title: embryo at 8-10hour, fraction 8-9,EDTA treated biological rep1


title: trMCF, biological rep1

data_processing: The data were analyzed with dChip softwareusing invariant-set normalization method.


title: embryo at 8-10hour, fraction 6-7,EDTA treated biological rep1


title: embryo at 4-6hour, fraction 10-12,EDTA treated biological rep1


title: embryo at 4-6hour, unfractionated, biological rep2


title: embryo at 0-2hour, fraction 10-12,EDTA treated biological rep1


title: embryo at 0-2hour, unfractionated, biological rep1


title: embryo at 4-6hour, fraction 6-7,EDTA treated biological rep1


title: embryo at 4-6hour, fraction 8-9,EDTA treated biological rep1


title: embryo at 0-2hour, fraction 6-7,EDTA treated biological rep1


title: embryo at 8-10hour, fraction 10, biological rep2

extract_protocol: the dechorionated embryos were first incubated with 0.1mg/ml cycloheximide in PBS for 10 minutes on ice, then homogenized with a motorized plastic pellet pestle in a lysis buffer (20mM Tris-HCl, pH7.4, 140mM Kcl, 5mM MgCl2, 0.5mM DTT, 1% Triton X-100, 0.1mg/ml cycloheximide, 1mg/ml heparin, 50unit/ml RNasin) and incubated for 10 minutes on ice. The nuclei and debris were removed by centrifugation at 12,000x g for 10min at 4oC, and supernatants was loaded onto 20-50% sucrose gradients with the same extraction buffer without Triton x-100.


