title: siRNA 1

description: Bicalutamide treated LNCaP cells not stimulated with DHT, biological replicate 1

source_name: siRNA treated U251 cells stimulated with DFO, biological replicate 1


title: thymocytes_DN3_1

status: Public on May 17 2007

type: RNA

city: Bunkyo-ku

first: Masahito

last: Kawazu

state: Tokyo

address: Hongo 7-3-1

department: Department of Hematology and Oncology

country: Japan

institute: University of Tokyo Hospital

description:
Cell source of DN2_1, DN3_1, and DN4_1 are identical.
Cell source of DN2_2, DN3_2, and DN4_2 are identical.
Cell source of DN2_3, DN3_3, and DN4_3 are identical.
Cell source of DN2_4, DN3_4, and DN4_4 are identical.
Each cell sorce was derived from four mice.

hyb_protocol: Following fragmentation, Biotin-labeled cRNA was hybridized to the Mouse Genome 430 2.0 Array® (Affymetrix®) for 16 h at 45°C as recommended by the manufacturer. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.

scan_protocol: The array was scanned with GeneChip Scanner 3000 7G.

data_processing: Expression data were extracted from image files produced on Affymetrix® GeneChip Operating Software 1.0® (GCOS®).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: double negative thymocytes subset DN3

label_protocol: Biotin-labeled cRNA probes were prepared using Two-Cycle cDNA synthesis kit® (Affymetrix®, Santa Clara, CA), according to Affymetrix protocol.

extract_protocol: RNA was extracted from sorted cells using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.

treatment_protocol:
FACS sorting
All antibodies used for cell sorting were purchased from BD Pharmingen (San Diego, CA). Thymocytes were harvested from 5- to 6-week-old female C57BL/6 mice. Four independent cell sortings were performed and four mice were sacrificed for each experiment. Before cell sorting, CD4+ cells and CD8+ cells were depleted using the MACS LD system (Miltenyi Biotec, Bergisch Gladbach, Germany). The remaining fraction was stained with anti-CD44 and anti-CD25 antibodies conjugated to FITC or PerCP-Cy5.5, respectively, and also with PE-conjugated antibodies to CD4, CD8, CD3, NK1.1, and TCRgamma-delta and sorted using a FACSAria cell sorter (BD Bioscience). DN2, DN3, and DN4 subsets were identified as FITC+PE-PerCP-Cy5.5+, FITC-PE-PerCP-Cy5.5+, FITC-PE-PerCP-Cy5.5- populations, respectively.

tag: Strain:C57BL/6, Gender:female, Age:5-6 weeks,


title: thymocytes_DN3_2


title: thymocytes_DN2_4

source_name: double negative thymocytes subset DN2


title: siRNA 2

city: Pasadena

first: Peter

last: Dervan

state: CA

address: 1200 East California Blvd

country: USA

institute: California Institute of Technology

description: Bicalutamide treated LNCaP cells not stimulated with DHT, biological replicate 2

hyb_protocol: Standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)

data_processing: Resolver (Rosetta Biosoftware, Seattle); Affymetrix GeneChip Operating Software (GCOS) integrated into the Rosetta Resolver gene expression data analysis system

organism: Homo sapiens

source_name: siRNA treated U251 cells stimulated with DFO, biological replicate 2

growth_protocol: U251 cells seeded in 12-well plates in 10% FBS RPMI for 1 day.

extract_protocol: Cells were harvested for RNA using the Qiagen RNEasy kit and protocol.  Control cells that were not treated with DFO were also harvested.

treatment_protocol: After the 1-day growth, media was changed and at this time 1 microM of polyamide targeted to the HRE or siRNA against HIF-1a (invitrogen, as per the invitrogen protocol) was added to appropriate wells.  Cells were grown for 48 hours more.  Echinomycin (100 nM) was added to the appropriate cells, incubataed for 2 hours.  DFO was added (300 microM) for 16 hours prior to harvest.

tag: cultured U251 cells

tag: refer to ATTC


title: thymocytes_DN3_4


title: Control 3

description: Untreated LNCaP cells stimulated with DHT, biological replicate 3

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

source_name: Untreated U251 cells stimulated with DFO, biological replicate 3


title: thymocytes_DN4_3

source_name: double negative thymocytes subset DN4


title: Control 2

description: Untreated LNCaP cells stimulated with DHT, biological replicate 2

source_name: Untreated U251 cells stimulated with DFO, biological replicate 2

label_protocol: Standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)


title: thymocytes_DN4_1


title: thymocytes_DN3_3


title: thymocytes_DN2_1

hyb_protocol: Following fragmentation, Biotin-labeled cRNA was hybridized to the Mouse Genome 430 2.0 Array® (Affymetrix®) for 16 h at 45°C as recommended by the manufacturer.  Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.

scan_protocol: The array wasscanned with GeneChip Scanner 3000 7G.

treatment_protocol:
FACS sorting
All antibodies used for cell sorting were purchased from BD Pharmingen (San Diego, CA).  Thymocytes were harvested from 5- to 6-week-old female C57BL/6 mice.  Four independent cell sortings were performed and four mice were sacrificed for each experiment.  Before cell sorting, CD4+ cells and CD8+ cells were depleted using the MACS LD system (Miltenyi Biotec, Bergisch Gladbach, Germany).  The remaining fraction was stained with anti-CD44 and anti-CD25 antibodies conjugated to FITC or PerCP-Cy5.5, respectively, and also with PE-conjugated antibodies to CD4, CD8, CD3, NK1.1, and TCRgamma-delta and sorted using a FACSAria cell sorter (BD Bioscience).  DN2, DN3, and DN4 subsets were identified as FITC+PE-PerCP-Cy5.5+, FITC-PE-PerCP-Cy5.5+, FITC-PE-PerCP-Cy5.5- populations, respectively.


title: GFP- CD25+ CD4+ CD8- thymocytes from Foxp3(gfp/gfp) mice

status: Public on May 18 2007

city: Seattle

first: Alexander

last: Rudensky

state: WA

address: 1959 Pacific St

department: Immunology

institute: University of Washington

description: Foxp3(gfp/gfp) homozygous female mice bear a GFP-Foxp3 fusion protein knockin allele, allowing for the visualization of regulatory T cells due to GFP-Foxp3 protein fluorescence.

hyb_protocol: Standard hybridization to Affymetrix 430_2.0 arrays.

scan_protocol: Standard scanning of Affymetrix 430_2.0 arrays.

data_processing: GCMRA, Bioconductor

source_name: thymocytes

label_protocol: RNA was converted to biotinylated cRNA (2 rounds of amplification) using commercially available reagent kits (Affymetrix, Santa Clara, CA) and were hybridized to Affymetrix mouse 430 2.0 microarrays.

extract_protocol: Qiagen RNeasy

treatment_protocol: Cells were isolated by magnetic bead sorting followed by fluorescence activated cell sorting.

tag: Strain

value: C57BL/6 backcross 4-6 from 129/Sv Gender:Female Age:6-8 weeks


title: ND017

status: Public on May 15 2007

city: Madison

first: Paul

last: Ahlquist

state: WI

address: 1525 Linden Dr.

department: Oncology

institute: University of Wisconsin-Madison

description: Head and neck cancer

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

scan_protocol: GeneChips were scanned using the scanner of the Affymetrix GeneChip Analysis System.

data_processing: The data were analyzed with the Bioconductor using Affymetrix package version 1.10.0. Probeset summary measures were computed by robust multiarray averaging applied to the combined set of 84 microarrays.

