title: U2OS_empty pSG213 vector_24 hours of doxycycline induction - Replica 2

description: U2OS cells transfected with an empty pSG213 vector after 24 hours of doxycycline induction - Replica 2

source_name: U2OS human osteosarcoma cell line, doxycycline-inducible vector pSG213, 24h induction

tag: U2OS (human osteosarcoma cell line) transfected with the doxycycline-inducible vector pSG213 treated for 24h with 2ug/ml doxycycline.


title: U2OS_HA-tagged PRDM5_24 hours of doxycycline induction - Replica 1

status: Public on Jan 26 2009

type: RNA

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: U2OS cells transfected with an HA-tagged PRDM5 cloned onto the pSG213 doxycycline-inducible vector, after 24 hours of doxycycline induction - Replica 1

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.

scan_protocol: Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.

data_processing: The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: U2OS human osteosarcoma cell line, HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213, 24h induction

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.  The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.

growth_protocol: U2OS cell lines were maintained in DMEM supplemented with 100 ug/ml streptomycin, 100 ug/ml penicillin, 2 mM glutamine, 10% tetracyclin free serum and 1,5 ug/ml puromycin at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the four independent RNA extractions.

treatment_protocol: Doxycycline treatments were performed by adding 2ug/ml oxycycline to the culture medium.

tag: U2OS (human osteosarcoma cell line) transfected with HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213 treated for 24h with 2ug/ml doxycycline to induce transgene expression.


title: U2OS_HA-tagged PRDM5_24 hours of doxycycline induction - Replica 2

description: U2OS cells transfected with an HA-tagged PRDM5 cloned onto the pSG213 doxycycline-inducible vector, after 24 hours of doxycycline induction - Replica 2


title: U2OS_empty pSG213 vector_24 hours of doxycycline induction - Replica 1

description: U2OS cells transfected with an empty pSG213 vector after 24 hours of doxycycline induction - Replica 1


title: Mammary Gland_WT_rep3

city: Philadelphia

first: Mathew

last: Casimiro

state: PA

address: 1035 BLSB, 233 South 10th street

department: Cancer Biology

country: USA

institute: Thomas Jefferson University

description: Gene expression data from WT mouse mammary gland compared to mice deficient for Caveolin-3

hyb_protocol: The hybridization protocol was followed for single probe array 49 format (standard)/64 format array outlined in genechip expression analysis technical manual provided by Affymetrix. This was also true for washing, staining and scanning procedures.

scan_protocol: Mouse 430 2.0 chips scanned using Gene chip scanner 3000 with autoloader following Affymetrix guidelines. Image aquired using Gene Chip Operating Sofware version 1.4.

data_processing: The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm.

label: Biotin

organism: Mus musculus

source_name: Mammary Gland

label_protocol: Total RNA (5µg of RNeasy purified) was reverse transcribed using Superscript III First-Strand Synthesis System (Invitrogen) using a HPLC purified T7-dT24 primer (Sigma Genosys) which contains the T7 polymerase promoter sequence. The single stranded cDNA was converted to double stranded cDNA using DNA polymerase I (promega) and purified by cDNA spin column purification using GeneChip Sample Cleanup Module (Affymetrix). The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix). 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module.

growth_protocol: No specific growth protocol

extract_protocol: Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.

treatment_protocol: No treatment

tag: FVB/N genetic background. 4-month old

tag: virgin female mice were used, mice were kept on a 12-hour

tag: light/dark cycle with ad libitum access to chow and water


title: U2OS_HA-tagged PRDM5_8 hours of doxycycline induction - Replica 1

description: U2OS cells transfected with an HA-tagged PRDM5 cloned onto the pSG213 doxycycline-inducible vector, after 8 hours of doxycycline induction - Replica 1

source_name: U2OS human osteosarcoma cell line, HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213, 8h induction

tag: U2OS (human osteosarcoma cell line) transfected with HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213 treated for 8h with 2ug/ml doxycycline to induce transgene expression.


title: U2OS_HA-tagged PRDM5_48 hours of doxycycline induction - Replica 2

description: U2OS cells transfected with an HA-tagged PRDM5 cloned onto the pSG213 doxycycline-inducible vector, after 48 hours of doxycycline induction - Replica 2

source_name: U2OS human osteosarcoma cell line, HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213, 48h induction

tag: U2OS (human osteosarcoma cell line) transfected with HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213 treated for 48h with 2ug/ml doxycycline to induce transgene expression.


title: Mammary Gland_WT_rep1


title: Mammary Gland_WT_rep2


title: U2OS_empty pSG213 vector_8 hours of doxycycline induction - Replica 2

description: U2OS cells transfected with an empty pSG213 vector after 8 hours of doxycycline induction - Replica 2

source_name: U2OS human osteosarcoma cell line, doxycycline-inducible vector pSG213, 8h induction

tag: U2OS (human osteosarcoma cell line) transfected with the doxycycline-inducible vector pSG213 treated for 8h with 2ug/ml doxycycline.


title: U2OS_HA-tagged PRDM5_8 hours of doxycycline induction - Replica 2

description: U2OS cells transfected with an HA-tagged PRDM5 cloned onto the pSG213 doxycycline-inducible vector, after 8 hours of doxycycline induction - Replica 2


title: Individual_4503_PP_sample

status: Public on Jan 25 2009

city: Ann Arbor

first: Goncalo

last: Abecasis

state: MI

address: 1420 Washington Heights

department: Biostatistics

institute: University of Michigan

hyb_protocol: Procedure used standard Affymetrix protocol.

data_processing: The raw data from 180 microarrays were processed using the Robust Multichip Average (RMA) method. The expression values in the table were after adjustment of RMA expression values (on the log scale) to account for batch and sex effects.

extract_protocol:
Two biopsies were taken from each patient; one 6mm punch biopsy was obtained from lesional skin of each patient (involved sample) and the other from non-lesional skin (uninvolved sample), taken at least 10 cm away from any active plaque. One biopsy was obtained from each healty control. The non-lesional and control biopsies were taken from the buttocks or upper thighs.
Biopsies were snap-frozen in liquid nitrogen, stored at -80°C.  At processing the biopsy samples were homogenized while still frozen and total RNA isolation was performed using RNeasy kit protocol (Qiagen, Chatsworth, Ca, USA).

tag: involved skin from cases


title: Individual_3937_PP_sample

scan_protocol: Procedure used standard Affymetrix protocol.


title: Individual_4093_PP_sample

label_protocol: Procedure used standard Affymetrix protocol.


