title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1015

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1015


title: SN:Human Glioblastoma Biopsy 10514

status: Public on Jun 20 2006

type: RNA

city: Los Angeles

first: Cho-Lea

last: Tso

state: CA

address: 10833 Le Conte Avenue

department: Surgery

country: USA

institute: University of California, Los Angeles

data_processing: rma

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: SN:Human Glioblastoma  10514

tag: Human Glioblastoma Biopsy


title: SN:Human Glioblastoma Biopsy 12376

source_name: SN:Human Glioblastoma  12376


title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1001

city: Rahway

first: Olivia

last: Fong

state: NJ

department: Molecular Profiling

institute: Merck & Co.

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1001

data_processing: Local background correction

organism: Rattus norvegicus

tag: Sprague Dawley CD, Approximately 8 wks at the onset of dosing, Vehicle Treated, extensor digitorum longus (EDL)

tag: Sprague Dawley CD, Approximately 8 wks at the onset of dosing, Fenofibrate; Wy-14,643; bezafibrate; rosiglitazone; all trans retinoic acid, extensor digitorum longus (EDL)


title: SN:Human Glioblastoma Biopsy 12378

source_name: SN:Human Glioblastoma  12378


title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1006

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1006


title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1012

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1012


title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1013

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1013


title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1004

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1004


title: SN:Human Glioblastoma Biopsy 10515

source_name: SN:Human Glioblastoma  10515


title: PPAR in Rat  EDL_2-Wy-14,643_d03_010.0mkd_#1174

description: EDL_ vehicle control pool_d03_000.0mkd_n=16 vs. EDL_2-Wy-14,643_d03_010.0mkd_#1174


title: SN:Human Glioblastoma Biopsy 10484

source_name: SN:Human Glioblastoma  10484


title: SN:Human Glioblastoma Biopsy 12369

source_name: SN:Human Glioblastoma  12369


title: PPAR in Rat  EDL_2-Wy-14,643_d03_010.0mkd_#1176

description: EDL_ vehicle control pool_d03_000.0mkd_n=16 vs. EDL_2-Wy-14,643_d03_010.0mkd_#1176


title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1002

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1002


title: SN:Human Glioblastoma Biopsy 10485

source_name: SN:Human Glioblastoma  10485


title: SN:Human Glioblastoma Biopsy 10459

source_name: SN:Human Glioblastoma  10459


title: SN:Human Glioblastoma Biopsy 10429

source_name: SN:Human Glioblastoma  10429


title: SN:Human Glioblastoma Biopsy 10457

source_name: SN:Human Glioblastoma  10457


title: SN:Human Glioblastoma Biopsy 10408

source_name: SN:Human Glioblastoma  10408


title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1011

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1011


title: SN:Human Glioblastoma Biopsy 10455

source_name: SN:Human Glioblastoma  10455


title: GMP3

city: Boston

first: Scott

middle: A.

last: Armstrong

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Children's Hospital

description: Sorted hematopoietic cells

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite Version 5

label: Biotin

organism: Mus musculus

source_name: bone marrow

label_protocol: Approx. 50 ng of total RNA was processed to produce biotinylated cRNA targets

extract_protocol: Approxaimately 50,000 sorted cells were put into trizol and isolated by standard methods

tag: normal GMP


title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1016

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1016


title: N_100G_12hr

city: Tsukuba

first: Masaki

last: Endo

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

country: Japan

institute: National Institute of Agrobiological Sciences

description: Arabidopsis ecotype Nossen wild-type plants were grown on solidified MS medium. Total RNAs were prepared from irradiated / non-irradiated seedlings using an RNeasy Mini Kit (Qiagen, Hilden, Germany). 400 ng of each RNA sample was reverse transcribed, labeled with Cy3, Cy5, and purified with an RNeasy Mini Kit (Qiagen). One microgram each of Cy3- and Cy5-labeled cRNA was added to 500 ul of the hybridization buffer and the mixtures were applied to microarrays under cover slips (Arabidopsis 2 Oligo Microarray, Agilent).

hyb_protocol: The slides were incubated in a hybridization chamber for 17 hr at 60 oC

data_processing: Signal quantification were performed using Agilent G2565AA Feature Extraction software

organism: Arabidopsis thaliana

source_name: Wild-type non-irradiated sample labeled by green (Cy3)

tag: Ecotype

value: Nossen

tag: Age

tag: Tissue

value: Rosette leaves

source_name: Wild-type 12 hr after 100 Gy of gamma-irradiation labeled by red (Cy5)

tag: Treatment

value: Seedlings were irradiated with 100 Gy of gamma-rays at a dose rate of 300 Gy/hr. Twelve hours after irradiation, samples were frozen in liquid nitrogen


title: SN:Human Glioblastoma Biopsy 10410

source_name: SN:Human Glioblastoma  10410


title: SN:Human Glioblastoma Biopsy 10406

source_name: SN:Human Glioblastoma  10406


title: SN:Human Glioblastoma Biopsy 10456

source_name: SN:Human Glioblastoma  10456


title: normal GMP

description: Sorted hematopoietic cells

tag: normal GMP isolated from bone marrow


title: SN:Human Glioblastoma Biopsy 10412

source_name: SN:Human Glioblastoma  10412


title: N_F2

description: Arabidopsis ecotype Nossen wild-type and fas2-2 mutant were grown on solidified MS medium. Total RNAs were prepared from each sample using an RNeasy Mini Kit (Qiagen, Hilden, Germany). 400 ng of each RNA sample was reverse transcribed, labeled with Cy3, Cy5, and purified with an RNeasy Mini Kit (Qiagen). One microgram each of Cy3- and Cy5-labeled cRNA was added to 500 ul of the hybridization buffer and the mixtures were applied to microarrays under cover slips (Arabidopsis 2 Oligo Microarray, Agilent).

source_name: Wild-type sample labeled by green (Cy3)

source_name: fas2-2 sample labeled by red (Cy5)

tag: Mutation

value: p60 subunit of CAF-1


title: N_100G_6hr

source_name: Wild-type 6 hr after 100 Gy of gamma-irradiation labeled by red (Cy5)

value: Seedlings were irradiated with 100 Gy of gamma-rays at a dose rate of 300 Gy/hr. Six hours after irradiation, samples were frozen in liquid nitrogen.


title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1003

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1003


title: SN:Human Glioblastoma Biopsy 10454

source_name: SN:Human Glioblastoma  10454


title: SN:Human Glioblastoma Biopsy 10453

source_name: SN:Human Glioblastoma  10453


title: N_F1

description: Arabidopsis ecotype Nossen wild-type and fas1-2 mutant were grown on solidified MS medium. Total RNAs were prepared from each sample using an RNeasy Mini Kit (Qiagen, Hilden, Germany). 400 ng of each RNA sample was reverse transcribed, labelled with Cy3, Cy5, and purified with an RNeasy Mini Kit (Qiagen). One microgram each of Cy3- and Cy5-labeled cRNA was added to 500 ul of the hybridisation buffer and the mixtures were applied to microarrays under cover slips (Arabidopsis 2 Oligo Microarray, Agilent).

hyb_protocol: The slides were incubated in a hybridisation chamber for 17 h at 60｡C.

data_processing: signal quantification were performed using Agilent G2565AA Feature Extraction software

source_name: wild-type sample labeled by green (Cy3)

value: rosette leaves

source_name: fas1-2 sample labeled by red (Cy5)

value: p150 subunit of CAF-1


title: SN:Human Glioblastoma Biopsy 10405

source_name: SN:Human Glioblastoma  10405


title: GMP2

description: Sorted hematopoietic cells


title: SN:Human Glioblastoma Biopsy 10401

source_name: SN:Human Glioblastoma  10401


title: SN:Human Glioblastoma Biopsy 10398

source_name: SN:Human Glioblastoma  10398


title: SN:Human Glioblastoma Biopsy 10404

source_name: SN:Human Glioblastoma  10404


title: SN:Human Glioblastoma Biopsy 10396

source_name: SN:Human Glioblastoma  10396


title: SN:Human Glioblastoma Biopsy 10392

source_name: SN:Human Glioblastoma  10392


title: SN:Human Glioblastoma Biopsy 10399

source_name: SN:Human Glioblastoma  10399


title: SN:Human Glioblastoma Biopsy 10397

source_name: SN:Human Glioblastoma  10397


title: SN:Human Glioblastoma Biopsy 10403

source_name: SN:Human Glioblastoma  10403


title: SN:Human Glioblastoma Biopsy 10402

source_name: SN:Human Glioblastoma  10402


title: SN:Human Glioblastoma Biopsy 10391

source_name: SN:Human Glioblastoma  10391


title: SN:Human Glioblastoma Biopsy 10400

source_name: SN:Human Glioblastoma  10400


title: SN:Human Glioblastoma Biopsy 10393

source_name: SN:Human Glioblastoma  10393


title: MCF-10F cells transformed by 17-beta-estradiol  caMCF, biological rep2

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

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

hyb_protocol: Following fragmentation, 8 microg of cRNA were hybridized for 16 hr at 45C on GeneChip 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 dChip softwareusing invariant-set normalization method.

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

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

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

tag: Genotype

value: slightly aneuploid


title: MCF-10F cells transformed by 17-beta-estradiol  caMCF, biological rep3


title: L_GMP 1

description: Sorted hematopoietic cells

source_name: bone marrow

tag: leukemic GMP from MLL-AF9 leukemia


title: AKLG-2

description: Sorted hematopoietic cells

source_name: L-GMP

tag: cells cultured in vitro derived from L-GMP


title: L_GMP_2

description: Sorted hematopoietic cells

source_name: Bone marrow

tag: L GMP from an MLL-AF9 leukemia


title: AKLG-1

description: Sorted hematopoietic cells

tag: cells cultures in vitro derived from L-GMP


title: SN:Human Glioblastoma Biopsy 10390

source_name: SN:Human Glioblastoma  10390


title: SN:Human Glioblastoma Biopsy 10383

source_name: SN:Human Glioblastoma  10383


title: Lin-, sca-, kit+, FCR+, CD34+ (L-GMP) rep5

description: Sorted leukemic cells

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label_protocol: Approximately 50ng of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Approximately 10,000 sorted cells were put into Trizol and RNA was isolated by standard methods

tag: leukemia, sorted cells


title: Lin-, sca-, kit+, FCR+, CD34+ (L-GMP) rep6

description: Sorted leukemic cells


title: L_GMP_3

description: Sorted hematopoietic cells

tag: L_GMP isolated from an MLL-AF9 leukemia


title: MCF-10F cells transformed by 17-beta-estradiol  caMCF, biological rep1


title: AKLG-3

description: Sorted hematopoietic cells

tag: cells cultured in vitro, and derived from L-GMP


title: Activation with Strontium Chloride (and cytochalasin D) at metaphase 2 stage St #3(16012165010099)

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: Universal Mouse Reference RNA

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

source_name: St #3

label_protocol: 2-round linear amplification method modified by Toshio Hamatani and Yulan Piao from Agilent protocol: Aliquots of mRNAs, equivalent to 25 embryos from each mRNA, were labeled with Cy3-dye by two-round linear amplification labeling reactions to make each cRNA target using a Fluorescent Linear Amplification Kit (Agilent Technologies, Palo Alto, CA). Briefly, mRNA was used to synthesize double-stranded cDNA with Moloney Murine Leukemia Virus (MMLV) reverse transcriptase in a reaction scaled-down to a total volume of 4 l, with half the standard T7-oligo-dT primer concentration and 125 ng/  l of T4 gp32 single-stranded DNA-binding protein (United States Biochemical, Cleveland, OH). Linear amplification was performed in a total volume of 16 l, with half the standard NTP concentration and no labeled CTP. For the second round of amplification, the product of the first reaction was divided into half, and labeled using the manufacturer ~Rs standard protocol, with the addition of T4gp32 in the cDNA synthesis reaction. Quality and size distribution of targets was determined by RNA 6000 Nano Lab-on-chip Assay (Agilent Technologies), and quantitation was determined using a NanoDrop microscale spectrophotometer (NanoDrop, Wilmington, DE). Similarly, universal mouse reference RNA (Stratagene, La Jolla, CA), which was used for all the hybridization as controls, was labeled with Cy5-dye by 1-round linear amplification labeling reactions.