source_name: Head and neck normal

label_protocol: Biotinylated cRNA were prepared using Enzo BioArray HighYield RNA Transcript Labeling Kit  according to manufacturer's instructions.

growth_protocol: Sample was harvested without further growth

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

treatment_protocol: Samples were fresh frozen in liquid nitrogen and collected with patients' consent under approval of the Institutional Review Boards.

tag: Case

value: Head and neck normal

tag: Anatomical sites

value: Oral Cavity

tag: gender

value: Male

tag: age

tag: Stage


title: HNN039

description: Head and neck cancer

value: tonsil

tag: Tumor Stage


title: HNN023

description: Head and neck cancer

value: uvula and palate

value: Female


title: HNC2914

description: Head and neck cancer

source_name: Head and neck cancer

value: Head and neck cancer

value: Pharynx

value: II


title: HNCS2

description: Head and neck cancer

value: IV


title: ND018

description: Head and neck cancer


title: ND011

description: Head and neck cancer


title: ND010

description: Head and neck cancer


title: HNC3092

description: Head and neck cancer

value: Tongue


title: HNCS1

description: Head and neck cancer

value: hypopharynx

value: III


title: ND004

description: Head and neck cancer


title: HNC3687

description: Head and neck cancer

value: Floor of mouth

value: No data


title: ND014

description: Head and neck cancer


title: HNN013

description: Head and neck cancer


title: HNC3046

description: Head and neck cancer


title: HNC2967

description: Head and neck cancer


title: HNC2907

description: Head and neck cancer

value: Larynx


title: HNC3003

description: Head and neck cancer


title: HNCS3

description: Head and neck cancer


title: ND012

description: Head and neck cancer


title: HNC2887

description: Head and neck cancer


title: HNC2942

description: Head and neck cancer

value: Oropharynx


title: HNC2966

description: Head and neck cancer


title: HNC3055

description: Head and neck cancer

value: Tonsil


title: HNN053

description: Head and neck cancer

value: Head and neck normal


title: HNCB1

description: Head and neck cancer

value: Male


title: HNN052

description: Head and neck cancer

value: tonsil


title: HNC2910

description: Head and neck cancer


title: ND007

description: Head and neck cancer

value: Oral Cavity


title: ND015

description: Head and neck cancer

value: Female


title: HNC2885

description: Head and neck cancer

value: Head and neck cancer


title: HNC2857

description: Head and neck cancer


title: HNC2816

description: Head and neck cancer


title: HNC2784

description: Head and neck cancer

value: Hypopharynx


title: HNC2836

description: Head and neck cancer


title: HNC2738

description: Head and neck cancer


title: HNC2743

description: Head and neck cancer


title: HNC2855

description: Head and neck cancer

value: Mouth


title: HNC2774

description: Head and neck cancer

value: II


title: HNC2725

description: Head and neck cancer

value: Tongue


title: HNC2814

description: Head and neck cancer


title: HNC2748

description: Head and neck cancer


title: HNC012

description: Head and neck cancer

value: IV


title: HNC017

description: Head and neck cancer


title: HNC001

description: Head and neck cancer


title: HNC004

description: Head and neck cancer


title: HNC008

description: Head and neck cancer

value: III


title: HNC2551

description: Head and neck cancer

value: I


title: HNC2714

description: Head and neck cancer

value: No data


title: HNC015

description: Head and neck cancer

value: no data


title: HNC005

description: Head and neck cancer

value: Oropharynx


title: HNC2719

description: Head and neck cancer


title: HNC2724

description: Head and neck cancer


title: HNC018

description: Head and neck cancer

value: Tonsil


title: HNC009

description: Head and neck cancer


title: HNC2686

description: Head and neck cancer


title: Murine_Bulk_Splenocytes_resting_3

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

description: Resting murine bulk splenocytes were lysed in Trizol and assessed for gene expression on Affy MOE430_2 microarray

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Transformation procedure used:GCOS 1.4

label: Biotinylated aRNA

source_name: Resting Murine bulk splenocytes

label_protocol: One cycle amplification by standard Affymetrix procedure

growth_protocol: None, splenocytes were used at rest

extract_protocol: Trizol, per manufacturers protocol


title: Murine_Bulk_Splenocytes_resting_4

treatment_protocol: Resting murine bulk splenocytes were lysed in Trizol


title: Murine_Bulk_Splenocytes_resting_2


title: Murine_Bulk_Splenocytes_resting_1


title: Murine_NK_IL-15_24h_3

description:
Murine NK cell were purified from wild type C57Bl/6 mice (>99% NK1.1+CD3-), stimulated with rmIL-15 for 24 hours,
and then lysed in Trizol and assessed for gene expression on Affy MOE430_2 microarray

source_name: Splenic NK cells, IL-15 activated for 24 hours

label_protocol: Two cycle amplification by standard Affymetrix procedure

growth_protocol: NK cells were stimulated with 100 ng/mL of rmIL-15

treatment_protocol:
Splenic NK cells were flow sorted to >99% NK1.1+CD3- purity, stimulated with 100 ng/mL of IL-15 and
then lysed in Trizol


title: Murine_NK_IL-15_24h_2


title: Murine_NK_Resting_1

description: Murine NK cell were purified from wild type C57Bl/6 mice (>99% NK1.1+CD3-) and immediately lysed in Trizol and assessed for gene expression on Affy MOE430_2 microarray

source_name: Splenic NK cells, resting

growth_protocol: None, NK cells were used at rest

treatment_protocol: Splenic NK cells were flow sorted to >99% NK1.1+CD3- purity and lysed in Trizol


title: Murine_NK_Resting_3

growth_protocol: NK cells were used at rest


title: huasa7_293_miRNA_r1

status: Public on May 11 2007

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: gene expression from 293 cells with pmiRNA cluster

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix F450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: 293 human embryonic kidney cells with pmiRNA cluster

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).

growth_protocol: grow 293 cells to 80% confluence in DMEM with 10% FBS, collected 2 samples each 2 days apart for a total of 4 experimental and 4 control samples

extract_protocol: Qiagen RNeasy according to manufacturer's instructions

treatment_protocol: 293 cells were stably expressing either pcDNA vector control or miRNA expressing vector while selected under 100 ug/mL G418

tag: expressing 10 KSHV encoded miRNAs


title: huasa7_293_CV_r3

description: gene expression from 293 cells with pcDNA3.1/V5/HisA

source_name: 295 human embryonic kidney cells with pcDNA3.1/V5/HisA

tag: expressing control vector pcDNA3.1/V5/HisA


title: huasa7_293_miRNA_r2

source_name: 294 human embryonic kidney cells with pmiRNA cluster


title: Expression analysis of differentiated Caco-2 replica 2

status: Public on May 10 2007

city: Copenhagen

first: Jesper

middle: T

last: Troelsen

address: Blegdamsvej 3b

country: Denmark

institute: Univ. of Copenhagen

description: Caco-2 cells were grown to ten days after confluence. The RNA from these differentiated cells were harvested and analysed.

