title: control_saline_pt9

city: Amsterdam

first: Aram

middle: Ben

last: Vroling

address: meibergdreef 9

department: ENT

institute: AMC

description: Gene expression data from cells after exposure to saline or HDM

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Affymetrix GeneChip® Operating Software using Affymetrix default analysis settings. Data were normalized using the robust multi-array average (RMA) algorithm

source_name: epithelial cells cultured from biobsy, saline exposed 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were isolated from biobsy by digesting biopsy with collagenase, cells were cultured in BEGM culture medium for app. 2 weeks.

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

treatment_protocol: cells were preincubated with HBSS 8 hours prior to adding stimulus, cells were exposed to stimulus for 24 hours.

tag: non allergic


title: cumulus cells-early cleavage-rep2

status: Public on Nov 10 2007

type: RNA

city: maastricht

first: Aafke

last: van Montfoort

department: Obstetrics & Gynaecology

country: Netherlands

institute: Academic hospital Maastricht

description: Comparison of cumulus cells from eight oocytes resulting in an early cleavage embryo (EC-CC; n=8) and from eight oocytes resulting in a non-EC embryo  (NEC-CC; n=8).

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 / 7G.

data_processing: Affymetrix GCOS, TGT value: 500, Norm Factor: 1

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: cumulus cells from oocyte resulting in an early cleavage embryo (i.e. cleaved between 23-26h post-injection or 25-28h post-insemination) from patient 2

label_protocol: Fifty ng total RNA was amplified using the two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, USA) in combination with the MEGAscript T7 in vitro transcription system (Ambion) and biotin labeled with GeneChip IVT labeling kit (Affymetrix).

growth_protocol: In consenting IVF patients, immediately following ultrasound-guided cumulus-oocyte-complex (COC) retrieval, a proportion of the cumulus cells surrounding a single oocyte were removed using a sharp needle.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, USA) according to the manufacturers’ instructions with some adaptations for the small quantity of RNA. RNA was precipitated with isopropyl alcohol for 2h and the RNA pellet was washed three times with 75% ethanol. To be able to track the small RNA pellet, 5 mg glycogen (Ambion, Woodward, USA) was added to the sample before RNA precipitation.

treatment_protocol: Cumulus cells were immediately lysed in 100 ml Trizol reagent (Invitrogen, Carlsbad, USA) supplemented with 1% (v/v) 2-mercapto-ethanol (Merck, Darmstadt, Germany), snap-frozen in liquid nitrogen and stored at -80°C (cumulus cells from one oocyte per vial).

tag: The oocyte enclosed by these cumulus cells was fertilized normally (2PN) and developed into a 4-cell embryo with good morphology on day 2 and no multinucleated blastomeres present.


title: control_HDM_pt7

source_name: epithelial cells cultured from biobsy, house dust mite exposed 24h


title: control_HDM_pt9


title: Allergic_HDM_pt5

tag: monotypic nouse dust mite allergic


title: Allergic_saline_pt5


title: Allergic_saline_pt4


title: control_saline_pt2


title: control_saline_pt8


title: control_HDM_pt2


title: control_saline_pt3


title: Allergic_HDM_pt1


title: control_HDM_pt8


title: control_HDM_pt3


title: Allergic_saline_pt1


title: control_saline_pt7


title: Allergic_HDM_pt3


title: Allergic_HDM_pt4


title: Allergic_HDM_pt2


title: Allergic_saline_pt3


title: 48 hrs infection 1

city: Galveston

first: Antonella

last: Casola

email: ancasola@utmb.edu, xibao@utmb.edu

state: TX

address: Children's Hospital. Rm#2.364, 301 University Blvd

department: Pediatrics

country: USA

institute: University of Texas Medical Branch(UTMB)

description: Gene Expression data A549 cells hmpv infected for 48 h

hyb_protocol: Follow fragmentation, 10ug of cRNA were hybridized for 16 hrs at 45C onto the HG U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Gene Array Scanner (Hewlett Packard)

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

source_name: airway epithelial cells A549 cells infected with hMPV for 48 h

label_protocol: Biotinylated cRNA were prepared accordiing to the standard Affymetrix protocol from 8.4 ug of total RNA

growth_protocol: F12K  medium containing 10% (v/v) FBS, 100 IU/ml penicillin and 100 μg/ml streptomycin

treatment_protocol: Cell monolayers were mock infected or infected with hMPV at MOI of 1 in serum-free medium containing 1 µg of trypsin/ml.RNAqueous®-Midi Kit (Ambion, Austin, TX),converted cDNA utilizing a T7-oligo (dT) primer was  used as a template to synthesis biotinylated cRNA, using bacteriophage T7 RNA polymerase


title: Allergic_saline_pt2


title: 48 hrs infection 3


title: 72 hrs infection 2

description: Gene Expression data A549 cells hmpv infected for 72 h

source_name: airway epithelial cells A549 cells infected with hMPV for 72 h


title: 72 hrs infection 1


title: 48 hrs infection 2


title: 24 hrs infection 3

description: Gene Expression data A549 cells hmpv infected for 24 h

source_name: airway epithelial cells A549 cells infected with hMPV for 24 h


title: 72 hrs infection 3


title: 6 hrs infection 3

description: Gene Expression data A549 cells hmpv infected for 6 h

source_name: airway epithelial cells A549 cells infected with hMPV for 6 h


title: 6 hrs infection 2


title: 24 hrs infection 1


title: 12 hrs infection 1

description: Gene Expression data A549 cells hmpv infected for 12 h

source_name: airway epithelial cells A549 cells infected with hMPV for 12 h


title: Drosophila 500µGy 60min repB

status: Public on Nov 09 2007

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: Ogura

state: Aomori

address: Takahoko, Hacchasawa,

department: AMBIC

country: Japan

institute: Institute for Environmental Science

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Single Array Analysis were calculated by  Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Drosophila melanogaster

source_name: Drosophila, 500µGy, 60min

label_protocol: cDNA were synthesized by GeneChip T7-Oligo(dT) Promoter Primer Kit（Affymetrix) and TaKaRa cDNA Synthesis Kit （TaKaRa Bio） from 3ug total RNA. Biotinylated cRNA were synthesized by IVT Labeling Kit(Affymetrix)

growth_protocol: About one thousand flies were put into a large bottle with egg collection medium and were allowed to lay eggs for one hour.  Then parental flies were discard and the embryos from six bottles were collected into a 1.5 ml plastic tube with screw cap.  The embryos were kept three hours at 23˚C and then frozen with liquid nitrogen.

extract_protocol: Total RNA was extracted from samples using TRIZOL reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

treatment_protocol: The irradiations with 500µGy gamma rays at 22.4mGy/h were carried out before 5, 30, 60 or 90 minutes to freeze embryos.

tag: Strain

value: w[1118], Embryo, 3-4 hours


title: 12 hrs infection 3


title: Drosophila 500µGy 90min repC

source_name: Drosophila, 500µGy, 90min


title: 24 hrs infection 2


title: Drosophila 0µGy  repB

source_name: Drosophila, control


title: Drosophila 0µGy repC


title: Drosophila 500µGy 5min repB

source_name: Drosophila, 500µGy, 5min


title: Drosophila 500µGy 30min repA

source_name: Drosophila, 500µGy, 30min


title: Control 2

description: Gene Expression data A549 cells mock infected for 48 h

source_name: airway epithelial cells A549 cells mock infected for 48 h


title: 12 hrs infection 2


title: Drosophila 500µGy 30min repB


title: 6 hrs infection 1


title: Drosophila 500µGy 60min repC


title: Drosophila 500µGy 90min repB


title: Drosophila 500µGy 5min repC


title: Drosophila 500µGy 30min repC


title: Control 1


title: Control 3


title: Drosophila 500µGy 60min repA


title: Drosophila 0µGy repA


title: Drosophila 500µGy 5min repA


title: hMSC_Donor240L_Passage2_Day2

status: Public on Nov 07 2007

city: Temple

first: Joni

last: Ylostalo

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

description:
Scale factor: 25.3
Background: 111
Noise (RawQ): 3.38
%Present: 39.1

hyb_protocol: The biotinylated and fragmented cRNA was hybridized on the HG-U133 Plus 2.0 microarray chips (Affymetrix). After washing, microarray chip was stained with streptavidin-phycoerythrin (Molecular Probes), amplified with biotinylated anti-streptavidin (Vector Laboratories) and stained with streptavidin-phycoerythrin.

scan_protocol: The microarray was scanned for fluorescence (GeneChip Scanner 3000, Affymetrix) using the GeneChip Operating software 1.0 (GCOS, Affymetrix).

data_processing: Data was scaled to the target value of 2500 with GCOS that also recorded intensities for perfect match (PM) and mismatch (MM) oligonucleotides, and determined whether genes were present (P), marginal (M) or absent (A).

label: Biotin

source_name: Passage 2 human MSC grown for 2 days

label_protocol: 5 μg of total RNA was used to synthesize double-stranded cDNA (Superscript Choice System/GIBCO BRL Life Technologies).  After synthesis, the double-stranded cDNA was purified by phenol/chloroform extraction (Phase Lock Gel, Eppendorf Scientific) and concentrated by ethanol precipitation.  In vitro transcription was used to produce biotin-labeled cRNA (BioArray HighYield RNA Transcription Labeling Kit, Enzo Diagnostics).  The biotinylated cRNA was then cleaned (RNAeasy Mini Kit Qiagen) and fragmented with metal induced hydrolysis.

extract_protocol: RNAqueous Kit (Ambion)

tag: Recovered passage 1 human Multipotent Stromal Cells (MSCs) donor 240L plated at 50 cells/cm2 in complete culture medium (CCM

value: alpha-MEM, 17% FBS, pen-strep, 2 mM L-glutamine) and grown for 2 days.


title: hMSC_Donor5064L_Passage2_Day2

description:
Scale factor: 17.4
Background: 132
Noise (RawQ): 3.92
%Present: 39.6

tag: Recovered passage 1 human Multipotent Stromal Cells (MSCs) donor 5064L plated at 50 cells/cm2 in complete culture medium (CCM


title: Drosophila 500µGy 90min repA


title: hMSC_Donor5064L_Passage2_Day7

description:
Scale factor: 24.8
Background: 92.1
Noise (RawQ): 2.90
%Present: 40.8

source_name: Passage 2 human MSC grown for 7 days

tag: Recovered passage 1 human Multipotent Stromal Cells (MSCs) donor 220R plated at 50 cells/cm2 in complete culture medium (CCM

value: alpha-MEM, 17% FBS, pen-strep, 2 mM L-glutamine) and grown for 7 days.


title: hMSC_Donor220R_Passage2_Day7

description:
Scale factor: 27.6
Background: 96.9
Noise (RawQ): 3.07
%Present: 39.3


title: Hsp-Gal4>EYA-E728Q-heatshocked-1

city: Chicago

first: Ilaria

last: Rebay

email: irebay@uchicago.edu, jcj27@mit.edu

state: IL

address: 929 East 57th Street Room W340

department: Ben May Department for Cancer Research

institute: University of Chicago

description: eya mutant transgene with the E728Q mutation

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: Chips were scanned using the GeneChip Scanner 3000 enabled for High-Resolution scanning.

data_processing: GeneChip Operating Software (GCOS) v1.1.1.  Global mean normalization was performed for samples, scaled so that each median is 100.  Detection P values were determined from raw data using GCOS software.

source_name: EYA-E728Q head, heatshocked 1hr@ 37C, recovered 3hrs @25C

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: Adult male and female flies were raised at 25C. W1118 was used as a control.  HspGal flies were crossed to flies carrying one of the folowing transgenes, UAS-EYA-wildtype, UAS-EYA-D493N or UAS-EYA-E728Q and flies carrying both the driver and UAS-EYA trangene were collected

extract_protocol: Flies were transferred to falcon tubes, frozen in liquid nitrogen and vortexed,  This was repeated two more times and fly heads were collected using a paint brush from an Rnase-free plate.  RNA was isolated from 200 adult heads (4 groups of 50) in Trizol according to the manufacturer's protocol and RNA was cleaned up using the Qiagen RNeasy kit.