title: Individual_4356_PP_sample


title: Individual_5849_PP_sample


title: Individual_3777_PP_sample


title: Individual_3983_PP_sample


title: Individual_4344_PP_sample


title: Individual_3992_PP_sample


title: Individual_3822_PP_sample


title: Individual_4089_PP_sample


title: Individual_4688_PP_sample


title: Individual_511_PP_sample


title: Individual_4389_PP_sample


title: Individual_5331_PP_sample


title: Individual_3586_PP_sample


title: Individual_4079_PP_sample


title: Individual_4160_PP_sample


title: Individual_4616_PP_sample


title: Individual_3591_PP_sample


title: Individual_5414_PP_sample


title: Individual_5177_PP_sample


title: Individual_3140_PP_sample


title: Individual_4609_PP_sample


title: Individual_4213_PP_sample


title: Individual_5325_PP_sample


title: Individual_953_PP_sample


title: Individual_5258_PP_sample


title: Individual_4368_PP_sample


title: Mammary Gland_Cav-3KO_rep2


title: Individual_4208_PP_sample


title: Individual_4294_PP_sample


title: Individual_4164_PP_sample


title: Individual_4362_PP_sample


title: Individual_4284_PP_sample


title: Individual_4426_PP_sample


title: Individual_4165_PP_sample


title: Individual_5242_PP_sample


title: Individual_4216_PP_sample


title: Individual_4177_PP_sample


title: Individual_4505_PP_sample


title: Individual_3171_PP_sample


title: Individual_4163_PP_sample


title: Individual_3059_PP_sample


title: Individual_4934_PP_sample


title: Individual_4697_PP_sample


title: Individual_4269_PP_sample


title: Individual_4247_PP_sample


title: Individual_4257_PP_sample


title: Individual_4298_PP_sample


title: Individual_3690_PP_sample


title: Individual_4339_PP_sample


title: Individual_4397_PP_sample


title: Individual_777_PP_sample


title: Individual_4334_PP_sample


title: Individual_4136_PP_sample


title: Individual_649_PP_sample


title: Individual_4162_PP_sample


title: Individual_4160_PN_sample

tag: uninvolved skin from cases


title: Individual_4503_PN_sample


title: Individual_5331_PN_sample


title: Individual_5414_PN_sample


title: Individual_4093_PN_sample


title: Individual_4213_PN_sample


title: Individual_3822_PN_sample


title: Individual_3777_PN_sample


title: Individual_3586_PN_sample


title: Individual_4609_PN_sample


title: Individual_511_PN_sample


title: Individual_5325_PN_sample


title: Individual_3591_PN_sample


title: Individual_3992_PN_sample


title: Individual_4089_PN_sample


title: Individual_3937_PN_sample


title: Individual_5849_PN_sample


title: Individual_3983_PN_sample


title: Individual_4688_PN_sample


title: Individual_3140_PN_sample


title: Individual_4344_PN_sample


title: Individual_5177_PN_sample


title: Individual_4616_PN_sample


title: Individual_582_PP_sample


title: Individual_4079_PN_sample


title: Individual_4389_PN_sample


title: Individual_4356_PN_sample


title: Individual_5258_PN_sample


title: Individual_953_PN_sample


title: Individual_4334_PN_sample


title: Individual_4257_PN_sample


title: Individual_4294_PN_sample


title: Individual_4208_PN_sample


title: Individual_3690_PN_sample


title: Individual_4397_PN_sample


title: Individual_4284_PN_sample


title: Individual_4426_PN_sample


title: Individual_4505_PN_sample


title: Individual_4368_PN_sample


title: Individual_777_PN_sample


title: Individual_4163_PN_sample


title: Individual_3059_PN_sample


title: Individual_4697_PN_sample


title: Individual_4136_PN_sample


title: Individual_4269_PN_sample


title: Individual_4216_PN_sample


title: Individual_4177_PN_sample


title: Individual_5242_PN_sample


title: Individual_4362_PN_sample


title: Individual_3171_PN_sample


title: Individual_4298_PN_sample


title: Individual_4247_PN_sample


title: Individual_582_PN_sample


title: Individual_4165_PN_sample


title: Individual_4162_PN_sample


title: Individual_4164_PN_sample


title: Individual_4934_PN_sample


title: Individual_649_PN_sample


title: Individual_4339_PN_sample


title: Individual_5749_NN_sample

tag: normal skin from controls


title: Individual_5919_NN_sample


title: Individual_5844_NN_sample


title: Individual_4977_NN_sample


title: Individual_5660_NN_sample


title: Individual_4778_NN_sample


title: Individual_4968_NN_sample


title: Individual_5575_NN_sample


title: Individual_5905_NN_sample


title: Individual_4708_NN_sample


title: Individual_5942_NN_sample


title: Individual_5579_NN_sample


title: Individual_4874_NN_sample


title: Individual_4607_NN_sample


title: Individual_5293_NN_sample


title: Individual_4124_NN_sample


title: Individual_5936_NN_sample


title: Individual_4618_NN_sample


title: Individual_5839_NN_sample


title: Individual_5883_NN_sample


title: Individual_4649_NN_sample


title: Individual_4990_NN_sample


title: Individual_5935_NN_sample


title: Individual_5305_NN_sample


title: Individual_5324_NN_sample


title: Individual_5295_NN_sample


title: Individual_4641_NN_sample


title: Individual_5346_NN_sample


title: Individual_5815_NN_sample


title: Individual_4378_NN_sample


title: Individual_5292_NN_sample


title: Individual_5223_NN_sample


title: Individual_5257_NN_sample


title: Individual_5248_NN_sample


title: Individual_5023_NN_sample


title: Individual_4992_NN_sample


title: Individual_5256_NN_sample


title: Individual_5281_NN_sample


title: Individual_4626_NN_sample


title: Individual_4391_NN_sample


title: Individual_999027_NN_sample


title: Individual_5008_NN_sample


title: Individual_5079_NN_sample


title: Individual_4935_NN_sample


title: Individual_5243_NN_sample


title: Individual_4999_NN_sample


title: Individual_5063_NN_sample


title: Individual_4952_NN_sample


title: Individual_5050_NN_sample


title: Individual_4382_NN_sample


title: Individual_5093_NN_sample


title: Individual_4981_NN_sample


title: Individual_5143_NN_sample


title: Individual_5144_NN_sample


title: Individual_5030_NN_sample


title: Individual_5147_NN_sample


title: Individual_5247_NN_sample


title: Individual_5142_NN_sample


title: Individual_4908_NN_sample


title: Individual_4598_NN_sample


title: Individual_4379_NN_sample


title: Individual_4288_NN_sample


title: Individual_4689_NN_sample


title: precise excision control starved L3 replicate 3

status: Public on Jan 24 2009

city: Salt Lake City

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah

description: Gene expression data from precise excision control L3 larvae that survived 24 hrs of wet starvation

hyb_protocol: standard Affymetrix 2.0 protocol

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

data_processing: The data were analyzed with dChip and global scaling as the normalization method. See GSE14531 for dCHIP data.

organism: Drosophila melanogaster

source_name: Drosophila control 3rd instar larvae starved for 24 hours

label_protocol: one-cycle cRNA biotin labeling

growth_protocol: All animals were fed a normal lab diet until late L2

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

treatment_protocol: Larvae were fed or isolated as late L2, washed, and starved for 24 hours

tag: Genotype

tag: Age

value: mid-L3 larvae


title: HNF4 null starved L3 replicate 2

description: Gene expression data from HNF4 null mutant L3 larvae that survived 24 hrs of wet starvation

source_name: Drosophila HNF4 null 3rd instar larvae starved for 24 hours


title: precise excision control starved L3 replicate 2


title: HNF4 null starved L3 replicate 1


title: precise excision control starved L3 replicate 1


title: HNF4 null fed L3 replicate 1

description: Gene expression data from HNF4 null mutant L3 larvae that were fed normal food the entire lifespan

source_name: Drosophila HNF4 null 3rd instar larvae fed normal food


title: HNF4 null fed L3 replicate 2


title: HNF4 null fed L3 replicate 3


title: precise excision control fed L3 replicate 3

description: Gene expression data from precise excision control L3 larvae that were fed normal food the entire lifespan

source_name: Drosophila control 3rd instar larvae fed normal food


title: precise excision control fed L3 replicate 1


title: precise excision control fed L3 replicate 2


title: HNF4 null starved L3 replicate 3


title: Individual_4394_NN_sample


title: Hippocampus, APP transgenic animals, BDNF treated, biological rep3

status: Public on Jan 23 2009

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: Gene expression data in brain regions after lentiviral infusion of BDNF, eGFP vs. control in APP transgenic and WT animals

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: RMA-normalized, log2 transformed data

source_name: Mouse brains 4 weeks after lentiviral infection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: APP transgenic and WT mice

extract_protocol: Entorhinal cortices and hippocampi were rapidly dissected from experimental subjects and snap frozen to -80oC.

treatment_protocol: Aged entorhinal cortex and hippocampus were examined one month after entorhinal administration of BDNF lentivirus and compared to controls.

tag: Region

value: Hippocampus

value: APP

tag: Treatment

value: BDNF


title: MM.1s, ATO 6 hours

city: Miami

first: Larry

last: Boise

state: FL

address: 1600 NW 10th Ave

department: Microbiology and Immunology

institute: University of Miami

description: Gene expression data from MM.1s myeloma cell line treated with inorganic arsenical arsenic trioxide (ATO) for 6 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 2.0 Plus Chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Affymetrix GCOS software was used

source_name: MM.1s human myeloma cell line, treated for 6 hours with 2 μM ATO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Multiple myeloma cell lines were cultured at 37°C in a humidified atmosphere with 5% CO2, in RPMI-1640 medium, supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 U/mL of penicillin, 100 μg/mL of streptomycin and 2 mmol/L of L-glutamine

extract_protocol: Total RNA was isolated using the RNeasy® Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Cell lines were treated for 0, 6, and 24 h (and 48 h ATO only) with 2 μM ATO or with either 4 μM DAR (U266), 3 μM DAR (KMS11 and MM.1s), 2 μM DAR (8226/S)

tag: Privately obtained cell line


title: Hippocampus, non-transgenic animals, sham lesion, biological rep2

value: non-transgenic

value: Sham lesion


title: MM.1s, ATO 48 hours

description: Gene expression data from MM.1s myeloma cell line treated with inorganic arsenical arsenic trioxide (ATO) for 48 hours

source_name: MM.1s human myeloma cell line, treated for 48 hours with 2 μM ATO


title: 8226/S, Control, 2

description: Gene expression data from untreated 8226/S myeloma cell line

source_name: 8226/S human myeloma cell line, untreated

tag: Commerical Cell line


title: 8226/S, ATO 24 hours

description: Gene expression data from 8226/S myeloma cell line treated with inorganic arsenical arsenic trioxide (ATO) for 24 hours

source_name: 8226/S human myeloma cell line, treated for 24 hours with 2 μM ATO

tag: Commercial Cell line


title: Hippocampus, non-transgenic animals, sham lesion, biological rep3


title: MM.1s, Control, 2

description: Gene expression data from untreated MM.1s myeloma cell line

source_name: MM.1s human myeloma cell line, untreated


title: KMS11, Control, 2

description: Gene expression data from untreated KMS11 myeloma cell line

source_name: KMS11 human myeloma cell line, untreated


title: MM.1s, ATO 24 hours

description: Gene expression data from MM.1s myeloma cell line treated with inorganic arsenical arsenic trioxide (ATO) for 24 hours

source_name: MM.1s human myeloma cell line, treated for 24 hours with 2 μM ATO


title: KMS11, ATO 48 hours

description: Gene expression data from KMS11 myeloma cell line treated with inorganic arsenical arsenic trioxide (ATO) for 48 hours

source_name: KMS11 human myeloma cell line, treated for 48 hours with 2 μM ATO


title: U266, ATO 48 hours

description: Gene expression data from U266 myeloma cell line treated with inorganic arsenical arsenic trioxide (ATO) for 48 hours

source_name: U266 human myeloma cell line, treated for 48 hours with 2 μM ATO


title: KMS11, ATO 24 hours

description: Gene expression data from KMS11 myeloma cell line treated with inorganic arsenical arsenic trioxide (ATO) for 24 hours

source_name: KMS11 human myeloma cell line, treated for 24 hours with 2 μM ATO


title: 8226/S, ATO 48 hours

description: Gene expression data from 8226/S myeloma cell line treated with inorganic arsenical arsenic trioxide (ATO) for 48 hours

source_name: 8226/S human myeloma cell line, treated for 48 hours with 2 μM ATO


title: Hippocampus, APP transgenic animals, BDNF treated, biological rep4


title: Hippocampus, APP transgenic animals, GFP treated, biological rep2

value: GFP


title: Hippocampus, APP transgenic animals, GFP treated, biological rep4


title: Hippocampus, non-transgenic animals, GFP treated, biological rep2


title: KMS11, DAR 24 hours

description: Gene expression data from KMS11 myeloma cell line treated with organic arsenical darinaparsin (DAR) for 24 hours

source_name: KMS11 human myeloma cell line, treated for 24 hours with 3 μM DAR


title: Hippocampus, APP transgenic animals, BDNF treated, biological rep1


title: 8226/S, DAR 24 hours

description: Gene expression data from 8226/S myeloma cell line treated with organic arsenical darinaparsin (DAR) for 24 hours

source_name: 8226/S human myeloma cell line, treated for 24 hours with 2 μM DAR


title: 8226/S, DAR 6 hours

description: Gene expression data from 8226/S myeloma cell line treated with organic arsenical darinaparsin (DAR) for 6 hours

source_name: 8226/S human myeloma cell line, treated for 6 hours with 2 μM DAR


title: 8226/S, Control, 1


title: 8226/S, ATO 6 hours

description: Gene expression data from 8226/S myeloma cell line treated with inorganic arsenical arsenic trioxide (ATO) for 6 hours

source_name: 8226/S human myeloma cell line, treated for 6 hours with 2 μM ATO


title: U266, ATO 24 hours

description: Gene expression data from U266 myeloma cell line treated with inorganic arsenical arsenic trioxide (ATO) for 24 hours

source_name: U266 human myeloma cell line, treated for 24 hours with 2 μM ATO


title: Hippocampus, APP transgenic animals, GFP treated, biological rep3

description: Gene expression data in brain regions after lentiviral infusion of BDNF, eGFP vs. control in APP transgenic and WT animals

source_name: Mouse brains 4 weeks after lentiviral infection


title: U266, ATO 6 hours

description: Gene expression data from U266 myeloma cell line treated with inorganic arsenical arsenic trioxide (ATO) for 6 hours

