title: Lens from Pax6 heterozygote rep 2

status: Public on Oct 17 2008

city: LYON

first: Jiri

last: ZAVADIL

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

description: Lenses were dissected from newborn Pax6 heterozygous and wildtype pups.

hyb_protocol: 2.2 micrograms of cDNA was hybridized for 17 hr to the Affymetrix array as described in the Ovation™ Biotin RNA Amplification and Labeling System manual. Genechips® were processed using protocol EukGE_WS2v4 450 for Genechip® fluidics station 450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring 7.2 program. No further adjustments were made to the data in the table.

source_name: Total RNA of eye lens of newborn Pax6-heterozygous mouse

label_protocol: Amplified cDNA was fragmented and biotin labeled according to manufacturer's instructions  (NuGEN Ovation ™ Biotin RNA Amplification and Labeling System ).

extract_protocol: Total RNA was extracted using RNeasy micro-elute columns (QIAGEN), according to manufacturer's instructions.

tag: Pax6 heterozygous RNA


title: Lens from Pax6 wild type rep 3

type: RNA

state: Other

country: France

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Total RNA of eye lens of newborn Pax6-wild-type mouse

tag: Pax6 wild-type RNA


title: 1212-6heart_Control

status: Public on Oct 01 2008

city: Cambridge

first: Jonathan

middle: Lee

last: Jesneck

state: MA

address: 7 Cambridge Center

department: Cancer Program

country: USA

institute: Broad Institute

description: Cardiac tissue from an embryonic OTT1 null/wt mouse was harvested. Gene expression was measured by Affymetrix 430A v2 chip.

hyb_protocol: cDNA was then hybridized to Affymetrix Mouse expression array 430A2.0 chips by the Dana Farber Microarray Core Facility (Boston, MA).

scan_protocol: Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis. The data is transferred to a file-system from which it can be downloaded via a password-protected URL.

data_processing:
The raw CEL files were preprocessed with the RMA algorithm.
(Irizarry R.A. et al. Exploration, normalization and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249-64 (2003)).

source_name: thorax from embryo of OTT1 null/wt E18.5 mouse

label_protocol: Amplified RNA was biotinylated with the FL-Ovation Biotin Module V2 (Nugen, San Carlos, CA) per the supplied protocol.

extract_protocol: RNA was extracted from 3 hearts each from  either Ott1null/nullSox2-cre or Ott1null/wtSox2-cre E18.5 embryos using the RNeasy Micro kit (Qiagen, Valencia, CA) and treated with RNAse-free DNAse (Qiagen, Valencia, CA). 50 ng of purified total RNA was linearly amplified using the Ovation RNA amplification system V2 (Nugen, San Carlos, CA).

treatment_protocol: Mice containing the Ott1flox and Ott1null alleles were generated as previously reported [Raffel, 2007 #218]. Tg-Sox2-cre animals were obtained from Jackson labs (Bar Harbor, ME). Genotyping was performed by PCR analysis of murine or embryonic tissue [Raffel, 2007 #218]. Timed matings were determined by presence of a vaginal plug at E0.5.

tag: OTT1 null/wt mouse

tag: sacrificed at gestational age


title: rs178_DC_MF_HI_24hr

status: Public on Sep 17 2008

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: RNA was pooled from 4 separate donors

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

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

organism: Homo sapiens

source_name: DCs from healthy donors treated with live microfilariae from Brugia Malayi

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

extract_protocol: RNeasy Mini extraction of 50,000 cells

tag: Age

value: RNA was pooled from 4 separate donors

tag: Gender

value: U

tag: Race

value: (Race Not Reported)

tag: Treatment

value: microfilariae from Brugia Malayi at [  50,000 mf/well   ] for 24hr

tag: Pathogen

value: microfilariae from Brugia Malayi


title: 1212-4heart_Control


title: Lens from Pax6 wild type rep 1


title: rs178_DC_MediaControl_24hr

description: RNA was pooled from 4 separate donors

source_name: DCs from healthy donors treated with media alone

value: Media Only 24hr


title: Lens from Pax6 heterozygote rep 3


title: 1212-3heart_OTT1KO

description: Cardiac tissue from an embryonic OTT1 knockout mouse was harvested. Gene expression was measured by Affymetrix 430A v2 chip.

source_name: thorax from embryo of OTT1 knockout E18.5 mouse

tag: OTT1 knockout mouse


title: 1212-1heart_OTT1KO


title: Lung_Control_3days

status: Public on Oct 23 2008

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Label, hybridization, and scan protocols were performed according to the Agilent manufacturer’s instructions.

hyb_protocol: The hybridization was performed according to the Agilent manufacturer’s instructions.

scan_protocol: Hybridized microarray slides were washed according to the manufacturer’s instructions, and were scanned with an Agilent DNA Microarray Scanner (#G2565BA, Agilent Technologies, Santa Clara, CA) at 5 micron resolution. The scanned images were analyzed numerically using the Agilent Feature Extraction Software version 9.5.3.1.

data_processing:
Normalized data were analyzed using GeneSpring GX version 10.0.1 software (Agilent Technologies, Santa Clara, CA).
Threshold: 1.0
Logbase: 2
Technology: Agilent.SingleColor.14879
Normalization: Shift to 50 percentile
Baseline Transformation: Median of Control Samples

organism: Rattus norvegicus

source_name: Lung, at 3days after inhalation exposure, Fresh air control group (n=3)

label_protocol: cRNA labeled with fluorescent Cyanine 3-CTP was used for hybridization onto the 4 X 44K Whole Rat Genome Oligo Multiplex Microarray slides (#G4131F, Agilent Technologies, Santa Clara, CA) containing approximately 41,000 oligonucleotide probes.

extract_protocol: The right lungs were homogenized with a Tissue Ruptor (Qiagen, Tokyo, Japan). Total RNA from the homogenates was extracted using the RNeasy Midi kit (Qiagen, Tokyo, Japan) following the manufacturer’s instructions. RNA quality and concentration were determined using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) and a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE).

tag: Male Wistar rats, 9 wk, Whole right lung


title: wt.sal.10: Striatum from saline treated control animal, biological rep. 1

status: Public on Sep 10 2008

city: Heidelberg

first: Jan

last: Rodriguez Parkitna

address: Im Neuenheimer Feld 581

country: Germany

institute: German Cancer Research Center

description: Gene expression data from mutant animals treated with cocaine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse 430A 2.0 arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Analysis of array data was performed using the R 2.4.1/Bioconductor 1.9 (Gentleman et al. 2004) . Data was normalized and expression values were computed using the gcrma method.

source_name: The striatum including nucleus accumbens

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

growth_protocol: 10 to 20 week-old littermate mice were single-caged and handled for 5 days

extract_protocol: Whole brains were removed and placed in RNAlater (Ambion) overnight. Brains were sliced into 150 μm-thick vibratome sections and the striatum including the nucleus accumbens was excised with thin needles. Total RNA was prepared with Rneasy RNA Mini kit (Qiagen) and its quality was assessed on RNA LabChips (Agilent).

treatment_protocol: Intra peritoneal injection of 25 mg/kg cocaine, animals were sacrificed one hour after the injection

tag: Mixed background C57BL6 and 129; D1Cre+, Camk4 flox/flox


title: 1212-5heart_Control


title: wt.coc.V: Striatum from cocaine treated control animal, biological rep. 6


title: Lens from Pax6 heterozygote rep 1


title: 1212-2heart_OTT1KO


title: wt.sal.8: Striatum from saline treated control animal, biological rep. 3


title: wt.coc.IV: Striatum from cocaine treated control animal, biological rep. 5


title: mut.sal.6: Striatum from saline treated mutant animal, biological rep. 3


title: wt.coc.12: Striatum from cocaine treated control animal, biological rep. 1


title: wt.coc.II: Striatum from cocaine treated control animal, biological rep. 4


title: wt.coc.2: Striatum from cocaine treated control animal, biological rep. 2


title: Lung_C60 Fullerene_3days

data_processing:
Normalized data were analyzed using GeneSpring GX version 10.0.1 software (Agilent Technologies, Santa Clara, CA).
Threshold: 1.0
Logbase: 2
Technology: Agilent.SingleColor.14879
Normalization: Shift to 50 percentile

source_name: Lung, at 3days after inhalation exposure, C60 Fullerene group (n=2)


title: wt.coc.7: Striatum from cocaine treated control animal, biological rep. 3


title: mut.coc.III: Striatum from cocaine treated mutant animal, biological rep. 5

description: Gene expression data from control animals treated with cocaine


title: mut.coc.VI: Striatum from cocaine treated mutant animal, biological rep. 6


title: Pilocytic astrocytoma, case PA3

status: Public on Sep 09 2008

city: London

first: Linda

middle: B

last: Moran

address: Fulham Palace Road

department: Neuropathology

country: United Kingdom

institute: Imperial College London

description: Gene expression data from human

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC to chip A of Affymetrix GeneChip Human Genome U95 Version (HG-U95A; Affymetrix). The GeneChips was washed and stained in an Affymetrix Fluidics Station 400. Standard Affymetrix Protocols were used (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).

scan_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).

data_processing: ArrayAssist 5.5 GC-RMA

source_name: Pilocytic astrocytoma, case PA3

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

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol (http://www.qiagen.com). Tissue samples (provided by M Deprez, Liege, Belgium) were mechanically disrupted using a rotary homogenizer, lysed in buffer containing guanidine isothiocyanate (GITC) and then further homogenized (Shredder tubes, Qiagen).