treatment_protocol: Adult flies of the above genotypes were subjected to a 1hr heatshock at 37C and then allowed to recover for 3hrs at 25C.

tag: Hsp-Gal4>UAS-EYA-E728Q(Transgene 4) adult male and female flies


title: Thy1+ 2dpp gonocytes control-2

city: Pullman

first: Lizhong

last: Yang

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

description: To detect changes in expression levels for gene transcripts, we used the Mouse Genome 430v2.0 GeneChip™ array (Affymetrix, Santa Clara, CA). This array contains more than 45,000 probe sets representing 39,000 transcripts and variants, and is currently the most comprehensive GeneChip array available for the mouse. Approximately 3.75 ìg of biotin-labeled, fragmented cDNA was hybridized to each array for 18 h at 45 °C. Washes and post hybridization processing were performed using the Fluidics Station 450 (Affymetrix) according to the manufacturers’ instructions, and the GeneChip™ arrays were scanned using a laser confocal slide scanner (GeneChip Scanner 3000, Affymetrix). Array quality was assessed and images were quantified using GeneChip™ Operating Software (GCOS) v1.2 (Affymetrix).

data_processing: For each microarray, probe set signal values were initially normalized by scaling to a target intensity of 125.

organism: Mus musculus

source_name: Thy1+ 2dpp gonocytes 8hr control-2

label_protocol: Approximately 75 ng total RNA from each sample was used to generate cDNA using the Ovation™ RNA Amplification System V2 (NuGEN, San Carlos, CA) according to the manufacturer’s instructions. Briefly, first and second strand cDNA were synthesized, followed by SPIA™ isothermal linear amplification to generate single stranded antisense cDNA. Single stranded antisense cDNA (3.75 ug) was then enzymatically fragmented and end-labeled with biotin using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA) following the manufactures protocol.

extract_protocol: Trizol reagent solution

tag: 129/c57BL/6 male, thy1+ gonocytes isolated from 2 dpp testes and treated with vehicle (ethanol) for 8hr


title: hMSC_Donor240L_Passage2_Day7

description:
Scale factor: 23.7
Background: 129
Noise (RawQ): 3.76
%Present: 38.6


title: Hsp-Gal4>EYA-Wildtype-heatshocked-2

description: wildtype with overexpressed eya transgene

source_name: EYA-Wildtype head, heatshocked 1hr@ 37C, recovered 3hrs @25C

tag: Hsp-Gal4>UAS-EYA-WT(Transgene IV) adult male and female flies


title: Hsp-Gal4>EYA-D493N-heatshocked-2

description: eya mutant transgene with the D493N mutation

source_name: EYA-D493N head, heatshocked 1hr@ 37C, recovered 3hrs @25C

tag: Hsp-Gal4>UAS-EYA-D493N(Transgene 6) adult male and female flies


title: Hsp-Gal4>EYA-E728Q-heatshocked-2


title: Thy1+ 2dpp gonocytes RA-2

hyb_protocol: To detect changes in expression levels for gene transcripts, we used the Mouse Genome 430v2.0 GeneChip™ array (Affymetrix, Santa Clara, CA). This array contains more than 45,000 probe sets representing 39,000 transcripts and variants, and is currently the most comprehensive GeneChip array available for the mouse. Approximately 3.75 ìg of biotin-labeled, fragmented cDNA was hybridized to each array for 18 h at 45 °C. Washes and post hybridization processing were performed using the Fluidics Station 450 (Affymetrix) according to the manufacturers’ instructions, and the GeneChip™ arrays were scanned using a laser confocal slide scanner (GeneChip Scanner 3000, Affymetrix). Array quality was assessed and images were quantified using GeneChip™ Operating Software (GCOS) v1.2 (Affymetrix).

source_name: Thy1+ 2dpp gonocytes 8hr RA-2

tag: 129/c57BL/6 male, thy1+ gonocytes isolated from 2 dpp testes and treated with RA for 8hr


title: hMSC_Donor220R_Passage2_Day2

description:
Scale factor: 27.1
Background: 120
Noise (RawQ): 3.56
%Present: 38.3


title: Thy1+ 2dpp gonocytes RA-1

scan_protocol: To detect changes in expression levels for gene transcripts, we used the Mouse Genome 430v2.0 GeneChip™ array (Affymetrix, Santa Clara, CA). This array contains more than 45,000 probe sets representing 39,000 transcripts and variants, and is currently the most comprehensive GeneChip array available for the mouse. Approximately 3.75 ìg of biotin-labeled, fragmented cDNA was hybridized to each array for 18 h at 45 °C. Washes and post hybridization processing were performed using the Fluidics Station 450 (Affymetrix) according to the manufacturers’ instructions, and the GeneChip™ arrays were scanned using a laser confocal slide scanner (GeneChip Scanner 3000, Affymetrix). Array quality was assessed and images were quantified using GeneChip™ Operating Software (GCOS) v1.2 (Affymetrix).

source_name: Thy1+ 2dpp gonocytes 8hr RA-1


title: Hsp-GAL4>EYA-Wildtype-heatshocked-1


title: control-head-heatshocked-2

description: controls without overexpressed eya

source_name: control head, heatshocked 1hr@ 37C, recovered 3hrs @25C

tag: w1118 male and female adult flies


title: Hsp-Gal4>EYA-D493N-heatshocked-1


title: Thy1+ 2dpp gonocytes control-1

source_name: Thy1+ 2dpp gonocytes 8hr control-1


title: control-head-heatshocked-1

description: controls without overexpressed eya


title: Slice10JW

status: Public on Nov 05 2007

city: Durham

first: Siobhan

middle: M

last: Brady

state: NC

department: Biology

institute: Duke University

description:
Arabidopsis, root cells, cross-section, cross-section 2 (approx 500 µm) of maturation section from root tip, root 2
Gene expression data from a cross-section (approximately 500 µm) of the root maturation zone, the second section from the root tip

hyb_protocol: Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

data_processing: Software described in Levesque et al. (2006), PLoS Biology, 4:e143 was used for normalization.  This uses the global normalization/linear modeling approach described in Chu et al. (2001). This method simultaneously considers the perfect match probeset data across all chips in an experiment.  Normalization across all chips was performed as follows: [Log2(IntensityPROBE, ARRAY) = logarithmic meanALLARRAY INTENSITY VALUES + residualsPROBE, ARRAY].  For each array, all probes were removed that were greater than two standard deviations from the probeset mean.  For all remaining probe values across replicates in a treatment, expression indices are calculated as:   2^r1 + 2^r2 + 2^rN/N

organism: Arabidopsis thaliana

source_name: root tissue

label_protocol: Fragmented cRNA probes were prepared using the two-cycle amplification protocol by Affymetrix.

growth_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water.  Seeds were stratified at 4˚C for 2 days before being planted on standard media.  Standard media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH.  Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh.

extract_protocol: RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH).

treatment_protocol: Samples were prepared as in Birnbaum et al. (2005) Nat. Methods for roots grown under standard conditions.

tag: Columbia ecotype

tag: Age

value: Seedling roots, 7 days after germination

tag: Growth media

value: standard media


title: Slice8JW

description:
Arabidopsis, root cells, cross-section, 1/2 of elongation zone, second elongation section from root tip, standard conditions, root2
Gene expression data from a cross-section of 1/2 of the root elongation zone, the second section from the root tip

scan_protocol: Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.


title: Slice7JW

description:
Arabidopsis, root cells, cross-section, 1/2 of elongation zone, first elongation section from root tip, standard conditions, root 2
Gene expression data from a cross-section of 1/2 of the root elongation zone, the first section from the root tip


title: Slice9JW

description:
Arabidopsis, root cells, cross-section, cross-section 1 (approx 500 µm) of maturation section from root tip, root 2
Gene expression data from a cross-section (approximately 500 µm) of the root maturation zone, the first section of the root maturation zone


title: Slice6JW

description:
Arabidopsis, root cells, cross-section, 1/6 of meristematic zone, sixth meristematic section from root tip, root 2
Gene expression data from a cross-section of 1/6 of the root meristematic zone, the sixth section from the root tip


title: Slice4JW

description:
Arabidopsis, root cells, cross-section, 1/6 of meristematic zone, fourth meristematic section from root tip, root 2
Gene expression data from a cross-section of 1/6 of the root meristematic zone, the fourth section from the root tip


title: Slice12JW

description:
Arabidopsis, root cells, cross-section, cross-section 4 (approx 500 µm) of maturation section from root tip, root 2
Gene expression data from a cross-section (approximately 500 µm) of the root maturation zone, the fourth section from the root tip


title: Slice11JW

description:
Arabidopsis, root cells, cross-section, cross-section 3 (approx 500 µm) of maturation section from root tip, root 2
Gene expression data from a cross-section (approximately 500 µm) of the root maturation zone, the third section from the root tip


title: Slice3JW

description:
Arabidopsis, root cells, cross-section, 1/6 of meristematic zone, third meristematic section from root tip,  root 2
Gene expression data from a cross-section of 1/6 of the root meristematic zone, the third section from the root tip


title: Slice5JW

description:
Arabidopsis, root cells, cross-section, 1/6 of meristematic zone, fifth meristematic section from root tip, root 2
Gene expression data from a cross-section of 1/6 of the root meristematic zone, the fifth section from the root tip


title: L10SB

description:
Arabidopsis, root cells, cross-section, cross-section 2 (approx 500 µm) of maturation section from root tip, root 1
Gene expression data from a cross-section (approximately 500 µm) of the root maturation zone, the second section from the root tip


title: Slice1JW

description:
Arabidopsis, root cells, cross-section, 1/6 of meristematic zone, first meristematic section from root tip, contains QC, root 2
Gene expression data from a cross section of 1/6 of the meristematic zone, the first section from the root tip


title: Slice2JW

description:
Arabidopsis, root cells, cross-section, 1/6 of meristematic zone, second meristematic section from root tip, root 2
Gene expression data from a cross-section of 1/6 of the root meristematic zone, the second section from the root tip


title: L8SB


title: L2SB

description:
Arabidopsis, root cells, cross-section, 1/6 of meristematic zone, second meristematic section from root tip, root 1
Gene expression data from a cross-section of 1/6 of the root meristematic zone, the second section from the root tip


title: L4SB

description:
Arabidopsis, root cells, cross-section, 1/6 of meristematic zone, fourth meristematic section from root tip, root 1
Gene expression data from a cross-section of 1/6 of the root meristematic zone, the fourth section from the root tip


title: L9SB

description:
Arabidopsis, root cells, cross-section, cross-section 1 (approx 500 µm) of maturation section from root tip, root 1
Gene expression data from a cross-section (approximately 500 µm) of the root maturation zone, the first section of the root maturation zone


title: L7SB

description:
Arabidopsis, root cells, cross-section, 1/2 of elongation zone, first elongation section from root tip, standard conditions, root 1
Gene expression data from a cross-section of 1/2 of the root elongation zone, the first section from the root tip


title: L3SB

description:
Arabidopsis, root cells, cross-section, 1/6 of meristematic zone, third meristematic section from root tip,  root 1
Gene expression data from a cross-section of 1/6 of the root meristematic zone, the third section from the root tip


title: L12SB

description:
Arabidopsis, root cells, cross-section, cross-section 4 (approx 500 µm) of maturation section from root tip, root 1
Gene expression data from a cross-section (approximately 500 µm) of the root maturation zone, the fourth section from the root tip