growth_protocol: Embryos were cultured in KSOM medium for 60 hours before embryo collection.

extract_protocol: mRNAs were extracted with QuickPrep Micro mRNA Purification Kit, Amersham, by Yulan Piao

tag: MF1 unknown sex embryo

source_name: Universal Mouse Reference RNA

tag: Universale Mouse Reference


title: MCF-10F cells transformed by 17-beta-estradiol  bcMCF, biological rep3

description: Gene expression data from the bsMCF cell clone

treatment_protocol: bsMCF cells were cloned and expanded


title: Activation with Strontium Chloride (and cytochalasin D) at metaphase 2 stage St #1(16012165010097)

description: Universal Mouse Reference RNA

source_name: St #1


title: MCF-10F cells transformed by 17-beta-estradiol  bcMCF, biological rep2


title: Activation with cyclohexamide (and cytochalasin D) at metaphase 2 stage Cx #3(16012165010096)

description: Universal Mouse Reference RNA

source_name: Cx #3


title: Lin-, sca-, kit+, FCR+, CD34+ (L-GMP) rep4

description: Sorted leukemic cells


title: Activation with Strontium Chloride (and cytochalasin D) at metaphase 2 stage St #2(16012165010098)

description: Universal Mouse Reference RNA

source_name: St #2


title: Activation with cyclohexamide (and cytochalasin D) at metaphase 2 stage Cx #1(16012165010094)

description: Universal Mouse Reference RNA

source_name: Cx #1


title: SN:Human Glioblastoma Biopsy 10382

source_name: SN:Human Glioblastoma  10382

tag: Human Glioblastoma Biopsy


title: SN:Human Glioblastoma Biopsy 07093

source_name: SN:Human Glioblastoma  07093


title: SN:Human Glioblastoma Biopsy 07091

source_name: SN:Human Glioblastoma  07091


title: SN:Human Glioblastoma Biopsy 07088

source_name: SN:Human Glioblastoma  07088


title: Lin-, sca-, kit+, FCR+, CD34+ (L-GMP)rep3

description: Sorted leukemic cells


title: Activation with cyclohexamide (and cytochalasin D) at metaphase 2 stage Cx #2(16012165010095)

description: Universal Mouse Reference RNA

source_name: Cx #2


title: SN:Human Glioblastoma Biopsy 07096

source_name: SN:Human Glioblastoma  07096


title: Hippocampus 2010 2 month Old

city: Vancouver

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

country: Canada

institute: University of British Columbia

description: (No additional Information)

hyb_protocol: Fragmented amplified RNA was hybridized to Affymetrix Murine Genome U74Av2 arrays (12,486 probe sets). Hybridized arrays were washed and stained as described in the Affymetrix signal antibody amplification protocol.

scan_protocol: Image data were acquired with a Hewlett-Packard GeneArray scanner. Signal values were generated by using the Affymetrix Microarray Suite 5.0 software.

data_processing: MAS 5.0, Target value 250

source_name: Hippocampus

label_protocol: According to the GeneChip Expression Analysis Technical Manual (Affymetrix).

growth_protocol: Housed in groups and according to standard IACUC protocol. Mice received food and water ad libitum and a 12-h light/12-h dark cycle.

extract_protocol: Hippocampi were homogenized, and total RNA was extracted by using TRIzol (Invitrogen Life Technologies). RNA was precipitated with isopropanol and glycogen, washed in 75% ethanol, and resuspended in RNAse free water (Ambion).

treatment_protocol:
Training of mice in the Morris water maze task was carried out between 10:00 am and 2:00 pm in four trials a day, with each
trial lasting a maximum of 120 sec with a 15-min intertrial interval. The task was performed as previously described (Malleret et al. 1999), with two training phases: 2 d with a visible platform followed by 7 d (spatial phase) with a hidden platform in the training quadrant. Probe trials (60 sec), during which the platform was removed, were performed to assess retention of the previously acquired information. Mice were killed by cervical dislocation and hippocampi were dissected out and immediately frozen in liquid nitrogen.

tag: Strain

value: 2 months

tag: Gender

value: Male

value: Whole hippocampus


title: SN:Human Glioblastoma Biopsy 07085

source_name: SN:Human Glioblastoma  07085


title: MCF-10F cells transformed by 17-beta-estradiol  bcMCF, biological rep1


title: SN:Human Glioblastoma Biopsy 07084

source_name: SN:Human Glioblastoma  07084


title: Hippocampus 2008 2 month Old

description: (No additional Information)

tag: Age

tag: Tissue


title: MCF-10F cells transformed by 17-beta-estradiol  bsMCF, biological rep2

description: Gene expression data from the trMCF cells that passed the Boyden chamber

treatment_protocol: trMCF cells selected by Boyden chamber migratory assay


title: SN:Human Glioblastoma Biopsy 07083

source_name: SN:Human Glioblastoma  07083


title: Hippocampus 2007 2 month Old

description: (No additional Information)


title: SN:Human Glioblastoma Biopsy 07082

source_name: SN:Human Glioblastoma  07082


title: SN:Human Glioblastoma Biopsy 07086

source_name: SN:Human Glioblastoma  07086


title: Lin-, sca-, kit+, FCR-, CD34- (MEP)rep2

description: Sorted hematopoietic cells

source_name: bone marrow

tag: Wild type, sorted cells


title: Lin-, sca-, kit+, FCR-, CD34- (MEP)rep3

description: Sorted hematopoietic cells


title: MCF-10F cells transformed by 17-beta-estradiol  trMCF, biological rep3

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

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


title: SN:Human Glioblastoma Biopsy 07080

source_name: SN:Human Glioblastoma  07080


title: Hippocampus 2006 2 month Old

description: (No additional Information)


title: Lin-, sca-, kit+, FCR+, CD34+ (L-GMP)rep2

description: Sorted leukemic cells


title: MCF-10F cells transformed by 17-beta-estradiol  bsMCF, biological rep1


title: Lin-, sca-, kit+, FCR-, CD34- (MEP)rep1

description: Sorted hematopoietic cells


title: SN:Human Glioblastoma Biopsy 07081

source_name: SN:Human Glioblastoma  07081


title: SN:Human Glioblastoma Biopsy 10394

source_name: SN:Human Glioblastoma  10394


title: Lin-, sca-, kit+, FCR+, CD34high(GMP)rep4

description: Sorted hematopoietic cells


title: Hippocampus 2005 2 month Old

description: (No additional Information)


title: MCF-10F cells transformed by 17-beta-estradiol  trMCF, biological rep2


title: MCF-10F cells transformed by 17-beta-estradiol  trMCF, biological rep1


title: Hippocampus 2003 2 month Old

description: (No additional Information)


title: SN:Human Glioblastoma Biopsy 07067

source_name: SN:Human Glioblastoma  07067


title: Lin-, sca-, kit+, FCR+, CD34high(GMP)rep3

description: Sorted hematopoietic cells


title: Breast epithelial cells derived from fibroadenoma  MCF-10F, biological rep3

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

source_name: breast epithelial cells derived from fibroadenoma

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


title: Hippocampus 2002 2 month Old

description: (No additional Information)


title: Hippocampus 2004 2 month Old

description: (No additional Information)


title: SN:Human Glioblastoma Biopsy 06735

source_name: SN:Human Glioblastoma  06735


title: Hippocampus 1995 15 month Old

description: (No additional Information)

value: 15 months


title: Lin-, sca-, kit+, FCR+, CD34high(GMP)rep2

description: Sorted hematopoietic cells


title: SN:Human Glioblastoma Biopsy 06731

source_name: SN:Human Glioblastoma  06731


title: Hippocampus 2001 2 month Old

description: (No additional Information)


title: Lin-, sca-, kit+, FCR+, CD34low(CMP)rep3

description: Sorted hematopoietic cells


title: SN:Human Glioblastoma Biopsy 06733

source_name: SN:Human Glioblastoma  06733


title: Breast epithelial cells derived from fibroadenoma  MCF-10F, biological rep2


title: Lin-, sca-, kit+, FCR+, CD34high(GMP)rep1

description: Sorted hematopoietic cells


title: SN:Human Glioblastoma Biopsy 06732

source_name: SN:Human Glioblastoma  06732


title: Lin-, sca-, kit+, FCR+, CD34low(CMP)rep4

description: Sorted hematopoietic cells


title: Hippocampus 1997 15 month Old

description: (No additional Information)


title: Breast epithelial cells derived from fibroadenoma  MCF-10F, biological rep1


title: SN:Human Glioblastoma Biopsy 06730

source_name: SN:Human Glioblastoma  06730


title: SN:Human Glioblastoma Biopsy 06728

source_name: SN:Human Glioblastoma  06728


title: SN:Human Glioblastoma Biopsy 06729

source_name: SN:Human Glioblastoma  06729


title: Lin-, sca-, kit+, FCR+, CD34low(CMP)rep2

description: Sorted hematopoietic cells


title: Lin-, sca+, kit+ (HSC enriched)rep5

description: Sorted hematopoietic cells


title: Hippocampus 1992 15 month Old

description: (No additional Information)

source_name: Hippocampus


title: Hippocampus 1988 15 month Old

description: (No additional Information)


title: Hippocampus 1989 15 month Old

description: (No additional Information)


title: Lin-, sca+, kit+ (HSC enriched)rep4

description: Sorted hematopoietic cells


title: Lin-, sca+, kit+ (HSC enriched)rep3

description: Sorted hematopoietic cells


title: SN:Human Glioblastoma Biopsy 06726

source_name: SN:Human Glioblastoma  06726


title: SN:Human Glioblastoma Biopsy 06725

source_name: SN:Human Glioblastoma  06725


title: SN:Human Glioblastoma Biopsy 06723

source_name: SN:Human Glioblastoma  06723


title: Lin-, sca+, kit+ (HSC enriched)rep2

description: Sorted hematopoietic cells

source_name: bone marrow


title: SN:Human Glioblastoma Biopsy 06712

source_name: SN:Human Glioblastoma  06712


title: Hippocampus 1984 15 month Old

description: (No additional Information)


title: Hippocampus 1985 15 month Old

description: (No additional Information)


title: MCF-10F cells transformed by 17-beta-estradiol  bsMCF, biological rep3


title: Lin-, sca-, kit+, FCR+, CD34+ (L-GMP)rep1

description: Sorted leukemic cells


title: Hippocampus 1986 15 month Old

description: (No additional Information)


title: Lin-, sca+, kit+ (HSC enriched)rep1

description: Sorted hematopoietic cells


title: Hippocampus 1980 15 month Old

description: (No additional Information)


title: Hippocampus 1982 15 month Old

description: (No additional Information)


title: GMP expressing GFPrep3

description: Sorted hematopoietic cells

tag: Wild type, sorted cells infected with a retrovirus that expresses GFP


title: GMP expressing MLL_AF9rep2

description: Sorted hematopoietic cells

tag: Wild type, sorted cells infected with a retrovirus that expresses MLL-AF9


title: Hippocampus 1987 15 month Old

description: (No additional Information)


title: Hippocampus 1981 15 month Old

description: (No additional Information)


title: GMP expressing MLL_AF9rep1

description: Sorted hematopoietic cells


title: Hippocampus 1983 15 month Old

description: (No additional Information)