tag: Pilocytic astrocytoma


title: mut.coc.9: Striatum from cocaine treated mutant animal, biological rep. 3

description: Gene expression data from control animals treated with saline


title: mut.coc.I: Striatum from cocaine treated mutant animal, biological rep. 4


title: Pilocytic astrocytoma, case PA5

description: Gene expression data from human

source_name: Pilocytic astrocytoma, case PA5


title: Pilocytic astrocytoma, case PA12

description: Gene expression data from human

source_name: Pilocytic astrocytoma, case PA12


title: mut.coc.5: Striatum from cocaine treated mutant animal, biological rep. 2


title: mut.sal.3: Striatum from saline treated mutant animal, biological rep. 2


title: mut.coc.1: Striatum from cocaine treated mutant animal, biological rep. 1


title: mut.sal.11: Striatum from saline treated mutant animal, biological rep. 1


title: Pilocytic astrocytoma, case PA6

description: Gene expression data from human

source_name: Pilocytic astrocytoma, case PA6


title: Pilocytic astrocytoma, case PA2

description: Gene expression data from human

source_name: Pilocytic astrocytoma, case PA2


title: Oligodendroglioma, case O8

description: Gene expression data from human

source_name: Oligodendroglioma, case O8

tag: Oligodendroglioma


title: Oligodendroglioma, case O4', replicate of case 4 (O4)

description: Gene expression data from human


title: Oligodendroglioma, case O7

description: Gene expression data from human

source_name: Oligodendroglioma, case O7


title: Control, case N7

description: Gene expression data from human

source_name: Control, case N7

tag: Control


title: Control, case N1

description: Gene expression data from human

source_name: Control, case N1


title: Control, case N11

description: Gene expression data from human

source_name: Control, case N11


title: Glioblastoma, case GB10

description: Gene expression data from human

source_name: Glioblastoma, case GB10

tag: Glioblastoma


title: Oligodendroglioma, case O6

description: Gene expression data from human

source_name: Oligodendroglioma, case O6


title: Oligodendroglioma, case O1

description: Gene expression data from human

source_name: Oligodendroglioma, case O1


title: Oligodendroglioma, case O4

description: Gene expression data from human

source_name: Oligodendroglioma, case O4


title: Pilocytic astrocytoma, case PA1

description: Gene expression data from human

source_name: Pilocytic astrocytoma, case PA1


title: Control, case N2

description: Gene expression data from human

source_name: Control, case N2


title: Oligodendroglioma, case O5

description: Gene expression data from human

source_name: Oligodendroglioma, case O5


title: Glioblastoma, case GB12

description: Gene expression data from human

source_name: Glioblastoma, case GB12


title: Glioblastoma, case GB7

description: Gene expression data from human

source_name: Glioblastoma, case GB7


title: Glioblastoma, case GB13

description: Gene expression data from human

source_name: Glioblastoma, case GB13


title: Control, case N6

description: Gene expression data from human

source_name: Control, case N6


title: Glioblastoma, case GB6

description: Gene expression data from human

source_name: Glioblastoma, case GB6


title: wt.sal.4: Striatum from saline treated control animal, biological rep. 2

source_name: The striatum including nucleus accumbens


title: Lens from Pax6 wild type rep 2

source_name: Total RNA of eye lens of newborn Pax6-wild-type mouse


title: Glioblastoma, case GB4

description: Gene expression data from human

source_name: Glioblastoma, case GB4


title: Glioblastoma, case GB1

description: Gene expression data from human

source_name: Glioblastoma, case GB1


title: control, BA10-60

status: Public on Sep 04 2008

city: Wako

first: Kazuya

last: Iwamoto

address: 2-1 Hirosawa

department: Brain Science Institute

institute: RIKEN

description: Gene expression data in human prefromtal cortex

hyb_protocol: Biotin-labeled cRNA sample was hybridized according to manufacture's instruction.

scan_protocol: Hybridization signal on the chip was scanned using an HP GeneArray scanner (Hewlett-Packard).

data_processing: The data were normalized by median centering by GeneSpring software (Agilent).

source_name: control

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

tag: prefrontal cortex (BA10)

tag: control


title: schizophrenia, BA10-56

source_name: schizophrenia

tag: schizophrenia


title: control, BA10-59


title: depression, BA10-57

source_name: depression

tag: depression


title: schizophrenia, BA10-46


title: depression, BA10-48


title: control, BA10-55


title: schizophrenia, BA10-45


title: bipolar disorder, BA10-51

source_name: bipolar disorder

tag: bipolar disorder


title: control, BA10-58


title: control, BA10-44


title: bipolar disorder, BA10-47


title: control, BA10-54


title: control, BA10-43


title: schizophrenia, BA10-41


title: control, BA10-50(2)


title: control, BA10-53


title: bipolar disorder, BA10-49


title: control, BA10-40


title: control, BA10-42


title: depression, BA10-38


title: schizophrenia, BA10-25


title: depression, BA10-33


title: depression, BA10-39


title: schizophrenia, BA10-37(3)


title: control, BA10-21


title: schizophrenia, BA10-15


title: bipolar disorder, BA10-19


title: control, BA10-30


title: bipolar disorder, BA10-31


title: depression, BA10-28(2)


title: schizophrenia, BA10-14(2)


title: depression, BA10-22(4)


title: schizophrenia, BA10-26


title: bipolar disorder, BA10-18


title: depression, BA10-9


title: depression, BA10-35


title: bipolar disorder, BA10-16


title: bipolar disorder, BA10-11


title: schizophrenia, BA10-12(3)


title: schizophrenia, BA10-29


title: bipolar disorder, BA10-13(2)


title: Cont subject 04

status: Public on Sep 03 2008

city: Odense

first: Casper

last: Frederiksen

address: Kloevervaenget 6

country: Denmark

institute: Odense University Hospital

description: control subject 04

hyb_protocol: 10 µg of fragmented cRNA were hybridised to a U95Av2 GeneChip (Affymetrix) using their standard procedure (45°C, 16-h). Washing and staining was performed in a Fluidics Station 400 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanned in an Affymetrix GeneChip 2500 scanner.

data_processing: Microarray normalisation and calculation of expression measures were performed using Robust Multiarray Average, implemented in the statistical package R provided by Bioconductor (Seattle, WA, USA). The expression values were log 2 transformed to obtain a normal distribution across arrays and samples. Before analysing the expression data we removed Affymetrix control probes, resulting in a total of 12,558 probes.

source_name: myotubes from control subject

label_protocol: In vitro transcription was performed on 1 µg of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics, USA)

extract_protocol: Total RNA was prepared from muscle cell cultures using RNeasy (Qiagen)

tag: The control subjects had normal glucose tolerance and no family history of diabetes.


title: Cont subject 06

description: control subject 06


title: control, BA10-4(2)


title: Cont subject 10

description: control subject 10


title: Cont subject 07

description: control subject 07


title: Cont subject 09

description: control subject 09


title: control, BA10-1


title: Cont subject 03

description: control subject 03


title: schizophrenia, BA10-6(2)


title: bipolar disorder, BA10-8(2)


title: depression, BA10-3


title: Cont subject 02

description: control subject 02


title: depression, BA10-2


title: schizophrenia, BA10-7(2)


title: Cont subject 01

description: control subject 01


title: type 2 diabetes subject 10

description: type 2 diabetes subject 10

source_name: myotubes from type 2 diabetes subject

tag: Only sedentary male subjects were recruited. Patients with type 2 diabetes were either treated by diet alone or in combination with sulphonylurea or metformin, which were withdrawn one week prior to the study. The patients were all GAD65 antibody negative and without signs of diabetic retinopathy, nephropathy, neuropathy or macrovascular complications.


title: Cont subject 05

description: control subject 05


title: type 2 diabetes subject 09

description: type 2 diabetes subject 09


title: bipolar disorder, BA10-5


title: Cont subject 08

description: control subject 08


title: type 2 diabetes subject 08

description: type 2 diabetes subject 08


title: type 2 diabetes subject 01

description: type 2 diabetes subject 01


title: type 2 diabetes subject 03

description: type 2 diabetes subject 03


title: type 2 diabetes subject 04

description: type 2 diabetes subject 04


title: type 2 diabetes subject 02

description: type 2 diabetes subject 02


title: WT/mdx_muscle_4 month

status: Public on Aug 30 2008

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: Blastocyst Injection of Wild Type Embryonic Stem Cells Induces Global Corrections in Mdx Mice.

hyb_protocol: 15ug of labeled cRNA were hybridized on the MOE 430A2.0 arrays

scan_protocol: according to manufacturer

data_processing: Overall intensity was targetted to 500. Signal intensities were generated using GCOS1.4

source_name: WT/mdx chimera_muscle_4 month

label_protocol: 1ug total RNA was labeled using the Magascript Ambion kit (cat#AM1334)

extract_protocol: RNeasy

tag: WT/mdx chimera_4 months old_pectoralis_male


title: K14E6_skin_Technical_replica

status: Public on Sep 01 2008

city: Mexico City

first: Alfredo

last: Hidalgo-Miranda

address: Periferico Sur 4124, Torre Zafiro II, piso 6

country: Mexico

institute: National Institute of Genomic Medicine

description: Pooled total RNA from three transgenic mice

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, then, 15 μg of the fragmentation product were used to prepare 300 μl hybridization cocktail (100mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20, 0.1 mg ml-1 of HS DNA, and 0.5 mg ml-1 acetylated bovine serum albumine). The cocktails were heated to 95°C and hybridized in the Mouse Genome 430A 2.0 Array (Affymetrix Inc.) for 16 hours at 45ºC .After hybridization, arrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: The GeneChip Scanner 3000 7G  (Affymetrix, Santa Clara CA) was used to collect fluorescence signal of 11um feature size resolution after excitation at 570 nm. GCOS software (Affymetrix, Santa Clara CA) was used to obtain intensity signal and quality data of the scanned arrays.