title: L6SB

description:
Arabidopsis, root cells, cross-section, 1/6 of meristematic zone, sixth meristematic section from root tip, root 1
Gene expression data from a cross-section of 1/6 of the root meristematic zone, the sixth section from the root tip


title: LCOLUMELLASB

description:
Arabidopsis, root cells, cross-section of columella below QC, replicate 1
Gene expression data from a cross section of the root tip containing columella cells


title: L5SB

description:
Arabidopsis, root cells, cross-section, 1/6 of meristematic zone, fifth meristematic section from root tip, root 1
Gene expression data from a cross-section of 1/6 of the root meristematic zone, the fifth section from the root tip


title: L11SB

description:
Arabidopsis, root cells, cross-section, cross-section 3 (approx 500 µm) of maturation section from root tip, root 1
Gene expression data from a cross-section (approximately 500 µm) of the root maturation zone, the third section from the root tip


title: SUC2

description:
Arabidopsis, root cells, phloem companion cells, standard conditions, replicate 1
Gene expression data from isolated phloem companion cells

source_name: Protoplasted and FACS sorted root cells

value: Seedling roots, 5-6 days after germination

tag: GFP reporter


title: L1SB

description:
Arabidopsis, root cells, cross-section, 1/6 of meristematic zone, first meristematic section from root tip, contains QC, root 1
Gene expression data from a cross section of 1/6 of the meristematic zone, the first section from the root tip


title: RM1000

description:
Arabidopsis, root cells, lateral root primordia initials, standard conditions, replicate 1
Gene expression data from isolated lateral root primordia cells


title: S32

description:
Arabidopsis, root cells, protophloem and metaphloem, standard conditions, replicate 1
Gene expression data from isolated protophloem and metaphloem cells


title: S4

description:
Arabidopsis, root cells, protoxylem and metaxylem, meristematic zone, standard conditions, replicate 1
Gene expression data from isolated protoxylem and metaxylem cells in the meristematic zone


title: JO121

description:
Arabidopsis, root cells, xylem pole pericycle, standard conditions, replicate 1
Gene expression data from isolated xylem pole pericycle cells


title: Young trained subject, biological replicate (YT5)

status: Public on Nov 01 2007

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

description: Expression of mRNA in Vastus Lateralis muscle,young trained subject

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

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

data_processing: The data were analyzed with dChip using quantile normalization and PM-only Model Based Expression Indexing.

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

extract_protocol: total RNAs were extracted using QIAGEN'S RNeasy Fibrous Tissue Kit

tag: no additional information


title: Young trained subject, biological replicate (YT11)

source_name: Vastus Lateralis muscle,young trained subject


title: J2501

description:
Arabidopsis, root cells, pericycle, protoxylem, metaxylem, phloem, standard conditions, replicate 1
Gene expression data from isolated pericycle, protoxylem, metaxylem and phloem cells


title: Young sedentary subject, biological replicate (YS12)

description: Expression of mRNA in Vastus Lateralis muscle,young sedentary subject


title: Young trained subject, biological replicate (YT3)


title: S17

description:
Arabidopsis, root cells, phloem pole pericycle, standard conditions, replicate 1
Gene expression data from isolated phloem pole pericycle cells

tag: GFP reporter:S17


title: Young sedentary subject, biological replicate (YS10)

source_name: Vastus Lateralis muscle,young sedentary subject


title: Young sedentary subject, biological replicate (YS8)


title: Young sedentary subject, biological replicate (YS9)


title: Young trained subject, biological replicate (YT7)


title: Young trained subject, biological replicate (YT10)


title: COBL9

description:
Arabidopsis, root cells, hair cells, standard conditions, replicate 1
Gene expression data from isolated hair cells


title: Young trained subject, biological replicate (YT1)


title: Young sedentary subject, biological replicate (YS6)


title: Young trained subject, biological replicate (YT2)


title: Young trained subject, biological replicate (YT4)


title: Young sedentary subject, biological replicate (YS11)


title: Young trained subject, biological replicate (YT9)


title: Young sedentary subject, biological replicate (YS4)


title: Young trained subject, biological replicate (YT8)


title: Young sedentary subject, biological replicate (YS3)


title: Old trained subject, biological replicate (OT2)

description: Expression of mRNA in Vastus Lateralis muscle,old trained subject


title: Old trained subject, biological replicate (OT5)

source_name: Vastus Lateralis muscle,old trained subject


title: Old trained subject, biological replicate (OT1)


title: Old trained subject, biological replicate (OT9)


title: Old trained subject, biological replicate (OT4)


title: Old sedentary subject, biological replicate (OS9)

description: Expression of mRNA in Vastus Lateralis muscle,old sedentary subject


title: Old sedentary subject, biological replicate (OS3)

source_name: Vastus Lateralis muscle,old sedentary subject


title: Old trained subject, biological replicate (OT3)


title: Old trained subject, biological replicate (OT20)


title: Old trained subject, biological replicate (OT7)


title: Young sedentary subject, biological replicate (YS2)


title: Young sedentary subject, biological replicate (YS1)


title: Old trained subject, biological replicate (OT10)


title: Old sedentary subject, biological replicate (OS6)


title: Old trained subject, biological replicate (OT8)


title: Old sedentary subject, biological replicate (OS8)


title: Old sedentary subject, biological replicate (OS2)


title: Old sedentary subject, biological replicate (OS7)


title: Old sedentary subject, biological replicate (OS1)


title: Old sedentary subject, biological replicate (OS4)


title: Old sedentary subject, biological replicate (OS10)


title: Old sedentary subject, biological replicate (OS5)


title: CD49a+ rep2 (stromal cell study)

city: Winston-Salem

first: Jennifer

middle: A

last: Hipp

address: Medical Center Blvd

institute: Wake Forest School of Medicine

description: Prostate stromal fibromuscular cells

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA of .cel files with Genespring 7.2

source_name: normal prostate

label_protocol: Approximately 200 ng of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Prostate tissue was MACS sorted for positive cells. Total RNA was extracted from the cell lysate using an RNeasy kit (Qiagen).

tag: CD49a+ MACS sorted cells


title: CD49a+ rep3 (stromal cell study)

description: Prostate stromal fibromuscular cells


title: CD49a+ rep5 (stromal cell study)

description: Prostate stromal fibromuscular cells


title: CD49a+ rep4 (stromal cell study)

description: Prostate stromal fibromuscular cells


title: CD31+ rep4 (endothelial study)

description: endothelial cells

tag: CD31+ MACS sorted cells


title: CD49a+ rep1 (stromal cell study)

description: Prostate stromal fibromuscular cells


title: CD31+ rep5 (endothelial study)

description: endothelial cells


title: CD31+ rep3 (endothelial study)

description: endothelial cells


title: CD31+ rep1 (endothelial study)

description: endothelial cells


title: CD31+ rep2 (endothelial study)

description: endothelial cells


title: cord blood 28

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description: Gene expression data from newborn cord blood

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.0

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

data_processing: The data were analyzed with Robust multichip analysis

source_name: cord blood arsenic exposure level 4.11

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

extract_protocol: globin reduction protocol rna easy extraction

tag: Cord blood arsenic exposure level 4.11


title: cord blood 29_2

source_name: cord blood arsenic exposure level 9.66

tag: Cord blood arsenic exposure level 9.66


title: cord blood 29


title: cord blood 32_2

source_name: cord blood arsenic exposure level 68.63

tag: Cord blood arsenic exposure level 68.63


title: cord blood 22_2

source_name: cord blood arsenic exposure level 0.7

tag: Cord blood arsenic exposure level 0.7


title: cord blood 31_2

source_name: cord blood arsenic exposure level 14.74

tag: Cord blood arsenic exposure level 14.74


title: H1 embryonic stem cells - GFP

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr.

scan_protocol: Once the probe array has been hybridized, washed, and stained, it is scanned.

data_processing: The data were analyzed with Robust Multi-Chip Analysis (RMA).

source_name: H1 undifferentiated embryonic stem cells - GFP

growth_protocol: see supplementary information Lu et.al, Nature Methods, 2007 Jun;4(6):501-9.

extract_protocol: Total RNA was extracted by Qiagen RNAeasy kiit and was performed according to the manufacturer's instructions.

tag: derived from H1-GFP labeled


title: cord blood 21_2

source_name: cord blood arsenic exposure level 0.66

tag: Cord blood arsenic exposure level 0.66


title: H9 blast cells

source_name: H9 blast cells

treatment_protocol: see supplementary information Lu et.al, Nature Methods, 2007 Jun;4(6):501-9.

tag: derived from H11


title: cord blood 21


title: cord blood 28_2


title: H9 embryoid bodies

source_name: H9 day3.5 embryoid bodies

tag: derived from H10


title: cord blood 32


title: cord blood 19

source_name: cord blood arsenic exposure level 0.5

tag: Cord blood arsenic exposure level 0.5


title: cord blood 31


title: H9 embryonic stem cells

source_name: H9 undifferentiated embryonic stem cells

tag: derived from H9


title: cord blood 27_2

source_name: cord blood arsenic exposure level 3.24

tag: Cord blood arsenic exposure level 3.24


title: cord blood 30_2

source_name: cord blood arsenic exposure level 10.02

tag: Cord blood arsenic exposure level 10.02


title: cord blood 22


title: H1 blast cells - GFP

source_name: H1 blast cells - GFP


title: H1 embryoid bodies - GFP

source_name: H1 day3.5 embryoid bodies - GFP


title: cord blood 19_2


title: cord blood 20_2

source_name: cord blood arsenic exposure level 0.63

tag: Cord blood arsenic exposure level 0.63


title: cord blood 20


title: cord blood 5

source_name: cord blood arsenic exposure level 0.32

tag: Cord blood arsenic exposure level 0.32


title: cord blood 27


title: cord blood 5_2


title: cord blood 9

source_name: cord blood arsenic exposure level 1.6

tag: Cord blood arsenic exposure level 1.6


title: cord blood 23

source_name: cord blood arsenic exposure level 0.74

tag: Cord blood arsenic exposure level 0.74


title: cord blood 11_2

source_name: cord blood arsenic exposure level 1.62

tag: Cord blood arsenic exposure level 1.62


title: cord blood 23_2


title: cord blood 30


title: cord blood 11


title: cord blood 9_2


title: cord blood 25_2

source_name: cord blood arsenic exposure level 1.76

tag: Cord blood arsenic exposure level 1.76


title: cord blood 12

source_name: cord blood arsenic exposure level 11.65

tag: Cord blood arsenic exposure level 11.65


title: rhPBEF rep3 (age 8-12 weeks)

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description: Gene expression data from lung tissue of control animal