hyb_protocol: performed according to the protocols published by the manufacturer (Affymetrix)

data_processing: RMA processing using quantile normalization

label_protocol: The total RNA 'One-Cycle Target Labeling Protocol' from Affymetrix was used

extract_protocol: Qiagen RNeasy total RNA extraction system with on column DNAse I digestion

tag: RNA isolated from differentiated Caco-2 cells


title: huasa7_293_miRNA_r4

source_name: 296 human embryonic kidney cells with pmiRNA cluster


title: huasa7_293_CV_r4

source_name: 296 human embryonic kidney cells with pcDNA3.1/V5/HisA


title: huasa7_293_CV_r1

source_name: 293 human embryonic kidney cells with pcDNA3.1/V5/HisA


title: Expression analysis of differentiated Caco-2 replica 3

hyb_protocol: performed according to the protocols published by the manufacturer (Affymetrix


title: huasa7_293_miRNA_r3

source_name: 295 human embryonic kidney cells with pmiRNA cluster


title: huasa7_293_CV_r2

source_name: 294 human embryonic kidney cells with pcDNA3.1/V5/HisA


title: Murine_NK_IL-15_24h_1

description: Murine NK cell were purified from wild type C57Bl/6 mice (>99% NK1.1+CD3-), stimulated with rmIL-15 for 24 hours, and then lysed in Trizol and assessed for gene expression on Affy MOE430_2 microarray

treatment_protocol: Splenic NK cells were flow sorted to >99% NK1.1+CD3- purity, stimulated with 100 ng/mL of IL-15 and then lysed in Trizol


title: Expression analysis of undifferentiated Caco-2 replica 2

description: Caco-2 cells were grown to 90 % confluence. The RNA from these undifferentiated cells were harvested and analysed.

scan_protocol: performed according to the protocols published by the manufacturer (Affymetrix)

tag: RNA isolated from undifferentiated Caco-2 cells


title: Expression analysis of undifferentiated Caco-2 replica 1


title: Expression analysis of differentiated Caco-2 replica 1


title: Expression analysis of undifferentiated Caco-2 replica 3


title: cry1_LL_C

status: Public on May 09 2007

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

country: Germany

institute: Ludwig-Maximilians-Universität München

description: Part of an experiment investigating transcriptome changes in of wt, cry1 and hy5 after high light and in wt after blue light treatment.

hyb_protocol: 15 μg of fragmented, biotinylated cRNA was used for hybridization. Hybridization was performed as in the Affymetrix technical manual.

scan_protocol: Washing, staining, and scanning procedures were performed as described in the Affymetrix technical manual. A Hybridization Oven 640, a Fluidics Station 450 and a GeneChip Scanner 3000 were used.

data_processing:
Normalization and expression estimate computation were calculated from the .CEL output files from the Affymetrix GCOS 1.1 software using gcRMA implemented in R using standard settings. Statistical testing for differential expression was performed with logit-t analysis (p < 0.025). The .CHP and logit-t files were loaded into GeneSpring 7.3 (Agilent Technologies). Affymetrix present, marginal and absent flags were used as an indicator of whether or not a gene was expressed. Genes called absent in both of the
compared conditions were removed from subsequent analyses.

label: Biotin

organism: Arabidopsis thaliana

source_name: cry1, control

label_protocol: 5 μg of total RNA was used in a reverse transcription reaction (Ambion MessageAmp kit) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription reaction to generate biotinylated cRNA. The quality of purified and fragmented cRNA was assessed by spectrophotometry and agarose gel electrophoresis.

growth_protocol: Arabidopsis thaliana seeds were sterilized (75 % ethanol, 0.01 % Triton X-100) for 15 min and washed three times with 95 % ethanol before spreading onto 0.27 % phytoagar plates containing 1x Murashige and Skoog basal salt mixture including vitamins (Duchefa) and 2 % sucrose. The plates were stratified two days in darkness at 4°C and then placed 7 d into continuous white light (100 micro mol quanta m-2 s-1, 22 °C).

extract_protocol: For total RNA isolation the RNeasy Plant Mini Kit (QIAGEN) was used according to the manufacturer’s instructions. The concentration of total RNA was determined with a Nanodrop ND-1000 spectrophotometer; quality of RNA was checked by agarose gel electrophoresis

tag: cry1, 7 d old seedlings


title: hy5_LL_A

source_name: hy5, control

tag: hy5, 7 d old seedlings


title: hy5_LL_C


title: hy5_LL_B


title: hy5_HL_A

source_name: hy5, 3 hours high light

treatment_protocol: For high light treatment seedlings were transferred for 3 h to 1000 micro mol quanta m-2 s-1 (metal halide HQI-T 400 W daylight light bulbs, Osram).


title: hy5_HL_B


title: hy5_HL_C


title: cry1_LL_B

data_processing:
Normalization and expression estimate computation were calculated from the .CEL output files from the Affymetrix GCOS 1.1 software using gcRMA implemented in R using standard settings. Statistical testing for differential expression was performed with logit-t analysis (p < 0.025; (21)). The .CHP and logit-t files were loaded into GeneSpring 7.3 (Agilent Technologies). Affymetrix present, marginal and absent flags were used as an indicator of whether or not a gene was expressed. Genes called absent in both of the
compared conditions were removed from subsequent analyses.

source_name: cry1, 3 hours blue light treatment

extract_protocol:
For total RNA isolation the RNeasy Plant Mini Kit (QIAGEN) was used according to the
manufacturer’s instructions. The concentration of total RNA was determined with a
Nanodrop ND-1000 spectrophotometer; RNA quality was checked by agarose gel electrophoresis.

tag: For blue light exposure HQI-T 400 W lamps were filtered through color filter #74, 400-540 nm, absorption maximum

value: 470 nm (Night Blue; Rosco International). Air temperature was 22°C. Seedlings (at least 10) were harvested and directly frozen in liquid nitrogen.


title: Col-O_LL_C

source_name: Col-O, control

tag: Col-O, 7 d old seedlings


title: cry1_HL_C

source_name: cry1, 3 hours high light


title: cry1_HL_A


title: Col-O_HL_C

source_name: Col-O, 3 hours high light

treatment_protocol: For high light treatment seedlingswere transferred for 3 h 1000 micro mol quanta m-2 s-1 (metal halide HQI-T 400 W daylight light bulbs, Osram).


title: Col-O_LL_B


title: Murine_NK_Resting_2


title: Col_HL_B


title: Col-O_BL_B

source_name: Col-O, 3 hours BL

treatment_protocol: For blue light exposure HQI-T 400 W lamps were filtered through color filter #74, 400-540 nm, absorption maximum: 470 nm (Night Blue; Rosco International). Air temperature was 22°C. Seedlings (at least 10) were harvested after 3 hours and directly frozen in liquid nitrogen.


title: Col-O_HL_A


title: cry1_LL_A


title: Col-O_BL_C


title: Col-O_LL_A


title: cry1_HL_B


title: Polyamide1_1

status: Public on May 05 2007

description: Polyamide 1 treated LNCaP cells not stimulated with DHT, biological replicate 1

data_processing: Resolver (Rosetta Biosoftware, Seattle)

growth_protocol: LNCaP cells seeded in 12-well plates at 90-100,000 cells per plate in 10% FBS RPMI for 3 days.

extract_protocol: Cells were harvested for RNA using the Qiagen RNEasy kit and protocol.  Control cells that were not treated with DHT were also harvested.

treatment_protocol: After the 2-day growth, media was changed to 10% charcoal-stripped FBS RPMI and at this time 10 microM of polyamide targeted to the ARE or 10 microM of a control polyamide were added.  Cells were grown for 48 hours more.  Bicalutamide (10 microM) was added to the appropriate cells, incubataed for 2 hours.  DHT was added (1 nM) for 16 hours.