data_processing: Chip scanning and expression analyisis of the .CHP files was performed using the MAS 5.0 software

source_name: K14E6_skin_pool of 3 mice

label_protocol: The quality and size distribution of the RNA were assessed with the RNA Nano Lab on a Chip kit (Agilent Technologies), which yielded RNA integrity numbers (RIN) from 6.5 to 9.2.  Total RNA collected from skin or cervical tissue from three female mice of each condition were pooled. Briefly, 3 μg of the total pooled RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer. Second strand cDNA synthesis was followed by an in vitro transcription reaction in which biotinylated CTP and UTP were incorporated to the generated transcripts.

extract_protocol: Collected tissues were homogenized by mortar in liquid nitrogen, total RNA was extracted using TRIZOL reagent (InVitrogen) and purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Tissue was immediately frozen in liquid nitrogen for later RNA isolation using Trizol.

tag: K14E6 transgenic 6-week-old virgin female mice were employed. All mice were sacrificed and shaved with razor. After sacrifice dorsal skin (approx. 1cm2) was removed and immediately frozen in liquid nitrogen for later RNA isolation.


title: WT1_muscle_4 month

source_name: WT_muscle_4 month

tag: B10_4 months old_pectoralis_male


title: FVB_non_transgenic_cervix

description: Pooled total RNA from three non-transgenic mice

source_name: FVB_non_transgenic_cervix_pool of 3 mice

tag: FVB type 6-week-old virgin female mice were employed. All mice were sacrificed and shaved with razor. After sacrifice lower reproductive tract (cervix and vagina) were removed. and immediately frozen in liquid nitrogen for later RNA isolation.


title: mdx/mdx chimera_muscle_4 month

source_name: mdx/mdx chimera_muscle_4 month


title: type 2 diabetes subject 07

description: type 2 diabetes subject 07


title: type 2 diabetes subject 06

description: type 2 diabetes subject 06


title: type 2 diabetes subject 05

description: type 2 diabetes subject 05


title: FVB_non_transgenic_skin_replica

source_name: FVB_non_transgenic_skin_pool of 3 mice

tag: FVB type 6-week-old virgin female mice were employed. All mice were sacrificed and shaved with razor. After sacrifice dorsal skin (approx. 1cm2) was removed and immediately frozen in liquid nitrogen for later RNA isolation.


title: K14E6_cervix

source_name: K14E6_cervix and vagina_pool of 3 mice

tag: K14E6 transgenic 6-week-old virgin female mice were employed. All mice were sacrificed and shaved with razor. After sacrifice lower reproductive tract (cervix and vagina) were removed. and immediately frozen in liquid nitrogen for later RNA isolation.


title: P21 Cochlear Nucleus, TTX_24h_2X

city: Seattle

first: Julie

last: Harris

state: WA

department: Otolaryngology-HNS

institute: University of Washington

description: Ipsilateral CN 24 h after TTX exposure in cochlea.  Replicate 2.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Normalization using GC-RMA

label: Biotin

source_name: P21 Cochlear Nucleus, TTX-treated

label_protocol: Affymetrix standard protocol

extract_protocol: Qiagen lipid RNeasy kit with on column DNAse digestion

treatment_protocol: TTX delivered to one cochlea unilaterally via osmotic pump for 24 h.  CN dissected fresh & snap frozen.

tag: Age P21, strain C57Bl6/J


title: P21 Cochlear Nucleus, TTX_24h_1X

description: Ipsilateral CN 24 h after TTX exposure in cochlea.  Replicate 1.


title: WT2_muscle_4 month

source_name: WT chimera_muscle_4 month

tag: WT_chimera_4 months old_pectoralis_male


title: K14E6_cervix_Technical_replica


title: mdx_muscle_4 month

source_name: mdx_muscle_4 month

tag: mdx_4 months old_pectoralis_male


title: FVB_non_transgenic_cervix_replica


title: P21 Cochlear Nucleus, TTX_24h_3X

description: Ipsilateral CN 24 h after TTX exposure in cochlea.  Replicate 3.


title: P21 Cochlear Nucleus, TTX_24h_3

description: Contralateral CN 24 h after TTX exposure in cochlea.  Replicate 3.

source_name: P21 Cochlear Nucleus, Control


title: P21 Cochlear Nucleus, TTX_24h_2

description: Contralateral CN 24 h after TTX exposure in cochlea.  Replicate 2.


title: CRC_nodrug_F4864

status: Public on Aug 21 2008

city: Chapel Hill

first: James

middle: Todd

last: Auman

state: NC

address: 3304 Kerr Hall, Campus Box 7360

department: Institute for Pharmacogenomics and Individualized Therapy

institute: University of North Carolina at Chapel Hill

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix .cel files were imported into GeneSpring GX 7.3 using GC-RMA File Preprocessor.  Data was normalized by (1) setting all expression measurements <0.01 to 0.01, (2) a per chip normalization to the 50th percentile, and (3) a per gene normalization to the median value across all chips.

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was isolated from surgically resected, histologically confirmed colorectal primary adenocarcinomas using a TRIzol RNA isolation kit (Invitrogen, Carlsbad, CA) according to the manufacturer’s recommended protocol at the Siteman Cancer Center Tissue Procurement Core (St. Louis, MO).

treatment_protocol: Patients undergoing surgical resection of histologically proven primary colorectal adenocarcinomas were consented for participation in the study.  The patients enrolled in this study were randomized to receive either 400 mg celecoxib two times per day (n=11) or no COX-2 inhibitor (n=12) for 7 days prior to surgical resection.

tag: Gender

value: Female

tag: AJCC Stage

value: II

tag: Pathological T

tag: Pathological N

tag: Pathological M

tag: Grade

value: moderate

tag: Tumor Site

value: Cecum

tag: Drug Treatment

value: NO


title: P21 Cochlear Nucleus, TTX_24h_1

description: Contralateral CN 24 h after TTX exposure in cochlea.  Replicate 1.


title: CRC_celecoxib_M4866

value: Male

value: IV

value: Ascending

value: YES


title: CRC_nodrug_F4882

value: Sigmoid


title: CRC_celecoxib_F4880


title: CRC_nodrug_F4862

value: Rectosigmoid


title: CRC_celecoxib_M4861

value: III


title: CRC_celecoxib_F4859

value: I


title: CRC_nodrug_F4879

value: well


title: CRC_nodrug_F4881


title: CRC_nodrug_F4863


title: CRC_nodrug_M4876


title: CRC_nodrug_M4865


title: CRC_celecoxib_F4874

value: Hepatic Flexure


title: CRC_celecoxib_F4873


title: CRC_celecoxib_M4877

value: poor


title: CRC_celecoxib_F4871


title: CRC_celecoxib_M4875

value: moderate to poor

value: Descending


title: CRC_nodrug_F4872

value: Female


title: CRC_celecoxib_M4867

value: II

value: moderate


title: CRC_nodrug_M4870

value: NO


title: CRC_celecoxib_M4858

value: Male


title: CRC_nodrug_F4860

value: Cecum


title: P371 dexamethasone pre-treatment

status: Public on Aug 04 2008

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

description:
human myeloma cell  P371 dexamethasone pre-treatment

The CEL file for this sample could not be recovered due to damaged DAT file

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

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

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.

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

extract_protocol: RNeasy Mini Kit(50)


title: Erythroid progenitor cells. Epo+insulin cells 8hr +9cRA 2.

status: Public on Jul 31 2008

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

description: Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.

hyb_protocol: Affymetrix arrays were prehybridized with 200 _l MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 _g of labeled cRNA in 200 _l MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.

data_processing: Data were normalized using MAS5 algorithm (scaled to 300) and further analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductor. Control probe sets were removed from global gene lists before normalization.

source_name: Cord blood derived erythroid progenitors. differentiation for 8hrs in Epo+insulin +9cRA

label_protocol:
In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.

growth_protocol:
Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M. Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.

extract_protocol: Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the manufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).

treatment_protocol: Erythroid progenitors were differentiated with Epo and insulin and simultaneously treated with retonic acid 9cRA (1x10-6M, Sigma) for 8 hrs

tag: Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) and T3, 9cRA or T3+9cRA for 8 hrs


title: P579 lenalidomide pre-treatment

description:
human myeloma cell  P579 lenalidomide pre-treatment

The CEL file for this sample could not be recovered due to damaged DAT file


title: P576 lenalidomide pre-treatment

description:
human myeloma cell  P576 lenalidomide pre-treatment

The CEL file for this sample could not be recovered due to damaged DAT file


title: P573 lenalidomide pre-treatment

description:
human myeloma cell  P573 lenalidomide pre-treatment

The CEL file for this sample could not be recovered due to damaged DAT file


title: Erythroid progenitor cells. Epo+insulin cells 48hr 2.

source_name: Cord blood derived erythroid progenitors. differentiation for 48 hrs in Epo+insulin

extract_protocol: Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the maufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).

tag: Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) for 48 hrs


title: P547 lenalidomide post-treatment

description:
human myeloma cell  P547 lenalidomide post-treatment

The CEL file for this sample could not be recovered due to damaged DAT file


title: P576 lenalidomide post-treatment

description:
human myeloma cell  P576 lenalidomide post-treatment

The CEL file for this sample could not be recovered due to damaged DAT file


title: Erythroid progenitor cells. Epo+insulin cells 24hr +T3 +9cRA 2.