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse320_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) for ABS_Call; Bioconductor GCRMA package for normalization;

source_name: Lung

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: standard conditions (12h light-dark cycle, 25-27ºC, ~40% humidity)

treatment_protocol: rhPBEF 20µg / mouse in 1.5µl water per gram body weight, intratracheal injection

tag: Age

value: 8-12 week


title: cord blood 10_2

source_name: cord blood arsenic exposure level 1.61

tag: Cord blood arsenic exposure level 1.61


title: VALI rep3 (age 8-12 weeks)

treatment_protocol: VILI (4 hours, 30 ml/kg tidal volume)


title: rhPBEF & VALI rep1 (age 8-12 weeks)

treatment_protocol: rhPBEF 20µg / mouse in 1.5µl water per gram body weight, intratracheal injection; VILI (4 hours, 30 ml/kg tidal volume)


title: rhPBEF & VALI rep3 (age 8-12 weeks)


title: rhPBEF & VALI rep2 (age 8-12 weeks)


title: cord blood 13

source_name: cord blood arsenic exposure level 13.76

tag: Cord blood arsenic exposure level 13.76


title: cord blood 13_2


title: rhPBEF rep2 (age 8-12 weeks)


title: rhPBEF rep1 (age 8-12 weeks)


title: Control rep3 (age 8-12 weeks)

treatment_protocol: PBS


title: cord blood 10


title: cord blood 25


title: VALI rep2 (age 8-12 weeks)


title: cord blood 8_2

source_name: cord blood arsenic exposure level 1.44

tag: Cord blood arsenic exposure level 1.44


title: cord blood 12_2


title: VALI rep1 (age 8-12 weeks)


title: cord blood 8


title: cord blood 7_2

source_name: cord blood arsenic exposure level 0.54

tag: Cord blood arsenic exposure level 0.54


title: cord blood 7


title: cord blood 6

source_name: cord blood arsenic exposure level 0.38

tag: Cord blood arsenic exposure level 0.38


title: cord blood 24_2

source_name: cord blood arsenic exposure level 1.74

tag: Cord blood arsenic exposure level 1.74


title: VILI PBEF+/- rep1

treatment_protocol: VILI (4 hours, 40 ml/kg tidal volume)

tag: Mouse C57BL/6J

tag: 129/Sv/Ola derived ES cell line; microinjection into B6/J mice; Founder mice were out-crossed to B6 mice for 4 generations to reach 85% congenic status;


title: cord blood 6_2


title: VILI PBEF+/- rep3


title: VILI PBEF+/- rep2


title: Control rep1 (age 8-12 weeks)


title: cord blood 24


title: cord blood 17

source_name: cord blood arsenic exposure level 0.17

tag: Cord blood arsenic exposure level 0.17


title: cord blood 16_2

source_name: cord blood arsenic exposure level 0.13

tag: Cord blood arsenic exposure level 0.13


title: cord blood 15_2

source_name: cord blood arsenic exposure level 0.12

tag: Cord blood arsenic exposure level 0.12


title: cord blood 16


title: cord blood 15


title: cord blood 17_2


title: PBEF+/- rep1

treatment_protocol: No VILI


title: PBEF+/- rep3


title: VALI rep4

tag: Wild type


title: cord blood 18_2

source_name: cord blood arsenic exposure level 0.2

tag: Cord blood arsenic exposure level 0.2


title: cord blood 14


title: Control rep3


title: VALI rep3


title: Control rep4


title: PBEF+/- rep2


title: Control rep2 (age 8-12 weeks)


title: VALI rep1


title: cord blood 14_2


title: cord blood 4_2


title: VALI rep2


title: cord blood 3_2

source_name: cord blood arsenic exposure level 0.14

tag: Cord blood arsenic exposure level 0.14


title: Control rep2


title: cord blood 3


title: cord blood 2_2


title: cord blood 1

source_name: cord blood arsenic exposure level 0.1

tag: Cord blood arsenic exposure level 0.1


title: cord blood 26_2

source_name: cord blood arsenic exposure level 2.29

tag: Cord blood arsenic exposure level 2.29


title: cord blood 4


title: Control rep1

tag: Age


title: cord blood 1_2


title: cord blood 2


title: cord blood 26


title: 01MKV: new onset sJIA

city: cincinnati

first: ndate

last: fall

state: OH

address: 3333 burnet av

department: rheumatology

institute: Cincinnati children's hospital medical center

hyb_protocol: Labeled cDNA was hybridized to Affymetrix U133plus2.0 Gene Chips

scan_protocol: A Affymetrix Scanner 3000 was used

data_processing: Expression values were derived using RMA preprocessing methods.  Each probe set was then normalized to the median expression of the control samples.

source_name: Ficoll/PBMC

label_protocol: Biotio-labeled cDNA was generated using the Nugen Ovation Biotin RNA Amplification and Labeling System

growth_protocol: Whole blood was collected into sodium heparin tubes.  PBMCs were separated and placed in Trizol within 4 hrs of blood collection and stored frozen at -80 degree celsius.

extract_protocol: RNA extraction using Trizol reagent was performed according to the manufacturer protocol.

tag: new onset sJIA


title: 01N0Y: new onset sJIA


title: 01N3C: new onset sJIA


title: 01N3M: new onset sJIA


title: 01N15: new onset sJIA


title: 01MCY: new onset sJIA


title: 01N1E: new onset sJIA


title: 01LPG: new onset sJIA


title: 01MLB: new onset sJIA


title: 01LN8: new onset sJIA


title: 01LMN: new onset sJIA


title: 01LMJ: new onset sJIA


title: 01J46: new onset sJIA


title: 061J4: normal control

tag: normal control


title: 061K0: normal control


title: 01LM6: new onset sJIA


title: 01JME: new onset sJIA


title: 01LN7: new onset sJIA


title: 061K3: normal control


title: 01J43: new onset sJIA


title: 061J3: normal control


title: E12.5 heart_wildtype_sample c

city: Rotterdam

first: Sjaak

last: Philipsen

address: Dr. Molewaterplein 50

department: Cell Biology

institute: Erasmus MC

description: No further description required.

hyb_protocol: According to standard Affymetrix protocol (GeneChip® Expression Analysis Technical Manual)

data_processing: Data extraction and normalization was done using Affymetrix Gene Chip Operating Software (GCOS) version 1.4. The overall intensity value of each GeneChip was scaled to an average value of 200 according to the method of global scaling provided by GCOS. Intensity values between 0 and 30 were set to 30. An unsupervised correlation analysis using all the probe sets expressed above detection level in at least one of the samples was performed with the OmniViz correlation tool (Omniviz, Maynard, MA); this measures correlation patterns by Pearson’s correlation coefficient. We used Robust Multichip Average (RMA) normalization to obtain a list of differentially expressed probe sets, using a fold-change of >1.5 and false discovery rate of 0.01 as criteria. This list was used for cluster analysis by standard hierarchical clustering methods with similarity measured by Euclidean distance, provided by OmniViz software. Potentially relevant biological processes were determined with Ingenuity Pathways Analysis software (Ingenuity, Redwood, CA). Functional annotation was manually curated using the Mouse Genome Informatics Web Site, The Jackson Laboratory (Bar Harbor, ME) (http://www.informatics.jax.org), Online Mendelian Inheritance in Man McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD) (http://www.ncbi.nlm.nih.gov/omim/), and the Ensembl genome database at the European Bioinformatics Institute (Hinxton, UK) (http://www.ensembl.org/), July 2007.

source_name: E12.5 heart

label_protocol: 1-cycle target labeling according to standard Affymetrix protocol (GeneChip® Expression Analysis Technical Manual)

extract_protocol: Total RNA isolated from single heart stored at -80 degrees Celsius, according to standard Affymetrix protocol (GeneChip® Expression Analysis Technical Manual)

tag: Heart dissected from wildtype E12.5 fetus.


title: E12.5 heart_Sp3 knockout_sample b

description: No further description required.

scan_protocol: According to standard Affymetrix protocol (GeneChip® Expression Analysis Technical Manual)

tag: Heart dissected from E12.5 fetus with a null mutation for the Sp3 transcription factor.


title: Columbia glabrous (C24) wild type pollen

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Wild type Columbia glabrous pollen

hyb_protocol: Following fragmentation, fifteen micrograms of cRNA were hybridized for 16 hr at 45°C with the GeneChip ATH1 Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating System 1.3 (GCOS 1.3) using default analysis settings and global scaling as a normalization method. The trimmed mean target intensity of each array was set to 500.

molecule: polyA RNA

source_name: Arabidopsis (C24 ecotype) pollen from stages 13 and 14 flowers

label_protocol: Fifteen micrograms of total RNA was poly(A)+ selected using Dynabeads mRNA purification kit (Dynal Inc.).  Double-stranded cDNAs were generated using Superscript Choice System (Invitrogen).  Biotinylated cRNAs were synthesized with the ENZO BioArray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences).

growth_protocol: Plants were grown in standard green house conditions using a 16:8 light-dark cycle.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) and poly(A)+ RNA was selected using Dynabeads mRNA Purification kit (Dynal Inc) according to the manufacturers.

tag: Arabidopsis Columbia glabrous ecotype (C24)


title: 061HZ: normal control


title: 061J0: normal control


title: 01N6Z: normal control


title: 01N71: normal control


title: E12.5 heart_Sp3 knockout_sample c

description: No further description required.


title: E12.5 heart_wildtype_sample a

description: No further description required.


title: 01N70: normal control


title: Tumor2

description: Gene expression data from H. hepaticus infected mouse; mouse liver to study H. hepaticus infection and liver cancer

hyb_protocol: Following fragmentation, cRNA was hybridized on Mouse genome 430 2.0 arrays

data_processing: The data were analyzed with Robust multichip analysis in RMA express

source_name: Male mouse infected with H. hepaticus; with liver tumor

growth_protocol: male mice 20 months old

extract_protocol: qiagen RNA extraction

treatment_protocol: H. hepaticus inoculated male mouse

tag: male mouse infected

tag: liver from infected male mouse


title: Columbia glabrous (C24) wild type stamen

description: Wild type Columbia glabrous stamens

source_name: Arabidopsis (C24 ecotype) stamens from stages 13 and 14 flowers


title: CaMV::DME stamen

description: CaMV::DME Columbia glabrous stamens

source_name: Arabidopsis (C24 ecotype) CaMV::DME stamen from stages 13 and 14 flowers


title: Hep2

source_name: Male mouse infected with H. hepaticus; and with dysplasia


title: Control

description: Gene expression data from normal mouse liver; mouse liver to study H. hepaticus infection and liver cancer

source_name: Male control mouse

treatment_protocol: sham inoculated male mouse

tag: male mouse uninfected

tag: liver from uninfected male mouse


title: CaMV::DME pollen

description: CaMV::DME Columbia glabrous pollen

source_name: Arabidopsis (C24 ecotype) CaMV::DME pollen from stages 13 and 14 flowers


title: Hep1


title: 01LQJ: normal control


title: Tumor1


title: 01LQK: normal control


title: E12.5 heart_wildtype_sample b

description: No further description required.


title: 01LQH: normal control


title: 01LNM: normal control


title: E12.5 heart_Sp3 knockout_sample a

description: No further description required.

extract_protocol: Total RNA isolated from single hearts stored at -80 degrees Celsius, according to standard Affymetrix protocol (GeneChip® Expression Analysis Technical Manual)


title: MutantHeart_LPS_30min_rep3

city: La Jolla

first: Yu

last: Xia

address: 10550, N. Torrey Pines Rd.

department: Genetics

institute: The Scripps Research Institute

description: Expression data from heart

hyb_protocol: Samples were hybridized to the Affymetrix Mouse 430 2.0 array using standard Affymetrix protocols.

scan_protocol: The chips were scanned using the Affymetrix ScanArray 3000 using default settings.

data_processing: A target intensity of 250 was used for scaling. Chips were included with a background less than 100 intensity units and a GAPDH 3':5'<3. The raw expression values were normalised using Robust Multichip Average. All further processing of the data were performed within the Bioconductor project and the R program software.

label_protocol: RNA was labeled using the MessageAmp II-Biotin Enhanced Single Round RNA Amplification Kit (Perkin-Elmer Inc.)

treatment_protocol: Hearts were homogenized in Trizol immediately following dissection.


title: 01LQD: normal control


title: 01LNJ: normal control


title: MutantHeart_PBS_3h_rep3

description: Expression data from heart


title: ControlHeart_LPS_30min_rep1

description: Expression data from heart


title: 01LLX: normal control


title: Control neonate valves -1

city: Darlinghurst

first: Christine

last: Biben

state: NSW

address: 384 Victoria Street

department: Developmental Biology

country: Australia

institute: Victor Chang Institute

description: Pools of 3 mutant samples (2 valves with 2-3 leaflets each, so 4-6 leaflets/mutant) and 3 wildtype littermates (6 leaflets/wildtype)

hyb_protocol: Biotinylated cRNA was fragmented and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0, following the protocol described in the Affymetrix manual. Typically, 10ug of probe was used per chip (300 ul hybridization mix).

scan_protocol: Each chip was scanned once on a GeneChip Scanner, according to manufacturer’s instructions. CEL files were acquired using GCOS (see supplementary information). CHP files were generated for deposition using Expression console.

data_processing: CHP files were generated from CEL files in Expression console using MAS5.0 normalisation with all probe sets scaled to TGT = 500.

label: Phycoerythrin

source_name: Neonatal semilunar (aortic and pulmonary) valve leaflets

label_protocol: 50ng of total RNA was subjected to two cycles of in vitro amplification following the instructions of the GeneChip Two cycle cDNA synthesis kit (Affymetrix #900432). Biotinylated antisense cRNA was prepared from 10ug of amplified RNA, according to the Affymetrix Small Sample Labeling Protocol II (GeneChip Expression 3’Amplification reagents, IVT labeling kit, Affymetrix #900449).