tag: cultured LNCaP cells


title: Polyamide1_2

description: Polyamide 1 treated LNCaP cells not stimulated with DHT, biological replicate 2

tag: refer to ATTC


title: Bicalutamide_2

source_name: Bicalutamide treated LNCaP cells not stimulated with DHT, biological replicate 2


title: Col-O_BL_A

tag: Arabidopsis Col-O, 7 d old seedlings


title: Polyamide1_3

description: Polyamide 1 treated LNCaP cells not stimulated with DHT, biological replicate 3


title: Control_1

description: Untreated LNCaP cells stimulated with DHT, biological replicate 1


title: Control_3

source_name: Untreated LNCaP cells stimulated with DHT, biological replicate 3


title: Bicalutamide_1

description: Bicalutamide treated LNCaP cells not stimulated with DHT, biological replicate 1


title: Polyamide2_1

description: Polyamide 2 treated LNCaP cells not stimulated with DHT, biological replicate 1


title: Bicalutamide_3

description: Bicalutamide treated LNCaP cells not stimulated with DHT, biological replicate 3


title: Polyamide2_2

description: Polyamide 2 treated LNCaP cells not stimulated with DHT, biological replicate 2


title: No_DHT_control_2

description: Untreated LNCaP cells not stimulated with DHT, biological replicate 2


title: No_DHT_control_1

description: Untreated LNCaP cells not stimulated with DHT, biological replicate 1


title: Polyamide2_3

description: Polyamide 2 treated LNCaP cells not stimulated with DHT, biological replicate 3


title: Control_2

description: Untreated LNCaP cells stimulated with DHT, biological replicate 2


title: SK-Mel-28 Human Cell Lines_affs431-MTf/B2

city: Sydney

first: Des

middle: Raymond

last: Richardson

state: New South Wales

address: 92-94 Parramatta Rd, Sydney

department: Bosch Institute

country: Australia

institute: University of Sydney

description: Standard Affymetrix Protocol on total RNA extracted from SK-Mel-28 cell line

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol, GeneChip Scanner 3000

data_processing: GeneChip Scanner 3000, GCOS v1.3, scaled to 1000

source_name: Human Melanotransferrin Downregulation - SK-Mel-28 Cell Line - MTf/B2

label_protocol: Standard Affymetrix Protocol

extract_protocol: Standard TRIzol RNA Extraction Protocol

tag: Cell Line

tag: Expression Vector

value: pSilencer™ 3.1-H1 neo

tag: Inserted Gene

value: Human Melanotransferrin siRNA (NM_005929; position:2048-2066 bp)


title: SK-Mel-28 Human Cell Lines_affs431-Scrambled

source_name: Human Melanotransferrin Downregulation - SK-Mel-28 Cell Line - Scrambled Control


title: Wild Type, biological rep2

status: Public on May 01 2007

city: Cambdridge

first: Dmitri

last: Wiederschain

state: MA

address: 250 Massachusetts Avenue

department: Oncolology

institute: Novartis

description: Gene expression data from wild type DAOY cells

hyb_protocol: The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.

scan_protocol: Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).

data_processing: Affymetrix Microarray Suite version 5.39

source_name: Human medulloblastoma DAOY cell line

label_protocol: cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)

growth_protocol: Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics.

extract_protocol: Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)

treatment_protocol: Cells were mock transduced and 2 x 105 cells were plated onto 60 mm dishes in triplicates and harvested 4 days later.

tag: Untransduced Wild Type DAOY Cells


title: SK-Mel-28 Human Cell Lines_affs431-MTf/B1

source_name: Human Melanotransferrin Downregulation - SK-Mel-28 Cell Line - MTf/B1


title: SK-N-MC Human Cell Lines_affs403-CMV1

description: Standard Affymetrix Protocol on total RNA extracted from SK-N-MC cell line

source_name: Human Melanotransferrin Hyperexpression - SK-N-MC Cell Line - Vector Control #1

value: SK-N-MC

value: pCMV-Script


title: LMTK Mouse Cell Lines_affs264-M6

description: Standard Affymetrix Protocol on total RNA extracted from LMTK cell line

source_name: Mouse Melanotransferrin Hyperexpression - LMTK Cell Line - Hyper Clone #6

value: LMTK

value: pCI-neo

value: Mouse Melanotransferrin (NM_013900)


title: Alk shRNA, biological rep3

description: Gene expression data from DAOY cells stably expressing Alk shRNA

data_processing: Affymetrix Microarray Suite version 5.33

growth_protocol: Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.

treatment_protocol: DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.

tag: Stable lentiviral shRNA


title: SK-N-MC Human Cell Lines_affs403-hlMTf4

source_name: Human Melanotransferrin Hyperexpression - SK-N-MC Cell Line - Hyper Clone #4

value: Human Melanotransferrin (NM_005929)


title: LMTK Mouse Cell Lines_affs264-M4

source_name: Mouse Melanotransferrin Hyperexpression - LMTK Cell Line - Hyper Clone #4


title: Alk shRNA, biological rep2

data_processing: Affymetrix Microarray Suite version 5.30


title: Wild Type, biological rep1

data_processing: Affymetrix Microarray Suite version 5.36


title: LMTK Mouse Cell Lines_affs264-V2

source_name: Mouse Melanotransferrin Hyperexpression - LMTK Cell Lines - Vector Control #2


title: Wild Type, biological rep3

data_processing: Affymetrix Microarray Suite version 5.42


title: LMTK Mouse Cell Lines_affs264-V1

source_name: Mouse Melanotransferrin Hyperexpression - LMTK Cell Line - Vector Control #1


title: Mel18 shRNA, biological rep3

description: Gene expression data from DAOY cells stably expressing Mel18 shRNA

data_processing: Affymetrix Microarray Suite version 5.15


title: Alk shRNA, biological rep1

data_processing: Affymetrix Microarray Suite version 5.27


title: Bmi1 Mel18 shRNA, biological rep2

description: Gene expression data from DAOY cells stably expressing Bmi1 and Mel18 shRNA

data_processing: Affymetrix Microarray Suite version 5.21


title: Bmi1 Mel18 shRNA, biological rep3

data_processing: Affymetrix Microarray Suite version 5.24


title: LSKCD34+Flt3hi (040128)

city: Lund

first: Robert

last: Månsson

address: Klinikgatan 26, BMC B12

department: Hemapotoietic stem cell biology

country: Sweden

institute: Lund University

description: Gene expression data from LSKCD34+Flt3hi cells FACS sorted from adult BM

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

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000. Chip target intensity was arbitrarily scaled to 100 before rendering CHP files.

data_processing: Expression values were calculated by RMA express (http://rmaexpress.bmbolstad.com/) using background adjustment and quantile normalization.

source_name: Adult murine BM from 10-14 weeks old mice

label_protocol: Biotinylated cRNA was prepared according to the standard AffymetrixTM; Small Sample Labelling Protocol v.2, with the exception that the second round of in vitro transcription (IVT) was performed using AffymetrixTM GeneChipTM Expression 3’amplification kit.

extract_protocol: Cells were directly sorted into buffer RLT and RNA prepared using RNeasy Micro (Qiagen) according to manufacturer's instructions.

tag: Wild type C57bl/6


title: LSKCD34+Flt3- (040128)

description: Gene expression data from LSKCD34+Flt3- cells FACS sorted from adult BM


title: Mel18 shRNA, biological rep1

data_processing: Affymetrix Microarray Suite version 5.9


title: Bmi1 shRNA, biological rep1

description: Gene expression data from DAOY cells stably expressing Bmi1 shRNA

data_processing: Affymetrix Microarray Suite version 5.0


title: Bmi1 shRNA, biological rep2

data_processing: Affymetrix Microarray Suite version 5.3


title: LSKCD34-Flt3- (040127)

description: Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM


title: LSKCD34+Flt3hi (040127)


title: Mel18 shRNA, biological rep2

data_processing: Affymetrix Microarray Suite version 5.12


title: C2C12_4.5_hr

city: Tempe

first: Kenro

last: Kusumi

state: AZ

department: School of Life Sciences

institute: Arizona State University

hyb_protocol: Hybridization was carried out according to Affymetrix protocol.