title: SN:Human Glioblastoma Biopsy 06486

source_name: SN:Human Glioblastoma  06486


title: EP66_adipose_pcos

status: Public on Jun 17 2006

city: MADRID

first: BELEN

last: PERAL

state: MADRID

address: ARTURO DUPERIER

country: Spain

institute: INSTITUTO DE INVESTIGACIONES BIOMEDICAS, CSIC-UAM

description: Total RNA was extracted from omental  adipose tissue from a PCOS subject

data_processing: MAS 5.0, scaled to 100 and RMA

source_name: Omental adipose tissue

tag: Morbidly obese PCOS patient


title: SN:Human Glioblastoma Biopsy 06487

source_name: SN:Human Glioblastoma  06487


title: SN:Human Glioblastoma Biopsy 06573

source_name: SN:Human Glioblastoma  06573


title: Hippocampus 1978 15 month Old

description: (No additional information)


title: GMP expressing GFPrep1

description: Sorted hematopoietic cells


title: SN:Human Glioblastoma Biopsy 06484

source_name: SN:Human Glioblastoma  06484


title: SN:Human Glioblastoma Biopsy 06485

source_name: SN:Human Glioblastoma  06485


title: GMP expressing GFPrep2

description: Sorted hematopoietic cells


title: SN:Human Glioblastoma Biopsy 06488

source_name: SN:Human Glioblastoma  06488


title: EP55_adipose_pcos


title: EP47_adipose_pcos


title: EP69_adipose_control

description: Total RNA was extracted from omental  adipose tissue from a control subject

tag: Morbidly obese control subject


title: EP49_adipose_control


title: EP37_adipose_control

tag: Total RNA was extracted from omental adipose tissue from a control subject


title: SN:Human Glioblastoma Biopsy 06527

source_name: SN:Human Glioblastoma  06527


title: EP34_adipose_pcos


title: EP31_adipose_control_rep2


title: EP23_adipose_control


title: EP10_adipose_pcos

description: Total RNA was extracted from omental  adipose tissue from a PCOS patient


title: EP1_adipose_pcos_rep2


title: EP31_adipose_control_rep1


title: EP18_adipose_pcos


title: Patient ID# M79

status: Public on Jun 16 2006

city: Stanford

first: Jacob

middle: M

last: Zahn

address: 279 Campus Dr.

department: Developmental Biology

institute: Stanford University

description: Gene expression data from human skeletal muscle samples.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix HU-133 2.0 GeneChip array.

data_processing: The data were analyzed and normalized using Dchip.  The expression model was positive probe only (PM only).  No lower cutoff was used.

source_name: Skeletal muscle taken from rectus abdominis

label_protocol: Biotinylated cRNA were prepared from 8 microg total RNA (Protocol at http://cmgm.stanford.edu/~kimlab/aging_muscle).

treatment_protocol: Muscle samples were surgically removed from patients, snap-frozen immediately after extraction in liquid nitrogen, and stored at -80C until total RNA extraction.

tag: Sex


title: EP3_adipose_control


title: Patient ID# M78


title: Patient ID# M76


title: Patient ID# M77

value: Female


title: Patient ID# M67


title: Patient ID# M70


title: EP71_adipose_control


title: Patient ID# M73


title: Patient ID# M74


title: Patient ID# M65


title: Patient ID# M71


title: EP1_adipose_pcos_rep1


title: Patient ID# M69


title: Patient ID# M68


title: Patient ID# M63


title: Patient ID# M72


title: Patient ID# M75


title: Patient ID# M66


title: Patient ID# M60


title: Patient ID# M61


title: EP32_adipose_pcos


title: Patient ID# M57


title: Lin-, sca-, kit+, FCR+, CD34low(CMP)rep1

description: Sorted hematopoietic cells


title: Patient ID# V1

source_name: Skeletal muscle taken from other anatomical region: NON-rectus abdominis


title: Patient ID# M54


title: Patient ID# M59


title: Patient ID# M55


title: Patient ID# M58


title: Patient ID# M49


title: GMP expressing MLL_AF9rep3

description: Sorted hematopoietic cells


title: Patient ID# M46


title: Patient ID# M43


title: Patient ID# M52


title: Patient ID# M53


title: Patient ID# M47


title: Patient ID# M50


title: Patient ID# M34


title: Patient ID# M40


title: Patient ID# M56


title: Patient ID# M31


title: Patient ID# M37


title: Patient ID# M48


title: Patient ID# M51


title: Patient ID# M44


title: Patient ID# M27


title: Patient ID# M38


title: Patient ID# M33


title: Patient ID# M24


title: Patient ID# M23


title: Patient ID# M14


title: Patient ID# M18


title: Patient ID# M10


title: Patient ID# M28


title: Patient ID# M05


title: Patient ID# M25


title: Patient ID# M11


title: Patient ID# M30


title: Patient ID# M08


title: Patient ID# M02


title: Patient ID# M07


title: Patient ID# M06


title: Patient ID# M09


title: Patient ID# M03


title: N1

city: Montréal

first: Antoine

last: Lampron

state: Qc

address: 3840 St-Urbain

department: Research Centre

institute: CHUM-Hotel Dieu

description:
GIP-dependent nodule
Developped in margin of a GIP-dependent AIMAH, available in the same serie (dataset G1)

data_processing: Data extracted from CEL files by GCOS using all genes and a target value of 500

label: Affymetrix

source_name: GIP-dependent nodule, Adrenal gland

tag: Cortisol prodcing GIP-dependent nodule developped on margin of a GIP-dependent AIMAH.


title: H5

description: ACTH-dependent adrenal hyperplasia. Cushing's syndrome secondary to a ACTH secreting pituitary tumor

source_name: Adrenal gland, Cushing's disease

tag: ACTH-dependent hypercorticism


title: Patient ID# M19


title: Patient ID# M04


title: SNP Analysis of Human Glioblastoma Cell Line (S-496)

type: genomic

description: SNP array analysis for identification of loss of heterozygosity and gene amplification in glioblastoma cell lines.

data_processing: GDAS

molecule: genomic DNA

source_name: Human Glioblastoma Cell Line

label_protocol: Affymetrix GeneChip Human Mapping 10K Array Xba131 Standard Protocol

tag: Human glioblastoma biopsy derived, permanent glioblastoma culture cell line.


title: Patient ID# M01


title: N2


title: A1

description: GIP-dependent adenoma

source_name: GIP-dependent adenoma, Adrenal gland

tag: Cortisol prodcing GIP-dependent adrenocortical adenoma.


title: Patient ID# M62


title: G5

description: Clinically well-defined GIP-dependent AIMAH.

molecule: nuclear RNA

source_name: GIP-dependent AIMAH, Adrenal gland

tag: Cortisol prodcing GIP-dependent AIMAH


title: SNP Analysis of Human Glioblastoma Cell Line (D-431)


title: H1


title: SNP Analysis of Human Glioblastoma Cell Line (W-98)

label: Biotin Labeled


title: Angio_Nonmetast_Dx

status: Public on Jun 15 2006

city: Toronto

first: Chung-Hae

last: Lee

state: ON

address: 9th Floor Rm. 717, 610 University Ave

department: Applied Molecular Oncology

institute: Ontario Cancer Institute, Princess Margaret Hospital

description: hybridized biotin-labeled cDNA were detected with CPD-Star Chemiluminescent Detection Kit;   NOTE: this data is linked to supplementary excel file AngioPlatform_NonmetastaticGroup_atDiagnosis_atSurgery.xls

data_processing: the mean of signal intensities from empty spots (see platform description) were subtracted from the raw intensities after which normalization was performed with the mean signal intensity of PPIA

label: biotin labeled cDNA detected with ECL

source_name: osteosarcoma tumor harvested at diagnosis

tag: Osteosarcoma harvested at time of diagnosis; patient was diagnosed as nonmetastatic


title: Angio_ Nonmetast_SX

source_name: osteosarcoma tumor at surgery

tag: Osteosarcoma harvested at time of surgery; patient was diagnosed as nonmetastatic


title: SNP Analysis of Human Glioblastoma Cell Line (F-502)


title: G4


title: H3


title: G2


title: Angio_NormalBone2

description:
hybridized biotin-labeled cDNA were detected with CPD-Star Chemiluminescent Detection Kit;

NOTE: this data is linked to supplementary excel file AngioPlatform_NonmetastaticGroup_atDiagnosis_atSurgery.xls

source_name: normal bone

tag: normal bone


title: G3


title: H4


title: Angio_Metast_SX

description: hybridized biotin-labeled cDNA were detected with CPD-Star Chemiluminescent Detection Kit;   NOTE: this data is linked to supplementary excel file AngioPlatform_MetastaticGroup_atSurgery_atMetastaticSite.xls

data_processing: the mean of signal intensities from empty spots (see platform description) were subtracted from the raw intensities after which normalization was performed with the mean signal intensity of ACTB

tag: tumor harvested at surgery from patient diagnosed with metastasis


title: Angio_Metast_Mets

description: hybridized biotin-labeled cDNA were detected with CPD-Star Chemiluminescent Detection Kit;    NOTE: this data is linked to supplementary excel file AngioPlatform_MetastaticGroup_atSurgery_atMetastaticSite.xls

source_name: osteosarcoma tumor at metastatic site

tag: Osteosarcoma harvested at metastatic site; patient was diagnosed with metastasis


title: G1


title: SNP analysis of fibroblasts

description: SNP array analysis of normal human fibroblast cell line used as a control for normal human cells.

source_name: Human fibroblast cell line

tag: Normal Human Fibroblast cell line. Hs.27 (ATCC)


title: Angio_NormalBone1

description:
hybridized biotin-labeled cDNA were detected with CPD-Star Chemiluminescent Detection Kit;

NOTE: this data is linked to supplementary excel file AngioPlatform_MetastaticGroup_atDiagnosis.xls


title: Angio_Metast_Dx

description: hybridized biotin-labeled cDNA were detected with CPD-Star Chemiluminescent Detection Kit;    NOTE: this data is linked to supplementary excel file AngioPlatform_MetastaticGroup_atDiagnosis.xls

source_name: osteosarcoma tumor at time of diagnosis

tag: osteosarcoma tumor tissue

tag: at diagnosis, patient diagnosed with metastasis at time of diagnosis


title: Cx_Nonmetast_SX

description: hybridized biotin-labeled cDNA were detected with CPD-Star Chemiluminescent Detection Kit;   NOTE: this data is linked to supplementary excel file ChemoPlatform_NonmetastaticGroup_atDiagnosis_atSurgery.xls

data_processing: the mean of signal intensities from empty spots (see platform description) were subtracted from the raw intensities after which normalization was performed with the mean signal intensity of PPIA, ACTB


title: Patient ID# M15


title: Cx_Nonmetast_Dx


title: Mets_NormalBone2

description:
hybridized biotin-labeled cDNA were detected with CPD-Star Chemiluminescent Detection Kit;

NOTE: this data is linked to supplementary excel file MetastasisPlatform_MetastaticGroup_atMetastaticSite.xls


title: Cx_NormalBone2


title: Effect of S185A mutation on global gene regulation by SATB1 in Jurkat cells from Galande Lab

city: Pune

first: Sanjeev

last: Galande

address: Ganeshkhind

country: India

institute: National Centre for Cell Science

description: Effect of S185A mutant SATB1 on regulation of global gene expression in T cells. S185A mutation abolishes phosphorylation of SATB1 by PKC.

data_processing: Data Aquired by GenePixPro v5.0; log-ratio taken was Cy3 / Cy5

source_name: Total RNA from Jurkat cells

tag: RNA from untransfected Jurkat cells

source_name: Total RNA from stably transfected Jurkat cells

tag: Total RNA from S185A stably transfected Jurkat cells.