source_name: U266 human myeloma cell line, treated for 6 hours with 2 μM ATO


title: U266, Control, 2

description: Gene expression data from untreated U266 myeloma cell line

source_name: U266 human myeloma cell line, untreated


title: Hippocampus, APP transgenic animals, BDNF treated, biological rep2


title: Hippocampus, non-transgenic animals, sham lesion, biological rep1


title: Entorhinal cortex, APP transgenic animals, BDNF treated, biological rep4

value: Entorhinal cortex


title: Entorhinal cortex, APP transgenic animals, GFP treated, biological rep3


title: Entorhinal cortex, APP transgenic animals, GFP treated, biological rep4


title: KMS11, DAR 6 hours

description: Gene expression data from KMS11 myeloma cell line treated with organic arsenical darinaparsin (DAR) for 6 hours

source_name: KMS11 human myeloma cell line, treated for 6 hours with 3 μM DAR


title: KMS11, Control, 1


title: Hippocampus, APP transgenic animals, GFP treated, biological rep1


title: Entorhinal cortex, APP transgenic animals, GFP treated, biological rep2


title: U266, DAR 24 hours

description: Gene expression data from U266 myeloma cell line treated with organic arsenical darinaparsin (DAR) for 24 hours

source_name: U266 human myeloma cell line, treated for 24 hours with 4 μM DAR


title: Entorhinal cortex, non-transgenic animals, sham lesion, biological rep3


title: MM.1s, Control, 1

description: Gene expression data from untreated MM.1s myeloma cell line

source_name: MM.1s human myeloma cell line, untreated


title: MM.1s, DAR 6 hours

description: Gene expression data from MM.1s myeloma cell line treated with organic arsenical darinaparsin (DAR) for 6 hours

source_name: MM.1s human myeloma cell line, treated for 6 hours with 3 μM DAR


title: Hippocampus, non-transgenic animals, GFP treated, biological rep1


title: U266, DAR 6 hours

description: Gene expression data from U266 myeloma cell line treated with organic arsenical darinaparsin (DAR) for 6 hours

source_name: U266 human myeloma cell line, treated for 6 hours with 4 μM DAR


title: MM.1s, DAR 24 hours

description: Gene expression data from MM.1s myeloma cell line treated with organic arsenical darinaparsin (DAR) for 24 hours

source_name: MM.1s human myeloma cell line, treated for 24 hours with 3 μM DAR


title: KMS11, ATO 6 hours

description: Gene expression data from KMS11 myeloma cell line treated with inorganic arsenical arsenic trioxide (ATO) for 6 hours

source_name: KMS11 human myeloma cell line, treated for 6 hours with 2 μM ATO


title: Entorhinal cortex, non-transgenic animals, sham lesion, biological rep2


title: Entorhinal cortex, non-transgenic animals, GFP treated, biological rep2


title: Entorhinal cortex, APP transgenic animals, BDNF treated, biological rep3


title: Entorhinal cortex, non-transgenic animals, sham lesion, biological rep1


title: Entorhinal cortex, APP transgenic animals, BDNF treated, biological rep2


title: Entorhinal cortex, APP transgenic animals, GFP treated, biological rep1


title: A549_miR-NC_rep2

city: Perth

first: Rebecca

last: Webster

address: Rear, 50 Murray St

country: Australia

institute: Western Australian Institute for Medical Research

description: Treatment of A549 cells with miR-NC negative control precursor, biological replicate #2.

hyb_protocol: Hybridization was performed according to the GeneChip Expression Analysis Technical Manual on the Hybridization Station 640. Washing was performed using the GeneChip Fluidics Station 450.

scan_protocol: Scanning was performed using standard Affymetrix procedures with the Affymetrix GeneArray Scanner 3000.

data_processing: Data was processed using the Affymetrix MAS5 statistical algorithm, scaling the target signal to 500 for all probe sets.

source_name: A549 lung carcinoma cell line

label_protocol: Labelling was performed using standard Affymetrix procedures.

extract_protocol: Cells were harvested 24 hours after transfection, using TRIzol Reagent (Invitrogen, Corp.) according to the manufacturer’s instructions up to the point of RNA precipitation in isopropanol. RNA samples were then purified using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions, and eluted in 30 mL of RNase-free water.

tag: Lung carcinoma cell line, ATCC number

value: CCL-185, Sex:Male, Age:58, Ethnicity:Caucasian


title: Entorhinal cortex, APP transgenic animals, BDNF treated, biological rep1


title: Entorhinal cortex, non-transgenic animals, GFP treated, biological rep1


title: A549_miR-NC_rep1

description: Treatment of A549 cells with miR-NC negative control precursor, biological replicate #1.


title: A549_miR-7_rep2

description: Treatment of A549 cells with miR-7 precursor, biological replicate #2.


title: LNCaP Vector 1a

status: Public on Jan 22 2009

city: Baltimore

first: Robert

middle: H

last: Getzenberg

state: MD

address: 600 North Wolfe St., 121 Marburg

department: James Buchanan Bradey Urological Institute

institute: The Johns Hopkins School of Medicine

description: Hybridization was performed by the Johns Hopkins Medical Institutions Microarray Core Facility.

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

source_name: Human prostate cancer cell line LNCaP

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

growth_protocol: RPMI-1640 plus 10% fetal bovine serum

extract_protocol: RNeasy Kit (QIAGEN)

treatment_protocol: LNCaPVector: LNCaP infected with Retroviral vectors, MSCV and selected with puromycin for 72hr (Vector-1a)

tag: The LNCaP androgen-dependent prostate cancer cell line was transfected with Retroviral vector MSCV


title: LNCaP PURa 1a

treatment_protocol: LNCaPPURa: LNCaP infected with Retroviral vectors, MSCVPURaMyc  and selected with puromycin for 72hr (PURa-1a)

tag: The LNCaP androgen-dependent prostate cancer cell line was transfected with Retroviral vector MSCVPURaMyc


title: U266, Control, 1


title: LNCaP PURa 2a

treatment_protocol: LNCaPPURa: LNCaP infected with Retroviral vectors, MSCVPURaMyc  and selected with puromycin for 72hr (PURa-2a)


title: LNCaP Vector 2a

treatment_protocol: LNCaPVector: LNCaP infected with Retroviral vectors, MSCV and selected with puromycin for 72hr (Vector-2a)


title: HeLa_ctrlsiRNA_IPedRNA_replicate4

city: Martinsried

first: Gunter

last: Meister

address: Am Klopferspitz 18

department: Center for Integrated Protein Science Munich (CIPSM)

country: Germany

institute: Max Planck Institute of Biochemistry

description: Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.

hyb_protocol: Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).

scan_protocol: Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.

data_processing: Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.

source_name: HeLa cells, control siRNA transfected

label_protocol: Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.

growth_protocol: HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.

extract_protocol: To analyze mRNA binding to endogenous Ago2, siRNA-transfected cells were harvested 4d post transfection and lysed in lysis buffer (150 mM KCl/25 mM Tris-HCl pH 7.5/2 mM EDTA/1mM NaF/0.5% NP-40/0.5 mM DTT/0.5 mM AEBSF/Ribolock, Fermentas, 1μl per ml of buffer). Lysates were cleared by centrifugation and incubated with anti-Ago2 protein G sepharose beads for 3 h at 4°C. Immunoprecipitates were washed three times with IP wash buffer (300 mM NaCl/50 mM Tris pH 7.5/1mM NaF, 0.01% NP-40/5 mM MgCl2) and once with PBS. IP samples were proteinase K-digested, followed by phenol/chloroform/isopropyl alcohol extraction and precipitation of RNA in 80% ethanol at -20°C. RNA was pelleted, dried and treated with DNaseI (Fermentas) for 30 min at 37°C, followed by thermal inactivation of DNaseI.

treatment_protocol: HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.

tag: HeLa S3 cells


title: HeLa_ctrlsiRNA_IPedRNA_replicate3


title: HeLa_ctrlsiRNA_IPedRNA_replicate1


title: HeLa_Imp8siRNA_IPedRNA_replicate1

source_name: HeLa cells, Importin8 siRNA transfected


title: HeLa_ctrlsiRNA_IPedRNA_replicate2


title: HeLa_TNRC6BsiRNA_totalRNA_replicate1

source_name: HeLa cells, TNRC6B siRNA transfected

extract_protocol: RNA for microarray analysis was isolated using PrepEase Kit for total RNA (USB, USA).


title: HeLa_Imp8siRNA_totalRNA_replicate2


title: HeLa_TNRC6BsiRNA_totalRNA_replicate2


title: HeLa_Imp8siRNA_IPedRNA_replicate3


title: HeLa_ctrlsiRNA_totalRNA_replicate1


title: HeLa_Imp8siRNA_IPedRNA_replicate4


title: primary colorectal adenocarcinoma R371: MSI

city: Aarhus N.

first: Claus

middle: Lindbjerg

last: Andersen

address: Brenstrupgaardsvej 100

department: Dept. of Molecular Medicine (MOMA)

country: Denmark

institute: Aarhus University Hospital

description: colorectal cancer microsatellite status: Microsatellite Instable (MSI)

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: ArrayAssist 3.3 (Stratagene) was used to calculate MAS5.0 calls. The MAS5.0 calls were subsequently quantile normalized and log-2 transformed.

source_name: primary colorectal adenocarcinoma

label_protocol: Approximately 5 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Total RNA was extracted from cancer tissue using Trizol reagent (Invitrogen).

tag: MSI


title: primary colorectal adenocarcinoma R396: MSI


title: HeLa_ctrlsiRNA_totalRNA_replicate2


title: primary colorectal adenocarcinoma R357: MSI


title: primary colorectal adenocarcinoma R395: MSI


title: HeLa_Imp8siRNA_totalRNA_replicate1


title: primary colorectal adenocarcinoma R344: MSI


title: primary colorectal adenocarcinoma R401: MSI


title: primary colorectal adenocarcinoma R368: MSI


title: primary colorectal adenocarcinoma R370: MSI


title: primary colorectal adenocarcinoma R391: MSI


title: A549_miR-7_rep1

description: Treatment of A549 cells with miR-7 precursor, biological replicate #1.