scan_protocol: Scans were carried out according to Affymetrix protocol.

data_processing: RMA method normalization implemented in Genespring GX 7.3

source_name: mouse C2C12 myoblast

label_protocol: Microarray target was prepared following the Affymetrix protocol.  In brief, cDNA was synthesized from total RNA using the SuperScript II double-stranded cDNA synthesis kit (Invitrogen), followed by in vitro transcription, where labeled cRNA was generated (Enzo).

extract_protocol: Total RNA was isolated from cells in culture using the RNeasy Mini Kit (Qiagen), according to manufacturer's protocol

tag: Tissue

value: mouse C2C12 myoblast, 4.5 hr after low-serum synchronization


title: C2C12_6.0_hr

value: mouse C2C12 myoblast, 6.0 hr after low-serum synchronization


title: C2C12_3.0_hr

value: mouse C2C12 myoblast, 3.0 hr after low-serum synchronization


title: C2C12_5.5_hr

value: mouse C2C12 myoblast, 5.5 hr after low-serum synchronization


title: Bmi1 shRNA, biological rep3

data_processing: Affymetrix Microarray Suite version 5.6


title: C2C12_4.0_hr

value: mouse C2C12 myoblast, 4.0 hr after low-serum synchronization


title: C2C12_3.5_hr

value: mouse C2C12 myoblast, 3.5 hr after low-serum synchronization


title: C2C12_5.0_hr

value: mouse C2C12 myoblast, 5.0 hr after low-serum synchronization


title: C2C12_2.5_hr

value: mouse C2C12 myoblast, 2.5 hr after low-serum synchronization


title: Bmi1 Mel18 shRNA, biological rep1

data_processing: Affymetrix Microarray Suite version 5.18


title: C2C12_2.0_hr

value: mouse C2C12 myoblast, 2.0 hr after low-serum synchronization


title: LSKCD34+Flt3- (040127)


title: C2C12_1.0_hr

value: mouse C2C12 myoblast, 1.0 hr after low-serum synchronization


title: MSE_N_M163

city: San Francisco

first: Linda

last: Giudice

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

hyb_protocol: cRNA was fragmented and hybridized overnight to Affymetrix U133 Plus 2.0 Genechips.

scan_protocol: Chips were scanned using the HR3000 scanner from Affymetrix.

data_processing: The data were analyzed using the Gene Chip Operating Software Version 1.2 using the Affymetrix default settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: uterus - Mid secretory endometrium from normal patient

label_protocol: biotinylated cRNA was generated from 5.0 ug total RNA using the Affymetrix labeling protocol.

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

tag: Mid Secretory Phase Normal


title: MSE_N_M153

description: Mid secretory endometrium from normal patient


title: C2C12_0.5_hr

value: mouse C2C12 myoblast, 0.5 hr after low-serum synchronization


title: C2C12_0_hr

source_name: mouse C2C12 myoblast 0 hour time point

value: mouse C2C12 myoblast


title: MSE_N_659


title: MSE_N_617


title: Cochlea_YC_4mo_3

first: Shinichi

last: Someya

address: 425 Henry Mall Dr

department: Medical Genetics

hyb_protocol: Hybridization (hybridization oven 640), and washing and staining (fluidics station 400) were accomplished according to the manufacturer’s instructions (Affymetrix).

scan_protocol: Arrays were scanned on the GeneChip Scanner 3000 (Affymetrix). Image analysis was performed using GCOS 1.3 (Affymetrix).

data_processing: GCOS 1.3 (Affymetrix), scaled to 1500

source_name: cochlea, young control, 4 month-old

label_protocol: cDNA synthesis from total RNA (Invitrogen) and cRNA amplification and labeling (Enzo BioArray IVT kit) were accomplished according to the manufacturer’s instructions (Affymetrix).

growth_protocol: All mice were raised under 12:12 dark/light conditions, and housed singly in the specific pathogen-free facility at University of Wisconsin-Madison, and provided a nonpurified diet and acidified water ad libitum.

extract_protocol: Total RNA was isolated from pooled cochlea tissue using the TriZol Reagent (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: To study the effects of CR, we reduced the caloric intake of mice to 74% of that fed to control animals in early adulthood (2 months of age), and this dietary regimen was maintained until 15 months of age. Each control mouse was fed 84 kcal/week of the control diet. Each CR mouse was fed 62 kcal/week of the restricted diet, resulting in a 26% reduction of calorie intake. Mice were divided into three groups: a 4-month-old young control (YC) group, a 15-month-old middle-age control (MC) group, and a 15-month-old calorie-restricted (CR) group. Cochlea tissues were taken from those three groups.

tag: Strain

tag: Gender

value: male

tag: Age

value: 4 months old

value: cochlea


title: MSE_N_M158


title: Cochlea_MC_15mo_3

source_name: cochlea, middle-age control, 15 month-old

value: 15 months old


title: C2C12_1.5_hr

value: mouse C2C12 myoblast, 1.5 hr after low serum synchronization


title: MSE_N_626


title: Cochlea_YC_4mo_1


title: Cochlea_MC_15mo_2


title: MSE_N_G98A


title: MSE_D_G73A

source_name: uterus - Mid secretory endometrium from patient with  endometriosis

tag: Mid Secretory Phase Endometriosis


title: MSE_N_610


title: MSE_D_645

description: Mid secretory endometrium from patient with  endometriosis


title: Cochlea_CR_15mo_2

source_name: cochlea, caloric restricted, 15 month-old

treatment_protocol: To study the effects of CR, we reduced the caloric intake of mice to 74% of that fed to control animals in early adulthood (2 months of age), and this dietary regimen was maintained until 15 months of age. Each control mouse was fed 84 kcal/week of the control diet. Each CR mouse was fed 62 kcal/week of the restricted diet, resulting in a 26% reduction of calorie intake. Mice were divided into three groups: a 4-month-old young control (YC) group, a 15-month-old control (MC) group, and a 15-month-old calorie-restricted (CR) group. Cochlea tissues were taken from those three groups.


title: MSE_D_G72A


title: Cochlea_CR_15mo_3


title: Cochlea_MC_15mo_1


title: Cochlea_YC_4mo_2


title: MSE_D_97A


title: Cochlea_CR_15mo_1


title: MSE_D_678


title: MSE_D_33A


title: MSE_D_543


title: MSE_D_516


title: ESE_N_664

source_name: uterus - Early secretory endometrium from normal patient

tag: Early Secretory Phase Normal


title: ESE_N_650

description: Early secretory endometrium from normal patient


title: ESE_N_629


title: ESE_D_599

source_name: uterus - Early secretory endometrium from patient with endometriosis

tag: Early Secretory Phase Endometriosis


title: ESE_D_489

description: Early secretory endometrium from patient with endometriosis


title: PE_N_M182

source_name: uterus - Proliferative endometrium from normal patient

tag: Proliferative Phase Normal


title: ESE_D_496


title: ESE_D_517


title: PE_D_594

source_name: uterus - Proliferative endometrium from patient with  endometriosis

tag: Proliferative Phase Endometriosis


title: ESE_D_27A


title: PE_D_651

description: Proliferative endometrium from patient with  endometriosis


title: PE_N_M169

description: Proliferative endometrium from normal patient


title: PE_N_598


title: PE_D_508


title: PE_N_562


title: PE_D_647


title: ESE_D_575


title: MSE_D_540


title: PE_D_587


title: PE_N_M165


title: PE_D_26A


title: control rep2

city: Kurashiki

first: Takashi

last: Hirayama

state: Okayama

department: Institute of Plant Science and Resources

institute: Okayama University

description: Gene expression data of wild type geminating seedlings undernomal condition

hyb_protocol: 30 ug cRNA was used. ATH1 GeneChip was used.