title: Mets_Nonmetast_SX

description: hybridized biotin-labeled cDNA were detected with CPD-Star Chemiluminescent Detection Kit;   NOTE: this data is linked to supplementary excel file MetastasisPlatform_NonmetastaticGroup_atDiagnosis_atSurgery.xls

data_processing: the mean of signal intensities from empty spots (see platform description) were subtracted from the raw intensities after which normalization was performed with the mean signal intensity of GAPD


title: Mets_Nonmetast_Dx


title: Mets_Metast_Mets

description: hybridized biotin-labeled cDNA were detected with CPD-Star Chemiluminescent Detection Kit;   NOTE: this data is linked to supplementary excel file MetastasisPlatform_MetastaticGroup_atMetastaticSite.xls


title: Wt vs Yap4 Osmotic Stress Response A

city: Oeiras

first: Claudina

last: Rodrigues-Pousada

address: Av da Republica (EAN)

country: Portugal

institute: Instituto de Tecnologia Quimica e Biologica

description: Details on the experiment

hyb_protocol: Add later

scan_protocol: Add later

data_processing: Raw data

organism: Saccharomyces cerevisiae

source_name: Wt 10', 0,4M NaCl

label_protocol: Add later.

growth_protocol: 10', 0,4M NaCl (details later)

extract_protocol: Protocol

treatment_protocol: Protocol

tag: Wt 10', 0,4M NaCl (strain charact)

source_name: Yap4 10', 0,4M NaCl

label_protocol: Same

growth_protocol: Same

extract_protocol: Same

treatment_protocol: Same

tag: Yap4 Mutant 10', 0,4M NaCl (Strain charact)


title: Cx_Metast_Mets

description: hybridized biotin-labeled cDNA were detected with CPD-Star Chemiluminescent Detection Kit;    NOTE: this data is linked to supplementary excel file ChemoPlatform_MetastaticGroup_atDiagnosis_atSurgery_atMetastaticSite.xls


title: Yap4 Osmotic Stress response C

description: Later

hyb_protocol: Later

scan_protocol: Later

source_name: Yap4 0'

label_protocol: Later

growth_protocol: Normal growth conditions

extract_protocol: Later

treatment_protocol: Later

tag: Yap4 0' (strain charact)

growth_protocol: 10', 0,4M NaCl (Details Later)

tag: Yap4 10', 0,4M NaCl (Strain charact)


title: 01-Control tissue

description: RNA was further purified on a Qiagen RNeasy MinElute column and its integrity was confirmed on a Agilent bioanalyzer 2100

data_processing: Data extracted from .cel files with GCOS 1.2 using all probesets and a target value of 500

label: Streptavidin-Phycoerythrin

source_name: Pool of adrenal gland, Commercially available, Contech #636528

tag: Pool of total RNA from adrenal glands of 62 caucasian subjects aged 15 to 61 years old


title: Wt vs Yap4 Osmotic Stress Response C

description: Later

source_name: Wt

tag: Wt (strain charact)

source_name: Yap4 Mutant

tag: Yap4 (Strain charact)


title: Yap4 Mutant Osmotic Stress Response A

description: Later

source_name: Yap4 Mutant 0'

tag: Yap4 Mutant 0' (strain charact)

source_name: Yap4 Mutant, 10' 0.4M NaCl

tag: Yap4 Mutant, 10' 0.4 M NaCl (strain charact)


title: Cx_Metast_SX

tag: Osteosarcoma harvested at time of surgery; patient was diagnosed with metastasis


title: Mets_NormalBone1

tag: normal bone


title: Cx_Metast_Dx1

description:
hybridized biotin-labeled cDNA were detected with CPD-Star Chemiluminescent Detection Kit;    NOTE: this data is linked to supplementary excel file
ChemoPlatform_MetastaticGroup_atDiagnosis_atSurgery_atMetastaticSite.xls

tag: Osteosarcoma harvested at time of diagnosis; patient was diagnosed with metastasis


title: Yap4 Mutant Osmotic Stress Response B

description: Later

tag: Yap4 Mutant 0' (Strain charact)

source_name: Yap4 Mutant 10', 0,4M NaCl

tag: Yap4 Mutant 10' 0,4M NaCl (Strain charact)


title: Wt Osmotic Stress Response B

description: Details on the experiment

source_name: Wt 0'

growth_protocol: Protocol: normal growth conditions

tag: wt 0' (strain charact)

source_name: Wt 10' Osmotic Stress

growth_protocol: 10', 0,4 M NaCl (details later)


title: Cx_NormalBone1

source_name: normal bone


title: Wt Osmotic Stress Response C

description: Details on the experiment

tag: wt (strain charact)

tag: Wt 10', 0,4M NaCl(strain charact)


title: Wt Osmotic Stress Response A

description: Details on the experiment

tag: Wt 0' strain (strain characteristics)

tag: Wt 10', 0,4M NaCl (strain characteristics)


title: Wt vs Yap4 Osmotic Stress Response B

description: Later

source_name: Wt 10' 0,4M NaCl

tag: Yap4 (strain charact)


title: Effect of K136A mutation on global gene regulation by SATB1 in HeLa cells from Galande Lab

description: K136A mutation in SATB1 abolishes its acetylation by PCAF.

source_name: HeLa total RNA

tag: Total RNA from untransfected Hela cells

source_name: HeLa (stably transfected with K136A mutant of SATB1)

tag: Total RNA from K136A mutant transfected HeLa cells


title: Global regulation of gene expression by SATB1 in Jurkat cells from Galande Lab

description: Jurkat cells were transfected with wild type SATB1 expressing construct to monitor the effect of overexpression of SATB1 on global gene expression in T cells.

source_name: Jurkat total RNA

tag: RNA from untransfected Jurkat cells

tag: RNA from wild type SATB1 transfected Jurkat cells


title: Effect of K136A mutation on global gene regulation by SATB1 in Jurkat cells from Galande Lab

description: Effect of K136A mutant SATB1 on regulation of global gene expression in T cells. K136A mutation abolishes acetylation of SATB1 by PCAF.

source_name: Total RNA from Jurkat cells

source_name: Total RNA from stably transfected Jurkat cells

tag: Jurkat cells were  stably transfected with K136A SATB1 mutant.


title: Global regulation of gene expression by SATB1 in HeLa cells from Galande Lab

description: HeLa cells do not express SATB1 endogenously.

tag: HeLa total RNA

source_name: HeLa (stably transfected with wild type SATB1)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h, rep 4 vs. pituitary reference pool (e11)

status: Public on Jun 14 2006

type: other

city: College Park

first: Tom

middle: Eric

last: Porter

address: Building #142

department: Animal and Avian Sciences

institute: University of Maryland

description: Chicken embryonic pituitary gland, embryonic day 11, replicate 4

hyb_protocol: The microarray was hybridized overnight at 42 C with Cy3-labeled embryonic day 11 cDNA and an aliquot of the Cy5-labeled reference pool cDNA using microarray hybridization buffer (Amersham Biosciences).  Slides were washed in increasing stringency using salt sodium citrate.

scan_protocol: The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

data_processing: The two images from each slide were processed with Spotfinder version 2.2.4 (The Institute for Genomic Research, Rockville, MD) using the following settings:  Otsu thresholding algorithm (minimum spot size 3 and maximum spot size 25); keep flagged values; keep raw data; and quality control filter set so 50% cutoff equals background plus 1 standard deviation.  Data were normalized using Microarray Data Analysis System (MIDAS) version 2.18 (The Institute for Genomic Research).  In MIDAS, channel A and B flags and channel A and B background checking were used, and the signal-to-noise threshold was set at 3.0.  Data from the Cy3 channel were first Lowess (LocFit) normalized by pin (block) using a smoothing parameter of 0.33 with Cy5 as the reference and then sujected to standard deviation regularization first by pin (block) then by slide with Cy5 as the reference.  The data from each spot on each slide were then expressed as log2-ratio, or log2(normalized Cy3/raw Cy5), which is given in the data table below.   Log2-ratios for the spots were statistically analyzed by one-way analysis of variance using Statistical Analysis Systems version 8.02 (SAS Institute, Cary, NC) to identify cDNAs that were differentially expressed on at least one of the time points (n = 4; P < 0.05), and a fold-change of > 2.0 was used as a filter for false positives.

organism: Gallus gallus

source_name: Chicken anterior pituitary gland cells, embryonic day 11

label_protocol: 1 microgram amplified antisense RNA (equivalent to 1 microgram mRNA) was converted to cDNA using random primers with the Amino Allyl cDNA Labeling Kit (Ambion), and Cy3-monoreactive NHS esters (Amersham Biosciences, Piscataway, NJ) were coupled to the cDNA.  Labeled cDNA was purified from unicorporated dye using CyScribe GFX Purification Kit (Amersham Biosciences).

growth_protocol: Fertilized chicken eggs were placed in 37.5 C humidified incubator on embryonic day 0 and removed from the incubator on embryonic day 11.  Pituitary glands from embryonic day 11 embryos were extracted and dispersed into individual cells by trypsin digestion and mechanical agitation.  Dispersed pituitary cells were plated in poly-L-lysine coated 12-well culture plates in serum-free medium supplemented with 0.1% bovine serum albumen (BSA), 5 µg/ml bovine insulin, 5 µg/ml human transferrin, 100 U/ml penicillin G, and 100 µg/ml streptomycin sulfate. Cells were allowed to attach for 1 h in a 37.5 °C, 5% CO2 atmosphere. Cells were then either 1) pretreated for 1.5 h with 10 microgram/ml cycloheximide and then subsequently cultured in the presence of corticosterone (10-9M) for 0, 1.5, 3, 6, 12, or 24 hrs, or (2) cultured with corticosterone (10-9M) with no cycloheximide pretreatment for 0, 1.5, 3, 6, 12, or 24 hours.

extract_protocol: Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Valencia, CA) and was amplifed using a modification of the Eberwine Procedure (Phillips J, Eberwine JH 1996 METHODS: A Companion to Methods in Enzymology 10: 283-288). Briefly, 500 ng was reverse-transcribed using SuperScript II (Invitrogen, Carlsbad, CA) and an oligo(dT) primer containing a T7 promoter site (5'-GGCCAGTGAATTGTAATATCGACTCACTATAGGGAGGCGGT24-3'; Affymetrix, Santa Clara, CA).  Following second strand synthesis and purification, double-stranded cDNA was used as a template for in vitro transcription using the T7 MEGAscript kit (Ambion, Austin, TX) and the resulting amplified antisense RNA was quantified with the Ribogreen RNA Quantitation Kit (Invitrogen, Carlsbad, CA).??

source_name: Reference pool of chicken embryonic pituitary gland amplified RNA, embryonic day 11

label_protocol: 1 microgram amplified antisense RNA (equivalent to 1 microgram mRNA) from the pool was converted to cDNA using random primers with the Amino Allyl cDNA Labeling Kit (Ambion) and Cy5-monoreactive NHS esters (Amersham Biosciences, Piscataway, NJ) were coupled to the cDNA.  Labeled cDNA was purified from unicorporated dye using CyScribe GFX Purification Kit (Amersham Biosciences) and a pool was made of all Cy5-labeled cDNA to be split among the 48 slides in the experiment.

extract_protocol: Extraction and amplification was conducted as described for channel 1 for each of the 48 samples used in the study, and a pool was made of 2 micrograms from each sample.

tag: Chicken embryonic pituitary amplified antisense RNA, pooled from all replicates (n=4) to be used as a reference sample (48 samples total)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 6 h, rep 4 vs. pituitary reference pool (e11)

tag: Chicken anterior pituitary gland cells, embryonic day 11


title: Effect of S185A mutation on global gene regulation by SATB1 in HeLa cells from Galande Lab

description: S185A mutation abolishes the phosphorylation of SATB1 by PKC.