title: primary colorectal adenocarcinoma R376: MSI


title: HeLa_Imp8siRNA_IPedRNA_replicate2


title: primary colorectal adenocarcinoma R399: MSI


title: primary colorectal adenocarcinoma R346: MSI


title: primary colorectal adenocarcinoma R362: MSI


title: primary colorectal adenocarcinoma R340: MSI


title: primary colorectal adenocarcinoma R356: MSI


title: primary colorectal adenocarcinoma R299: MSI


title: primary colorectal adenocarcinoma R316: MSI


title: primary colorectal adenocarcinoma R330: MSI


title: primary colorectal adenocarcinoma R292: MSI


title: primary colorectal adenocarcinoma R268: MSI


title: primary colorectal adenocarcinoma R283: MSI


title: primary colorectal adenocarcinoma R255: MSI


title: primary colorectal adenocarcinoma R277: MSI


title: primary colorectal adenocarcinoma R232: MSI


title: primary colorectal adenocarcinoma R338: MSI


title: primary colorectal adenocarcinoma R314: MSI


title: primary colorectal adenocarcinoma R265: MSI


title: primary colorectal adenocarcinoma R312: MSI


title: primary colorectal adenocarcinoma R237: MSI


title: primary colorectal adenocarcinoma R245: MSI


title: primary colorectal adenocarcinoma R202: MSI


title: primary colorectal adenocarcinoma R326: MSI


title: primary colorectal adenocarcinoma R291: MSI


title: primary colorectal adenocarcinoma R320: MSI


title: primary colorectal adenocarcinoma R264: MSI


title: primary colorectal adenocarcinoma R240: MSI


title: primary colorectal adenocarcinoma R239: MSI


title: primary colorectal adenocarcinoma R276: MSI


title: primary colorectal adenocarcinoma R191: MSI


title: primary colorectal adenocarcinoma R275: MSI


title: primary colorectal adenocarcinoma R187: MSI


title: primary colorectal adenocarcinoma R163: MSI


title: primary colorectal adenocarcinoma R180: MSI


title: primary colorectal adenocarcinoma R157: MSS

description: colorectal cancer microsatellite status: Microsatellite Stable (MSS)

tag: MSS


title: primary colorectal adenocarcinoma R153: MSS


title: primary colorectal adenocarcinoma R158: MSS


title: primary colorectal adenocarcinoma R151: MSS


title: primary colorectal adenocarcinoma R154: MSS


title: primary colorectal adenocarcinoma R156: MSI


title: primary colorectal adenocarcinoma R152: MSS


title: primary colorectal adenocarcinoma R145: MSS


title: primary colorectal adenocarcinoma R159: MSS


title: primary colorectal adenocarcinoma R147: MSS


title: primary colorectal adenocarcinoma R146: MSS


title: primary colorectal adenocarcinoma R267: MSI


title: primary colorectal adenocarcinoma R182: MSI


title: primary colorectal adenocarcinoma R148: MSS


title: primary colorectal adenocarcinoma R150: MSS


title: primary colorectal adenocarcinoma R155: MSS


title: primary colorectal adenocarcinoma R143: MSS


title: primary colorectal adenocarcinoma R144: MSS


title: primary colorectal adenocarcinoma R138: MSI


title: primary colorectal adenocarcinoma R141: MSS


title: primary colorectal adenocarcinoma R136: MSI


title: primary colorectal adenocarcinoma R137: MSS


title: primary colorectal adenocarcinoma R139: MSS


title: primary colorectal adenocarcinoma R142: MSS


title: primary colorectal adenocarcinoma R135: MSS


title: primary colorectal adenocarcinoma R132: MSS


title: primary colorectal adenocarcinoma R140: MSS


title: primary colorectal adenocarcinoma R134: MSS


title: primary colorectal adenocarcinoma R133: MSS


title: primary colorectal adenocarcinoma R127: MSS


title: primary colorectal adenocarcinoma R128: MSS


title: primary colorectal adenocarcinoma R124: MSS


title: primary colorectal adenocarcinoma R129: MSS


title: primary colorectal adenocarcinoma R123: MSS


title: primary colorectal adenocarcinoma R120: MSS


title: primary colorectal adenocarcinoma R125: MSS


title: primary colorectal adenocarcinoma R130: MSS


title: primary colorectal adenocarcinoma R121: MSS


title: primary colorectal adenocarcinoma R122: MSS


title: primary colorectal adenocarcinoma R126: MSI


title: primary colorectal adenocarcinoma R131: MSS


title: primary colorectal adenocarcinoma R113: MSS


title: primary colorectal adenocarcinoma R109: MSS


title: primary colorectal adenocarcinoma R117: MSI


title: primary colorectal adenocarcinoma R115: MSI


title: primary colorectal adenocarcinoma R114: MSI


title: primary colorectal adenocarcinoma R116: MSS


title: primary colorectal adenocarcinoma R118: MSI


title: primary colorectal adenocarcinoma R119: MSI


title: primary colorectal adenocarcinoma R111: MSS


title: primary colorectal adenocarcinoma R112: MSS


title: primary colorectal adenocarcinoma R108: MSS


title: primary colorectal adenocarcinoma R106: MSI


title: primary colorectal adenocarcinoma R110: MSS


title: primary colorectal adenocarcinoma R104: MSI


title: primary colorectal adenocarcinoma R107: MSI


title: primary colorectal adenocarcinoma R214: MSI


title: primary colorectal adenocarcinoma R105: MSS


title: primary colorectal adenocarcinoma R223: MSI


title: primary colorectal adenocarcinoma R103: MSI


title: primary colorectal adenocarcinoma R095: MSS


title: primary colorectal adenocarcinoma R100: MSI


title: primary colorectal adenocarcinoma R101: MSI


title: primary colorectal adenocarcinoma R097: MSS


title: primary colorectal adenocarcinoma R089: MSS


title: primary colorectal adenocarcinoma R098: MSS


title: primary colorectal adenocarcinoma R088: MSS


title: primary colorectal adenocarcinoma R102: MSS


title: primary colorectal adenocarcinoma R099: MSS


title: primary colorectal adenocarcinoma R094: MSS


title: primary colorectal adenocarcinoma R035: MSI


title: primary colorectal adenocarcinoma R056: MSI


title: primary colorectal adenocarcinoma R096: MSI


title: primary colorectal adenocarcinoma R059: MSI


title: primary colorectal adenocarcinoma R077: MSI


title: primary colorectal adenocarcinoma R092: MSI


title: primary colorectal adenocarcinoma R090: MSS


title: primary colorectal adenocarcinoma R030: MSS


title: primary colorectal adenocarcinoma R073: MSI


title: primary colorectal adenocarcinoma R031: MSS


title: primary colorectal adenocarcinoma R027: MSS


title: primary colorectal adenocarcinoma R029: MSS


title: primary colorectal adenocarcinoma R091: MSS


title: primary colorectal adenocarcinoma R026: MSS


title: primary colorectal adenocarcinoma R025: MSS


title: primary colorectal adenocarcinoma R040: MSI


title: primary colorectal adenocarcinoma R028: MSS


title: primary colorectal adenocarcinoma R093: MSS


title: primary colorectal adenocarcinoma R023: MSI


title: primary colorectal adenocarcinoma R018: MSI


title: primary colorectal adenocarcinoma R016: MSI


title: primary colorectal adenocarcinoma R024: MSS


title: primary colorectal adenocarcinoma R012: MSS


title: primary colorectal adenocarcinoma R022: MSS


title: primary colorectal adenocarcinoma R020: MSI


title: primary colorectal adenocarcinoma R019: MSS


title: primary colorectal adenocarcinoma R011: MSS


title: primary colorectal adenocarcinoma R017: MSS


title: primary colorectal adenocarcinoma R009: MSI


title: primary colorectal adenocarcinoma R015: MSS


title: Expression data from liver of the KRAP deficient mice (WT2)

city: Fukuoka

first: takahiro

last: fujimoto

state: Fukuoka

address: 7-45-1 nanakuma,jonan-ku

department: Faculty of medicine,Department of cell biology

country: Japan

institute: fukuoka university

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

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Liver

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

extract_protocol: Trizol extraction of total RNA followed by purification using Rneasy kit was performed according to the manufacturer's instructions.

tag: C57BL6J-backcrossed, male


title: primary colorectal adenocarcinoma R021: MSI


title: Expression data from liver of the KRAP deficient mice (KO3)


title: Expression data from liver of the KRAP deficient mice (KO1)


title: Expression data from liver of the KRAP deficient mice (WT3)


title: primary colorectal adenocarcinoma R013: MSS


title: Expression data from liver of the KRAP deficient mice (WT1)


title: primary colorectal adenocarcinoma R008: MSS


title: primary colorectal adenocarcinoma R010: MSI


title: primary colorectal adenocarcinoma R006: MSS


title: Expression data from liver of the KRAP deficient mice (KO2)


title: primary colorectal adenocarcinoma R004: MSS


title: Expression data from BAT of the KRAP deficient mice (WT3)

source_name: brown adipose tissue


title: primary colorectal adenocarcinoma R007: MSS


title: male APP, biological rep1

city: München-Neuherberg

first: Dietrich

last: Trümbach

address: Ingolstädter Landstraße 1

department: Institute for Developmental Genetics

institute: Helmholtz Zentrum München German Research Center for Environmental Health

description: mono-transgenic

hyb_protocol: Affymetrix standard protocol

scan_protocol: The expression profiling analysis for mono-transgenic mice (ADAM10, dnADAM10 mice and non-transgenic FVB/N control animals) was carried out at RZPD (Berlin, Germany). Samples from double-transgenic mice (ADAM10/APP[V717I, dnADAM10/APP[V717I] mice and mono-transgenic APP[V717I] control mice) were analyzed at the Microarray Facility (Tübingen, Germany).

data_processing:
For the first series (mono-transgenic mice) 9 gene chip arrays, and for the second series (double-transgenic mice) 18 gene chip arrays were analyzed. Data mining was performed by using the ChipInspector analysis software (Genomatix, Munich, Germany) which identifies significant changes based on single probes. The corresponding transcripts were then assigned after a user-defined number of significant probes. For all analyses, a transcript coverage greater than three probes was chosen. After intensity normalisation of each array, significantly changed genes were determined by significance analysis of microarrays (SAM), (Tusher et al., 2001)

ChipInspector carries out significance analysis on the single probe level.  Normalized probe set level data not provided.

source_name: APP[V717I] control, whole mouse brain

label_protocol: Affymetrix standard protocol

extract_protocol: Total RNA from whole mouse brains was isolated by using the RNeasy Kit (Qiagen, Germany) including on-column DNase I digestion according to the manufacturer´s recommendations. The quality of isolated RNA was controlled by the Lab-on-Chip-System Bioanalyser 2100 (Agilent Technologies, Inc., Palo Alto, CA, USA).