scan_protocol: using GSC3000 scanner according to the manufacturer’s recommendation

data_processing: RMA normalized using Cel file with affllmGUI

source_name: 3normal segregants from 3-week-old plant

label_protocol: First-strand of cDNA was synthesized using 16 µg of total RNA and SuperScript Double-stranded cDNA Synthesis kit (Invitrogen). The labeled cRNA was synthesized using BioArray RNA Transcripts Labeling Kit (T7) (ENZO Life Sciences inc.). After labeling, the cRNA was digested partially by incubating in 40 mM Tris-acetate, pH8.0, 100 mM KOAc, 30 mM MgOAc, at 94°C for 35 min. Then 30 µg cRNA was used for microarrary hybridization.

growth_protocol: The plates were kept in a growth chamber with a conditions; 23°C, 16 hr light and 8 hr dark cycles

extract_protocol: Total RNA was extracted from frozen tissue using TRIzol reagent (Invitrogen) and purified using a RNease MinElute Cleanup Kit (Qiagen).

treatment_protocol: grown on 1/2 MS plant containing 2% sucrose

tag: Nossen, normal phenotype segregants of Ds insertion line 13-2198-1


title: LSKCD34-Flt3- (040203)


title: control rep1

source_name: normal segregants from 3-week-old plant


title: albino rep1

source_name: albino segregants from 3-week-old plant

tag: Nossen, albino segregants of Ds insertion line 13-2198-1


title: albino rep2


title: ahg3-1 rep1

scan_protocol: Using GSC3000 scannar according to the manufacturer’s recommendation

source_name: ABA hypersensitive mutant ahg3-1 seedlings

treatment_protocol: After stratification at 4°C for 4 days, seeds were allowed to germinate on the MS-2% sucrose plate containing 0.5 uM ABA for two days

tag: ABA hypersensitive mutant ahg3-1 columbia back ground


title: No ABA control rep1

source_name: Columbia wild type seedlings

treatment_protocol: After stratification at 4°C for 4 days, seeds were allowed to germinate on the MS-2% sucrose plate for two days

tag: Columbia wild type


title: ahg1-1 rep2

source_name: ABA hypersensitive mutant ahg1-1 seedlings

tag: ABA hypersensitive mutant ahg1-1 columbia back ground


title: ahg1-1 rep1


title: ABA control rep2


title: WT_total_rep1

city: Knoxville

first: Albrecht

middle: G

last: von Arnim

state: TN

address: M407 Walters Life Science Building

department: Biochemistry, Cellular and Molecular Biology

institute: The University of Tennessee

hyb_protocol: not provided

scan_protocol: not provided

data_processing: MAS 5.0

source_name: aerial part

label_protocol: not provided

extract_protocol: standard total RNA isolation

tag: [Ecotype] Columbia, WT, [Age] 10-day-old


title: ahg3-1 rep2


title: WT_non-polysome_rep1

type: other

molecule: other

extract_protocol: polysomal and non-polysomal RNA samples were isolated by sucrose density gradient method (Kim et al., 2004, Plant Cell 16:3341-3356).


title: eif3h_total_rep1

tag: [Ecotype] Columbia, eif3h-1 mutant, [Age] 10-day-old


title: eif3h_polysome_rep2


title: WT_polysome_rep2


title: No ABA control rep2


title: WT_total_rep2


title: WT_non-polysome_rep2


title: eif3h_non-polysome_rep2


title: ABA control rep1


title: B307 Monocytes treated with anti-FcgRIIB antibody for 24 hrs

status: Public on Apr 30 2007

city: New Haven

first: Kavita

last: Dhodapkar

address: 333 Cedar Street

institute: Yale

description: Data was scanned using Genechip scanner 3000 using the manufacturer’s protocol.

hyb_protocol: 1-2 ug of total RNA was labeled and hybridized using the ENZO T7 labeling kit (Life Sciences) as per the manufacturer’s protocol, on Affymetrix Human Genome U133 Plus 2.0 microarrays (Affymetrix).

scan_protocol: Washing and scanning was done on fluidics station 400 and GeneChip scanner 3000 using the manufacturer’s protocol.

data_processing: Affymetrix GCOS 1.2 software was used to obtain the raw signal and present / absent gene data.

extract_protocol: Cells were pelleted in the RLT buffer. Total RNA was extracted using the RNeasy kit (Qiagen) following the manufacturer’s protocol.

tag: CD14+ macs bead seperated monocytes


title: WT_polysome_rep1


title: eif3h_total_rep2


title: eif3h_non-polysome_rep1


title: eif3h_polysome_rep1


title: B240 MOnocytes treated with anti-FcgRIIB antibody for 24 hrs

source_name: B240 Monocytes treated with anti-FcgRIIB antibody

label_protocol: 1-2 ug of total RNA was labeled and hybridized using the ENZO T7 labeling kit (Life Sciences) as per the manufacturer’s protocol, on Affymetrix Human Genome U133 Plus 2.0 microarrays (Affymetrix).

tag: CD14+ macs bead separated monocytes


title: Tumor from MYF-5 CRE/SSM2 mouse CC17-B

city: Salt Lake City

first: Jeffrey

last: Hancock

state: UT

address: 2000 Circle of Hope Dr

department: Huntsman Cancer Institute

institute: University of Utah

description: Gene expression data from SYT-SSX murine tumor

hyb_protocol: cRNA (15 ug) was fragmented following the Affymetrix protocol, added to 270 ul of hybridization buffer, and hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 arrays (P/N 900495)

scan_protocol: The arrays were scanned using an Affymetrix GeneChip Scanner 3000 enabled for High-Resolution Scanning, and the raw images were converted to .CEL files using Affymetrix GCOS software

data_processing: The MAS5 algorithm was used to accomplish the mean scaling normalization and scaling to 500.

source_name: Tumor from MYF-5 CRE/SSM2 mouse

label_protocol: labeled target RNA was prepared from total tissue RNA using the One-Cycle Target Labeling Kit and Control Reagents