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen Life Technologies, Mt Waverley, Australia) according to the manufacturer's instructions.
RNA concentration, integrity and purity were determined with an Agilent 2100 Bioanalyzer and the RNA 6000 Nano assay kit (Agilent Technologies) according to the manufacturer's instructions.

treatment_protocol: Neonates were sacrificed and hearts dissected. Cardiac semilunar valves were isolated under the microscope in PBS. Valve leaflets (3/valve) were collected for each valve and stored in trizol reagent on ice during the dissection then at -80.

tag: Pool of semilunar valve leaflets of 3-4 wildtype neonates (mix of genders)

tag: C57BL/6 pure genetic background


title: ControlHeart_PBS_3h_rep2

description: Expression data from heart

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


title: ControlHeart_LPS_30min_rep2

description: Expression data from heart


title: 01LKV: normal control


title: MutantHeart_LPS_30min_rep2

description: Expression data from heart


title: MutantHeart_PBS_3h_rep2

description: Expression data from heart


title: ControlHeart_PBS_3h_rep3

description: Expression data from heart


title: Cxcr7-/- neonate valves – 1

tag: Pool of semilunar valve leaflets of 3-4 Cxcr7-/- neonates (mix of genders)


title: MutantHeart_LPS_30min_rep1

description: Expression data from heart


title: Control neonate valves -2


title: 01LQE: normal control


title: 01LLE: normal control


title: Cxcr7-/- neonate valves – 2


title: 01LLB: normal control


title: 01LKT: normal control


title: 01LNL: normal control


title: 01LLR: normal control


title: MutantHeart_PBS_3h_rep1

description: Expression data from heart


title: 01LNH: normal control


title: 01LNK: normal control


title: 01L4P: normal control


title: ControlHeart_LPS_30min_rep3

description: Expression data from heart


title: 01L4N: normal control


title: 01L4M: normal control


title: ControlHeart_LPS_3h_rep2

description: Expression data from heart


title: 01L4G: normal control


title: MutantHeart_LPS_3h_rep3

description: Expression data from heart


title: ControlHeart_LPS_3h_rep1

description: Expression data from heart


title: ControlHeart_LPS_3h_rep3

description: Expression data from heart


title: 01L4J: normal control


title: colonic_mucosa_non_inflamed_744

status: Public on Oct 31 2007

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: The sample is a part of an analysis of colonic gene expression in patients with ulcerative colitis

hyb_protocol: The Affymetrix GeneChip® Hybridization, Wash, and Stain kit was used according to the protocol supplied with the kit.

scan_protocol: The Affymetrix system was used and the protocols supplied by Affymetrix followed.

data_processing: Log(2) transformed expression measures were calculated with the RMA procedure using the software from www.Bioconductor.org

source_name: Colonic mucosal endoscopic pinch biopsy

label_protocol: First strand cDNA was synthesized from 1 ug total RNA by incubation (42C, 1 hr) in a 20 ul reaction volume containing 2.5 mM T7-(dT)24 primer, 50 mM Tris-HCl pH 8.3, 75 mM KCL, 3 mM MgCl2, 10 mM DTT and 500 mM dNTP, 10 U/ml Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA, USA).Second strand cDNA was synthesized directly by adding 91 ul RNase free water, 30 ul 5 times second strand reaction buffer (Invitrogen), 3 ul 10 mM dNTP, 1 ul Escherichia coli DNA ligase (10 U/ml), 4 ul E. coli DNA polymerase I (10 U/ml), 1 ul E. coli RNase H (2 U/ml) followed by incubation (2 hr, 16C). The ends of the double-stranded cDNA were polished using T4 DNA polymerase (20 U, 5 min, 16C). The cDNA was purified and concentrated by phenol/ chloroform extraction and ethanol precipitation.

extract_protocol: RNA was extracted with Trizol

tag: Ulcerative colitis patient, biopsy taken from the colon, no macroscopic signs of inflammation.


title: colonic_mucosa_non_inflamed_722

tag: Control subject, biopsy taken from the colon, no macroscopic signs of inflammation.


title: colonic_mucosa_non_inflamed_741


title: colonic_mucosa_non_inflamed_728

tag: Control subject, biopsy taken from the sigmoideum, no macroscopic signs of inflammation.


title: colonic_mucosa_non_inflamed_758

tag: Ulcerative colitis patient, biopsy taken from the sigmoideum, no macroscopic signs of inflammation.


title: colonic_mucosa_non_inflamed_93

tag: Ulcerative colitis patient, biopsy taken from the descending colon, no macroscopic signs of inflammation.


title: colonic_mucosa_non_inflamed_95


title: colonic_mucosa_non_inflamed_122


title: colonic_mucosa_non_inflamed_881


title: colonic_mucosa_inflamation_125

tag: Ulcerative colitis patient, biopsy taken from the descending colon, macroscopic inflammation vissible


title: colonic_mucosa_non_inflamed_125


title: colonic_mucosa_non_inflamed_94


title: colonic_mucosa_non_inflamed_877


title: colonic_mucosa_non_inflamed_721


title: MutantHeart_LPS_3h_rep1

description: Expression data from heart


title: MutantHeart_LPS_3h_rep2

description: Expression data from heart


title: colonic_mucosa_non_inflamed_75


title: colonic_mucosa_non_inflamed_743


title: colonic_mucosa_inflamation_119


title: colonic_mucosa_non_inflamed_123


title: colonoc_mucosa_non_inflamed_30


title: colonic_mucosa_non_inflamed_76


title: Colonic_mucosa_inflammation_26

hyb_protocol: Hybridization protocol The Affymetrix GeneChip® Hybridization, Wash, and Stain kit was used according to the protocol supplied with the kit.

extract_protocol: RNA was extracted using Trizol


title: colonic_mucosa_inflamation_76


title: colonic_mucosa_inflamation_94


title: colonic_mucosa_inflamation_95


title: colonic_mucosa_inflamation_93


title: colonic_mucosa_inflammation_30


title: eutopic endometrium from patients with endometriosis, biological rep4

city: BeiJing

first: Guihua

last: Sha

address: 1 Wangfujing, Shuaifuyuan

country: China

institute: Peking Union Medical College Hospital

description: Gene expression data from ectopic endometrium

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

scan_protocol: GeneChips were scanned using the genechip Scanner 3000.

data_processing: A global scaling procedure was performed to normalize the different arrays using dChip software. In a comparison analysis, we applied two class unpaired method in the SAM (Significant Analysis of Microarray ) software to identify significantly differentially expressed genes between the EM group and non-EM group.

source_name: endometrial endothelial cell from eutopic endometrium

label_protocol: Biotinylated cRNA were prepared according to instruction manual of Single Round aRNA Amplification Kit from 2 microg total RNA (MessageAmp? II-Bintin Enhaned KIT, Ambion).

growth_protocol: DMEM with 20% FBS, 100 ug/ml ECGS

treatment_protocol: primary in vitro culture followed by two passages.

tag: endothelium from a patient with endometriosis


title: eutopic endometrium from patients with endometriosis, biological rep3


title: eutopic endometrium from patients without endometriosis, biological rep2

description: Gene expression data from eutopic endometrium

treatment_protocol: primary in vitro culture followed by two passages

tag: endothelium from normal control


title: 6 hr RSL1, biological rep 1

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

description: Gene expression data from clone 7-11 cells, 6 hr following addition of RSL1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C to GeneChip U133 Plus 2.0 Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 G7.

data_processing: The data were analyzed with LimmaGUI software (Bioconductor). Data was normalized by RMA method.

source_name: Cells exposed to RSL1 for 6 hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 50 ug streptomycin/ml and 100 IU penicillin/ml. Cells were grown at 37 C in 5% CO2.

extract_protocol: Total RNA was isolated from cells using Trizol Reagent, according to the manufacturer’s protocol (Invitrogen).

treatment_protocol: Cells were incubated in medium containing vehicle alone (Control) or in medium containing RSL1 (500 nM) for 6 or 24 hr.

tag: LNCaP prostate cancer cells, clone 7-11, 6 hr after induction of AIbZIP expression


title: eutopic endometrium from patients without endometriosis, biological rep3


title: eutopic endometrium from patients without endometriosis, biological rep4


title: eutopic endometrium from patients without endometriosis, biological rep5

label_protocol: Biotinylated cRNA were prepared according to instruction manual of Single Round aRNA Amplification Kit from 2 microg total RNA (MessageAmp II-Bintin Enhaned KIT, Ambion).


title: eutopic endometrium from patients without endometriosis, biological rep1


title: Control, biological rep 2

description: Gene expression data from clone 7-11 cells, prior to addition of RSL1

source_name: Control cells

tag: LNCaP prostate cancer cells, clone 7-11, prior to induction of AIbZIP expression


title: 6 hr RSL1, biological rep 2


title: eutopic endometrium from patients with endometriosis, biological rep1


title: eutopic endometrium from patients with endometriosis, biological rep5

growth_protocol: DMEM with 20% FBS, 100 ug/ml ECGS"


title: 24 hr RSL1, biological rep 2

description: Gene expression data from clone 7-11 cells, 24 hr following addition of RSL1

source_name: Cells exposed to RSL1 for 24 hr

tag: LNCaP prostate cancer cells, clone 7-11, 24 hr after induction of AIbZIP expression


title: colon_IBD_939

city: Budapest

first: Balazs

last: Györffy

address: Bókay 53

country: Hungary

institute: Hungarian Academy of Sciences

description: total RNA extracted from cells obtained using biopsy in a patient having inflammatory bowel disease