source_name: Cord blood derived erythroid progenitors. differentiation for 24hrs in Epo+insulin +T3 +9cRA

treatment_protocol: Erythroid progenitors were differentiated with Epo and insulin and simultaneously treated with thyroid hormone T3 (1x10-7 M, Sigma) and retonic acid 9cRA (1x10-6M, Sigma) for 24 hrs

tag: Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) and T3, 9cRA or T3+9cRA for 24 hrs.


title: P519 lenalidomide pre-treatment

description:
human myeloma cell  P519 lenalidomide pre-treatment

The CEL file for this sample could not be recovered due to damaged DAT file


title: Erythroid progenitor cells. Epo+insulin cells 8hr +T3 2.

source_name: Cord blood derived erythroid progenitors. differentiation for 8hrs in Epo+insulin +T3

treatment_protocol: Erythroid progenitors were differentiated with Epo and insulin and simultaneously treated with thyroid hormone T3 (1x10-7 M, Sigma) for 8 hrs


title: Erythroid progenitor cells. Epo+insulin cells 8hr +T3 +9cRA 2.

source_name: Cord blood derived erythroid progenitors. differentiation for 8hrs in Epo+insulin +T3 +9cRA

treatment_protocol: Erythroid progenitors were differentiated with Epo and insulin and simultaneously treated with thyroid hormone T3 (1x10-7 M, Sigma) and retonic acid 9cRA (1x10-6M, Sigma) for 8 hrs

tag: Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) and T3, 9cRA or T3+9cRA


title: Erythroid progenitor cells. Epo+insulin cells 48hr +T3 +9cRA 2.

source_name: Cord blood derived erythroid progenitors. differentiation for 48hrs in Epo+insulin +T3 +9cRA

treatment_protocol: Erythroid progenitors were differentiated with Epo and insulin and simultaneously treated with thyroid hormone T3 (1x10-7 M, Sigma) and retonic acid 9cRA (1x10-6M, Sigma) for 48 hrs

tag: Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) and T3, 9cRA or T3+9cRA for 48 hrs.


title: P482 dexamethasone post-treatment

description:
human myeloma cell  P482 dexamethasone post-treatment

The CEL file for this sample could not be recovered due to damaged DAT file


title: P554 lenalidomide post-treatment

description:
human myeloma cell  P554 lenalidomide post-treatment

The CEL file for this sample could not be recovered due to damaged DAT file


title: CRC_nodrug_M4868


title: Erythroid progenitor cells. SCF+Epo cells 0hr 1.

hyb_protocol: Affymetrix arrays were prehybridized with 200 ml MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 mg of labeled cRNA in 200 ml MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

source_name: Cord blood derived erythroid progenitors cultured in SCF+Epo.

growth_protocol:
Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l b-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M Dexamethasone (Dex). Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.

extract_protocol: Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the maufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 mg total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).

tag: Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells).


title: Erythroid progenitor cells. Epo+insulin cells 48hr 1.


title: Erythroid progenitor cells. Epo+insulin cells 24hr 2.

source_name: Cord blood derived erythroid progenitors. differentiation for 24 hrs in Epo+insulin

tag: Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) for 24 hrs


title: Erythroid progenitor cells. Epo+insulin cells 8hr 1.

data_processing: Data were normalized using MAS5 algorithm (scaled to 300) and further analysed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductur. Control probe sets were removed from global gene lists before normalization.

source_name: Cord blood derived erythroid progenitors. differentiation for 8hrs in Epo+insulin

tag: Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) for 8 hrs.


title: cell at T01.biological rep1

status: Public on Jul 24 2008

city: Seoul

first: Dong-Wook

last: Kim

address: 221, Heukseok-Dong, Dongjak-Ku

department: Lifescience

country: South Korea

institute: Chung-Ang University

description: Gene expression data from ESP_treated cells for 0hr

hyb_protocol: 750 ng of cRNA was hybridized to a human-8 expression bead array for 16 hr at 58¡É

scan_protocol: Scans are performed on the illumine BeadArray Reader scanner.

data_processing: The data were extracted using the Bead Studio v 2.1.12. Quantile normalization.

source_name: Hucct1 cells after 0hr of ESP treatment

label_protocol: Biotinylated cRNA was prepared using Ambio Illumina RNA amplification kits (Ambion, Austin, TX, USA) according to the manufacturer¡¯s protocols.

growth_protocol: HuCCT1 cells were cultured in RPMI1640 medium

extract_protocol: Total RNA was extracted from the ESP-treated cells using TRIzol according to the manufacturer¡¯s protocols.

treatment_protocol: HuCCT1 cells were gradually depreived of serum by 1% FBS for overnight. These serum-starved cells were treated with 800ng/ml ESP and incubated for the indicated times (T01-T05)

tag: tissue

value: Bile duct carcinoma


title: Erythroid progenitor cells. Epo+insulin cells 8hr 2.


title: MEF E2F4 KO 4-rep1

status: Public on Jul 11 2008

city: East Lansing

first: Eran

last: Andrechek

state: MI

address: 2120 BPS Building

department: Physiology

institute: Michigan State University

description: Gene expression data from E2F4 null MEFs.

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: MAS 5.0 algorithm

source_name: Primary MEF from 13.5 dpc E2F4 null mouse

label_protocol: standard affymetrix protocol

extract_protocol: standard affymetrix protocol

tag: Genotype

value: E2F4 Null


title: Erythroid progenitor cells. SCF+Epo cells 0hr 2.

source_name: Cord blood derived erythroid progenitors cultured in SCF+Epo

growth_protocol: Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M

tag: Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells)


title: MEF E2F4 KO 5-rep2


title: MEF E2F4 KO 2-rep2


title: MEF Wild Type 3-rep3

description: Gene expression data from wild type MEFs

source_name: Primary MEF from 13.5 dpc wild type mouse

value: Wild Type


title: MEF E2F4 KO 5-rep1


title: MEF E2F4 KO 4-rep2


title: MEF E2F4 KO 3-rep1


title: Erythroid progenitor cells. Epo+insulin cells 24hr 1.

tag: Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) for 24 hrs.


title: MEF E2F4 KO 2-rep1


title: MEF E2F4 KO 3-rep2


title: MEF E2F4 KO 1-rep1


title: MEF E2F4 KO 1-rep2


title: MEF Wild Type 3-rep1


title: MEF Wild Type 3-rep4


title: MEF Wild Type 2-rep1


title: coch_16_6_-_- biological replicate 3

status: Public on Jun 20 2008

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

description: Gene expression data from 4 cochleas disected from E18.5 Ig-1 -/- mouse embryos.

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

scan_protocol: GeneChips were scanned at 3-mm density with a GeneChip® Scanner 3000 7G 4C (Affymetrix).

data_processing: The data were analyzed with puma package, propagating uncertainty in Microarray data (www.bioconduct.org). Fold change cut-off was set at 1 in log2 scale. Cut-off of probability of positive ratio for the analysis of DE genes was set at 0.95

source_name: RNA pool from 4 cochleas from Igf-1 +/+ mouse E18.5, biological replicate 3

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: Heterozygous male and female with a genetic background C57BL/6J were mated to obtain embryos 18.5 days post coitus (E18.5).

extract_protocol: RNA was isolated by using the Trizol (Invitrogen) method following manufacturer’s instructions. Trizol-purified RNA was then treated with RNase-free DNase I (Roche) and mRNA purified with RNeasy spin columns (Qiagen). RNA quantity and quality was assessed with an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Cochlear tissues included the otic capsule but not vestibular tissues.

tag: genetic background C57BL/6J

tag: Age

value: E18.5 embryos


title: MEF Wild Type 1-rep1


title: coch_16_2_+_+ biological replicate 3

description: Gene expression data from 4 cochleas disected from E18.5 Ig-1 +/+ mouse embryos.

source_name: RNA pool from 4 cochleas from Igf-1 +/+ mouse E18.5, biological replicate 2


title: MEF Wild Type 3-rep2


title: coch_14_5_+_+ biological replicate 1

source_name: RNA pool from 4 cochleas from Igf-1 +/+ mouse E18.5


title: MEF Wild Type 2-rep3


title: coch_14_6_-_- biological replicate 1

source_name: RNA pool from 4 cochleas from Igf-1 +/+ mouse E18.5,


title: coch_16_1_+_+ biological replicate 2

source_name: RNA pool from 4 cochleas from Igf-1 +/+ mouse E18.6, biological replicate 1


title: MEF Wild Type 1-rep3


title: coch_16_4_-_- biological replicate 2


title: Coch_4_1+_+

status: Public on Jun 19 2008

description: Gene expression data from 8 cochleas disected from E18.5 Ig-1 -/- mouse embryos.

source_name: Cochlear RNA from E18.5 Igf-1 -/- mouse


title: Coch_4_2-_-

description: Gene expression data from 8 cochleas disected from E18.5 Ig-1 +/+ mouse embryos.

source_name: Cochlear RNA from E18.5 Igf-1 +/+ mouse


title: MEF Wild Type 1-rep2


title: liver_T-TSU_#14

status: Public on Jun 18 2008

city: Hamamatsu

first: M

last: Yamamoto

address: 1-20-1 Handayama, Higashiku

department: 2nd Dept. Surgery

institute: Hamamatsu Univ. Sch. of Med.

description: All procedures of sample and array preparation are according to manufacturer's instructions (Affymetrix Eukaryotic Sample and Array Processing).

hyb_protocol: Hybridize for 16h, 45C, 60rpm

scan_protocol: Affymetrix GeneChip scanner 3000 was used.