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and was further purified using RNeasy kit (Qiagen)

treatment_protocol: Tissue and tumor samples were excised and subjected to manual disruption prior to total RNA extraction

tag: Adolescent mouse tumor sample


title: B240 monocytes treated with isotype control antibody for 24 hrs

source_name: B240 Monocytes treated with isotype control antibody for 24 hrs

tag: CD14+ Macs bead separated  monocytes


title: Tumor from MYF-5 CRE/SSM2 mouse SSM4


title: Tumor from MYF-5 CRE/SSM2 mouse SSM5


title: Tumor from MYF-5 CRE/SSM2 mouse CC17-A


title: B307 Monocytes treated with isotype control antibody for 24 hrs


title: B227 immature DCs treated with anti- FcgRIIB antibody for 24 hrs

source_name: B227 Immature Dcs treated with anti-FcgRIIB antibody

tag: monocyte derived DCs


title: Tumor from MYF-5 CRE/SSM2 mouse CC23


title: Wild Type Skeletal Muscle Sample (forelimb)

description: Gene expression data from normal mouse skeletal muscle tissue

source_name: Normal Mouse Skeletal Muscle

tag: Mature mice skeletal muscle sample from the forelimb


title: B227 immature DCs treated with inflammatory cytokines for 24 hrs


title: B239 Monocytes treated with isotype control antibody for 24 hrs

tag: CD14+ Macs bead separated monocytes


title: Wild Type Skeletal Muscle Sample (Hind limb)

tag: Mature mice skeletal muscle sample from the hind limb


title: B195 DCs treated with isotype control antibody for 24 hrs


title: Wild Type Skeletal Muscle Sample (Intercostal)

tag: Mature mice skeletal intercostal muscle sample


title: B195 DCs treated with inflammatory cytokines for 24 hrs


title: Wild Type Skeletal Muscle Sample (Hind limb 2)

tag: Mature mice skeletal muscle sample from the hind limb 2


title: B239 monocytes treated with anti-FcgRIIB antibody for 24 hrs

source_name: B239 monocytes traeted with anti-FcgRIIB antibody


title: B227 immature DCs treated with isotype control antibody for 24 hrs

source_name: B227 Immature DCs treated with isotype control antibody


title: B195 DCs treated with anti-FCgRIIB antibody for 24 hrs

source_name: B195 DCs treated with anti-FcgRIIB antibody for 24 hrs


title: B226 Immature DCs treated with anti-FcgRIIB antibody for 24 hrs


title: 131 Immature DCs treated with anti-FcgRIIB antibody for 24 hrs

source_name: 131 immature DCs treated with anti-FcgRIIb antibody for 24 hrs


title: B158 DCs treated with inflammatory cytokines for 24 hrs


title: B158 DCs treated with isotype antibody

source_name: Immature DCs treated with isotype control antibody for 24 hrs


title: B158 DCs treated with anti-FcgRIIB antibody for 24 hrs


title: B226 immature DCs treated with isotype control antibody

source_name: B195 Immature Dcs treated with isotype control antibody


title: Immature DCs without IFN alpha treatment

hyb_protocol: 1-2 ug of total RNA was labeled and hybridized using the ENZO T7 labeling kit (Life Sciences) as per the manufacturer’s protocol, on Affymetrix U133Plus 2.0 microarrays (Affymetrix).

scan_protocol: Washing and scanning was done on fluidics station 400 and GeneChip scanner 3000 using the manufacturer’s protocol. Affymetrix GCOS 1.2 software was used to obtain the raw signal and present / absent gene data.

data_processing:
o	Data was scanned using Genechip scanner 3000 using the manufacturer’s protocol.
o	Affymetrix GCOS 1.2 software was used to obtain the raw signal and present / absent gene data.

source_name: Immature Dcs without IFN alpha treatment

extract_protocol: Cells were pelleted in the RLT buffer. Total RNA was extracted using the RNeasy kit (Qiagen) following the manufacturer’s protocol


title: B305 immature DCs without IFN alpha treatment

description: o	Data was scanned using Genechip scanner 3000 using the manufacturer’s protocol.

label_protocol: 1-2 ug of total RNA was labeled and hybridized using the ENZO T7 labeling kit (Life Sciences) as per the manufacturer’s protocol, on Affymetrix U133Plus 2.0 microarrays (Affymetrix).


title: Immature Dcs treated with IFN alpha

source_name: Immature Dcs treated with IFN alpha


title: B226 Immature DCs treated with inflammatory cytokines for 24 hrs


title: B305 Immature DCs treated with IFNa

source_name: Immature DCs treated with IFNalpha


title: B131 isotype treated DCs

source_name: Isotype treated immature Dcs


title: B304 immature DCs no interferon alpha treatment

source_name: immature DCs without IFN alpha treatment 24 hrs


title: B304 immature Dcs IFN alpha treatment

source_name: b304 immature dcs with ifn alpha treatment 24 hrs

tag: monocyte derived Dcs


title: Teratozoospermic individual: Sample T7

status: Public on Apr 27 2007

city: Detroit

first: Stephen

middle: A

last: Krawetz

state: MI

address: 275 East Hancock, CS Mott Center

institute: Wayne State University

description: Spermatozoal RNA profile from an infertile individual with a consistent severely teratozoospermic semen profile.  The individual demonstrated no other abnormal semen characteristics.

hyb_protocol: Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).

scan_protocol: Scanning procedures were carried out as described by Affymetrix, Santa Clara.

data_processing: The data were analyzed with DChip using invariant set normalization and PM-only MBEI model settings.

source_name: Human Sperm from an infertile male with a consistent severe teratozoospermia

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

growth_protocol: Human donor

extract_protocol: Semen was collected then treated with Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100) on ice for 30 minutes.  Lack of somatic cell contamination and sperm count were established by microscopic examination.  RNA was isolated from sample using a modified RNeasy protocol (Qiagen Inc. Valencia, CA).  RNA was eluted from collection columns using 50 microL of nuclease-free water twice for a final volume of 100 microL.  Dithiothreitol (DTT) was added to eluted samples to a final concentration of 10 mM.  A total of 40 units RNase block (Strategene, La Jolla, CA) was added to each sample prior to a 20-minute treatment with RNase-free DNase I (Ambion, Austin, TX) at 37°C.

tag: Fertility Status

value: Infertile


title: Teratozoospermic individual: Sample T6


title: Teratozoospermic individual: Sample T4


title: Normospermic individual: Sample N8

description: RNA abundance profile from a normospermic semen sample

source_name: Normal Human Sperm

growth_protocol: Healthy human donor

extract_protocol: Semen was collected then treated with Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100) on ice for 30 minutes.  Lack of somatic cell contamination and sperm count were established by microscopic examination.  RNA was isolated from sample using Trizol.  Samples were then treated with RNase-free DNase I.