tag: HeLa cells

source_name: HeLa (stably transfected with S185A mutant of SATB1)

tag: Stably transfected HeLa cells


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 1.5 h, rep 4 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CORT for 1.5 hr, rep 4 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells non-treated, rep 4 vs. pituitary reference pool (e11)

description: Chicken e11 pituitary cells, replicate 4

growth_protocol: Fertilized chicken eggs were placed in 37.5 C humidified incubator on embryonic day (e) 0 and removed from the incubator on e11.  Pituitary glands from e11 embryos were extracted and dispersed into individual cells by trypsin digestion and mechanical agitation.  Dispersed pituitary cells were plated in poly-L-lysine coated 12-well culture plates in serum-free medium supplemented with 0.1% bovine serum albumen (BSA), 5 µg/ml bovine insulin, 5 µg/ml human transferrin, 100 U/ml penicillin G, and 100 µg/ml streptomycin sulfate. Cells were allowed to attach for 1 h in a 37.5 °C, 5% CO2 atmosphere. Cells were then either 1) pretreated for 1.5 h with 10 microgram/ml cycloheximide (CHX) and then subsequently cultured in the presence of corticosterone (CORT) (10-9M) for 0, 1.5, 3, 6, 12, or 24 hrs, or (2) cultured with CORT with no CHX pretreatment for 0, 1.5, 3, 6, 12, or 24 hours.

source_name: Reference pool of chicken e11 pituitary amplified RNA

label_protocol: 1 microgram amplified antisense RNA (equivalent to 1 microgram mRNA) from the pool was converted to cDNA using random primers with the Amino Allyl cDNA Labeling Kit (Ambion) and Cy5-monoreactive NHS esters (Amersham Biosciences, Piscataway, NJ) were coupled to the cDNA.  Labeled cDNA was purified from unicorporated dye using CyScribe GFX Purification Kit (Amersham Biosciences) and a pool was made of all Cy5-labeled cDNA to be split among the 16 slides in the experiment.

tag: Chicken e11 pituitary amplified antisense RNA, pooled from all replicates (n=4) to be used as a reference sample (48 samples total)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 24 h, rep 4 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CORT for 3 h, rep 4 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CORT for 6 h, rep 4 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 24 h, rep 3 vs. pituitary reference pool (e11)

description: Chicken embryonic pituitary gland, embryonic day 11, replicate 3


title: Chicken e11 pituitary cells treated with CORT for 6 h, rep 3 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CORT for 12 h, rep 3 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 1.5 h, rep 3 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CORT for 1.5 hr, rep 3 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CORT for 12 h, rep 4 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 12 h, rep 4 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h, rep 3 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CORT for 24 h, rep 4 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 3 h, rep 3 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells non-treated, rep 3 vs. pituitary reference pool (e11)

description: Chicken e11 pituitary cells, replicate 3


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 6 h, rep 3 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CORT for 3 h, rep 3 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 12 h, rep 3 vs. pituitary reference pool (e11)


title: H2

description: ACTH-dependent adrenal hyperplasia. Cushing's syndrome secondary to a ACTH secreting pituitary tumor

source_name: Adrenal gland, Cushing's disease

tag: ACTH-dependent hypercorticism


title: Chicken e11 pituitary cells treated with CORT for 24 h, rep 2 vs. pituitary reference pool (e11)

description: Chicken embryonic pituitary gland, embryonic day 11, replicate 2


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 3 h, rep 4 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h, rep 2 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 1.5 h, rep 2 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 12 h, rep 2 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CORT for 24 h, rep 3 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CORT for 12 h, rep 1 vs. pituitary reference pool (e11)

description: Chicken embryonic pituitary gland, embryonic day 11, replicate 1


title: 4.5 dpc normal mouse embryo, slide stage 4.5dpc Alexa647

city: Roma

first: Francesca

last: Amati

address: Via Montpellier 1

department: Biomedicine and Prevention

country: Italy

institute: University of Rome Tor Vergata

description: Synthesis of the labelled first strand cDNA was conducted using Invitrogen Superscript II reverse transcript system with starting material of 10 ug of total RNA. The amino-allyl labeled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA probes were purified using a the Purification Module (Invitrogen). Probe mixtures were evaporated in a vacuum centrifuge, and the cDNA pellet was resuspended in 3 uL of water. The dye coupling reactions were performed by mixing the cDNA samples with AlexaFluor Dyes 555 or 647 and incubating for overnight in the dark. The reactions were purified with Purification Module (Invitrogen) to remove the unincorporated/quenched dyes. After the purification samples were combined for hybridization. The labeled cDNAs were co-hybridized to cDNA microarrays in duplicate, with one dye swap. Slides were scanned on the GenePix 4000A Microarray Scanner at the optimal wavelength for theAlexa555 (F532) and Alexa647 (F635) using lasers.

data_processing: The acquired images were analyzed with Genepix Pro 5.0 (Axon instruments, Union City). DNA spots were automatically segmented, total intensities as well as the fluorescence ratios of the two dyes were calculated for each spot. The spots were flagged when they exhibited poor hybridization signals, when they were saturated (F635 median = 65534 or F532 = 65534), or when their signal to background ratio were below two. We removed systematic bias in the data by applying the dye-swap normalization (Sanchez-Cabo et.al. 2006) in order to have the least possible information loss. Dye-swap normalization directly makes use of the reverse labelling in the two microarray replicates, and is particularly suited for experiments in which a large number of the spotted genes are expected to significantly change their expression level. Correlations between raw intensity and background were computed for each spot; and background was not subtracted because of the low observed correlations, as suggested by Scharpf et. al. (2005).

source_name: 4.5 dpc normal mouse embryo

tag: Total RNA from mouse embryos at specific developmental stages was obtained by Seegene (Seegene Inc, Korea). Embryo samples from 4.5 dpc to 6.5 dpc include extra-embryonic tissues and maternal uterus.

source_name: RNA reference

tag: The RNA reference used in this study was obtained by pooling different CD1 mouse embryos at 18.5 dpc; total RNA was isolated by the TRIZOL standard protocol (Invitrogen).


title: Chicken e11 pituitary cells treated with CORT for 12 h, rep 2 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CORT for 1.5 hr, rep 2 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 24 h, rep 1 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 6 h, rep 2 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CORT for 6 h, rep 2 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 12 h, rep 1 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CORT for 3 h, rep 1 vs. pituitary reference pool (e11)


title: 14.5 dpc normal mouse embryo, slide stage 14.5dpc Alexa555

source_name: 14.5 dpc normal mouse embryo

tag: Total RNA from mouse embryos at specific developmental stages was obtained by Seegene (Seegene Inc, Korea). The samples from 10.5 dpc to 14.5 dpc are solely embryos.


title: Chicken e11 pituitary cells treated with CORT for 6 h, rep 1 vs. pituitary reference pool (e11)


title: 11.5 dpc normal mouse embryo, slide stage 11.5dpc Alexa555

source_name: 11.5 dpc normal mouse embryo


title: Chicken e11 pituitary cells treated with CORT for 24 h, rep 1 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 1.5 h, rep 1 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 3 h, rep 2 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells non-treated, rep 2 vs. pituitary reference pool (e11)

description: Chicken e11 pituitary cells, replicate 2


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 24 h, rep 2 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 6 h, rep 1 vs. pituitary reference pool (e11)


title: 4.5 dpc normal mouse embryo, slide stage 4.5dpc Alexa555


title: Chicken e11 pituitary cells treated with CHX for 1.5 h, rep 1 vs. pituitary reference pool (e11)


title: Chicken e11 pituitary cells non-treated, rep 1 vs. pituitary reference pool (e11)

description: Chicken e11 pituitary cells, replicate 1


title: Chicken e11 pituitary cells treated with CHX for 1.5 h then CORT for 3 h, rep 1 vs. pituitary reference pool (e11)


title: 9.5 dpc normal mouse embryo, slide stage 9.5dpcAlexa555

source_name: 9.5 dpc normal mouse embryo

tag: Total RNA from mouse embryos at specific developmental stages was obtained by Seegene (Seegene Inc, Korea). Samples from 7.5 dpc to 9.5 dpc are conceptuses, including embryo and extra-embryonic tissues.


title: Chicken e11 pituitary cells treated with CORT for 3 h, rep 2 vs. pituitary reference pool (e11)


title: 8.5 dpc normal mouse embryo, slide stage 8.5dpcAlexa647

source_name: 8.5 dpc normal mouse embryo

tag: Total RNA from mouse embryos at specific developmental stages was obtained by Seegene (Seegene Inc, Korea). Samples form 7.5 dpc to 9.5 dpc are conceptuses, including embryo and extra-embryonic tissues.


title: 11.5 dpc normal mouse embryo, slide stage 11.5dpc Alexa647


title: 6.5 dpc normal mouse embryo, slide stage 6.5dpc Alexa647

source_name: 6.5 dpc normal mouse embryo


title: 7.5 dpc normal mouse embryo, slide stage 7.5dpcAlexa647

source_name: 7.5 dpc normal mouse embryo


title: 9.5 dpc normal mouse embryo, slide stage 9.5dpcAlexa647

tag: Total RNA from mouse embryos at specific developmental stages was obtained by Seegene (Seegene Inc, Korea). Samples form 7.5 dpc to 9.5 dpc are conceptuses, including embryo and extra-embryonic tissues


title: 14.5 dpc normal mouse embryo, slide stage 14.5dpc Alexa647


title: 6.5 dpc normal mouse embryo, slide stage 6.5dpcAlexa555

source_name: reference RNA


title: 7.5dpc normal mouse embryos, slide stage 7.5dpcAlexa555

data_processing: The acquired images were analyzed with Genepix Pro 5.0 (Axon instruments, Union City).  DNA spots were automatically segmented, total intensities as well as the fluorescence ratios of the two dyes were calculated for each spot. The spots were flagged when they exhibited poor hybridization signals, when they were saturated (F635 median = 65534  or F532 =  65534), or when their signal to background ratio were below two. We removed systematic bias in the data by applying the dye-swap normalization (Sanchez-Cabo et.al. 2006) in order to have the least possible information loss. Dye-swap normalization directly makes use of the reverse labelling in the two microarray replicates, and is particularly suited for experiments in which a large number of the spotted genes are expected to significantly change their expression level. Correlations between raw intensity and background were computed for each spot; and background was not subtracted because of the low observed correlations, as suggested by Scharpf et. al. (2005).

source_name: Reference RNA

label: Alexa 555

source_name: 7.5dpc normal mouse embryos


title: 8.5 dpc normal mouse embryos, slide stage 8.5dpcAlexa555

source_name: 8.5 dpc normal mouse embryos


title: Chicken e11 pituitary cells treated with CORT for 1.5 hr, rep 1 vs. pituitary reference pool (e11)

source_name: Chicken anterior pituitary gland cells, embryonic day 11


title: chitinoligomer treatment (CEBiP-specific knock-down)

status: Public on Jun 13 2006

city: tsukuba

first: Chiharu

last: Akimoto-Tomiyama

address: 2-1-2 kannonndai

institute: NIAS

description: To see the function of CEBiP in the chitin elicitor signaling in rice cells, a plasmid for the gene-specific knock-down by RNA interference (RNAi) was constructed by using a sequence for the 3’-terminal region of CEBiP and transformed into the rice cells by using Rhizobium radiobacter (Agrobacterium tumefaciens).  chitinoligomer was added (or not added) to the medium. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract the total RNA.

data_processing: Feature Extraction ver.6

organism: Oryza sativa

tag: chitinoligomer treatment for CEBiP-specific knock-down rice cells

source_name: non treated control (CEBiP-specific knock-down)

tag: non treated control (CEBiP-specific knock-down rice cells)


title: WCHI_F057_02-02-05

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

description: lin-35(n745) vs N2

data_processing: log base 2 ratio of cy5 to cy3

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: EXP: lin-35(n745) mRNA

tag: lin-35(n745) mRNA

source_name: REF: N2 mRNA

tag: N2 mRNA


title: chitinoligomer treatment (WT) color-swap

description: Chitinoligomer was added (or not added)to the suspension culture of Oryza sativa L. cv. nipponbare (WT) that maintained using modified N6 medium. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract the total RNA.