tag: Gender

value: male

value: 5 months

tag: Strain background

value: FVB/N


title: Expression data from BAT of the KRAP deficient mice (KO3)


title: Expression data from BAT of the KRAP deficient mice (WT1)


title: primary colorectal adenocarcinoma R005: MSS


title: male APP, biological rep2

description: mono-transgenic


title: female APP, biological rep1

description: mono-transgenic

value: female


title: primary colorectal adenocarcinoma R014: MSS


title: primary colorectal adenocarcinoma R002: MSI


title: Expression data from BAT of the KRAP deficient mice (KO2)


title: primary colorectal adenocarcinoma R003: MSS


title: male dnADAM10/APP, biological rep3

description: double-transgenic

source_name: dnADAM10/APP[V717I], whole mouse brain


title: female APP, biological rep2

description: mono-transgenic


title: Expression data from BAT of the KRAP deficient mice (WT2)


title: male APP, biological rep3

description: mono-transgenic


title: primary colorectal adenocarcinoma R001: MSS


title: female dnADAM10/APP, biological rep3

description: double-transgenic


title: female APP, biological rep3

description: mono-transgenic


title: female dnADAM10/APP, biological rep2

description: double-transgenic


title: male ADAM10/APP, biological rep3

description: double-transgenic

source_name: ADAM10/APP[V717I], whole mouse brain


title: female dnADAM10/APP, biological rep1

description: double-transgenic


title: male dnADAM10/APP, biological rep2

description: double-transgenic


title: female ADAM10/APP, biological rep3

description: double-transgenic


title: male ADAM10/APP, biological rep1

description: double-transgenic


title: female ADAM10/APP, biological rep2

description: double-transgenic


title: female ADAM10/APP, biological rep1

description: double-transgenic


title: Expression data from BAT of the KRAP deficient mice (KO1)


title: Adrenocortical Carcinoma 098

first: Rork

last: Kuick

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

description: Comparison of patients with adrenocortical carcinomas, adrenocortical adenomas and normal adrenal cortex samples.

data_processing: Ann Arbor quantile-normalized trimmed-mean method

source_name: Adrenocortical Carcinoma

label_protocol: 3-5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the tissue lysate using Trizol (Invitrogen) and cleanup performed with an RNeasy kit (Qiagen)

tag: age

tag: Sex

value: F

tag: side of body

value: not applicable

tag: cinical characteristics

value: Status post adrenalectomy

tag: tumor diameter (cm)

value: unknown

tag: tumor weight (gm)

tag: weiss grade of tumor

value: Low

tag: mitotic rate of tumor

tag: tumor stage

tag: adrenocortical carcinoma cluster in our analysis

tag: years to last followup

tag: dead or alive at last followup

value: alive

tag: first principal component for 33 accs


title: FVB/N, biological rep3

description: non-transgenic

source_name: FVB/N control, whole mouse brain

tag: Age


title: Adrenocortical Carcinoma 101

value: M

value: Left

value: Left adrenal mass


title: Adrenocortical Carcinoma 084

value: Tumor of left hepatic lobe

value: High

value: dead


title: Adrenocortical Carcinoma 051

value: Right

value: Right adrenal mass; elevated androgens and cortisol


title: Adrenocortical Carcinoma 102


title: Adrenocortical Carcinoma 055

value: History of Adrenocortical carcinoma


title: Adrenocortical Carcinoma 053


title: FVB/N, biological rep2

description: non-transgenic

value: 5 months

value: FVB/N


title: Adrenocortical Carcinoma 056

value: F

value: Hyperaldosteronism


title: Adrenocortical Carcinoma 094


title: Adrenocortical Carcinoma 057

value: Cortisol secreting tumor


title: Adrenocortical Carcinoma 058

value: unknown


title: Adrenocortical Carcinoma 054

value: Low


title: Adrenocortical Carcinoma 048

value: Liver tumor; Severe abdominal pain

value: alive


title: male ADAM10/APP, biological rep2

description: double-transgenic

value: male


title: Adrenocortical Carcinoma 103

value: Left

value: Left adrenal mass


title: FVB/N, biological rep1

description: non-transgenic

value: female


title: Adrenocortical Carcinoma 042

value: Cushing Syndrome

value: High

value: dead


title: Adrenocortical Carcinoma 046


title: Adrenocortical Carcinoma 047

value: Elevated serum aldosterone and DHEA-S; History of left nephrectomy


title: dnADAM10, biological rep3

description: mono-transgenic

source_name: dnADAM10, whole mouse brain

value: 5 months


title: dnADAM10, biological rep2

description: mono-transgenic

value: FVB/N


title: dnADAM10, biological rep1

description: mono-transgenic


title: ADAM10, biological rep1

description: mono-transgenic

source_name: ADAM10, whole mouse brain


title: Adrenocortical Carcinoma 039

value: F

value: Right


title: Adrenocortical Carcinoma 034

value: Right adrenal mass


title: Adrenocortical Carcinoma 038

value: Cushing Syndrome; Right adrenalectomy 4 years prior

value: unknown


title: ADAM10, biological rep3

description: mono-transgenic


title: Adrenocortical Carcinoma 035

value: M

value: Low


title: ADAM10, biological rep2

description: mono-transgenic


title: Adrenocortical Carcinoma 019

value: Right flank pain; Masses in right kidney, liver and both lungs


title: Adrenocortical Carcinoma 032

value: Left

value: Cushing Syndrome; Left adrenalectomy 3 years prior for adrenocortical tumor


title: Adrenocortical Carcinoma 033

value: Increased testosterone


title: Adrenocortical Carcinoma 016

value: Virilization and microcephaly

value: alive


title: Adrenocortical Carcinoma 014

value: Right adrenal tumor; Leg edema

value: High

value: dead


title: Adrenocortical Carcinoma 017

value: History of adrenal mass; 2 month history of abdominal pain


title: Adrenocortical Adenoma 082

source_name: Adrenocortical Adenoma

value: F

value: Bilateral adrenal masses

value: not applicable


title: Adrenocortical Adenoma 072

value: Left adrenal mass


title: Adrenocortical Adenoma 077

value: Cushing Syndrome


title: Adrenocortical Carcinoma 013

value: History of Adrenocortical carcinoma with lung, liver and bone metastises 1 year prior


title: Adrenocortical Adenoma 099

value: M


title: Adrenocortical Adenoma 080

value: Hyperaldosteronism


title: Adrenocortical Carcinoma 008

value: Left


title: Adrenocortical Adenoma 079

value: Right


title: Adrenocortical Adenoma 029


title: Adrenocortical Adenoma 081

value: Right adrenal mass


title: Adrenocortical Adenoma 075

value: Abdominal pain


title: Adrenocortical Adenoma 095


title: Adrenocortical Adenoma 070

value: Right pheochromocytoma


title: Adrenocortical Adenoma 078

value: Aldosteronoma


title: Adrenocortical Adenoma 068

value: unknown


title: Adrenocortical Carcinoma 001

value: Low

value: dead


title: Adrenocortical Carcinoma 011

value: F

value: History of Adrenocortical carcinoma

value: High


title: Adrenocortical Carcinoma 089


title: Adrenocortical Adenoma 030

value: not applicable


title: Adrenocortical Adenoma 064


title: Adrenocortical Carcinoma 018

value: Cushing Syndrome


title: Adrenocortical Adenoma 040


title: Adrenocortical Adenoma 071

value: Conn's syndrome


title: Adrenocortical Adenoma 028


title: Adrenocortical Adenoma 059


title: Adrenocortical Adenoma 065

value: M

value: Left adrenal mass


title: Adrenocortical Adenoma 022

value: Left


title: Adrenocortical Adenoma 021

value: Right

value: Hypertension


title: male dnADAM10/APP, biological rep1

description: double-transgenic

value: male

value: 5 months

value: FVB/N


title: Normal Adrenal Cortex 097

source_name: Normal Adrenal Cortex

value: Adrenalectomy for pheochromocytoma


title: Normal Adrenal Cortex 088

value: Adrenalectomy for renal cell carcinoma


title: Normal Adrenal Cortex 092

value: unknown


title: Normal Adrenal Cortex 069


title: Normal Adrenal Cortex 006

value: F

value: Adrenalectomy for metastatic lung carcinoma


title: Normal Adrenal Cortex 083

value: Adrenalectomy for ACA


title: Normal Adrenal Cortex 085

value: Adrenalectomy for pheochromocytoma (Multiple Endocrine Neoplasia, Type IIA)

value: not applicable


title: Normal Adrenal Cortex 063

value: Adrenalectomy for ACA; Conn's syndrome


title: Normal Adrenal Cortex 076

value: M


title: T-ALL_#9

status: Public on Jan 21 2009

city: Rotterdam

first: Bas

last: Wouters

address: P.O. Box 2040, room Ee1330B

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: RMA, log2 transformation

source_name: T-ALL blasts

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was extracted by lysis with guanidium isothiocyanate followed by cesium chloride gradient purification.

tag: Male, 23 years, CD7++, CD2+-, CD5+-, CD1a+, cyCD3++, CD4+, CD8 +-, cyTdT+, CD45 dim


title: T-ALL_#7

tag: Male, 39 years, TCRgd+-, TCRab+-, CD7+, CD2+, CD5+, CD1a+, cyCD3+, CD3+ CD4+, CD8 +-, CD10+ cyTdT+, CD45 dim


title: Normal Adrenal Cortex 087

value: Adrenalectomy for multinodular cortical hyperplasia; Conn's syndrome


title: T-ALL_#5

tag: Male, 29 years, TCRab+, CD7+, CD2+, CD5+, cyCD3+, CD3+, CD4+, CD8 +-, cyTdT+, CD45 dim


title: T-ALL_#3

tag: Male, 35 years, CD7+, CD2+, CD5+, CD1a+, cyCD3+, CD4+, CD8 +-, CD10+, cyTdT+, CD45 dim


title: T-ALL_#1


title: wild type (ProβCG:GUS) sample_biological replicate 2

city: London

first: Mohan

last: babu

state: Ontario

address: 1391 Sandford

department: Virology

country: Canada

institute: AAFC

description: The Affymetrix Arabidopsis ATH1-whole genome array, containing 22,810 probe sets representing approximately 24,000 genes, was used for the analysis.

hyb_protocol: Labelling, hybridization, and detection were performed at the McGill University and Genome Quebec Innovation Centre (http://genomequebec.mcgill.ca).

data_processing: The raw MAS 5.0 data files obtained from scanned array images are then imported into GeneSpring 7.3.1 (Silicon Genetics). Only genes with Present (P) calls were included in the analysis. Raw signals of each gene were normalized with the median of all measurements on the chip. The average normalized value of the signal intensity for each gene in three replicate hybridization experiments was adopted as the expression value of the gene. The normalized values were used to identify the differentially regulated genes by calculating the log2 ratios, where the normalized mean intensity values of brm-5 were divided by respective values from ProβCG:GUS. Fold changes of differentially regulated genes in brm-5 compared with ProβCG:GUS were calculated from these ratios.For multiple comparisons among slides, a false discovery rate (FDR) multiple testing correction (Benjamini and Hochberg, 1995) was applied to generate adjusted p-values in GeneSpring 7.3.1 Using a FDR at 5% (p-value=0.05), we selected only the statistically significant genes that were regarded as differentially regulated only if their fold-change was ≥ 2.0 for up- and ≤ -2.0 fold for downregulated.

organism: Arabidopsis thaliana

source_name: wild type (ProβCG:GUS)

growth_protocol: All plants were grown under 16-h-light (22°C)/8-h-dark (20°C) cycles, either grown on soil or on plates with MS media containing 1.5% sucrose and 0.8% agar with appropriate selection markers. All seeds were vernalized at 4oC for 3 days before placement in a growth environment.