data_processing: Each data was processed using Affymetrix - GeneChip® Operating Software

source_name: liver, tumor-bearing mouse, treated with TSU68

label_protocol: Biotin-labeled complementary RNA (cRNA) was synthesized from 5 μg of total RNA using the One-Cycle cDNA Synthesis Kit and the GeneChip IVT Labeling Kit (Affy-metrix, Santa Clara, CA) according to the manufacturer’s instructions.

extract_protocol: Total RNA was isolated using an Isogen kit (Wako, Osaka, Japan), following purification with an RNeasy mini kit (Qiagen, Valencia, CA).

tag: Total RNA extracted from the liver of a tumor-bearing 6-week-old male BALB/c nu/nu mouse in which colon cancer was transplanted orthotopically. Samples were extracted after 7 days treatment of the angiogenic inhibitor TSU68.


title: liver_T-TSU_#2


title: liver_T-Co_#10

source_name: liver, tumor-bearing mouse, treated with control

tag: Total RNA extracted from the liver of a tumor-bearing 6-week-old male BALB/c nu/nu mouse in which colon cancer was transplanted orthotopically. Samples were extracted after 7 days treatment of control vehicle.


title: liver_T-TSU_#12


title: liver_T-Co_#13


title: liver_T-Co_#9


title: liver_NT-Co_#11

source_name: liver, non-tumor-bearing mouse, treated with control

tag: Total RNA extracted from the liver of a non-tumor-bearing 6-week-old male BALB/c nu/nu mouse with 7 days treatment of control vehicle.


title: GW 3 (set 1)

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: 4 wks GW treatment

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Expression Array 430A and Mouse Genome 430A 2.0 Array.

scan_protocol: Gene chips were scanned using Affymetrix High Resolution Genechip scanner 3000

data_processing: Data was processed using Affymetrix Microarray Suite 5.0 software.  The trimmed mean signal of all probe sets was adjusted to a user specific target signal value for each array for global scaling.

source_name: Rodent quadricep muscles

label_protocol: Double straned DNA was prepared from 10ug of total RNA, which in turn was biotinylated using standard protocol.

extract_protocol: Total RNA from the frozen samples was extracted using Trizol method.  For each sample, total RNA from 3 mice within the group was pooled.

treatment_protocol: Sedentary and Exercise trained mice were treated with vehicle or GW1516 (5mg/kg/day) for 4 weeks.  At the end of treatment, mice in each group were euthanized, quadricep muscle were immediately disceted and flash frozen in liquid nitrogen.

tag: 10 wks old C57Bl/6J mice


title: GW 2 (set 1)

description: 4 wks GW treatment


title: GW + Exercise 3 (set 1)

description: combined GW treatmet and exercise for 4 wks


title: GW 1 (set 1)

description: 4 wks GW treatment


title: GW + Exercise 2 (set 1)


title: GW + Exercise 1 (set 1)


title: Exercise 3 (set 1)

description: Exercised on treadmill for 4 wks


title: Vehicle 3 (set 1)

description: Treated with vehicle for 4 wks


title: Vehicle 2 (set 1)

description: Treated with vehicle for 4 wks


title: Exercise 2 (set 1)

description: Exercised on treadmill for 4 wks


title: Spermatogonial stem cells, replicate 2

status: Public on Jun 05 2008

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

description: Gene expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse 430A2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with the Midi_Euk_2v3 protocol.

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

data_processing: RNA preparations were analyzed by in vitro amplification and hybridization to DNA microarrays containing about 14,000 genes (Mouse Genome 430A 2.0, Affymetrix, Santa Clara, CA, USA). Absolute and comparison analyses of the mouse oligonucleotide arrays were conducted using the statistics-based Affymetrix software MAS-5.0 (GeneChip Software) with the default settings. We used the MAS5 algorithm (Affymetrix) to determine the `present' and `absent' calls for each probe set. Quantitative expression values were obtained with the robust microarray analysis (RMA) algorithm, which uses a method based on quantile normalization to calculate an expression value for each probe set.

source_name: CD4-positive cells purified from testis of CD4HAglo transgenic mice

label_protocol: 2 mg of RNA from each sample was used to synthesize biotinylated probes, using 1 round of cRNA amplification with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from cell fractions using Trizol (Invitrogen, Cergy Pontoise, France) according to the manufacturer's instructions. Ten to 20 µg of stem cell RNA was obtained per SSC preparation. Quality of RNA was checked by agarose gel electrophoresis and using an Agilent bioanalyser

treatment_protocol: Total germ cells were prepared as described previously (Vidal et al., 2001). Immunomagnetic isolation of huCD4-positive cells from total testicular cells of Stra8-CD4HAglo mice was performed using the CD4-positive Isolation Kit (Dynal, Oslo, Norway) according to the manufacturer's instructions. For each SSC preparation, 50 transgenic males were used for a final yield of 2x106 cells corresponding to the expected number of 20,000 stem cells per testis (de Rooij and Grootegoed, 1998).

tag: Spermatogonial stem cells from CD4HAglo transgenic mice


title: Spermatogonial stem cells, replicate 1

description: Gene expression data

tag: Spermatogonial stem cells from CD4HAglo transgenic mice (CD4-positive population)


title: Exercise 1 (set 1)

description: Exercised on treadmill for 4 wks


title: Vehicle 1 (set 1)

description: Treated with vehicle for 4 wks


title: Total testicular cells, replicate 3

description: Gene expression data

source_name: CD4-negative cells purified from testis of CD4HAglo transgenic mice

tag: Testicular cells from CD4HAglo transgenic mice (CD4-negative population)


title: liver_NT-Co_#8


title: Spermatogonial stem cells, replicate 3

description: Gene expression data


title: Total testicular cells, replicate 2

description: Gene expression data


title: Total testicular cells, replicate 1

description: Gene expression data


title: liver_NT-Co_#10


title: Liver_control for acute stress_bio rep 2

status: Public on Jun 01 2008

city: Greifswald

first: Maren

last: Depke

address: F.-L.-Jahn-Str. 15a

department: Department of Functional Genomics

institute: Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics

description: Control mice were kept isolated from stressed animals during stress exposure to avoid any acoustic or olfactory communication between the groups. All successive experiments and analyses were performed starting at 1000 a.m. on the day of experiment.

hyb_protocol: For hybridization 15 µg of cRNA were fragmented in 1x fragmentation buffer according the the manufacturer’s instructions, of which  10 µg fragmented cRNA were added to the hybridization cocktail with final concentrations of 0.05 nM B2 Oligo, 1x hybridization controls, 0.1 mg/ml Herring Sperm DNA, 0.5 mg/ml acetylated BSA and 10% DMSO in 1x hybridization buffer and denatured. After prehybridization Affymetrix GeneChip Mouse Expression Arrays 430A 2.0 were loaded with 130 µl hybridization cocktail and hybridized 16 h at 45°C with rotation at 60 rpm.

scan_protocol: Arrays were washed and stained using the GeneChip FluidicsStation 450 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol and scanned using the Scanner 3000 (Affymetrix, Santa Clara, CA, USA) under the control of GeneChip Operating Software GCOS (Affymetrix, Santa Clara, CA, USA).

data_processing: Analysis of CEL-files was performed in GeneChip Operating Software GCOS 1.4 (Affymetrix, Santa Clara, CA, USA). CHP-files were generated with standard expression analysis settings (MAS algorithm) using the scaling procedure and a target value of 500.

source_name: Liver, control for acute stress, bio rep 2

label_protocol: The GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA, USA) were used for synthesis of labeled material for hybridization. The protocol started with reverse transcription of 5 µg of total RNA of sample pools and was followed by the synthesis of double stranded DNA, DNA purification, in-vitro transcription for amplification and labeling, and purification of resulting cRNA according to the manufacturer’s protocols. Concentration and quality of cRNA were measured with a photometer and an Agilent 2100 Bioanalyzer, respectively.

growth_protocol: Female BALB/c mice aged 6-8 weeks were randomly grouped into the experimental and control groups starting at least 4 weeks before being used in experiments. The group size in different experiments differed from 6-12 mice per cage. Animals stayed in their group until the end of the experiments and were not mixed up to avoid social stress. All animals were maintained with sterilized food (ssniff R-Z, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water ad libitum for adaptation under minimal stress conditions. Animal rooms were on 12:12 light/dark cycle and were maintained at a constant environment prior to the experiment. In order to avoid any additional effect (for example acoustic or olfactory effects) the handling of mice during the adaptation period and during the experiments was restricted to one investigator. All animal procedures were carried out as approved by the Ethics Committee for Animal Care of Mecklenburg-Vorpommern, Germany.

extract_protocol: Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation. For liver samples a small piece of tissue was immediately homogenized with a micropestle in 350 µl Buffer RLT/ 1% β-Mercapoethanol (QIAGEN GmbH, Hilden, Germany/Sigma-Aldrich Chemie GmbH, München, Germany). The liver lysates were shock frozen in liquid nitrogen. All samples were stored at -70°C. Liver sample lysates were thawed and processed at room temperature for RNA preparation with a RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer’s instructions. After ethanol precipitation the RNA was quantified spectrophotometrically and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA). RNA pools were prepared from equal amounts of RNA of each sample from the mice belonging to the group and used for subsequent array analysis.