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite version 5.0

label: standard Affymetrix procedure

source_name: colon biopsy

label_protocol: standard Affymetrix procedure

extract_protocol: Qiagen Rneasy

tag: biopsy specimen


title: colon_IBD_1533


title: Control, biological rep 3


title: 6 hr RSL1, biological rep 3


title: 24 hr RSL1, biological rep 1


title: 24 hr RSL1, biological rep 3


title: Control, biological rep 1


title: eutopic endometrium from patients with endometriosis, biological rep2


title: colon_IBD_1606


title: colon_IBD_1665


title: colon_IBD_1156


title: colon_IBD_1368


title: colon_IBD_1060


title: colon_IBD_1118


title: colon_IBD_1175


title: colon_IBD_1537


title: colon_CRC_1494

description: total RNA extracted from cells obtained using biopsy in a patient having colorectal cancer


title: colon_IBD_1802


title: colon_IBD_1670


title: colon_CRC_1499


title: colon_CRC_1761


title: colon_IBD_1110


title: colon_CRC_1377


title: colon_CRC_1883


title: colon_CRC_1158


title: colon_CRC_1739


title: colon_CRC_1479


title: colon_CRC_1293


title: colon_IBD_1017


title: ControlHeart_PBS_3h_rep1

description: Expression data from heart


title: colon_CRC_1316


title: colon_CRC_1651


title: colon_CRC_1708


title: colon_CRC_1486


title: colon_adenoma_983

description: total RNA extracted from cells obtained using biopsy in a patient having colon adenoma


title: colon_IBD_923


title: colon_CRC_1146


title: colon_CRC_1556


title: colon_adenoma_980


title: colon_adenoma_956


title: colon_adenoma_995


title: colon_adenoma_1832


title: colon_adenoma_1312


title: colon_adenoma_1700


title: colon_adenoma_1419


title: colon_adenoma_1187


title: colon_adenoma_1830


title: colon_adenoma_1138


title: colon_adenoma_1748


title: colon_adenoma_1115


title: colon_adenoma_1141


title: colon_adenoma_1154


title: Newborn Mouse Ovary_C57/129 WT_3

city: Houston

first: Aleksandar

last: Rajkovic

address: One Baylor Plaza

institute: Baylor College of Medicine

description: Wild type mouse

hyb_protocol: HYBRIDIZATION COCKTAIL  Euk 20X must be heated 5 minutes before using it.  Vortex before using and spin down.  Put on ice when you’re finished with it but not before adding it to MasterMix. (multiply all by 3.5)	MasterMix components  2X Hybe Buffer			150.0 µL				525.0 µL DEPC H20			54.0 µL (to bring volume up to 300.0µL)	189.0 µL 100% DMSO			30.0 µL					105.0 µL Eukaryotic 20X Control	***	15.0 µL					52.5 µL Oligo B2			5.0 µL					17.5 µL Herring Sperm DNA		3.0 µL					10.5 µL BSA				3.0 µL					10.5 µL cRNAfragmented			40.0 µL (if you retrieve all from NanoDrop) you have these separate  1. Keep cRNA in tubes labeled FRAG. 2. Prepare MasterMix in 15mL corning tube. 3. Mix after each component by pipetting several times. 4. Add 260.0 µL of the Hybe MasterMix to each fragmented sample.  You total volume should be 300.0 µL. 5. If you are not hybridizing right away, store the cRNA-HybeCocktail mix in the -20°C until you’re ready to use it.  HYBRIDIZATION  Thaw Hybe Cocktails if they are frozen before heating. Pull arrays out of 4°C Deli Fridge 30 minutes before you want to load them.  They must be at room temperature before you pierce the septa to prevent leakage.  1. Put tube hats on to prevent popping open at high heat. 2. Place the tubes into the 95°C heating block for 5 minutes. 3. Move the tubes to the 45°C heating block, again for 5 minutes. 4. Spin in MicroFuge at max. speed for 5 minutes. 5. Load 250.0 µL into each array. 6. Put in Hybe Oven, set at 60rpm and 45°C for 16 hours.  After 16 hours of hybridization, remove the hybridization cocktail from the probe array and fill the probe array completely with the appropriate volume of Non-Stringent Wash Buffer (Wash Buffer A)  Wash Buffer A: Non-Stringent Wash Buffer  (6X SSPE, 0.01% Tween-20) For 1,000 mL: 300 mL of 20X SSPE 1.0 mL of 10% Tween-20 699 mL of water Filter through a 0.2 μm filter EukGE-WS2v5* Midi_euk2* 10 cycles of 2 mixes/cycle with Wash Buffer A at 30°C 6 cycles of 15 mixes/cycle with Wash Buffer B at 50°C Stain the probe array for 5 minutes in SAPE solution at 35°C 10 cycles of 4 mixes/cycle with Wash Buffer A at 30°C Stain the probe array for 5 minutes in antibody solution at 35°C Stain the probe array for 5 minutes in SAPE solution at 35°C 15 cycles of 4 mixes/cycle with Wash Buffer A at 35°C. The holding temperature is 25°C

scan_protocol: [Scanner] Pixel Size	1.56 hardware: GeneChip Scanner 3000 Affymetrix® Microarray Suite Filter	570 Pixel Size	1.56 Scanner ID	50101490 Number of Scans	1 Scanner Type	M10 As affymetrix protocol.

data_processing: Data in value column is scaled by affymetrix Mas5/GCOS scanning software, but is not normalized.

source_name: Postnatal Day 0.5 Ovarian Tissue WT

label_protocol:
Test RNA sample on NanoDrop.  Concentration must be 500_g/µL or more. Calculate the volume of RNA sample necessary to start protocol with 5µg. i.e. (5 µg) / (NanoDrop concentration reading in µg/µL) =      µL

RNA		  	 x uL
DEPC H20	      10-x uL
oligo T7	 	 2.0 µL

1. Add all components together in a 0.2µL strip tube.
2. Mix well and spin down.
3. Place in thermalcycler at 70°C for 10 minutes. Should be warming up to 70°C while you prep. the samples.
4. Allow thermalcycler to ramp down to 4°C.
5. 4°C for 2 minutes.  Spin down and put on ice.
6. Prepare the 1st Strand MasterMix.

Reverse Transcription (RT) 1st Strand

You should have thawed and vortexed the components during the 70°C-10 minute step.
5X 1st Strand Mix	(4.0 µL) /sample
0.1M DTT		(2.0 µL) /sample
10mM dNTPs		(1.0 µL) /sample
7.0 µL total
1. Add 7.0 µL 1st Strand MasterMix to each sample.  Mix.
2. Put on thermalcycler 42°C-1 Hour. Set timer for 2 minutes.
(This setting is actually programmed for 42°C for 1 hour and 3 minutes, to compensate for the extra 2
minutes at the beginning before adding the SuperScript II.
3. After 2 minutes at 42°C add 1.0 µL of SSII enzyme. (Addition should be done on thermalcycler)
4. The rest of the program will run, 1 hour at 42°C.
5. Proceed to 2nd Strand.
(components should be thawed ~10 minutes before thermalcycler finishes.)

Reverse Transcription (RT) 2nd Strand

DEPC H20				91.0 µL /sample
5X 2nd Strand Mix			30.0 µL /sample
E. coli DNA Polymerase I (DNA Pol I)	  4.0 µL /sample
10mM dNTPs				  3.0 µL /sample
E. coli DNA ligase (ligase)		  1.0 µL /sample
RNase H				  1.0 µL /sample

1. Put samples on thermalcycler, 16°C for 2 hours.
2. At 2 hours, add 2.0 µL of T4 DNA Polymerase.  Mix.
3. Run additional 5 minutes at 16°C.
4. Transfer samples to 1.5mL tube with 10.0 µL of 0.5M EDTA.  Vortex.
5. Use cDNA Clean-Up Module to clean up samples.

Clean-Up of Double Stranded cDNA

Necessary components:
1.5mL tube with cDNA and EDTA, mixed.
cDNA Binding Buffer
cDNA Wash Buffer (ethanol added by MCF)
cDNA Elution Buffer
cDNA clean-up column (in 4°C Deli Fridge)
Empty Collection Tube (provided in clean-up module)
Empty 1.5mL tube labeled with sample name for collecting final eluate.
MicroFuge 18 Centrifuge to spin down samples.

cDNA Wash Buffer is supplied as a concentrate and you have to add ethanol before using.  Check the tube before use to make sure that etOH has been added.

1. Label Collection Tube with sample name (on side).
2. Add 600.0 µL of cDNA Binding Buffer (yellow) into tube with sample and EDTA.
3. Vortex.  Spin down briefly (2 sec.)
4. Add 500.0 µL sample-Binding Buffer mix onto column.
5. Spin in MicroFuge 18 Centrifuge, 14,000rpm for 1 minute.
6. Pour eluate down sink.  Keep same collection tube.
7. Add the remaining cDNA-Binding Buffer mix onto column.
8. Spin 14K rpm for 1 minute.
9. Discard that collection tube and place column into new, labeled tube.
10. Add 720.0 µL cDNA Wash Buffer (ETOH added) to the column.
11. Spin 14K rpm for 1 minute.
12. Discard eluate into sink.  Replace column into collection tube.
13. Spin empty column with the lid open for 5 minutes at 14K rpm.
14. Place column into labeled 1.5mL tube.  Discard collection tube.
15. Air dry column for an additional minute (cover with KimWipe).
16. Add 14.0 µL Elution Buffer onto the center of the column.
17. Let sit at room temp for 1 minute.
18. Spin at 14K for 1 minute.
19. Discard column.
20. Measure the eluate volume.
21. Bring volume up to 20.0 µL with DEPC H20.
22. Store at -20ºC until ready to proceed with IVT step.

InVitro Transcription Reaction (IVT): production of biotin-labeled cRNA

cDNA should be at 20.0 µL before adding IVT MasterMix components.
IVT kit components should be thawed to room temp. ~20 minutes before using.
10X IVT Labeling Buffer (may have precipitate, mix well.) 	(4.0 µL) /sample
IVT Labeling NTP Mix					(12.0 µL) /sample
IVT Labeling Enzyme Mix	 			(4.0 µL) /sample

1. Mix components.  Spin briefly.
2. Add 20.0 µL IVT MasterMix to each sample.  Mix by pipetting.
3. 37 ºC for 16 hours in thermalcycler.
4. Clean-up cRNA with cRNA Clean-Up Module.

Clean-Up of Biotinylated cRNA with cRNA Clean-Up Module

Necessary Components:
cRNA Binding Buffer
cRNA Wash Buffer (ethanol added by MCF)
cRNA clean-up column (stored at 4°C in deli fridge)
Collection Tube (labeled with sample name on side)
DEPC H20
100% Ethanol
80% Ethanol
2 clean, labeled 1.5mL tubes

1. Transfer cRNA samples into clean, labeled 1.5mL tubes for clean-up.
2. Add 60.0 µL to each sample.  Vortex to mix and spin down.
3. Add 350.0 µL cRNA Binding Buffer to each sample.  Vortex and spin down.
4. Add 250.0 µL 100% ETOH to each sample.  Mix by pipetting.
5. Add cRNA-Binding Buffer-ETOH mix onto column (it all fits).
6. Spin at 14,000rpm on “Short Spin” setting (30 seconds).
7. Place columns into clean, labeled collection tube.  Discard previous tubes with eluate.
8. Add 500.0 µL cRNA Wash Buffer to each column.
9. Spin at 14K for “Short Spin”.
10. Discard eluate in sink but replace column into collection tube.
11. Add 500.0 µL 80% ETOH onto column.
12. “Short Spin” at 14K.
13. Discard eluate and replace columns into collection tube again.
14. Spin 14K for 5 minutes to dry column.
15. Put column into clean, labeled 1.5mL tube.  (This tube should have the request number, the term “IVT” and the sample name on top.  On the side put the PI last name and the date.)
16. Pipet 11.0 µL DEPC H20 onto center of column.
17. Spin 14K for 1 minute.
18. Add another 10.0 µL DEPC H20 onto center of column.
19. Spin 14K for 1 minute.
20. Measure volume of eluate.  Record the volume in your lab notebook.
21. NanoDrop samples.  Dilute with DEPC H20 if you need to, to get concentration into read-able range for NanoDrop (under 3000_g).
22. Make a dilution of the IVT samples for testing on the Agilent.

Perform calculations to determine adjusted cRNA amount.  Enter the total µg into MAID. Perform calculations for Fragmentation step and record the volumes in your lab notebook.  Calculations are done with the IVT NanoDrop adjusted cRNA concentrations acquired with the formula provided by Affy.