extract_protocol: Total RNA was isolated in three biological replicates from leaves of two-week-old wild type (ProβCG:GUS) and mutant (essp3/brm-6) seedlings grown on MS agar plates (1.5% sucrose) using the RNeasy Plant Mini Kit (QIAGEN).

tag: Two-week-old wild type (ProβCG:GUS) seedlings were used in the analysis


title: essp3/brm5 mutant sample_biological replicate 2

scan_protocol: Labelling, hybridization, and detection were performed at the McGill University and Genome Quebec Innovation Centre (http://genomequebec.mcgill.ca).

source_name: essp3 or brm5 mutant

tag: Leaf tissues from two-week-old mutant (essp3/brm-5) seedlings


title: EScell shGFP rep2

status: Public on Jan 20 2009

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

hyb_protocol: 20 micrograms of biotin labeled RNA was fragmented to ~100 bp fragments by incubating in a buffer containing 200 mM Tris-Acetate pH 8.2, 500 mM Potassium Acetate and 500 Magnesium Acetate for 35 minutes at 95C. Fragments were hybridized to Affymetrix 430 2.0 chips for 16 hrs, washed and stained on an Affymetrix fluidics station.

scan_protocol: Scanning was performed with the Affymetrix GeneChip scanner using default settings.

data_processing: Raw signal values were normalized using RMA.

source_name: mouse E14Tg2 Embryonic Stem Cells

label_protocol: Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.

extract_protocol: Total RNA extraction was performed using a Qiagen RNeasy mini kit following the manufacturer's directions.

tag: mES were transfected with GFP shRNA (control) pLKO-based  constructs (Open Biosystems), selected with puromycin for 72 hours to remove non-transfectants, and harvested at 96hours for microarray analysis


title: T-ALL_#6

tag: Male, 51 years, TCRab+, CD7+, CD2+, CD5+, CD1a+, cyCD3+, CD3+, CD4+, CD8 +-, CD10+ cyTdT+, CD45 dim


title: T-ALL_#4

tag: Male, 29 years, TCRab+ CD7+, CD2+, CD5+-, CD1a+-, cyCD3+, CD3+, CD4+, CD10+-, cyTdT+, CD45 dim


title: wild type (ProβCG:GUS) sample_biological replicate 3

label_protocol: Labelling, hybridization, and detection were performed at the McGill University and Genome Quebec Innovation Centre (http://genomequebec.mcgill.ca).


title: EScell shGFP rep1


title: EScell BrgKD rep1

tag: mES were transfected with Brg shRNA pLKO-based  constructs (Open Biosystems), selected with puromycin for 72 hours to remove non-transfectants, and harvested at 96hours for microarray analysis


title: essp3/brm5 mutant sample_biological replicate 1


title: wild type (ProβCG:GUS) sample_biological replicate 1


title: T-ALL_#8

tag: Male, 18 years, CD7+, CD2+, CD5+, CD1a+, cyCD3+, CD4+, CD8 +-, cyTdT+, CD45 dim


title: EScell BrgKD rep2


title: T-ALL_#2

tag: Male, 31 years, CD7+, CD2+, CD5+, cyCD3+, cyTdT+, CD45 dim


title: essp3/brm5 mutant sample_biological replicate 3


title: EScell BrgKD rep3


title: EScell shGFP rep3


title: Exendin-4_30min

status: Public on Jan 19 2009

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

scan_protocol: standard Affymetrix procedures using GCS3000 scanner

data_processing: gcRMA, unlogged

label_protocol: 5 ug total RNA was used in a standard Affymetrix single amplification protocol.

extract_protocol: Total RNA was isolated from cell pellets using the RNeasy kit (Qiagen, Valencia, CA, USA). The integrity and concentration of RNA was determined by microfluidic analysis on an Experion instrument (BioRad).

treatment_protocol: R7T1 beta-cells treated with compounds at the indicated time points


title: DMSO_6h


title: BayK8644(2a)_6h


title: Exendin-4_2h


title: Exendin-4_6h


title: BayK8644(2a)_24h


title: BayK8644(2a)_Exendin-4_30min


title: BayK8644(2a)_2h


title: BayK8644(2a)_Exendin-4_2h


title: DMSO_24h


title: BayK8644(2a)_Exendin-4_6h


title: BayK8644(2a)_Exendin-4_24h


title: Exendin-4_24h


title: DMSO_30min


title: liver 4

status: Public on Jan 18 2009

first: rafael

last: irizarry

institute: Johns Hopkins University

description: Gene expression data obtained from post-mortem liver tissue

hyb_protocol: cRNA was fragmented and 10ug hybridized to an Affymetrix U133A or U133A Plus 2.0 arrays for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: The data were processed with RMA (Bioconductor, R). Brain (U133A) and liver (U133A_Plus 2.0) data was processed together but only probes common to both arrays were used in the analysis. The data from tumor and matched normal colon samples was analyzed independently from the brain and liver samples.

source_name: normal liver

label_protocol: Preparation of biotinylated cRNA was performed according to the standard (one-cycle) Affymetrix U133A 2.0 sample preparation protocol, starting with 1ug of total RNA

growth_protocol: no growth

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications

treatment_protocol: no treatment

tag: Tissue

value: normal liver


title: liver 5


title: 3 normal

description: Gene expression data obtained from normal colon mucosa

source_name: normal colon mucosa

value: normal colon


title: 1 normal


title: BayK8644(2a)_30min


title: 1 tumor

description: Gene expression data obtained from colon tumor tissue

source_name: colon tumor tissue

value: colon tumor


title: 4 tumor


title: 3 tumor


title: 2 tumor


title: 2 normal


title: 4 normal


title: liver 1


title: DMSO_2h


title: liver 2


title: liver 3


title: DLBCL-B CD19+ - mAdbID:60516

status: Public on Jan 16 2009

city: Bethesda

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 60516

hyb_protocol: Affymetrix Hybridization Protocol Other: Following fragmentation, 11 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affy Scanning Protocol Other: Scanning was performed by the Affymetrix 3000 Scanner.

data_processing:
MAS 5.0 Data Processing Protocol
Calculation Method: 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.

source_name: DLBCL-B CD19+

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
Sample RNA Extraction Protocol
Other: Total RNA was extracted using All Prep RNA/DNA kit (Qiagen, Valencia, CA) according to the manufacturers' protocols.

tag: Gender

value: lymph node

tag: Disease state

value: Lymphoma

tag: Individual

tag: Clinical info

value: Submitting diagnosis:NA

value: Final microarray diagnosis:NA

value: Follow up status:NA

value: Follow up years:NA

value: ECOG performance status:NA

value: LDH ratio:NA

value: Number of extranodal sites:NA


title: DLBCL-C CD19+ - mAdbID:60514

description: mAdb experiment ID: 60514

source_name: DLBCL-C CD19+

tag: Age


title: DLBCL-A CD19+ - mAdbID:60517

description: mAdb experiment ID: 60517

source_name: DLBCL-A CD19+


title: DLBCL-B CD19- - mAdbID:60515

description: mAdb experiment ID: 60515

source_name: DLBCL-B CD19-


title: HeLa_siDGCR8_24_rep2

city: Seoul

first: Jinju

last: Han

address: 599 Gwanangno, Gwanak-gu

country: South Korea

institute: Seoul National University

description: Expression changes of HeLa mRNA after DGCR8 knockdown for 24hrs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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.

source_name: HeLa total RNA, 24hrs after transfection of siRNA against DGCR8

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

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS.

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

treatment_protocol: 32nM of siRNAs (Samchully Phamaceuticals) were transfected into HeLa cells with lipofectamine 2000 (InvitroGen).

tag: Cervical cancer cell line


title: HeLa_siDrosha_48_rep2

description: Expression changes of HeLa mRNA after Drosha knockdown for 48hrs

source_name: HeLa total RNA, 48hrs after transfection of siRNA against Drosha


title: DLBCL-A CD19- - mAdbID:60518

description: mAdb experiment ID: 60518

source_name: DLBCL-A CD19-


title: DLBCL-C CD19- - mAdbID:60505

description: mAdb experiment ID: 60505

source_name: DLBCL-C CD19-


title: HeLa_siDGCR8_48_rep1

description: Expression changes of HeLa mRNA after DGCR8 knockdown for 48hrs

source_name: HeLa total RNA, 48hrs after transfection of siRNA against DGCR8


title: HeLa_siDrosha_48_rep1


title: HeLa_siGFP_48

description: Expression changes of HeLa mRNA after GFP knockdown for 48hrs

source_name: HeLa total RNA, 48hrs after transfection of siRNA against GFP


title: HeLa_siDGCR8_48_rep2


title: HeLa_siGFP_24

description: Expression changes of HeLa mRNA after GFP knockdown for 24hrs

source_name: HeLa total RNA, 24hrs after transfection of siRNA against GFP


title: HeLa_siGFP_24_rep1


title: HeLa_siDGCR8_24_rep1


title: HeLa_siGFP_48_rep1


title: HeLa_siDrosha_24_rep1

description: Expression changes of HeLa mRNA after Drosha knockdown for 24hrs

source_name: HeLa total RNA, 24hrs after transfection of siRNA against Drosha


title: HeLa_siDrosha_24_rep2


title: 6356

city: Houston

first: Roel

last: Verhaak

state: TX

address: 1400 Pressler St

department: Bioinformatics and Comp Bio

institute: MD Anderson Cancer Center

description: Blasts and mononuclear cells were purified from bone marrow or peripheral blood aspirates of AML patients. Samples contained 80-100 percent blast cells.

hyb_protocol: Affymetrix protocol.

scan_protocol: Affymetrix protocol.

data_processing: MAS5 with global scaling to target value 100, followed by setting all values lower than 30 at 30, and then log2 transformation.

source_name: Blasts and mononuclear cells, AML patient

label_protocol: Affymetrix protocol.

tag: female, 64 years, FAB M2, cytogenetic poor risk, CEBPA wild type


title: C7H2-24h-EtOH-Exp1

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

hyb_protocol: On rotation (60 rpm) hybridization at 45C for 16 hours

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software.

data_processing: Raw signal intensities were preprocessed with the GCRMA algorithm. Preprocessing was performed in R (version  2.6) with Bioconductor's (version 2.1) gcrma package.

label: R-Phycoerythrin

source_name: CCRF-CEM-C7H2 cell line

label_protocol: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.

extract_protocol: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), treated for 24h with 0.1% ethanol (EtOH) as carrier control, experiment 1.