treatment_protocol: Mice were exposed to a single 2 h combined acoustic and restraint stress cycle in the morning (0800-1000 a.m.). For immobilization mice were placed in 50-ml conical centrifuge tubes with multiple ventilation holes without penning the tail. Acoustic stress was induced by a randomized ultrasound emission device between 19 and 25 kHz with 0-35 dB waves in attacks (SiXiS; Pat.NO.109977, Taiwan) allowing the mice no adaptation to the stressor (8, 14). Control mice were kept isolated from stressed animals to avoid any acoustic or olfactory communication between the groups. All successive experiments and analyses were performed starting at 1000 a.m. on the day of experiment.

tag: strain

value: BALB/c

tag: gender

value: female

tag: age

value: 10 to 12 weeks


title: Liver_acute stress 0h_bio rep 2

description: Mice were exposed to a single 2 h combined acoustic and restraint stress cycle in the morning (0800-1000 a.m.). Analyses were performed immediately after the stress session.

source_name: Liver, acute stress 0h, bio rep 2

tag: Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation


title: Liver_acute stress 0h_bio rep 1

source_name: Liver, acute stress 0h, bio rep 1


title: Liver_control for acute stress_bio rep 1

source_name: Liver, control for acute stress, bio rep 1


title: 5IR; Atm-/-

status: Public on May 15 2008

description: Affymetrix MOE430A2.0

hyb_protocol: 15ug of labeled cRNA were hybridized on the MOE430A2.0 arrays according to Affymetrix's instructions.

data_processing: Overall intensity was targetted at 500. Signal intensities were generated using GCOS 1.4

source_name: thymocytes from 129SvEv/C57B6 mixed background

label_protocol: 1ug ot total RNA was labeled using the Megascript Ambion kit (cat # AM1334)  according the manufacturer's instructions

extract_protocol: total RNA was extracted from cell pellet using Trizol (invitrogen)

tag: status after 24hrs treatment

tag: Atm-/-

tag: IR


title: 5mock; Atm-/-

description: Affymetrix MOE430A2.0

tag: mock


title: 3IR; Chk2-/-

description: Affymetrix MOE430A2.0


title: 7IR; Wild type

description: Affymetrix MOE430A2.0

tag: Wild type


title: 14IR; Wild type

description: Affymetrix MOE430A2.0


title: 3mock; Chk2-/-

description: Affymetrix MOE430A2.0


title: 12mock; Atm-/-

description: Affymetrix MOE430A2.0


title: 2IR; Chk2-/-

description: Affymetrix MOE430A2.0


title: 12IR; Atm-/-

description: Affymetrix MOE430A2.0


title: 2mock; Chk2-/-

description: Affymetrix MOE430A2.0


title: 7mock; Wild type

description: Affymetrix MOE430A2.0


title: 14mock; Wild type

description: Affymetrix MOE430A2.0


title: Mock-infected monocyte, biological rep3

status: Public on May 13 2008

city: Shreveport

first: Andrew

middle: D.

last: Yurochko

state: LA

address: 1501 Kings Highway

department: Microbiology & Immunology

institute: LSUHSC-S

description: A total of 6 replicates from mock-infected and 6 replicates from HCMV-infected monocytes were analyzed in this study.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U95Av2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling with a target intensity value of 2500 as normalization method.

source_name: Mock-infected monocytes at 4 hours post infection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Monocytes were incubated in RPMI supplemented with 10% human AB serum at 37C and 5% CO2.

extract_protocol: RNA STAT-60 extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Isolated monocytes were HCMV infected (MOI 15) and incubated nonadherently at 37C for 4 hours.

tag: Tissue

value: Peripheral blood

tag: Virus Strain

value: Towne/E


title: Mock-infected monocyte, biological rep5


title: Mock-infected monocyte, biological rep6


title: Mock-infected monocyte, biological rep4


title: Mock-infected monocyte, biological rep2


title: Mock-infected monocyte, biological rep1


title: crem.ht.cocaine.2023: Striatum from saline treated control animal, biological rep. 2

status: Public on Apr 03 2008

city: Heidelberg

first: Jan

last: Rodriguez Parkitna

address: Im Neuenheimer Feld 581

institute: German Cancer Research Center

description: Gene expression data from control animals treated with saline

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse 430A 2.0 arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Analysis of array data was performed using the R 2.4.1/Bioconductor 1.9 (Gentleman et al. 2004) . Data was normalized and expression values were computed using the gcrma method.

source_name: The striatum including nucleus accumbens

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

growth_protocol: 5 to 6 week-old littermate female mice were single-caged and handled for 5 days

extract_protocol: Whole brains were removed and placed in RNAlater (Ambion) overnight. Brains were sliced into 150 μm-thick vibratome sections and the striatum including the nucleus accumbens was excised with thin needles. Total RNA was prepared with Rneasy RNA Mini kit (Qiagen) and its quality was assessed on RNA LabChips (Agilent).

tag: Female, mixed background C57Bl6 and 129, Cre+, Creb1 flox/flox, Crem +/-


title: Bone marrow transduced with MSCV-NUP98/HHEX-IRES-GFP at 72h - Experiment 1

status: Public on Apr 01 2008

city: Basel

first: Juerg

last: Schwaller

address: Hebelstrasse 20

department: Biomedicine

country: Switzerland

institute: Universityhospital of Basel

description: gene expression data

hyb_protocol: Following fragmentation, 6.5 ug cRNA was hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430A 2.0. 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 were normalized using the VSN algorithm

source_name: Bone marrow cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells are grown RPMI1640 with IL-3, IL-6, mSCF, and 10% fetal bovine serum with Penicillin/Streptomycin in a humidified chamber at 37°C.

extract_protocol: Ion-exchange chromatography with RNAmini (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: No treatment was performed

tag: Bone marrow BALB/C 6-10 weeks


title: Bone marrow transduced with MSCV-NUP98/HOX-IRES-GFP at 72h - experiment 3

description: gene expression data


title: crem.ht.cocaine.2009: Striatum from saline treated control animal, biological rep. 1


title: Bone marrow transduced with MSCV-IRES-GFP at 72h - experiment 1

description: gene expression data


title: Bone marrow transduced with MSCV-NUP98/HOX-IRES-GFP at 72h - experiment 2

description: gene expression data


title: Bone marrow transduced with MSCV-NUP98/HHEX-IRES-GFP at 72h -experiment 3

description: gene expression data


title: Bone marrow transduced with MSCV-IRES-GFP at 72h - experiment 2

description: gene expression data


title: Bone marrow transduced with MSCV-IRES-GFP at 72h - experiment 3

description: gene expression data


title: Bone marrow transduced with MSCV-NUP98/HHEX-IRES-GFP at 72h - experiment 2

description: gene expression data


title: Nm-KCl Replicate 4 (Dye Swap)

status: Public on Mar 18 2008

city: Delhi

first: Abhay

last: Sharma

state: Delhi

address: Delhi University campus, Mall Road

department: Functional Genomics Unit

country: India

institute: CSIR-Institute of Genomics and Integrative Biology (IGIB)

description: The data in the file is normalized ratio. The ratio in the Value column was derived from normalized data.

hyb_protocol: The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65ºC and applied onto cDNA microarray slides (Drosophila_Oligo14k1, CDMC, Toronto). The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37ºC for 16 hrs.

scan_protocol: Microarray slides were scanned at 10µm resolution in GenePix 4000A Microarray Scanner (Molecular Devices), using both green and red lasers. The 16 bit TIFF images were preprocessed and quantified using Gene Pix Pro 6.0 software (Molecular Devices).

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), had relatively uniform intensity and uniform background (Rgn R2 (635/532) >= 0.6) and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 3.0, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster, unmated, untreated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA) were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies, a laboratory stock of which was obtained and subsequently maintained by the corresponding author for around eight years, were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 + 1oC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing NF in batches of 30 individuals

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from eight pools of frozen heads, each representing flies collected from four vials two times of which comprised a single parallel set of treatment, using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in normal media  for three days .The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

value: Oregon-R

value: 10-11 days old

tag: sex

tag: tissue

value: Head

source_name: Drosophila melanogaster,  unmated, treated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA) were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in normal media containing 100 mM KCl for three days .The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: Nm-KCl Replicate 3 (Dye Swap)

description: The data in the file is normalized ratio. The ratio in the Value column was derived from normalized data as discussed in the manuscript.

treatment_protocol: Flies were maintained at 24 +/- 1 ºC in the treatment vessel in normal media  for three days .The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy3 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA) were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: Flies were maintained at 24 +/- 1 ºC in the treatment vessel in normal media containing 100 mM KCl for three days .The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: crem.ht.cocaine.2035: Striatum from saline treated control animal, biological rep. 3

treatment_protocol: Intra peritoneal injection of 25 mg/kg cocaine, animals were sacrificed one hour after the injection


title: Nm-KCl Replicate 2

source_name: Drosophila melanogaster, unmated, treated


title: MEF Wild Type 2-rep2

source_name: Primary MEF from 13.5 dpc wild type mouse

tag: Genotype


title: Bone marrow transduced with MSCV-NUP98/HOX-IRES-GFP at 72h - Experiment 1

description: gene expression data


title: Nm-KCl Replicate 1

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), had relatively uniform intensity and uniform background (Rgn R2 (635/532) >= 0.5) and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 3.0, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations.

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy5 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA) were purified by Microarray Target Purification Kit (Roche).

source_name: Drosophila melanogaster, 3-4 day old, unmated, untreated


title: transduced with caspase-resistant Bcl-2 (938)

status: Public on Mar 05 2008

city: Auckland

first: Cris

last: Print

address: Grafton Campus, Park Rd

country: New Zealand

institute: Auckland University

description: Gene expression data from HUVEC cultured in different conditions or differently genetically modified

hyb_protocol: After fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 dgrees C to the geneChips, which were then washed and stained according to standard Affymetrix protocols.

scan_protocol: Scanned with GeneArray Scanner G2500A.