Fragmentation:

cRNA			      (X uL) 15ug
DEPC H20(variable)	 (32-x) µL
5X Fragmentation Buffer	   8.0  µL
40.0  uL
1. Add 8.0 µL 5X Frag. Buffer to each empty 1.5mL tube.
2. Add the required amount of water to each tube.  This amount will depend on the concentration of cRNA- how much cRNA to make 15 µg of fragmented cRNA, then how much DEPC H20 to bring the final volume to 40.0 µL?
3. Add the required amount of cRNA to each tube.
4. Make sure the 1.5mL tube is clearly labeled FRAG so that you can tell it apart from the IVT cRNA tube.
5. Put the FRAG tube onto the 99°C heat block for 35 minutes.
6. After fragmentation put the tube on ice.  Let it cool about 5 minutes on ice.
7. Spin in the MicroFuge at max. speed to get the condensation out of the lid.
8. Vortex and spin.
9. Test FRAG on NanoDrop.  Needs to be 15 µg or more.  (15 µg/40 µL=0.375 µg/µL or more)

Put the FRAG into hybridization cocktail and store at -20°C until you are ready to load it onto a chip.

extract_protocol: 50 ovaries were pooled per affymetrix array.  RNA was isolated using Qiagen RNeasy mini kits.  On column DNase digestion was used.  RNA was eluted in RNase free water and frozen at -80 degrees Celsius until sample quality could be assessed with the Agilent Bioanalyzer system.

treatment_protocol: Ovaries were dissected from day 0.5 animals and placed in RNAlater (Ambion) for 24 hours at 4 degrees Celsius.  After 24 hours, the RNAlater was removed and the ovaries were frozen on dry ice and placed in a -80 degree freezer.

tag: Background Srain

value: C57/BL6/129SVEV Hybrid

tag: Gender

value: Female

tag: Tissue

value: Ovary

tag: Age

value: .5 Days Postnatal


title: colon_normal_1456

description: total RNA extracted from cells obtained using biopsy of the colon in a healthy control


title: Newborn Mouse Ovary_C57/129 WT_2

description: Wild type mouse


title: Newborn Mouse Ovary_LHX8 Null_2

description: Lhx8 is a homeobox gene expressed in oocytes

data_processing: Data in value is raw data (Mas5 scaled) unaltered by normalizations.

source_name: Postnatal Day 0.5 Ovarian Tissue LHX8 Null

extract_protocol: 50 ovaries were pooled per affymetrix array.  RNA was isolated using Qiagen RNeasy mini kits.  On column DNase digestion was used.  RNA was eluted in RNase free water and frozen at -80 degrees Celsius until sample quality could be assessed with the Agilent Bioanalyzer system


title: colon_normal_1357


title: Newborn Mouse Ovary_Nobox Null_2

description: Nobox is a homeobox gene expressed in oocytes

source_name: Postnatal Day 0.5 Ovarian Tissue Nobox Null


title: colon_normal_1081


title: colon_normal_1440


title: colon_normal_1122


title: Newborn Mouse Ovary_LHX8 Null_1


title: colon_normal_1431


title: colon_normal_1024


title: C2 Thymus

status: Public on Oct 30 2007

city: Seattle

first: John

last: Gosink

address: 1201 Amgen Court West

institute: Amgen

description: non-transgenic mouse

hyb_protocol: 10 μg biotinylated cRNA was hybridized to mouse Affymetrix U430 2.0 chips.  Hybridized chips were stained and washed on an Affymetrix FS400 fluidics station using the Affymetrix antibody amplification protocol.

scan_protocol: Chips were scanned using an Affymetrix Gene Array 2500 Scanner.

data_processing: The Rosetta Resolver System 5.1 (Rosetta Biosoftware, Seattle, Washington) was used for data normalization and analysis.

source_name: Thymus, wild type mouse #2

label_protocol: 5 μg total RNA was labeled with biotin according to standard protocols (affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was isolated from each tissue using the Rneasy Total RNA Isolation kit (Qiagen, Valencia, CA).

value: Female, Age:12 weeks, Strain:C57BL/6


title: colon_normal_1114


title: C1 Thymus

description: non-transgenic mouse

source_name: Thymus, wild type mouse #1


title: C3 spleen

description: non-transgenic mouse

source_name: Spleen, wild type mouse # 3


title: T4 CD2-CD30L spleen

description: Transgenic mice were generated with constitutive T cellspecific overexpression of CD30L as a tool to help unravel the consequences of CD30/CD30L interactions in vivo.

source_name: Spleen, CD30L transgenic mouse # 4


title: T3 CD2-CD30L spleen

source_name: Spleen, CD30L transgenic mouse # 3


title: Newborn Mouse Ovary_Nobox Null_3


title: C2 spleen

description: non-transgenic mouse

source_name: Spleen, wild type mouse # 2


title: T4 CD2-CD30L Thymus

source_name: Thymus, CD30L transgenic mouse # 4


title: T2 CD2-CD30L Thymus

source_name: Thymus, CD30L transgenic mouse # 2


title: C4 Thymus

description: non-transgenic mouse

source_name: Thymus, wild type mouse #4


title: T3 CD2-CD30L Thymus

source_name: Thymus, CD30L transgenic mouse # 3


title: Newborn Mouse Ovary_LHX8 Null_3


title: C4 spleen

description: non-transgenic mouse

source_name: Spleen, wild type mouse # 4


title: C3 Thymus

description: non-transgenic mouse

source_name: Thymus, wild type mouse #3


title: C1 spleen

description: non-transgenic mouse

source_name: Spleen, wild type mouse # 1


title: T1 CD2-CD30L Thymus

source_name: Thymus, CD30L transgenic mouse # 1


title: C2 mesenteric lymph node

description: non-transgenic mouse

source_name: Mesenteric lymph node, wild type mouse # 2


title: T1 CD2-CD30L mesenteric lymph node

source_name: Mesenteric lymph node, CD30L transgenic mouse # 1


title: T3 mesenteric lymph node

source_name: Mesenteric lymph node, CD30L transgenic mouse # 3


title: T1 CD2-CD30L spleen

source_name: Spleen, CD30L transgenic mouse # 1


title: T2 CD2-CD30L spleen

source_name: Spleen, CD30L transgenic mouse # 2


title: C3 mesenteric lymph node

description: non-transgenic mouse

source_name: Mesenteric lymph node, wild type mouse # 3


title: T2 CD2-CD30L mesenteric lymph node

source_name: Mesenteric lymph node, CD30L transgenic mouse # 2


title: CSP-inducible_plus Dox_TNF_1

city: San Diego

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: HeLa cells bearing the delta CS construct were first induced with doxycycline for 17 hours and then exposed to TNF-alpha (40ng/ml).  RNA samples were collected after 6 hours

hyb_protocol: standard Affymetrix procedures

source_name: CSP-inducible_plus Dox_TNF_1

label_protocol: 5 micrograms of total RNA was processed to produce biotinylated cRNA targets using standard Affymetrix protocols

extract_protocol: Trizol followed by RNeasy cleanup

tag: CSP-inducible_plus Dox_TNF_1


title: CSP-inducible_plus Dox_TNF_3

source_name: CSP-inducible_plus Dox_TNF_3

tag: CSP-inducible_plus Dox_TNF_3


title: T4 mesenteric lymph node

source_name: Mesenteric lymph node, CD30L transgenic mouse # 4


title: C4 mesenteric lymph node

description: non-transgenic mouse

source_name: Mesenteric lymph node, wild type mouse # 4


title: C1 mesenteric lymph node

description: non-transgenic mouse

source_name: Mesenteric lymph node, wild type mouse # 1


title: CSP-inducible_plus Dox_TNF_2

source_name: CSP-inducible_plus Dox_TNF_2

tag: CSP-inducible_plus Dox_TNF_2


title: minus Dox_1

description: HeLa cells

source_name: minus Dox_1

tag: minus Dox_1


title: plus Dox_TNF_3

description: HeLa cells were first induced with doxycycline for 17 hours and then exposed to TNF-alpha (40ng/ml).  RNA samples were collected after 6 hours

source_name: plus Dox_TNF_3

tag: plus Dox_TNF_3


title: minus Dox_3

description: HeLa cells

source_name: minus Dox_3

tag: minus Dox_3


title: plus Dox_TNF_1

source_name: plus Dox_TNF_1

tag: plus Dox_TNF_1


title: plus Dox_TNF_2

source_name: plus Dox_TNF_2

tag: plus Dox_TNF_2


title: T4 CD2-CD30L peripheral lymph node

source_name: Peripheral lymph node, CD30L transgenic mouse # 4


title: C3 peripheral lymph node

description: non-transgenic mouse

source_name: Peripheral lymph node, wild type mouse # 3


title: C4 peripheral lymph node

description: non-transgenic mouse

source_name: Peripheral lymph node, wild type mouse # 4


title: C2 peripheral lymph node

description: non-transgenic mouse

source_name: Peripheral lymph node, wild type mouse # 2


title: minus Dox_2

description: HeLa cells

source_name: minus Dox_2

tag: minus Dox_2


title: T2 CD2-CD30L peripheral lymph node

source_name: Peripheral lymph node, CD30L transgenic mouse # 2


title: Shoot Selenate rep2

status: Public on Oct 24 2007

city: Fort Collins

first: Douglas

last: Van Hoewyk

state: CO

address: 1521 Crestmore PL

department: Biology Department

institute: Colorado State University

description: Gene expression data from roots of plants vertically grown for 10 days on 0.5 MS media + 40 micromolar selenate.

hyb_protocol: Following fragmentation, 15 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 the Gene Array Scanner (Agilent Technologies, Palo Alto, CA).

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.

source_name: Arabidopsis shoot tissue from plants grown on selenate

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

growth_protocol:
WS plants were grown at 22C under 16h light and 8 hour dark cycle.
Plants were grown on 40 micromolar selenate.

extract_protocol: Total RNA was prepared using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Root samples were transferred to liquid nitrogen before RNA extraction.

tag: Arabidopsis thaliana, ecotype WS


title: C1 peripheral lymph node

description: non-transgenic mouse

source_name: Peripheral lymph node, wild type mouse # 1


title: T3 CD2-CD30L peripheral lymph node

source_name: Peripheral lymph node, CD30L transgenic mouse # 3


title: IhoCa3, mother of the index patient IhoCa1

city: Helsinki

first: Antti

last: Kokko

address: POBOX 63 (Haartmaninkatu 8)

department: Dept of Medical Genetics

country: Finland

institute: University of Helsinki

description: Gene expression data from human peripheral blood

source_name: blood

label_protocol: standard Affymetrix procedures from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: PAXgene Blood RNA extraction

tag: blood


title: Root control rep 2

description: Gene expression data from roots of plants vertically grown for 10 days on 0.5 MS media.

source_name: Arabidopsis roots

growth_protocol: WS plants were grown at 22C under 16h light and 8 hour dark cycle.


title: Acromegaly 1, control


title: Shoot control rep2

description: Gene expression data from roots of plants vertically grown for 10 days on 0.5 MS  media.

source_name: Arabidopsis shoots


title: classIIhiMECs LTBRWT rep3

status: Public on Oct 23 2007

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: MHC class II high thymic medullary epithelial cells, LTBRWT jos3491

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

label_protocol: BioArray High Yield RNA Transcript Labeling T7 Kit (Enzo Life Sciences)

extract_protocol: RNA isolated with Trizol reagent and amplified twice with the MessageAmp aRNA Kit (Ambion)

value: male Age:3-4.5 weeks Isolation:FACS of CD45-G8.8+Ly51intclassIIhi TECs Strain:C57BL/6


title: Root control rep 1

tag: Arabidopsis thaliana, ecotype WS ecotype


title: Lymf_9, control


title: Root Selenate rep 2

description: Gene expression data from roots of plants vertically grown for 10 days on 0.5 MS + 40 micromolar selenate media.

source_name: Root tissue from plants grown on selenate


title: T1 CD2-CD30L peripheral lymph node

source_name: Peripheral lymph node, CD30L transgenic mouse # 1


title: IhoCa2, father of the index patient IhoCa1


title: High R:FR 16 degrees

status: Public on Oct 28 2007

city: Leicester

first: Keara

last: Franklin

address: University Road

country: United Kingdom

institute: University of Leicester

description: Affymetrix standard protocols.

hyb_protocol: Hybridization was carried out by the John Innes Centre Genome Laboratory (http://jicgenomelab.co.uk) according to Affymetrix standard protocols (http://www.affymetrix.com).