title: ANAC102 knock-out seeds low oxygen treated biological rep 3

city: Acton

first: Jed

last: Christianson

state: ACT

address: Clunies Ross Road

institute: CSIRO Plant Industry

description:
Seeds were sown on 0.6% agarose in water. Seeds were treated for six days in the light.
extraction_method: Hot Borate extraction of total RNA was performed as described in  Cadman et al., Plant J 46: 805-822,  2006

hyb_protocol: Following fragmentation, cRNA was hybridized to the ATH1 Arabidopsis Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix genechip scanner 3000 7G

data_processing: The data analysed using the limma Bioconductor package in R. Array data was normalized using the EXPRESSO function (Gautier et al., 2005). A robust multi-chip average was calculated using quantile normalization, background correction and the median polish method as recommended by (Bolstad et al., 2003) and (Irizarry et al., 2003).

source_name: Arabidopsis whole seeds

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

growth_protocol: Plants or seeds for all experiments were kept in a growth room at 22° C with a day:night period of 16:8-hrs and fluorescent lighting  levels of ~75E.

extract_protocol: Plants or seeds were flash frozen and ground in liquid nitrogen.

treatment_protocol: Plants or seeds were placed in anaerobic microbial chambers (Oxoid, Adelaide, SA, Australia) and the chambers were flushed with a gas mixture of 0.1% Oxygen, balance Nitrogen at a flow rate of ~10L/min. for 20 minutes. Chambers were then sealed.

tag: Col-0 ecotype bearing a T-DNA insertion in the second exon of the ANAC102 gene


title: Col-0 low oxygen treated biological rep 2

description:
plants were grown on MS media with 3% sucrose and 0.8% agar and transferred to liquid MS media containign 3% sucrose one day prior to treatment. Low oxygen treatment was performed for four hours in darkened chambers.
extraction_method: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

source_name: Whole three week old Arabidopsis plants

tag: Col-0 ecotype


title: C7H2-24h-GC-Exp2

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone (a GC) 10e-7M for 24h, experiment 2.


title: C7H2-6h-EtOH-Exp1

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), treated for 6h with 0.1% ethanol (EtOH) as carrier control, experiment 1.


title: C7H2-6h-EtOH-Exp3

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), treated for 6h with 0.1% ethanol (EtOH) as carrier control, experiment 3.


title: ANAC102 knock-out seeds low oxygen treated biological rep 2


title: C7H2-24h-GC-Exp3

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone (a GC) 10e-7M for 24h, experiment 3.


title: C7H2-6h-EtOH-Exp0

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), treated for 6h with 0.1% ethanol (EtOH) as carrier control, experiment 0.


title: C7H2-24h-EtOH-Exp2

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), treated for 24h with 0.1% ethanol (EtOH) as carrier control, experiment 2.


title: C7H2-24h-GC-Exp1

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone (a GC) 10e-7M for 24h, experiment 1.


title: C7H2-24h-EtOH-Exp3

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), treated for 24h with 0.1% ethanol (EtOH) as carrier control, experiment 3.


title: Col-0 seeds low oxygen treated biological rep 2


title: Col-0 low oxygen treated biological rep 1


title: C7H2-6h-GC-Exp3

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone (a GC) 10e-7M for 6h, experiment 3.


title: Col-0 seeds low oxygen treated biological rep 1


title: Col-0 seeds low oxygen treated biological rep 3


title: urothelium8

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:10728

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 10ug

scan_protocol: Affymetrix standard protocol

data_processing: Analysis method: Affymetrix GCOS and Genespring and Avadis programs GCOS Tgt value: 1500

source_name: bladder epithelial cells

treatment_protocol:
pool size: NA
Pooled sample: no
Dissection Method: Bladder microdissected and treated with 20 µM EDTA to dissociate the mesenchyme from the epithelium.
FVB/N mice were time mated. At embryonic day 13 mice were euthanized by decapitation and the bladders were micro-dissected, cut just above the ureters and treated with 20 µM EDTA for 20 minutes. Mesenchymal and epithelial compartments were then separated by rimming the bladder with a needle and harvested in RLT. Total RNA was isolated for gene expression analysis using the Affymetrix MOE430 microarray chip.

tag: gene reported

value: wild-type

tag: strain

value: FVB/N

tag: Sex

value: unknown

tag: developmental stage

tag: theiler stage

tag: somite count

tag: developmental landmark


title: Col-0 biological rep 1

description:
plants were grown on MS media with 3% sucrose and 0.8% agar and transferred to liquid MS media containign 3% sucrose one day prior to sampling
extraction_method: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: Col-0 ecotype


title: C7H2-6h-GC-Exp0

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone (a GC) 10e-7M for 6h.


title: urothelium7

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:10727


title: ANAC102 knock-out low oxygen treated biological rep 2

tag: Col-0 ecotype bearing a T-DNA insertion in the second exon of the ANAC102 gene


title: ANAC102 knock-out low oxygen treated biological rep 1


title: ANAC102 knock-out seeds low oxygen treated biological rep 1


title: urothelium5

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:10726


title: Col-0 biological rep 2


title: C7H2-6h-GC-Exp1

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone (a GC) 10e-7M for 6h, experiment 1.


title: mesenchyme4

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:10725

source_name: bladder mesenchymal cells


title: mesenchyme2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:10724


title: C24 biological rep 1

tag: C24 ecotype


title: ANAC102 knock-out biological rep 1


title: BaF3 cells

status: Public on Jan 15 2009

city: Boston

first: George

middle: Q

last: Daley

state: MA

address: 300 Longwood Avenue

institute: Children's Hospital

description: No additional description needed

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Each chip was normalized to the median expression on the chip. A threshold value of 50 was set for all genes and the list of genes filtered to include only those that had at least one Present flag ("P" flag) in one of the 4 conditions.

label: Standard Affymetrix protocol

source_name: BaF3 cells

label_protocol: Standard Affymetrix protocol

growth_protocol: Cells were actively in complete RPMI  supplemented with 10% conditioned medium from WEHI-3B cells (as a source of IL-3).

extract_protocol: Standard Affymetrix protocol

tag: BaF3 cells are a murine pro-B cell line. The cell line used to generate this sample was not transduced with an exogenous cDNA.


title: ANAC102 over-expressor biological rep 2

tag: C24 ecotype bearing an ANAC102 overexpression construct


title: Six2_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:10722

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 5ug

data_processing:
Analysis method: Affymetrix GCOS, Gene Spring and Avadis programs.
GCOS Tgt value: 1500

source_name: Cap mesenchyme

extract_protocol: Potter protocol: 'RNA purification'

treatment_protocol:
pool size: approx 5-10 E15.5 kidneys
Pooled sample: Yes
Dissection Method: Trypsinization & FACS
Six2 transgenic mice are time-mated.  Pregnant Six2 transgenic mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal kidneys are dissected from fetuses and placed in ice-cold PBS.  Embryonic kidneys are incubated in the presence of 300ul of trypsin for 5 minutes at 37 ºC.  Kidneys are then dissociated by titurating in the presence of 600ul of ice-cold 10%FBS/PBS.  The kidneys are pelleted at 5000 rpm, 4 ºC for 5 minutes.  The media is aspirated and the cell pellet is resuspended in 200ul of ice-cold 2%FBS/PBS.  Filter cells through 70 micron mesh filter and proceed with FACS.

value: Tg(Six2-EGFP/cre)1Amc / MGI:3845228

tag: sex


title: C24 biological rep 2


title: BAF3 cells expressing ICSBP

description: No additional description needed

source_name: BAF3 cells expressing ICSBP

tag: BaF3 cells are a murine pro-B cell line. BaF3 cells expressing ICSBP were generated by infecting BaF3 cells with a retroviral construct encoding ICSBP


title: BAF3 cells expressing Bcr-Abl

description: No additional description needed

source_name: BAF3 cells expressing Bcr-Abl

tag: BaF3 cells are a murine pro-B cell line. BaF3 cells expressing BCR-ABL were generated by infecting BaF3 cells with a retroviral construct expressing bcr-abl.


title: Six2_1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:10720

tag: gene reported


title: Young hippocampus 6

city: Greenwood

first: Traci

middle: L

last: Pawlowski

state: SC

address: 113 Gregor Mendel Circle

department: molecular research

institute: Greenwood Genetic Center

description: spatial memory unimpaired

source_name: Young hippocampus

tag: male C57BL/6J NIA mouse age 2 months


title: Young hippocampus 5

description: spatial memory unimpaired


title: Young hippocampus 1

description: spatial memory unimpaired


title: HSC_untreated_Rep2

city: Heidelberg

first: Andreas

last: Trumpp

address: Im Neuenheimer Feld 280

department: Division of Stem Cells and Cancer

institute: Deutsches Krebsforschungszentrum (DKFZ)

description: Murine HSC untreated Replicate 2

hyb_protocol: Hybridization performed on a Affymetrix Fluidics Station

scan_protocol: Array scanning and raw data processing were done using GCOS software (Affymetrix)

data_processing: Data processing was performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org).  Data was normalized using RMA.

source_name: Bone marrow sorted for Lin neg cKit+ CD150+ CD48neg HSCs

label_protocol: Biotin labelling of cRNA was performed utilizing the Affymetrix GeneChip IVT labelling kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated from sorted lineage-cKit+CD150+CD48- cells using the Qiagen RNA isolation kit (Qiagen AG, Basel,CH). Per condition 3 independent samples were analysed. Two rounds of amplification for each RNA sample were performed utilizing the Nugen WT-Ovation Pico RNA Amplification System (Nugen, San Carlos, CA, USA).