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 100. The data were then normalised by chips using he loess method in R.

source_name: transduced with caspase-resistant

label_protocol: Biotinylated cRNAs were prepared from 5 micrograms total RNA according to the standard Affymetrix protocol.

growth_protocol: Genetically-modified HUVEC grown on a variety of substrates and in a variety of geometries were comared.

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

treatment_protocol: Cultured cells were overlayed with approximately 10x their mass of Trizol then disrupted with a cell scraper.

tag: human umbilical vein endotelial cells (HUVEC)

tag: cultured in collagen in 3D, transduced with caspase-resistant Bcl-2


title: transduced with caspase-resistant Bcl-2 (1124)


title: transduced with eGFP (1132)

source_name: transduced with eGFP

tag: cultured on plastic in 2D, transduced with eGFP


title: transduced with eGFP (935)


title: high titre virus wild type Bcl-2 (1871)

source_name: high titre virus wild type

tag: cultured on collagen in 2D, expressing wild type Bcl-2, transfected with high titre virus


title: transduced with caspase-resistant Bcl-2 (1131)

tag: cultured on plastic in 2D, transduced with caspase-resistant Bcl-2


title: transduced with caspase-resistant Bcl-2 (936)


title: transduced with caspase-resistant Bcl-2 (934)


title: untransduced (1123)

source_name: untransduced

tag: cultured in collagen in 3D, untransfected


title: high titre virus wild type Bcl-2 (1872)


title: transduced with caspase-resistant Bcl-2 (1133)


title: high titre virus G145E mutant Bcl-2 (1867)

source_name: high titre virus G145E mutant

tag: cultured in 3D collagen, expressing G145E mutant Bcl-2, transfected with high titre virus


title: high titre virus wild type Bcl-2 (1870)

tag: cultured on gelatin, expressing wild type Bcl-2, transfected with high titre virus


title: transduced with eGFP (1127)

tag: cultured in collagen in 3D, transduced with eGFP


title: high titre virus G145E mutant Bcl-2 (1869)


title: SEB-1 treated biological replicate 2

status: Public on Mar 04 2008

city: Hershey

first: Diane

middle: M

last: Thiboutot

state: PA

address: 500 University Drive

department: Department of Dermatology; Jake Gittlen Res. Fnd.

institute: The Pennsylvannia State University College of Medicine

description: Gene expression data from SEB-1 cell line with 72hr, 0.1uM 13-cis retinoic acid treatment

hyb_protocol: Biotinylated cRNA, produced through in vitro transcription, was fragmented and hybridized to an Affymetrix human U95Av2 microarray.

scan_protocol: The arrays were processed on a Gene Chip Fluidics Station 450 and scanned on a Affymetrix GeneChip Scanner (Santa Clara, CA).

data_processing: The expression values were normalized by using the R-Affy package from Bioconductor version 1.1 to remove background noise and non-biologival variations among arrays. The background noise was removed from the PM probe intensities using the "RMA" method. Normalization was performed using the quantile normalization method (Bolstad et. al., 2003).  To remove the effects of outlier probes and sumerize probe intensities within one probe set to a single expression value, the "Tukey Biweight" method was applied to the background adjusted, normalized PM intensities and not the PM-MM, because it is believed that MM intensities reflect background noise as well as probe-specific signals. Significant gene expression alterations were identified using the computer software: Significance Analysis of Microarrays (Tusher et. al.,2001).

source_name: sebocyte cell line, SV-40 immortalized, 13-cis retinoic acid treated

growth_protocol: SEB-1 sebocytes were cultured in standard culture medium according to established procedures (Thiboutot et al, 2003).

extract_protocol: Total RNA was isolated and DNase I treated using the Rneasy Kit (Qiagen, Valencia, CA). RNA was quantified using a spectrophotometer. Approximately 2 micrograms of total RNA from each sample was used to generate double-stranded cDNA using a T7-oligo (dT) primer.

treatment_protocol: SEB-1 sebocytes (p23) were treated in triplicate with 0.1 uM 13-cis RA or vehicle (DMSO) control for 72 hours. Each culture plate was considered an independent sample.

tag: sebocytes cultured from M, 55, normal preauricular sebaceous glands and SV-40 immortalized


title: high titre virus wild type Bcl-2 (1868)

tag: cultured in 3D collagen, expressing wild type Bcl-2, transfected with high titre virus


title: transduced with caspase-resistant Bcl-2 (1129)


title: SEB-1 treated biological replicate 3

label_protocol: Biotinylated cRNA, produced through in vitro transcription


title: SEB-1 treated biological replicate 1


title: SEB-1 vehicle control biological replicate 3

description: Gene expression data from SEB-1 cell line with 72hr, ethanol vehicle treatment

source_name: sebocyte cell line, SV-40 immortalized, ethanol treated


title: high titre virus wild type Bcl-2 (1866)


title: SEB-1 vehicle control biological replicate 1


title: primary keratinocytes, Trp63-specific siRNA oligo (C-7)

status: Public on Mar 01 2008

city: Naples

first: Diego

last: di Bernardo

address: Via P Castellino 111

country: Italy

institute: Telethon Institute of Genetics and Medicine

description: transient transfection with trp63 siRNA

data_processing: The data were analyzed with dChip

source_name: Primary keratinocytes

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


title: primary keratinocytes, non-specific siRNA oligo (E_6)

description: transient transfection with control siRNA


title: primary keratinocytes, non-specific siRNA oligo (E_5)


title: primary keratinocytes, Trp63-specific siRNA oligo (C-1)

description: transient transfection with trp63 siRNA


title: primary keratinocytes, Trp63-specific siRNA oligo (C-4)

description: transient transfection with trp63 siRNA


title: primary keratinocytes, 180 min after Tamoxifen

description: Primary keratinocytes were infected with an EMPTY retrovirus and treated with with Tamoxifen


title: primary keratinocytes, 120 min after Tamoxifen


title: SEB-1 vehicle control biological replicate 2


title: primary keratinocytes, 240 min after Tamoxifen


title: primary keratinocytes, Trp63-specific siRNA oligo (C-2)

description: transient transfection with trp63 siRNA


title: transduced with eGFP (1126)


title: primary keratinocytes, Trp63-specific siRNA oligo (C-3)

description: transient transfection with trp63 siRNA


title: primary keratinocytes, 40 min after Tamoxifen


title: primary keratinocytes, 60 min after Tamoxifen


title: primary keratinocytes, 20 min after Tamoxifen


title: primary keratinocytes, untreated (DB30)


title: primary keratinocytes, untreated (DB29)


title: ERDNp63a primary keratinocytes, 200 min after Tamoxifen

description: Primary keratinocytes infected with a retrovirus carryng the DNp63alpha isform fused to estrogen receptor domain, and induced with tamoxifen


title: ERDNp63a primary keratinocytes, 40 min after Tamoxifen


title: ERDNp63a primary keratinocytes, 180 min after Tamoxifen


title: ERDNp63a primary keratinocytes, 140 min after Tamoxifen


title: ERDNp63a primary keratinocytes, 160 min after Tamoxifen


title: ERDNp63a primary keratinocytes, 100 min after Tamoxifen


title: ERDNp63a primary keratinocytes, 80 min after Tamoxifen


title: ERDNp63a primary keratinocytes, untreated


title: ERDNp63a primary keratinocytes, 120 min after Tamoxifen


title: normal donors XCH1

status: Public on Feb 14 2008

city: New York

first: Taras

last: Antoniv

address: 535 East 70th Street

department: Research

institute: Hospital for Special Surgery

description: blood-derived macrophages from healthy donors

hyb_protocol: Samples from healthy donors were pooled before hybridization. Then hybridized to Affymetrix HG U95 Av2 GeneChip using Affymetrix fluidics station according to the instructions of the manufacturer

scan_protocol: Affymetrix Gene-Array Scanner

data_processing: Affymetrix Microarray Suite MAS 5.0. Images were scaled to an average hybridization intensity of 250. Further data analysis was performed using GeneSpring software.

source_name: normal donors

label_protocol: Labeled cDNA was prepared with BioArray High Yield RNA Transcription Kit (Enzo Life Sciences, Farmingdale,NY)

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: no treatment

tag: blood-derived macrophages


title: normal donors XH1

hyb_protocol: Samples from healthy donors were pooled before hybridization. hybridized to Affymetrix HG U95 Av2 GeneChip using Affymetrix fluidics station according to the instructions of the manufacturer


title: normal donors TA1


title: ERDNp63a primary keratinocytes, 20 min after Tamoxifen


title: ERDNp63a primary keratinocytes, 60 min after Tamoxifen


title: rheumatoid arthritis 1152

description: Synovial fluid macrophages from individual RA donor

hyb_protocol: hybridized to Affymetrix HG U95 Av2 GeneChip using Affymetrix fluidics station according to the instructions of the manufacturer

source_name: RA patient

tag: synovial fluid macrophages


title: ERDNp63a primary keratinocytes, 240 min after Tamoxifen


title: rheumatoid arthritis 1032


title: rheumatoid arthritis 2-21


title: rheumatoid arthritis 121102


title: CP_cDNA_vs_gDNA

status: Public on Feb 13 2008

type: mixed

city: Calgary

first: Sean

middle: Michael

last: Caffrey

state: Alberta

address: 2500 University Dr NW

department: Biological Scineces

country: Canada

institute: University of Calgary

hyb_protocol: Dried probes from the treatment condition (cDNA) and universal reference (gDNA) were mixed and diluted to 40 µl using a hybridization solution containing 50% (vol/vol) formamide, 5x SSC, 0.1% (wt/vol) SDS and 0.1 mg/ml herring sperm DNA. This solution was then incubated at 98 °C for 5 minutes and then kept at 60 °C. 16 ul of 3x SSC solution was added to the wells at the ends of the microarray slides to maintain proper chamber humidity, and then the hybridization solution was applied to the Corning UltraGAPS microarray slide which had been pre-washed according to manufacturer specification (Corning, New York). The slides were incubated for 17 hours in Corning hybridization chambers and then washed according the manufacturer’s specifications and dried in a centrifuge.