title: embryo at 4-6hour, fraction 1-5,EDTA treated biological rep1


title: embryo at 0-2hour, fraction 1-5,EDTA treated biological rep1


title: embryo at 8-10hour, fraction 12, biological rep2


title: embryo at 8-10hour, fraction 11, biological rep2


title: embryo at 0-2hour, fraction 8-9,EDTA treated biological rep1


title: bcMCF, biological rep3


title: embryo at 8-10hour, fraction 10, biological rep1


title: embryo at 8-10hour, fraction 1-5, biological rep2


title: embryo at 8-10hour, fraction 12, biological rep1


title: embryo at 8-10hour, fraction 7, biological rep2


title: embryo at 8-10hour, fraction 8, biological rep2


title: embryo at 8-10hour, fraction 7, biological rep1


title: embryo at 8-10hour, fraction 8, biological rep1


title: embryo at 8-10hour, fraction 6, biological rep2


title: embryo at 8-10hour, fraction 6, biological rep1


title: embryo at 8-10hour, fraction 1-5, biological rep1


title: embryo at 8-10hour, fraction 9, biological rep1


title: embryo at 4-6hour, fraction 12, biological rep2


title: embryo at 4-6hour, fraction 10, biological rep2


title: embryo at 4-6hour, fraction 7, biological rep2


title: embryo at 4-6hour, fraction 8, biological rep2


title: embryo at 4-6hour, fraction 6, biological rep2


title: embryo at 8-10hour, fraction 11, biological rep1


title: embryo at 4-6hour, fraction 12, biological rep1


title: embryo at 4-6hour, fraction 1-5, biological rep2


title: embryo at 4-6hour, fraction 11, biological rep2


title: embryo at 4-6hour, fraction 7, biological rep1


title: embryo at 4-6hour, fraction 9, biological rep2


title: embryo at 4-6hour, fraction 6, biological rep1


title: embryo at 4-6hour, fraction 11, biological rep1


title: embryo at 4-6hour, fraction 8, biological rep1


title: embryo at 4-6hour, fraction 1-5, biological rep1


title: embryo at 0-2hour, fraction 12, biological rep2


title: embryo at 4-6hour, fraction 10, biological rep1


title: embryo at 0-2hour, fraction 9, biological rep2


title: embryo at 8-10hour, fraction 9, biological rep2


title: embryo at 0-2hour, fraction 10, biological rep2


title: embryo at 4-6hour, fraction 9, biological rep1


title: embryo at 0-2hour, fraction 9, biological rep1


title: embryo at 0-2hour, fraction 6, biological rep2


title: embryo at 0-2hour, fraction 11, biological rep1


title: embryo at 0-2hour, fraction 8, biological rep2


title: embryo at 0-2hour, fraction 7, biological rep1


title: embryo at 0-2hour, fraction 10, biological rep1


title: embryo at 0-2hour, fraction 12, biological rep1


title: embryo at 0-2hour, fraction 7, biological rep2


title: embryo at 0-2hour, fraction 1-5, biological rep1


title: embryo at 0-2hour, fraction 8, biological rep1


title: embryo at 0-2hour, fraction 11, biological rep2


title: embryo at 0-2hour, fraction 6, biological rep1


title: embryo at 0-2hour, fraction 1-5, biological rep2


title: LPS DONOR 2

city: Los Angeles

first: Benhur

last: Lee

address: 609 Charles E Young Dr East

department: MIMG

institute: UCLA

description: LPS matured MDDCs

data_processing: GCOS v 1.2 normalized to all probe sets

source_name: monocyte derived dendritic cells

tag: LPS matured MDDCs


title: Vehicle Control DONOR 3

description: MDDCS treated with vehicle only

tag: MDDCS treated with vehicle only


title: Vehicle Control DONOR 2

description: MDDCS treated with vehicle only


title: Galectin-1 DONOR 1

description: mature MDDCs

tag: galectin-1 matured MDDCs


title: Vehicle Control DONOR 1

description: MDDCS treated with vehicle only


title: LPS DONOR 3

description: LPS matured MDDCs


title: untreated DONOR 2

description: immature monocyte derived dendritic cells


title: untreated DONOR 1

description: immature MDDCs

tag: immature MDDCs


title: untreated DONOR 3

description: immature MDDCs

tag: immatured monocyte derived dendritic cells


title: Galectin-1 DONOR 3

description: galectin-1 matured monocyte derived dendritic cells


title: LPS DONOR 1

description: LPS matured MDDCs


title: Galectin-1 DONOR 2

tag: galectin-1 matured dendritic cells


title: StratUnivRNA_10ug_Rep_2

status: Public on Jul 25 2006

city: Tampa

first: Sean

last: Yoder

state: FL

address: 12902 Magnolia Dr.

department: Molecular Genomics Core Facility

institute: Moffitt Cancer Center & Research Institute

description: Stratagene Universal Human Reference RNA

hyb_protocol: Affymetrix eukaryotic target prep

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: MAS 5.0 scaled to 500

label_protocol: Affymetrix eukaryotic target prep

extract_protocol: MAS 5.0 Signal Intensity


title: StratUnivRNA_5ug_Rep_2

source_name: Stratagene Universal Human Reference RNA


title: StratUnivRNA_10ug

source_name: Stratagene Universal Reference RNA

tag: Stratagene Universal Reference RNA


title: StratUnivRNA_2ug_3

tag: Stratagene Universal Human Reference RNA


title: StratUnivRNA_1ug_1_Rep_2


title: StratUnivRNA_2ug_2


title: StratUnivRNA_1ug_3_Rep_2


title: StratUnivRNA_1ug_2


title: StratUnivRNA_1ug_2_Rep_2


title: StratUnivRNA_2ug_5


title: StratUnivRNA_5ug


title: StratUnivRNA_1ug_1


title: StratUnivRNA_2ug_4

source_name: MAS 5.0 Signal Intensity

tag: MAS 5.0 Signal Intensity


title: StratUnivRNA_2ug_1


title: StratUnivRNA_2ug


title: StratUnivRNA_2ug_Rep_2


title: KPL_pnd0.5_20_refLitter_Mouse430_2_KWGU011601_a

status: Public on Jul 22 2006

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix
Target Amplified protocol: Affymetrix Two-Cycle cDNA synthesis protocol (701025 Rev 5)
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2235

hyb_protocol: Affymetrix standard protocol (701021 Rev 4) Amount labeled  target hybridization to array: 15 ug

data_processing: Analysis method: Affymetrix GCOS and SAS Microarray Solutions GCOS Tgt value: 500

source_name: Whole animal

extract_protocol: Gaido protocol: 'RNA isolation from whole testes'

treatment_protocol:
pool size: 8 whole embryos (4 male & 4 female)
Pooled sample: Yes
Dissection Method: NA
Experimental Design: P0.5 whole embryo RNA (4 male & 4 female) provided by Steve Potter.  This sample represents the universal standard for cross comparison of microarray data.

tag: gene reported

value: wild-type

tag: strain

tag: Sex

value: both (male & female)

tag: developmental stage

value: pnd 0.5

tag: theiler stage

tag: somite count

tag: developmental landmark


title: StratUnivRNA_1ug_3


title: KPL_gd11_19_ovary_Mouse430_2_KWGU011601_a

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix
Target Amplified protocol: Affymetrix Two-Cycle cDNA synthesis protocol (701025 Rev 5)
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2234

source_name: Gonad (Ovary)

treatment_protocol:
pool size: 3
Pooled sample: Yes
Dissection Method: Whole organ excision
CD-1 mice are time-mated within a 2 hour window.  Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal ovaries are removed from fetuses at gestation days 11, 12, 14, 16, 18, and postnatal day 2, snap frozen in liquid nitrogen and stored at -80ºC.

value: gd 11


title: KPL_gd11_18_ovary_Mouse430_2_KWGU011601_a

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix
Target Amplified protocol: Affymetrix Two-Cycle cDNA synthesis protocol (701025 Rev 5)
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2233

source_name: Gonad (Ovary) & mesonephros

value: Female


title: KPL_gd11_16_ovary_Mouse430_2_KWGU011601_a

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix
Target Amplified protocol: Affymetrix Two-Cycle cDNA synthesis protocol (701025 Rev 5)
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2232


title: KPL_gd14_10_ovary_Mouse430_2_KWGU011601_a

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix
Target Amplified protocol: Affymetrix Two-Cycle cDNA synthesis protocol (701025 Rev 5)
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2226

source_name: Ovary

value: gd 14


title: KPL_gd14_12_ovary_Mouse430_2_KWGU011601_a

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix
Target Amplified protocol: Affymetrix Two-Cycle cDNA synthesis protocol (701025 Rev 5)
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2228