tag: Strain

value: C57Bl/6 mice

tag: Tissue

value: Bone marrow sorted Lin neg cKit+ CD150+ CD48neg HSCs

tag: Timepoint

value: 16h after initiation of IFNa treatment, untreated were littermate controls which received no treatment


title: ANAC102 over-expressor biological rep 1


title: HSC_IFNa_treated_Rep2

description: Murine HSC treated with IFNa Replicate 2

value: 16h after initiation of IFNa treatment


title: Young hippocampus 3

description: spatial memory unimpaired


title: HSC_IFNa_treated_Rep1

description: Murine HSC treated with IFNa Replicate 1


title: Aged unimpaired hippocampus 6

description: spatial memory unimpaired

source_name: Aged unimpaired hippocampus

tag: male c57BL/6J NIA mouse age 23 months


title: Aged unimpaired hippocampus 4

description: spatial memory unimpaired


title: HSC_untreated_Rep3

description: Murine HSC untreated Replicate 3

source_name: Bone Marrow sorted for Lin neg cKit+ CD150+ CD48neg HSCs


title: HSC_IFNa_treated_Rep3

description: Murine HSC treated with IFNa Replicate 3


title: Young hippocampus 2

description: spatial memory unimpaired


title: Young hippocampus 4

description: spatial memory unimpaired


title: Aged unimpaired hippocampus 5

description: spatial memory unimpaired


title: Aged unimpaired hippocampus 3

description: spatial memory unimpaired


title: HSC_untreated_Rep1

description: Murine HSC untreated Replicate 1


title: Aged unimpaired hippocampus 2

description: spatial memory unimpaired


title: ANAC102 knock-out biological rep 2


title: Aged impaired hippocampus 4

description: spatial memory impaired

source_name: Aged impaired hippocampus


title: Aged impaired hippocampus 2

description: spatial memory impaired


title: Aged impaired hippocampus 6

description: spatial memory impaired


title: Aged impaired hippocampus 3

description: spatial memory impaired


title: Six2_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:10721

tag: strain

tag: developmental stage

tag: theiler stage

tag: somite count

tag: developmental landmark


title: Aged unimpaired hippocampus 1

description: spatial memory unimpaired


title: PPARg2 expression construct, 72 hrs, No Rosiglitazone (PPAR_72_2)

city: Bar Harbor

first: Keith

last: Shockley

state: ME

address: 600 Main Street

department: Computational and Systems Biology

institute: The Jackson Laboratory

description: Murine marrow-derived U-33 cells (previously referred as UAMS-33) represent a clonal cell line spontaneously immortalized in long term bone marrow cultures. To study the effect of PPARg2 on marrow mesenchymal stem cell differentiation, U-33 cells were stably transfected with either a PPARg2 expression construct (U-33/g2 cells) or an empty vector control (U-33/c cells). Several independent clones were retrieved after transfection and carefully analyzed for their phenotype. Clone 28.6 (representing U-33/g2 cells) and clone gammac2 (representing U-33/c cells) were used in the presented experiments.  Cells were maintained in alphaMEM supplemented with heat-inactivated 10% FBS (Hyclone, Logan, UT), 0.5 mg/ml G418 for positive selection of transfected cells, 100 U/ml penicillin, 100 ug/ml streptomycin, and 0.25 ug/ml amphotericin (Sigma) at 37oC in a humidified atmosphere containing 5% CO2. Media and additives were purchased from Life Technologies (Gaithersburg, MD).

hyb_protocol: The resulting biotinylated cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 Array (Affymetrix, Inc.). The arrays were washed and stained using the Affymetrix Model 450 Fluidics Station by the University of Iowa DNA Core Facility according to the protocols recommended by the manufacturer.

scan_protocol: The arrays were scanned using the Affymetrix Model 3000 scanner by the University of Iowa DNA Core Facility according to the protocols recommended by the manufacturer.

data_processing: The RMA method was used to adjust the background of perfect match (PM) probes, apply a quantile normalization of the corrected PM values and calculate final expression measures using the Tukey median polish algorithm.

source_name: -Rosi, +PPAR, 72hrs

label_protocol: RNA quality was assessed using the Agilent Model 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). For each microarray five micrograms of total RNA was processed using the Affymetrix GeneChip® one-cycle target labeling kit (Affymetrix, Inc., Santa Clara, CA) according to the protocol recommended by the manufacturer.

extract_protocol: For each experiment a fresh batch of cells was used, which was stored in liquid nitrogen. Cells were propagated for one passage and then seeded at the density of 3×105 cells/cm2. After 48h of growth, when cultures achieved about 80% confluency, cells were treated with either 1 uM Rosi or the same volume of vehicle (DMSO) for 2, 24, and 72h. RNA was isolated for each time point using the RNeasy kit (QIAGEN Inc., Valencia, CA). Replicate experiments were performed independently on a fresh batch of cells.

tag: Cells:U-33 cells stably transfected with a PPARg2 expression construct (U-33/g2 cells)

tag: Time

value: 72 hrs

tag: Drug

value: No Rosiglitazone present


title: Aged impaired hippocampus 5

description: spatial memory impaired


title: Empty vector control, 2 hrs, No Rosiglitazone (NONE_2_2)

source_name: -Rosi, -PPAR, 2hrs

tag: Cells:U-33 cells stably transfected with an empty vector control (U-33/c cells)

value: 2 hrs


title: Aged impaired hippocampus 1

description: spatial memory impaired


title: PPARg2 expression construct, 2 hrs, Rosiglitazone (ACT_2_2)

source_name: +Rosi, +PPAR, 2hrs

value: Rosiglitazone present


title: BAF3 cells expressing Bcr-Abl and ICSBP

description: No additional description needed

source_name: BAF3 cells expressing Bcr-Abl and ICSBP

tag: BaF3 cells are a murine pro-B cell line. BaF3 cells expressing Bcr-Abl and ICSBP were generated by infecting BaF3 cells with retroviral constructs for bcr-abl and ICSBP.


title: mesenchyme1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:10723

tag: Sex


title: Empty vector control, 2 hrs, Rosiglitazone (ROS_2_1)

source_name: +Rosi, -PPAR, 2hrs


title: PPARg2 expression construct, 2 hrs, No Rosiglitazone (PPAR_2_1)

source_name: -Rosi, +PPAR, 2hrs


title: PPARg2 expression construct, 24 hrs, No Rosiglitazone (PPAR_24_2)

source_name: -Rosi, +PPAR, 24hrs

value: 24 hrs


title: PPARg2 expression construct, 72 hrs, Rosiglitazone (ACT_72_2)

source_name: +Rosi, +PPAR, 72hrs


title: Empty vector control, 72 hrs, Rosiglitazone (ROS_72_2)

source_name: +Rosi, -PPAR, 72hrs


title: Empty vector control, 72 hrs, Rosiglitazone (ROS_72_1)


title: PPARg2 expression construct, 24 hrs, No Rosiglitazone (PPAR_24_1)


title: Empty vector control, 72 hrs, No Rosiglitazone (NONE_72_2)

source_name: -Rosi, -PPAR, 72hrs


title: PPARg2 expression construct, 72 hrs, Rosiglitazone (ACT_72_1)


title: Empty vector control, 24 hrs, No Rosiglitazone (NONE_24_2)


title: PPARg2 expression construct, 72 hrs, No Rosiglitazone (PPAR_72_1)


title: PPARg2 expression construct, 2 hrs, No Rosiglitazone (PPAR_2_2)


title: PPARg2 expression construct, 24 hrs, Rosiglitazone (ACT_24_2)

source_name: +Rosi, +PPAR, 24hrs


title: PPARg2 expression construct, 24 hrs, Rosiglitazone (ACT_24_1)


title: Empty vector control, 72 hrs, No Rosiglitazone (NONE_72_1)


title: Empty vector control, 2 hrs, Rosiglitazone (ROS_2_2)


title: PPARg2 expression construct, 2 hrs, Rosiglitazone (ACT_2_1)


title: Empty vector control, 2 hrs, No Rosiglitazone (NONE_2_1)


title: Empty vector control, 24 hrs, Rosiglitazone (ROS_24_2)


title: Empty vector control, 24 hrs, No Rosiglitazone (NONE_24_1)

source_name: - Rosiglitazone, - PPARg, 24 hrs


title: Human embryonic kidney cells (HEK293) treated with epoxomicin for 1hr, replicate 4

first: Allen

middle: HK

last: Chang

address: 50 South Drive, Bldg.50, Rm.2347

institute: NIH\NHLBI

description: gene expression data from human embryonic kidney cells (cell culture) treated with epoxomicin for 1hr

hyb_protocol: Fragmented RNA was hybridized to Affymetrix HG-U133 plus 2.0 chips for 16 hours, washed, stained on an Affymetrix fluidics station.

scan_protocol: Hybridized chips were scanned using Affymetrix genechip scanner 3000

data_processing: The data were first processed with GCOS1.4 using Affymetrix default analysis settings. The trimmed mean target intensity of each array was arbitrarily set to 1000. Intensities obtained in CHP file generated by GCOS were normalized using an adaptive variance-stabilizing quantile normalization (Munson, P.J., GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using Affymetrix’s IVT labeling kit following the manufacturer’s directions.

growth_protocol: HEK293 cells are maintained in DMEM supplemented with 10% fetal bovine serum in 3% oxygen, 5% carbon dioxide, 37 degrees Celsius humidified incubator.

extract_protocol: Total RNA was extracted from HEK293 cells using Qiagen RNeasy Mini Kit according to manufacturer’s instructions.

treatment_protocol: 1 uM epoxomicin is added to HEK293 cells and incubated for 1 and 6 hours before RNA extraction. RNA was extracted from cells without treatment at zero time point as control.

tag: HEK293 cells


title: Human embryonic kidney cells (HEK293) treated with epoxomicin for 6hr, replicate 2

description: gene expression data from human embryonic kidney cells (cell culture) treated with epoxomicin for 6hr


title: Human embryonic kidney cells (HEK293) treated with epoxomicin for 1hr, replicate 1


title: Human embryonic kidney cells (HEK293) treated with epoxomicin for 6hr, replicate 3


title: Human embryonic kidney cells (HEK293) treated with epoxomicin for 6hr, replicate 1


title: Human embryonic kidney cells (HEK293) at 0hr, replicate 3

description: gene expression data from human embryonic kidney cells (cell culture)


title: Human embryonic kidney cells (HEK293) treated with epoxomicin for 6hr, replicate 4


title: Empty vector control, 24 hrs, Rosiglitazone (ROS_24_1)

source_name: + Rosiglitazone, - PPARg, 24 hrs


title: Human embryonic kidney cells (HEK293) treated with epoxomicin for 1hr, replicate 3


title: Human embryonic kidney cells (HEK293) at 0hr, replicate 4


title: Human embryonic kidney cells (HEK293) at 0hr, replicate 2


title: Human embryonic kidney cells (HEK293) treated with epoxomicin for 1hr, replicate 2


title: Human embryonic kidney cells (HEK293) at 0hr, replicate 1


title: TEM2-5_1

city: Iowa City

first: Justin

last: Drake

state: IA

address: 6-509 Bowen Science Building

institute: The University of Iowa

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: MAS 5

label: According to Affymetrix protocol

source_name: TEM2-5 cell line, replicate 1

label_protocol: According to Affymetrix protocol

growth_protocol: DMEM/F12 with 10% FBS

extract_protocol: We used TRIzol reagent and RNeasy cleanup kit.  We followed both protocols according to manufacturer's instructions.

tag: A PC-3 cell line that was isolated, separately from TEM4-18, after transendothelial migration across human microvascular endothelial cells from the lung.  These cells are derived from ATCC PC-3 cells and termed TEM2-5.  This cell line expresses luciferase.


title: TEM4-18_2

source_name: TEM4-18 cell line, replicate 2

tag: A PC-3 cell line that was isolated after transendothelial migration across human microvascular endothelial cells from the lung.  These cells are derived from ATCC PC-3 cells and termed TEM4-18.  This cell line expresses luciferase.


title: TEM2-5_2