scan_protocol: The hybridized slides were scanned on a PerkinElmer Scanarray 5000 scanner (PerkinElmer, Massachusetts).

data_processing:
Spot and background intensities were quantified using TIGR’s Spotfinder software. The gDNA channel was used as the control for spot uniformity and labeling efficiency. Spots were flagged and rejected if the spot was saturated, of irregular size, missing in one channel or had a poor signal to noise ratio (lower than 2 times the median local background). Data was normalized with a lowpass filter and with total intensity normalization.
Raw data from 4 arrays (with duplicate spots) were used to generate 8 columns of data. The data is the ratio of RNA (cDNA) intensity versus genomic DNA (gDNA) intensity. The gDNA was used as a universal reference to control for spot morphology and density. This data underwent a lowpass filter and total intensity normalization in both the RNA and gDNA channels. These normalized data columns were then analyzed with Stanford Tools SAM (Significance Analysis of Microarrays) which median centered the data averaged the duplicate spots and replicate arrays and generated a q-value to represent the probability that the if the spot is included as differentially expressed that it is a false positive.

label: Alexa Flour 647

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Cathode protection fed culture

label_protocol: Amino modified cDNA was generated from 10 ug of total RNA using indirect cDNA labeling and random hexamers utilizing the Indirect SuperScript labeling kit from invitrogen. Amino-modified gDNA was generated using 1 µg of gDNA using indirect labeling with random hexamers utilizing the Bioprime indirect labeling kit from Invitrogen. The amino-modified cDNA was then coupled with Alexa fluor 647 and the amino-modified gDNA with Alexa fluor 555.

growth_protocol: For Cathode Protectoin (CP) condition D. vulgars was cultured at 30 °C in a biocorrosion reactor with a working volume of 400ml containing defined Widdel-Pfenning (WP) medium containing 3 mM acetate and 28 mM sulfate. The medium was bubbled with oxygen-free mixed gas consisting of 10% CO2 and 90% N2. A negative potential of -1.1V was supplied to the iron working electrode. For 50% hydrogen, 5% hydrogen and lactate growth conditions D. vulgaris was cultured at 30 °C in 1 L Erlenmeyer flasks containing 500 ml of defined Widdel-Pfenning (WP) medium containing 3 mM acetate and 28 mM sulfate. The medium was bubbled with oxygen-free mixed gas consisting of either 0.5% (vol/vol), 5% or 50% hydrogen, 10% CO2 and the balance made up by N2. Alternatively, 65 mM lactate was the sole electron donor in cultures gassed with 10% CO2 and 90% N2. Gas was delivered at 100 ml/min after passing through a heated (325 °C) copper reduction tube for oxygen removal.

extract_protocol: Total RNA was extracted from mid-log phase cells using Invitrogen Trizol and Bacterial Max reagents. The RNA was purified with the Qiagen RNA Easy kit with on column DNase digestion. RNA quality and quantity were assessed using the absorbance ratio at 260 and 280 nm (A260/A280), denaturing agarose gel electrophoresis with ethidium bromide staining and with a Qubit fluorometer. To extract genomic DNA (gDNA) cell pellets were resuspended in NaCl-EDTA with lysozime, SDS, NaCL04, and chloroform:isoamylalcohol. This solution was centrifuged for 3 minutes at 10xg and the supernatant was added to 2 volumes of 95% EtOH to precipitate the DNA. Once the ethanol was removed the DNA is dissolved in TE and DNAse-Free RNAase and Proteinase K are used to remove contaminates. A phenol extraction and ethanol precipitation is then used to isolate the purified DNA. Quantification of DNA was conducted using absorbance ratio at 260 and 280 nm (A260/A280), agrose gel electrophoresis and with a Qubit fluorometer.

tag: Cathode Protection Condition

label: Alexa Flour 555

molecule: genomic DNA

source_name: reference genomic DNA

tag: reference genomic DNA


title: lactate_cDNA_vs_gDNA

source_name: Lactate fed culture

tag: lactate condition


title: 50%_cDNA_vs_gDNA

source_name: 50% hydrogen fed culture

tag: 50% hydrogen condition


title: rheumatoid arthritis 9252

tag: Synovial fluid macrophages


title: CD16-

status: Public on Feb 05 2008

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description: The biotin-labeled target synthesis reactions as well as the Affymetrix HG-U95Av2 GeneChip arrays hybridisation, staining and scanning were performed, starting from 2 ug of total cellular RNA, using the Affymetrix standard protocols (Affymetrix, Santa Clara, CA, USA).

hyb_protocol: The fragmented cRNA was then hybridized to an identical lot of Affymetrix HG-U95Av2 GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.

scan_protocol: GeneChip were finally scanned using the GA2500 Affymetrix GeneChip scanner.

data_processing: The GeneChip Operating Software (GCOS) absolute analysis algorithm was used to determine the amount of a transcript mRNA (signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.

label: biotin-label

source_name: eosinophils

label_protocol: Biotin-labeled labeled cRNA was purified using RNeasy spin columns (Qiagen, Valencia, CA) and fragmented (20 µg) following the Affymetrix GeneChip protocol. The assessment of cRNA concentration/quality and fragmentation was performed with the Agilent RNA chips.

extract_protocol:
Total RNA was isolated from each cell population (2x105 cells) of each donor using a modification of the guanidinium isothiocyanate procedure and ultracentrifugation on cesium chloride gradient. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 bioanalyzer.
RNAs originating from 12 donors were pooled in order to obtain at least 2 ug per sample.

treatment_protocol: Eosinophils (CD16-) were isolated from the peripheral blood of 12 healthy donors using magnetic cell-sorting procedures. Briefly, the peripheral blood was subjected to centrifugation on a Ficoll-Hypaque gradient. CD16- cells were isolated by depletion from the pellet using CD16 MicroBeads (Miltenyi Biotech, Auburn, CA, USA).

tag: CD16- from peripheral blood.


title: 04-20L-rep2

status: Public on Jan 31 2008

city: Chicago

first: Pan

last: Du

state: IL

address: 676 N ST Clair St, 1200#

institute: Northwestern University

description:
04-20L b
African American with glaucoma

hyb_protocol: Purified biotin-labeled cRNA was fragmented before the hybridization. Hybridization of the labeled cRNA to Human Genome U133A 2.0 and U95 chips (Affymetrix, Santa Clara, CA) was carried out by using Genechip Instrument System (Affymetrix) at the Genechip Core Facility of Washington University (Saint Louis, MO).

scan_protocol: The arrays were washed and stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR) followed by scanning on an Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA), and then scanned by an Affymetrix Genearray Scanner.

data_processing: RMA normalized using affy Bioconductor package

source_name: Human optic nerve head astrocytes, glaucoma

label_protocol: cRNA was synthesized from 2-5 µg purified RNA by using Superscript Choice system (Gibco BRL Life Technologies, Gaithersburg, MD ) and  T7-(dT)24 primer (GENSET, La Jolla, CA). Using Bioassay High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY), in vitro transcription was carried out by using the cleaned double-stranded cDNA as a template in the presence of biotinylated UTP and CTP.

growth_protocol: Four explants from each lamina cribrosa were dissected and placed into 25-cm2 Primaria tissue culture flasks and maintained in DMEM-F12 supplemented with 10% FBS and antibiotics.Cells were kept in a 37oC, 5% CO2 incubator. After 2-4 weeks, primary cultures were purified by using modified immunopanning procedure described by Mi and Barres (1999). Purified cells were expanded after characterization by immunostaining for astrocyte markers GFAP and NCAM as described (Yang and Hernandez, 2003). Second passage cell cultures were stored in RPMI 1640 with 10% DMSO in liquid nitrogen until use.

extract_protocol: Total RNA was extracted using Qiagen RNeasy mini kits (Qiagen, Valencia, CA). RNA was then purified and quantified by measuring absorbance at 260 nm. Quality and intactness of the RNA was assessed by capillary electrophoresis analysis using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: African American, male, age 67, glaucoma


title: CD14+

description: The biotin-labeled target synthesis reactions as well as the Affymetrix HG-U95Av2  GeneChip arrays hybridisation, staining and scanning were performed, starting from 2 ug of total cellular RNA, using the Affymetrix standard protocols (Affymetrix, Santa Clara, CA, USA).

source_name: monocytes CD14+

treatment_protocol: Monocytes (CD14+ cells) were isolated from the peripheral blood of 12 healthy donors using magnetic cell-sorting procedures. Briefly, the peripheral blood was subjected to centrifugation on a Ficoll-Hypaque gradient; CD14+ cells were purified from PBMC utilizing the CD14 MicroBeads kit (Miltenyi Biotech, Auburn, CA, USA)

tag: CD14+ from peripheral blood.


title: 5%_cDNA_vs_gDNA

source_name: 5% hydrogen fed culture

tag: 5% hydrogen condition


title: 04-24R-rep1

description:
04-24R a
African American with glaucoma

tag: African American, female, age 53, glaucoma