source_name: non treated control (WT)

tag: non treated control (WT)

source_name: chitinoligomer treatment (WT)

tag: chitinoligomer treatment (WT)


title: WCHI_D026_10-02-03

description: lin-35(n745) vs N2


title: WCHI_D032_10-28-03

description: dpl-1(n3316) unc-4(e120) vs unc-4(e120) prep 3

source_name: REF: unc-4(e120) mRNA

tag: unc-4(e120) mRNA


title: Second replicate Hybrid simulans x mauritiana testes  / D. melanogaster whole fly

status: Public on Jun 12 2006

city: Hamilton

first: Rama

middle: S.

last: Singh

state: Ontario

address: 1280 Main Street West

department: Biology Department

institute: McMaster University

description: Labelling and hybridizations were performed at the Canadian Drosophila Microarray Centre according to the CDMC protocols http://www.flyarrays.com/downloads.html

data_processing: Data procesing was performed using GeneTraffic Duo (Iobion Informatics). Spots presenting a ratio probe intensity / backgroung intensity lower than 2 were removed, as spots with a probe intensity lower than 2 times the local background. Spots from the three replicates with a covariance greater than 150% were rejected. Before statistical analysis genes with less than 2/3 of valid spots were removed.

organism: Drosophila melanogaster

source_name: 4 days old whole D. melanogaster male

growth_protocol: temperature 25°C, 12 h light/dark cycle. Flies were bred on cornmeal and molasses medium

extract_protocol: Trizol extraction on whole D. melanogaster male

treatment_protocol: temperature 25°C, 12 h light/dark cycle. Flies were bred on cornmeal and molasse medium

tag: strain

value: 14021-0231.00, Gender:male, Age:4 days old, whole fly

organism:
Drosophila mauritiana
Drosophila simulans

source_name: Hybrid D. simulans x D. mauritiana testes

extract_protocol: Extraction using the RiboPure Kit (Ambion) was performed on a pool of 200 testes. A one round of RNA amplification was performed using the MessageIIAmp aRNA kit (Ambion) according to the specifications of the manufacturer

treatment_protocol: Testes of 4 days old males were dissected in PBS buffer and kept in RNAlater.

tag: Hybrids were obtained by crossing 10 females D. simulans (strain 14021-0251.2) with 15 males D. mauritiana (strain 14021-0241.1)  per vial. Gender

value: male, Age:4 days old, tissue:testes without accessory glands.


title: chitinoligomer treatment (CEBiP-specific knock-down) color swap

source_name: non treatment control (CEBiP-specific knock-down)

tag: non treatment control (CEBiP-specific knock-down rice cells)

tag: chitinoligomer treatment (CEBiP-specific knock-down rice cells)


title: WCHI_F058_02-02-05

description: lin-35(n745) vs N2


title: Third replicate Hybrid simulans x melanogaster testes  / D. melanogaster whole fly

extract_protocol: Trizol extraction on whole D. melanogaster males

organism:
Drosophila melanogaster
Drosophila simulans

source_name: Hybrid D. simulans x D. melanogaster testes

tag: Hybrids were obtained by crossing 10 females D. simulans (strain 14021-0251.2) with 15 males D. melanogaster (strain 14021-0231.00)  per vial. Gender


title: WCHI_D031_10-28-03

description: dpl-1(n3316) unc-4(e120) vs unc-4(e120) prep 2


title: GM15851 control cells treated with FA1 at 2uM 3

city: La Jolla

first: Ryan

middle: Stephen

last: Burnett

address: 10550 N. Torrey Pines Road, MB-27

department: Molecular Biology

institute: The Scripps Research Institute

description: Normal and patient cells were treated with pyrrole-imidazole made to target GAA repeats.

data_processing: RMAExpress and BRBArraytools

label: Caltech core facility labeled

tag: GM15851 control cells treated with FA1 at 2uM.


title: WCHI_D030_10-28-03

description: dpl-1(n3316) unc-4(e120) vs unc-4(e120) prep 1


title: chitinoligomer treatment (WT)

description: Chitinoligomer was added to the suspension culture of Oryza sativa L. cv. nipponbare (WT) that maintained using modified N6 medium. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract the total RNA.

source_name: chitinoligomer treated sample labeled by green (Cy3)

tag: chitinoligomer treatment (wild type)

source_name: Non treated sample labeled by red (Cy5)

tag: non treated control (wild type)


title: First replicate Hybrid simulans x melanogaster testes  / D. melanogaster whole fly


title: Second replicate D. mauritiana testes RNA  / D. melanogaster whole fly RNA

description:
Labelling and hybridizations were performed at the Canadian Drosophila Microarray Centre according to the CDMC protocols.

http://www.flyarrays.com/downloads.html

data_processing: Data procesing was performed using GeneTraffic Duo (Iobion Informatics). Spots presenting a ratio probe intensity / backgroung intensity lower than 2 were removed, as spots with a probe intensity lower than 2 times the local background. Spots from the four replicates with a covariance greater than 150% were rejected. Before statistical analysis genes with less than 2/3 of valid spots were removed.

tag: Gender

value: male

tag: Age

value: 4 days old

tag: whole fly

organism: Drosophila mauritiana

source_name: D. mauritiana testes

tag: tissue

value: testes without accessory glands


title: First replicate D. melanogaster testes  / D. melanogaster whole fly

description:
Labelling and hybridizations were performed at the Canadian Drosophila Microarray Centre according to their protocols

http://www.flyarrays.com/downloads.html

source_name: 4 day old whole D. melanogaster male

growth_protocol:
temperature 25°C
12 h light/dark cycle
Flies were bred on cornmeal and molasses medium

treatment_protocol:
temperature 25°C
12 h light/dark cycle
Flies were bred on cornmeal and molasse medium

value: 4 day old

source_name: D. melanogaster testes

extract_protocol:
Extraction using the RiboPure Kit (Ambion) was performed on a pool of 200 testes.
A one round of RNA amplification was performed using the MessageIIAmp aRNA kit (Ambion) according to the specifications of the manufacturer


title: WCHI_D012_01-28-04

description: efl-1(n3639) vs N2

source_name: EXP: efl-1(n3639) mRNA

tag: efl-1(n3639) mRNA


title: Third replicate D. melanogaster testes RNA  / D. melanogaster whole fly RNA

description: Labelling and hybridizations were performed at the Canadian Drosophila Microarray Centre according to their protocols. http://www.flyarrays.com/downloads.html

value: 14021-0231.00, Gender:male, Age:4 day old, tissue:testes without accessory glands


title: WCHI_D013_01-28-04

description: efl-1(n3639) vs N2

tag: N2 mRNA


title: Fourth replicate D. mauritiana testes RNA/D. melanogaster whole fly RNA

description: Labelling and hybridizations were performed at the Canadian Drosophila Microarray Centre according to the CDMC protocols. http://www.flyarrays.com/downloads.html

data_processing: Data procesing was performed using GeneTraffic Duo (Iobion Informatics). Spots presenting a ratio probe intensity / backgroung intensity lower than 2 were removed, as spots with a probe intensity lower than 2 times the local background. Spots from the three replicates with a covariance greater than 150% were rejected. Before statiscal analysis genes with less than 2/3 of valid spots were removed.

value: 14021-0241.1, Gender:male, Age:4 days old, tissue:testes without accessory glands


title: WCHI_D041_01-09-04

description: efl-1(n3639) vs N2


title: OltactoryEpithelium_mutant_biolrepli3

status: Public on Jun 10 2006

city: New York

first: Friedrich

middle: Bernhard

last: Laub

state: NY

address: 535 East 70th Street

department: Research

institute: Hospital for Special Surgery

description: RNA was amplified and converted into cDNA with the NuGEN Ovation™ Biotin RNA Amplification and Labeling System {http://www.nugentechnologies.com/html/03_products2.html}

hyb_protocol: Affymetrix Standard. Performed at Microarray Core Facility of Weill Medical College of Cornell University, New York

data_processing: dChip

source_name: Olfactory Epithelium from P1 mice, mutant

extract_protocol: Qiagen RNeasy mini

tag: Strain

value: Mix of C57Black6/J and 129SvJ; Age:1 day; Tissue:Olfactory Epithelium


title: Third replicate Hybrid simulans x mauritiana testes  / D. melanogaster whole fly


title: First replicate Hybrid simulans x mauritiana testes  / D. melanogaster whole fly


title: First replicate D. mauritiana testes  / D. melanogaster whole fly


title: Third replicate D. mauritiana testes RNA  / D. melanogaster whole fly RNA

extract_protocol: Trizol extraction


title: WCHI_D042_01-09-04

description: efl-1(n3639) vs N2


title: OltactoryEpithelium_mutant_biolrepli2

scan_protocol: Affymetrix Standard. Performed at Microarray Core Facility of Weill Medical College of Cornell University, New York

label_protocol: NuGEN Ovation™ Biotin RNA Amplification and Labeling System


title: yWt5-1 and yTaut5-1

status: Public on Jun 09 2006

city: Duesseldorf

first: Birgit

last: Andree

address: Moorenstr. 5

country: Germany

institute: BMFZ

description: For normalization the upper 20% and the lower 20% of signals were excluded. The remaining signals were used for a global normalization approach. Normalization was carried out for each channel independently.

hyb_protocol: Slides were processed with the automated slide processor (ASP, Amersham). Slides were prehybridized with 5xSSC, 0,1% SDS, 1% BSA for 1 h at 42°C. Probes were denaturated at 95°C for 5 min and hybridized in 5xSSC, 0,1%SDS, 40% Formamid at 42°C for 16h. Washing was performed at 30°C with 2xSSC/0.1%SDS, 1xSSC and 0.5xSSC for 10 min each. Slides were dried and scanned (FLA800, Fuji).

data_processing: Images were analysed with Aida Image Analyzer v.3.50 (Raytest).Two colour hybridizations were compared using Aida Array Compare v.3.50 (Raytest).

label_protocol: Fluorescent cDNA was reverse transcribed from 25 mg total RNA using 0.5 mg oligo dT-primer (Invitrogen). The reaction mixture was heated to 70°C for 5 min, and placed at room temperature for 10 min to allow primer annealing. The mixture was added with 1x first-strand buffer, 10 mM dithiothreitol, 200 mM dNTP (dATP, dCTP, and dGTP), 80 mM dTTP, 20 U RNAseout (Invitrogen), and 200 U Superscript III (Invitrogen), 40 mM Cy3- or Cy5-dUTP (Amersham-Pharmacia). Reverse transcription was carried out at 46°C for 2h. The reaction was stopped with 50 mM EDTA, followed by adding 25 mM sodium hydroxide at 37°C for 15 min to hydrolyze the RNA template, and neutralized with 600 mM Hepes. The unincorporated nucleotides were removed by using QIAquick PCR purification columns (Qiagen). The labeling efficency was calculated from NanoDrop (PeqLab) measurements.

extract_protocol: Total RNA was isolated from mouse hearts using Trizol reagent (Invitrogen). The total RNA was further purified via Rneasy columns (Qiagen).

tag: Wt mouse, heart tissue without atria, 2 months old

tag: Taut -/- mouse, heart tissue without atria, 2 months old


title: yWt2-2 and yTaut2-2

scan_protocol: Slides were dried and scanned (FLA800, Fuji).