scan_protocol: Scanning was carried out by the John Innes Centre Genome Laboratory (http://jicgenomelab.co.uk) according to Affymetrix standard protocols (http://www.affymetrix.com).

data_processing: Microarray suite 5.0 (Affymetrix) was used for image analysis and to determine probe signal levels. Normalization procedures can be found at http://jicgenomelab.co.uk. Data from MAS 5.0 was analysed in GeneSpring software version 5.1 (Silicon Genetics, Redwood City, CA).

source_name: High R:FR, 16 degrees

label_protocol: Labelling was carried out by the John Innes Centre Genome Laboratory (http://jicgenomelab.co.uk) according to Affymetrix standard protocols (http://www.affymetrix.com).

growth_protocol: Seedlings were grown for 5 days on soil in 100µmolm-2s-1 of white light (R:FR 4.4) at 16 degrees.

extract_protocol: RNA was extracted from cotyledon (and a small amount of hypocotyl) tissue using RNeasy kits (Qiagen) followed by extraction with acid phenol chloroform and precipitation with ethanol to a concentration > 3mg/ml.

tag: Accession

value: La-er

tag: Mutant

value: phyA-2 (WHitelam et al., 1993, Plant Cell 5, 757-768)

value: 5 days


title: Index patient IhoCa1

scan_protocol: standard Affymetrix procedures


title: classIIhiMECs LTBRKO rep2

description: MHC class II high thymic medullary epithelial cells, LTBRKO jos3490

tag: Gender


title: classIIhiMECs LTBRKO rep3

description: MHC class II high thymic medullary epithelial cells, LTBRKO jos3492


title: Shoot Selenate rep1


title: Lymf_6, control


title: Low R:FR, 22 degrees

description: Affymetrix standard protocols.

source_name: Low R:FR, 22 degrees

growth_protocol: Seedlings were grown for 4 days on soil in 100µmolm-2s-1 of white light (R:FR 4.4) at 22 degrees before transfer to low R:FR (R:FR 0.1) for 24 h.

treatment_protocol: 4-day-old seedlings were treated with low R:FR (0.1) for 24 h before harvesting

value: phyA-2 (Whitelam et al., 1993, Plant Cell 5, 757-768)


title: LCL721.174 (TAP1/2 -/-)

status: Public on Oct 27 2007

city: Tuebingen

first: Andreas

middle: Oliver

last: Weinzierl

address: Auf der Morgenstelle 15

department: Department of Immunology

country: Germany

institute: University of Tuebingen

description: Salter, Immunogenetic 1985,21:235

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. Incubation, washing, and staining were carried out according to the GeneChip Mapping Assay Manual, using standard protocols on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene-Chip Scanner 3000.

data_processing: Data were analyzed with the GCOS software (Affymetrix), using default settings for all parameters. Pairwise comparisons were calculated using the respective normal kidney array as baseline. For normalization, 100 housekeeping genes provided by Affymetrix were used (http://www.affymetrix.com/support/ technical/mask_files.affx). Relative expression values were calculated from the signal log ratios given by the software.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: suspension cells grown in RPMI + 10%FCS, split 1:5 every 3-4 days

treatment_protocol: cells (gwoing in log-phase) were centrifuged, the pellet was directly lysed in Trizol.

tag: human B-LCL, TAP deficient HLA-typing


title: Root Selenate rep 1

tag: Arabidopsis thanlia, ecotype WS


title: classIIhiMECs LTBRKO rep1

description: MHC class II high thymic medullary epithelial cells, LTBRKO jos3389


title: High R:FR 22 degrees

description: Affymetrix standard protocols.

source_name: High R:FR, 22 degrees

growth_protocol: Seedlings were grown for 5 days on soil in 100µmolm-2s-1 of white light (R:FR 4.4) at 22 degrees.

tag: mutant

tag: Age 5 days


title: Low R:FR, 16 degrees

description: Affymetrix standard protocols.

source_name: Low R:FR, 16 degrees

growth_protocol: Seedlings were grown for 4 days on soil in 100µmolm-2s-1 of white light (R:FR 4.4) at 16 degrees before transfer to low R:FR (R:FR 0.1) for 24 h.

value: phyA (Whitelam et al., 1993, Plant Cell 5, 757-768)

tag: Age


title: Shoot control rep1


title: LCL721.45 (TAP1/2 +/+)

description: Karathas, PNAS 1980,77:4251

tag: human B-LCL, TAP expressing, HLA-typing


title: classIIhiMECs LTaKO rep2

description: MHC class II high thymic medullary epithelial cells, LTaKO jos3514


title: classIIhiMECs B6aireKO rep3

description: MHC class II high thymic medullary epithelial cells, B6aireKO jos3484

value: male Age:3-4.5 weeks Isolation:FACS of CD45-G8.8+Ly51intclassIIhi TECs


title: classIIhiMECs LTBRWT rep2

description: MHC class II high thymic medullary epithelial cells, LTBRWT jos3489


title: classIIhiMECs LTaWT rep2

description: MHC class II high thymic medullary epithelial cells, LTaWT jos3513


title: classIIhiMECs LTBRWT rep1

description: MHC class II high thymic medullary epithelial cells, LTBRWT jos3388


title: classIIhiMECs LTaWT rep3

description: MHC class II high thymic medullary epithelial cells, LTaWT jos3515


title: classIIhiMECs B6aireKO rep1

description: MHC class II high thymic medullary epithelial cells, B6aireKO jos3387


title: classIIhiMECs LTaWT rep1

description: MHC class II high thymic medullary epithelial cells, LTaWT jos3511

tag: Strain


title: classIIhiMECs B6aireWT rep1

description: MHC class II high thymic medullary epithelial cells, B6aireWT

value: male

value: 3-4.5 weeks

tag: Isolation

value: FACS of CD45-G8.8+Ly51intclassIIhi TECs


title: classIIhiMECs B6aireWT rep2

description: MHC class II high thymic medullary epithelial cells, B6aireWT jos3481


title: classIIhiMECs LTaKO rep3

description: MHC class II high thymic medullary epithelial cells, LTaKO jos3516


title: wildtype cumulus cells #3

status: Public on Oct 22 2007

city: Bar Harbor

first: You-Qiang

last: Su

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description:
References cited
Cui, X. and Churchill, G. A. (2003). Statistical tests for differential expression in cDNA microarray experiments. Genome Biol, Epub 2003 Mar 17.
Cui, X., Hwang, J. T., Qiu, J., Blades, N. J. and Churchill, G. A. (2005). Improved statistical tests for differential gene expression by shrinking variance components estimates. Biostatistics 6, 59-75.
Gautier, L., Cope, L., Bolstad, B. M. and Irizarry, R. A. (2004). affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20, 307-15.
Irizarry, R. A., Bolstad, B. M., Collin, F., Cope, L. M., Hobbs, B. and Speed, T. P. (2003). Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31.
Storey, J. D. and Tibshirani, R. (2003). Statistical significance for genomewide studies. Proc Natl Acad Sci U S A, Epub 2003 Jul 25.
Wu H, K. M., Cui X, Churchill GA. (2003). MAANOVA: A Software Package for the Analysis of Spotted cDNA Microarray Experiments. In The Analysis of Gene Expression Data: An Overview of Methods and Software,  (ed. G. E. Parmigiani G, Irizarry RA, Zeger SL), pp. 313-431. New York: Springer.

hyb_protocol: Equal amounts, 15 µg, of fragmented and biotin-labeled cRNA from each sample were then hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays for 16 h at 45°C.  Post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: After the post-hybridization staining and washing, the arrays were scanned with a GeneChip™3000 laser confocal slide scanner (Affymetrix) and the images were quantified using Gene Chip Operating Software version 1.2 (GCOS, Affymetrix).

data_processing: Probe level data were imported into the R software environment and expression values were summarized using the RMA (Robust MultiChip Average) function (Irizarry et al., 2003) in the R/affy package (Gautier et al., 2004). Using the R/maanova package (Wu H, 2003), an analysis of variance (ANOVA) model was applied to the data, and F1, F2, F3 and Fs test statistics were constructed along with their permutation p-values(Cui and Churchill, 2003; Cui et al., 2005). False discovery rate (FDR) (Storey and Tibshirani, 2003) was then assessed using the R/qvalue package to estimate q-values from calculated Fs test statistics.  Three pair-wise comparison analyses: DM vs. WT, Bmp15-/- vs. WT, and DM vs. Bmp15-/-, were generated, and the significantly changed transcripts were identified using the criteria of FC (fold change) p < 0.01. Results were annotated using information provided by Affymetrix (12/20/2005 release).

source_name: Cumulus cells from PMSG (48h) primed adult wildtype ovarian follicles

label_protocol: Ten nanograms of total RNA from each sample was employed in the two-round cDNA synthesis and subsequent in vitro-transcription according to the Two-Cycle Eukaryotic Target Labeling Assay (Affymetrix Expression Analysis Technical Manual: “ Section 2: Eukaryotic Sample and Array Processing” (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

extract_protocol: Female WT, Bmp15-/-, and DM mice were primed with eCG (5IU/mouse, EMD Biosciences, Inc., Calbiochem, La Jolla, CA) for 48 hours to stimulate follicle development.  Cumulus-oocyte complexes (COCs) were released by puncturing large antral follicles on ovarian surface with a pair of 26 gauge needles.  Released COCs were collected and washed for three times by passing through 3 dishes of medium.  Cumulus cells were then stripped from the oocyte by passing COCs several times through a hand-drawn small fine glass pipette with an inner diameter slightly narrower than the oocyte.  After removing all of the denuded oocytes, cumulus cells were gathered together by gently swirling the dish, and were transferred into a 1.5 ml eppendorf centrifuge tube.  The cells were finally spun down by gentle centrifugation, and the pellet was re-suspended in 350 µl of RLT buffer (Qiagen, Valencia, CA) after removing the supernatant.  After brief vortexing, the cumulus cell lysate was snap frozen in liquid nitrogen and temporarily stored at -80°C until RNA isolation.  Three sets of WT, Bmp15-/- and DM cumulus cell samples were collected and employed in microarray study.  For each sample, about 75-100 COCs, obtained from 3-4 mice, were used for cumulus cell collection.  Medium used for cumulus cells isolation was MEM-α (Invitrogen Corporation, Grand Island, NY) supplemented with 3 mg/ml of crystallized lyophilized bovine serum albumin (Sigma, St. Louis, MO), 75 mg/liter of penicillin G (Sigma) and 50 mg/liter streptomycin sulfate (Sigma).  Milrinone (Sigma), a selective inhibitor of oocyte-specific phosphodiesterase (PDE3), was added into the medium at the concentration of 5 µM to prevent the GV-stage oocytes from undergoing maturation during the process of COC and cumulus cell isolation.  Total RNA was extracted from cumulus cells using the RNeasy Micro Kit (Qiagen, Valencia, CA) according to the manufacturer’s instruction.  The RNA quality and yield of each sample were determined using the Bioanalyzer 2100 and RNA 6000 Pico LabChip assay (Agilent Technologies Inc, Palo Alto, CA) in combination with Quant-iTTM RiboGreen Reagent according to supplied protocols (Invitrogen, Carlsbad, CA).

value: wildtype on B6/129 background; Gender:females; Age:4-5 months old; Follicle stage:large antral follicles


title: Bmp15-/- cumulus cells #1

source_name: Cumulus cells from PMSG (48h) primed adult Bmp15-/- ovarian follicles

value: Bmp15-/- on B6/129 background; Gender:females; Age:4-5 months old; Follicle stage:large antral follicles


title: DM cumulus cells #3

source_name: Cumulus cells from PMSG (48h) primed adult DM ovarian follicles

value: DM on B6/129 background; Gender:females; Age:4-5 months old; Follicle stage:large antral follicles