title: yWt4-1 and yTaut4-1


title: yWt3-1 and yTaut3-1


title: Wt4-2 and Taut4-2

tag: Wt mouse, heart tissue without atria, 15 - 16 months old

tag: Taut -/- mouse, heart tissue without atria, 15 - 16 months old


title: yWt4-2 and yTaut4-2


title: yWt1-2 and yTaut1-2


title: yWt5-2 and yTaut5-2


title: Wt2-2 and Taut2-2

tag: Wt mouse,

tag: heart tissue without atria, 15 - 16 months old

source_name: Taut 2-2

tag: Taut -/- mouse,


title: yWt2-1 and yTaut2-1


title: Wt3-2 and Taut 3-2

source_name: Taut 3-2


title: yWt3-2 and yTaut3-2


title: Wt4-1 and Taut4-1


title: yWt1-1 and yTaut1-1


title: Wt3-1 and Taut 3-1

tag: wt mouse,


title: OltactoryEpithelium_mutant_biolrepli1


title: Madin-Darby bovine kidney epithelial cells BEKC 46496 sodium butyrate treated BT3

city: Beltsville

first: Robert

middle: W

last: Li

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

description: After the hybridization and washing, the biotin labels were detected with Cy3-streptavidin

data_processing: Quantitle Normalization

organism: Bos taurus

source_name: The Madin-Darby bovine kidney epithelial cells, when at approximately 50% confluence (during the exponential phase), butyrate treated (BT treated, BT3)

tag: The Madin-Darby bovine kidney epithelial cells, when at approximately 50% confluence (during the exponential phase), 10 mM sodium butyrate treated (BT treated, BT3) for 24h


title: Wt2-1 and Taut2-1

source_name: Taut 2-1

tag: taut -/- mouse,


title: Wt1-2 and Taut1-2

tag: WT mouse,

tag: Heart tissue without atria, 15 - 16 months old

source_name: Taut 1-2


title: Second replicate Hybrid simulans x melanogaster testes  / D. melanogaster whole fly

tag: strain

tag: Hybrids were obtained by crossing 10 females D. simulans (strain 14021-0251.2) with 15 males D. melanogaster (strain 14021-0231.00)  per vial. Gender


title: Madin-Darby bovine kidney epithelial cells BEKC 66693 Control C3

source_name: The Madin-Darby bovine kidney epithelial cells, when at approximately 50% confluence (during the exponential phase), untreated (control, C3) for 24h


title: OltactoryEpithelium_wildtype_biolrepli3

source_name: Olfactory Epithelium from P1 mice, wildtype


title: OlfactoryEpithelium_wildtype_biolrepli1


title: Wt1-1 and Taut1-1

data_processing: Images were analysed with Aida Image Analyzer v.3.50 (Raytest).Two colour hybridizations were compared using Aida Array Compare  v.3.50 (Raytest).

label_protocol: Fluorescent cDNA was reverse transcribed from 25 mg total RNA using 0.5 mg  oligo dT-primer (Invitrogen). The reaction mixture was heated to 70°C for 5 min, and placed at room temperature for 10 min to allow primer annealing. The mixture was added with 1x first-strand buffer, 10 mM dithiothreitol, 200 mM dNTP (dATP, dCTP, and dGTP), 80 mM dTTP, 20 U RNAseout (Invitrogen), and 200 U Superscript III (Invitrogen), 40 mM Cy3- or Cy5-dUTP (Amersham-Pharmacia). Reverse transcription was carried out at 46°C for 2h. The reaction was stopped with 50 mM EDTA, followed by adding 25 mM sodium hydroxide at 37°C for 15 min to hydrolyze the RNA template, and neutralized with 600 mM Hepes. The unincorporated nucleotides were removed by using QIAquick PCR purification columns (Qiagen). The labeling efficency was calculated from NanoDrop (PeqLab) measurements.

source_name: Taut 1-1


title: Second replicate D. melanogaster testes RNA  / D. melanogaster whole fly RNA

source_name: 4 days old whole D. melanogaster male

value: 14021-0231.00, Gender:male, Age:4 days old, tissue:testes without accessory glands


title: DR AA4+ replicate 2

city: Milwaukee

first: Lisa

middle: Ann

last: Meyer

state: WI

address: 8701 Watertown Plank Rd

department: Pediatrics

institute: Medical College of Wisconsin

description: BioBreeding DR+/+ rat, day 65, mast cells derived from pancreatic lymph node.

data_processing: Signal scaled to target value of 150

source_name: BB Rat day 65 female diabetic resistant mast cells from pancreatic lymph node


title: DP AA4+ replicate 1

description: BioBreeding  DRlyp/lyp rat, day 65, mast cells derived from pancreatic lymph node

data_processing: Scaled to target of 150

source_name: BB Rat day 65 female diabetic prone mast cells from pancreatic lymph node


title: salmonella_5d_822_3

status: Public on Jun 08 2006

city: Seattle

first: William

middle: Wiley

last: Navarre

state: WA

address: 1959 NE Pacific Street Room K455

department: Laboratory Medicine

institute: University of Washington

description: hns-mutant and wild-type Salmonella

scan_protocol: Fluorescent array images were collected at two PMT settings for both Cy3 and Cy5 with a PerkinElmer ScanArray 5000 fluorescent scanner, to yield high and low intensity images per each fluorophore. Image intensity data were extracted and analyzed with MolecularWare AnalyzerDG analysis software.

data_processing: Raw spot intensities were integrated between high and low intensity scans, followed by background subtraction and median normalization between the Cy3 and Cy5 channels.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: wild type Salmonella typhimurium 14028s

label_protocol: Total RNA (50  micrograms) was annealed with 2.4  micrograms random hexamer oligo, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.2 mM dTTP and 0.7 mM Cy3 or Cy5-dUTP.  RNA was subsequently hydrolyzed by the addition of 0.2 M NaOH (10 min at 70 degrees C) and the solution was quenched with 0.2 M HCl. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit, vacuum dried and suspended in 25% formamide, 5X SSC, 0.1% SDS, 10 mg/ml BSA (bovine serum albumin) for hybridization to the microarray.

growth_protocol:
An overnight starter culture of a single colony, grown in Luria Broth (LB) for 12 to 14 hours at 37 degrees C, was diluted 1:200 into 50 ml of fresh LB media and grown (37 degrees C, shaking 250 rpm in a 250 ml Erlenmeyer flask) to an optical density (600 nm wavelength) of 2.0 before 10 ml was removed and added to 20 ml Qiagen Bacterial RNA Protect reagent to kill cells and stop RNA degragation.
An overnight starter culture of a single colony, grown in Luria Broth (LB) for 12 to 14 hours at 37 degrees C, was diluted 1:200 into 50 ml of fresh LB media and grown (37 degrees C, shaking 250 rpm in a 250 ml Erlenmeyer flask) to an optical density (600 nm wavelength) of 2.0 before 10 ml was removed and added to 20 ml Qiagen Bacterial RNA Protect reagent to kill cells and stop RNA degragation.

extract_protocol: RNA isolation was accomplished with Qiagen RNeasy Midi Kit reagents and resuspended in Rnase free water.

tag: wild type Salmonella typhimurium 14028s lab ID# WN150

source_name: hns mutant Salmonella typhimurium

tag: hns-mutant Salmonella typhimurium 14028s lab ID# WN342


title: salmonella_5d_822_1

description: hns-mutant and wild-type Salmonella


title: salmonella_5d_819_2

description: hns-mutant and wild-type Salmonella

source_name: hns-mutant Salmonella typhimurium 14028s

source_name: wild-type Salmonella typhimurium

tag: wild-type Salmonella typhimurium 14028s lab ID# WN150


title: DR AA4+ replicate 1

description: BioBreeding DR+/+ rat, day 65, mast cells derived from pancreatic lymph node

data_processing: Signal scaled to targe value of 150


title: salmonella_5d_821_3

description: hns-mutant and wild-type Salmonella


title: salmonella_5d_820_1

description: hns-mutant and wild-type Salmonella


title: salmonella_5d_822_2

description: hns-mutant and wild-type Salmonella


title: salmonella_5d_819_1

description: hns-mutant and wild-type Salmonella


title: DP AA4+ replicate 2

description: BioBreeding DRlyp/lyp rat, day65, mast cells derived form pancreatic lymph node


title: salmonella_5d_819_3

description: hns-mutant and wild-type Salmonella


title: salmonella_5d_820_2

description: hns-mutant and wild-type Salmonella


title: salmonella_5d_818_3

description: hns-mutant and wild-type Salmonella


title: Feeding Male with Females 3

city: Stillwater

first: Richard

middle: C.

last: Essenberg

state: OK

address: 246 NRC

department: Department of Biochemistry and Molecular Biology

institute: Oklahoma State University

description: Comparison of salivary glands from males feeding in the presence of females and partially fed (50-200 mg) females

hyb_protocol: Hybridization followed the protocol from Genisphere. cDNAs resulting from two independent samples to be compared were pooled together and hybridized in a formamide-based hybridization solution in a total volume of 25μl. Hybridization was performed overnight at 42°C in CMT™ hybridization chambers (Corning, NY). After hybridization, slides were washed then fixed in 95% ethanol. The second hybridization with the 3DNA™ reagents was performed in a formamide solution containing anti-fade reagent in a total volume of 25μl for 4 hours at 42°C after which slides were washed and dried.

scan_protocol: Slides were scanned after hybridization in a ScanArray Express confocal laser scanner (Perkin-Elmer) using the software that came with the instrument.

data_processing: The tiff files from the scanner were analyzed using GenePix Pro, v. 4.0 (Molecular Devices) software to find spots, determine local backgrounds and integrate spot intensities. Statistical package R, and library LIMMA (Linear Models for Microarray Data) (Smyth GK, Yang YH, Speed T. 2003. Methods Molec. Biol., 224: 111-136) were used for data filtering, data transformation, background correction, and normalization. Genepix flagged spots and spots whose intensities after background subtraction were lower than 200 in both channels were filtered out for normalization. Background was corrected using RMA, a non-linear method included in the LIMMA library. The log2 of the resulting intensity data was used to calculate the gene expression value, log2 (treatment/control), which was normalized to get the VALUE data presented. Local print-tip loess normalization was used for within-array normalization and quantile normalization was used for across-array normalization.

organism: Amblyomma americanum

source_name: Male in presence of females - Salivary gland - feeding

label_protocol: ArrayControl™ control spikes (Ambion, TX) were added to the RNA samples before labeling. Indirect labeling of RNA was performed with 3DNA® Array 50™ DNA Dendrimer Alexa Fluor 546™/Alexa Fluor 647™ kit (Genisphere, PA) following the manufacturer’s instructions. Ten μg of total RNA samples were precipitated with ethanol overnight at -20°C. RNA pellets were reconstituted with water and the cDNA synthesis was done according to the manufacturer’s protocol using SuperScript™ II RNase reverse transcriptase (Invitrogen, CA) with a dye-specific oligo dT primer.

growth_protocol: Adult male ticks were grown on sheep according to Patrick & Hair (1975, J. Med. Entomol. 12: 389-390) in cells containing females.

extract_protocol: Salivary glands were excised and stored in RNAlater™ (Ambion, TX) at -20°C till the RNA extraction. The total RNA was extracted using an RNAqueous™ -Mini kit (Ambion, TX).

tag: Feeding adult male salivary gland

tag: Females present

source_name: Female - Salivary gland - partially fed

growth_protocol: Adult female ticks were grown on sheep according to Patrick & Hair (1975, J. Med. Entomol. 12: 389-390) and pulled off at a weight of 50-200 mg.

tag: Feeding adult female salivary gland

tag: Weight range


title: salmonella_5d_818_1

description: hns-mutant and wild-type Salmonella


title: salmonella_5d_821_2

description: hns-mutant and wild-type Salmonella


title: Feeding Male with Females 2


title: salmonella_5d_817_2

description: hns-mutant and wild-type Salmonella


title: salmonella_5d_820_3

description: hns-mutant and wild-type Salmonella


title: Male Unfed 1

description: Comparison of unfed male and partially fed (50-200 mg) female tick salivary glands

source_name: Male - Salivary gland - unfed

label_protocol: ArrayControl™ control spikes (Ambion, TX) were added to the RNA samples before labeling. Indirect labeling of RNA was performed with 3DNA® Array 50™ DNA Dendrimer Cy3™/Alexa Fluor 647™ kit (Genisphere, PA) following the manufacturer’s instructions. Ten μg of total RNA samples were precipitated with ethanol overnight at -20°C. RNA pellets were reconstituted with water and the cDNA synthesis was done according to the manufacturer’s protocol using SuperScript™ II RNase reverse transcriptase (Invitrogen, CA) with a dye-specific oligo dT primer.

growth_protocol: Male ticks were grown on sheep to the adult stage according to Patrick & Hair (1975, J. Med. Entomol. 12: 389-390).

tag: Unfed adult male salivary gland


title: Feeding Male with Females 1


title: salmonella_5d_821_1

description: hns-mutant and wild-type Salmonella


title: Female Unfed S05

description: Comparison of unfed and partially fed (50-200 mg) female tick salivary glands

source_name: Female - Salivary gland - unfed

growth_protocol: Female ticks were grown on sheep to the adult stage according to Patrick & Hair (1975, J. Med. Entomol. 12: 389-390).

extract_protocol: alivary glands were excised and stored in RNAlater™ (Ambion, TX) at -20°C till the RNA extraction. The total RNA was extracted using an RNAqueous™ -Mini kit (Ambion, TX).

tag: Unfed adult female salivary gland

source_name: Female - Salivary gland - partially fed - pool

extract_protocol: Salivary glands were excised and stored in RNAlater™ (Ambion, TX) at -20°C till the RNA extraction. The total RNA was extracted using an RNAqueous™ -Midi kit (Ambion, TX).

tag: Pool from 400 ticks


title: Feeding Male without Females 1

description: Comparison of salivary glands from males feeding in the absence of females and partially fed (50-200 mg) females

source_name: Male in absence of females - Salivary gland - feeding

growth_protocol: Adult male ticks were grown on sheep according to Patrick & Hair (1975, J. Med. Entomol. 12: 389-390) in cells containing no females.

tag: No females present


title: salmonella_5d_817_1

description: hns-mutant and wild-type Salmonella


title: Female Fast Feeding S04

description: Comparison of fast feeding (300-550 mg) and partially fed (50-200 mg) female tick salivary glands

source_name: Female - Salivary gland - Fast Feeding

growth_protocol: Adult female ticks were grown on sheep according to Patrick & Hair (1975, J. Med. Entomol. 12: 389-390) and pulled off at a weight of 300-550 mg.


title: Female Fast Feeding S02


title: Female Unfed S01


title: salmonella_5d_817_3

description: hns-mutant and wild-type Salmonella


title: Feeding Male without Females 2


title: Female Replete S05

description: Comparison of replete and partially fed (50-200 mg) female tick salivary glands

source_name: Female - Salivary gland - replete

growth_protocol: Adult female ticks were grown on sheep according to Patrick & Hair (1975, J. Med. Entomol. 12: 389-390) until they detached.

tag: Replete, detached from host


title: Female Partially fed S04

description: Comparison of partially fed (50-200 mg) and partially fed (50-200 mg) female tick salivary glands

label: Alexa 647


title: salmonella_5d_818_2

description: hns-mutant and wild-type Salmonella


title: Female Partially fed S03


title: Female Partially fed S01

extract_protocol: alivary glands were excised and stored in RNAlater™ (Ambion, TX) at -20°C till the RNA extraction. The total RNA was extracted using an RNAqueous™ -Midi kit (Ambion, TX).


title: Female Partially fed S02


title: Female Replete S02


title: Female Unfed S03


title: Female Unfed S02


title: Female Fast Feeding S06


title: Female Fast Feeding S01


title: Female Replete S01


title: Female Fast Feeding S03


title: Female Replete S03


title: Female Early fed S01

description: Comparison of early fed (<5 mg) and partially fed (50-200 mg) female tick salivary glands

source_name: Female - Salivary gland - early fed

growth_protocol: Adult female ticks were grown on sheep according to Patrick & Hair (1975, J. Med. Entomol. 12: 389-390) and pulled off at a weight of <50 mg.

tag: pooled from 400 ticks


title: Rpc130_2_wt

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: Schizosaccharomyces pombe cells, Rpc130 ChIP(chromatin immunoprecipitation)-on-chip, replicate 2

hyb_protocol: 500 ng of Cy3 labeled WCE DNA was mixed with 500 ng of Cy5 labeled ChIP DNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer

scan_protocol: Slides were scanned using Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software version 7.5

data_processing: Log ratios of ChIP over WCE were obtained by dividing normalized median Cy5 value over its corrresponding Cy3 value

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe whole cell extract (WCE) genomic DNA

label_protocol: WCE DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy3 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked at 18C with paraformaldehyde for 30 minutes

extract_protocol: Chromatin was extracted from cross-linked cells following lysis with bead beater and sonication.  After reverse cross-linked and digested with Rnase A and proteinase K, DNA was recovered by phenol/chloroform extraction and ethanol precipitation

treatment_protocol: Schizosaccharomyces pombe cells crosslinked with paraformadehyde/dimethyl adipimidate

source_name: Schizosaccharomyces pombe chromatin immunoprecipitated DNA

label_protocol: ChIP DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy5 mono  NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked with paraformaldehyde at 18C for 30 minutes

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for Rpc130 chromatin with anti-Rpc130 rabbit polyclonal antibody.


title: salmonella_5d_163_1

description: hns-mutant and wild-type Salmonella

label_protocol: Total RNA (50 micrograms) was annealed with 2.4 micrograms random hexamer oligo, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.2 mM dTTP and 0.7 mM Cy3 or Cy5-dUTP.  RNA was subsequently hydrolyzed by the addition of 0.2 M NaOH (10 min at 70 degrees C) and the solution was quenched with 0.2 M HCl. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit, vacuum dried and suspended in 25% formamide, 5X SSC, 0.1% SDS, 10 mg/ml BSA (bovine serum albumin) for hybridization to the microarray.


title: salmonella_5d_164_3

description: hns-mutant and wild-type Salmonella


title: Sfc6_1_wt

description: Schizosaccharomyces pombe cells, Sfc6 ChIP(chromatin immunoprecipitation)-on-chip, replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for Sfc6 chromatin with anti-Sfc6 rabbit polyclonal antibody.


title: Female Early fed S02

hyb_protocol: Hybridization followed the protocol from Genisphere.  cDNAs resulting from two independent samples to be compared were pooled together and hybridized in a formamide-based hybridization solution in a total volume of 25μl.  Hybridization was performed overnight at 42°C in CMT™ hybridization chambers (Corning, NY). After hybridization, slides were washed then fixed in 95% ethanol. The second hybridization with the 3DNA™ reagents was performed in a formamide solution containing anti-fade reagent in a total volume of 25μl for 4 hours at 42°C after which slides were washed and dried.

source_name: Female - Salivary gland - partially fed -pool

tag: Pooled from 400 ticks


title: OlfactoryEpithelium_wildtype_biolrepli2

description: RNA was amplified and converted into cDNA with the NuGEN Ovation™ Biotin RNA Amplification and Labeling System {http://www.nugentechnologies.com/html/03_products2.html}

source_name: Olfactory Epithelium from P1 mice, wildtype

tag: Strain


title: salmonella_5d_164_1

description: hns-mutant and wild-type Salmonella

source_name: wild type Salmonella typhimurium 14028s

tag: wild type Salmonella typhimurium 14028s lab ID# WN150


title: salmonella_5d_163_2

description: hns-mutant and wild-type Salmonella

tag: hns-mutant Salmonella typhimurium 14028s lab ID# WN342


title: Female Early fed S03


title: Sfc6_2_wt

description: Schizosaccharomyces pombe cells, Sfc6 ChIP(chromatin immunoprecipitation)-on-chip, replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells


title: salmonella_5d_164_2

description: hns-mutant and wild-type Salmonella

source_name: hns mutant Salmonella typhimurium


title: Female Early fed S05


title: salmonella_5d_163_3

description: hns-mutant and wild-type Salmonella

source_name: hns-mutant Salmonella typhimurium 14028s

tag: wild-type Salmonella typhimurium 14028s lab ID# WN150


title: Female Early fed S04


title: Rpc130_1_wt

description: Schizosaccharomyces pombe cells, Rpc130 ChIP(chromatin immunoprecipitation)-on-chip, replicate 1


title: MPI-171

status: Public on Jun 07 2006

city: Berlin

first: Michael

last: Hummel

address: Hindenburgdamm 30

department: Institute of Pathology

institute: Universitätsmedizin Berlin, Campus Benjamin Franklin

description: Mature aggressive B-cell lymphoma

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536).  Probe-set summarization was performed using the median polish method on the normalized data (Irrizary et al. Nucleic Acids Research 2003, PMID: 12582260).

source_name: Frozen tissue

tag: Relapse

value: unk

tag: Age

tag: Sex

value: female

value: DLBCL

value: present

value: absent

value: IG-MYC

tag: Lesions

tag: Radiotherapy

tag: RITUXIMAB

tag: Chemotherapy

value: mBL

value: GCB

value: Training

value: no


title: MPI-187

description: Mature aggressive B-cell lymphoma

value: intermediate


title: MPI-242

description: Mature aggressive B-cell lymphoma

value: aggressive B-NHL.unclassifiable

value: MYC-negative

value: III

value: nodal + extranodal

value: dead

value: Progress

value: CHOP-like


title: MPI-230

description: Mature aggressive B-cell lymphoma

value: unk

value: female

value: non-mBL

value: ABC


title: MPI-172

description: Mature aggressive B-cell lymphoma

value: present

value: absent

value: IG-MYC


title: MPI-147

description: Mature aggressive B-cell lymphoma

value: male

value: atypical BL

value: II

value: nodal

value: alive

value: CRu

value: ALL-like

value: mBL

value: GCB

value: Test


title: MPI-170

description: Mature aggressive B-cell lymphoma

value: unk

value: DLBCL

value: MYC-negative

value: I

value: dead

value: no

value: CR

value: other

value: Training


title: MPI-116

description: Mature aggressive B-cell lymphoma

value: male

value: present

value: IG-MYC

value: absent

value: intermediate


title: MPI-138

description: Mature aggressive B-cell lymphoma

value: atypical BL

value: mBL


title: MPI-117

description: Mature aggressive B-cell lymphoma

value: aggressive B-NHL.unclassifiable

value: extranodal

value: alive

value: ALL-like

value: GCB

value: Test


title: MPI-140

description: Mature aggressive B-cell lymphoma

value: no

value: DLBCL

value: IV

value: nodal + extranodal

value: dead

value: Progress

value: CHOP-like


title: MPI-144

description: Mature aggressive B-cell lymphoma

value: unk

value: male

value: present

value: absent

value: IG-MYC

value: Training


title: MPI-101

description: Mature aggressive B-cell lymphoma

value: atypical BL

value: other

value: mBL


title: MPI-112

description: Mature aggressive B-cell lymphoma

value: female

value: intermediate

value: GCB

value: Test


title: MPI-155

description: Mature aggressive B-cell lymphoma

value: DLBCL

value: MYC-negative

value: I

value: extranodal

value: alive

value: yes

value: no

value: CR

value: non-mBL

value: unclassified


title: MPI-095

description: Mature aggressive B-cell lymphoma

value: male

value: BL

value: present

value: absent

value: IG-MYC

value: II

value: nodal

value: ALL-like

value: Training


title: MPI-123

description: Mature aggressive B-cell lymphoma

value: atypical BL

value: nodal + extranodal

value: mBL

value: GCB


title: MPI-114

description: Mature aggressive B-cell lymphoma

value: unk

value: yes


title: MPI-087

description: Mature aggressive B-cell lymphoma

value: aggressive B-NHL.unclassifiable

value: no


title: MPI-089

description: Mature aggressive B-cell lymphoma