value: Fertile


title: Teratozoospermic individual: Sample T5


title: Teratozoospermic individual: Sample T8


title: Teratozoospermic individual: Sample T1


title: Normospermic individual: Sample N13


title: Normospermic individual: Sample N6


title: Teratozoospermic individual: Sample T3


title: Normospermic individual: Sample N5


title: Normospermic individual: Sample N11


title: Normospermic individual: Sample N12


title: Normospermic individual: Sample N10


title: Normospermic individual: Sample N7


title: Normospermic individual: Sample N4


title: Normospermic individual: Sample N9


title: Normospermic individual: Sample N3


title: Normospermic individual: Sample N2


title: Teratozoospermic individual: Sample T2


title: MYB51_OE_rep1

status: Public on Apr 26 2007

city: Rehovot

first: Eyal

last: Blum

address: P.O. Box 26

department: Plant

country: Israel

institute: Weizmann Institute of Science

description: In most angiosperms, polarity of leaves in the adaxial-abaxial sides could be associated with differences in morphology and anatomy that reflect the function of either side surfaces. Since dissecting these two parts is technically difficult, examples of metabolic pathways activated in one side of leaves and not in the other are scarce. In this study we used a developmental genetic approach to elucidate the molecular machinery that controls polarity in Arabidopsis leaves. One significant outcome of this strategy was the discovery that expression of three R2-R3 MYB factors, controlling a major pathway of secondary metabolism in Arabidopsis, was localized to the abaxial regions of young leaves. Herein we present in planta evidence that these three genes together with a second group of genes that includes the previously described ATR1 factor and its closest homolog, play a critical role in the transcriptional control of the biosynthetic pathways leading to the formation of the two most prominent classes of GSs in Arabidopsis. Silencing of either one of these two groups of genes using synthetic microRNAs resulted in reduced levels of GSs in leaves. Overexpression of the MYB28-like clade members (MYB28, MYB29 and MYB76) and the ATR1-like members [MYB51, MYB34 (ATR1)] in Arabidopsis led to induction of gene expression and metabolism associated with aliphatic glucosinolates (AGs) and indole glucosinolates (IGs), respectively. At the same time, overexpression of either clade members suppressed expression and metabolism associated with the other pathway, signifying a reciprocal, negative feedback control in between the two GSs pathways. Furthermore, we found that both members of the ATR1-like clade were not only key controllers of IGs homeostasis, but also effected metabolism of auxin and the phytoalexin camalexin. The availability of plants producing high levels of either IGs or AGs allowed us to compare between the capacities of these two types of GSs to deter herbivory. The results demonstrated that AGs exhibit more potent deterrent properties against the whitefly, Bemisia tabaci, a major agricultural pest of field and horticultural crops. Taken as a whole, this work provides a framework for dissecting the spatial regulation of metabolic pathways associated with secondary metabolism and its co-evolution with insect behavior.

hyb_protocol: Labeled cRNA was prepared and hybridized to Affymetrix ATH1 GeneChips, according to the manufacturer's guidelines (Affymetrix, Santa Clara, CA)

source_name: MYB51 OE 14 day seedling

growth_protocol: Arabidopsis seedlings were grown in short day conditions (10h L/14h D, 20°C). These conditions were applied in order to prevent the plant from entering the reproductive stage. Using micro scissors, plants were collected from 14 days old whose cotyledons and hypocotyls were removed.

extract_protocol: Total RNA (15 μg) was extracted with the RNeasy RNA isolation kit (Qiagen).

tag: 14 day seedling


title: MYB29_OE_rep1

scan_protocol: Labeled cRNA was prepared and hybridized to Affymetrix ATH1 GeneChips, according to the manufacturer's guidelines (Affymetrix, Santa Clara, CA)

source_name: MYB29 OE 14 day seedling


title: 35S:MYB28_like_miR_rep2

source_name: 35S:ATR1 14 day seedling

label_protocol: Labeled cRNA was prepared and hybridized to Affymetrix ATH1 GeneChips, according to the manufacturer's guidelines (Affymetrix, Santa Clara, CA)


title: 35S:ATR1_like_miR_rep2

source_name: 14 days seedling

tag: 14 days seedling


title: 35S:ATR1_like_miR_rep1


title: 35S:MYB28_like_miR_rep1

extract_protocol: Total RNA (15 μg) was extracted with the RNeasy RNA isolation kit (Qiagen). Labeled cRNA was prepared and hybridized to Affymetrix ATH1 GeneChips, according to the manufacturer's guidelines (Affymetrix, Santa Clara, CA).


title: MYB76_OE_rep2

source_name: MYB76 OE 14 day seedling


title: ATR1_OE_rep1

source_name: ATR1 OE 14 day seedling


title: MYB29_OE_rep2


title: WT_for_miR_rep1

source_name: miR WT 14 day seedling


title: MYB76_OE_rep1


title: ATR1_OE_rep2


title: WT_for_ATR1/MYB51_rep2

source_name: ATR1 WT 14 day seedling


title: WT_for_miR_rep2


title: WT_for_MYB29/76_rep3

source_name: MYB29 WT 14 day seedling


title: WT_for_MYB29/76_rep2


title: WT_for_ATR1/MYB51_rep1


title: WT_for_MYB29/76_rep1


title: Normospermic individual: Sample N1


title: DC_Stimulated_Rep2

status: Public on Apr 24 2007

city: Oxford

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

country: United Kingdom

institute: University of Oxford

description: Circulating monocyte derived DCs were isolated from buffy coats by adherence and culture in IL-4 and granulocyte-macrophage colony-stimulating factor (GM-CSF). DC preparations analyzed were more than 98% pure. At day four 10 million immature DCs were either left unstimulated or stimulated using plate bound anti-DC-SIGN antibody for 2 hr. Three replicates of non-stimulated or stimulated cells were taken and used to extract total RNA.

hyb_protocol: Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). A 200µl of this hybridization cocktail was used on the chip and incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v5, Affymetrix) of double-staining and post-hybridisations washes.

scan_protocol: Fluorescent images were captured using gene Array Scanner 3000 and GCOS1.2 software (Affymetrix).

data_processing: We have used the genechip robust multi-array average expression measurements (GC-RMA) (37-39) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 54,675 probe sets (transcripts) on each of these arrays.

source_name: primary dendritic cells (DCs)

label_protocol: 2 microgram RNA together with appropriate dilutions of GeneChip eukaryotic poly-A RNA spike controls (Affymetrix # 900433) was converted to double-stranded cDNA with superscript II (Invitrogen #11917-010) using T7-(dT)24 primer (Affymetrix 900375). This was used in an in vitro transcription to generate biotin-labelled cRNA probes.

growth_protocol: DCs were grown in R10 with IL4 and GM-CSF. Media changes occured every 48-72hr

extract_protocol: Total RNA was extracted using RNeasy kits (Qiagen).

treatment_protocol: Circulating myeloid DCs were isolated from buffy coats by adherence and culture in IL-4 and granulocyte-macrophage colony-stimulating factor (GM-CSF). Immature primary monocyte derived DCs were stimulated for 2hr using plate bound anti-DC-SIGN antibody. To investigate the molecular nature of DC-SIGN signalling in primary dendritic cells (DCs), an antibody was identified that induces signalling in a similar manner to that produced following exposure of DCs to HIV-1. This antibody was used to activate primary DCs for two hours and the global gene expression profile documented.

tag: Buffy coats were obtained from the National Blood Centre. Circulating myeloid dendritic cells (DCs) were isolated from buffy coats by adherence and culture in IL-4 and granulocyte-macrophage colony-stimulating factor (GM-CSF). DC preparations analyzed were more than 98% pure.


title: DC_Stimulated_Rep3


title: 04-147 Transcriptome map

status: Public on Apr 23 2007

city: Amsterdam

first: Roel

last: van Driel

address: Kruislaan 318

department: BioCentrum

country: Netherlands

institute: University of Amsterdam

description:
Data accompanying the paper: "The 3D structure of human interphase
chromosomes is related to the transcriptome map. Goetze et al.,
(submitted).

hyb_protocol: Protocol 	10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol.

data_processing: Expression data (.cel files) were normalized with the MAS5 algorithm (target signal = 100) using GCOS software (Affymetrix). Data from the duplicate arraying experiments were averaged and further analyzed.

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation

growth_protocol: 04-147 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer's protocol.

tag: Human primary fibroblasts derived from female skin


title: DC_Stimulated_Rep1


title: HCT116 Transcriptome map

source_name: HCT116 cells

growth_protocol: H116 cells were cultured in McCoy’s 5 medium (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

tag: human colon carcinoma cells


title: DC_Unstimulated_Rep3

extract_protocol: RNA was extracted using RNeasy kits (Qiagen).

treatment_protocol: Circulating myeloid DCs were isolated from buffy coats by adherence and culture in IL-4 and granulocyte-macrophage colony-stimulating factor (GM-CSF).


title: DC_Unstimulated_Rep2

tag: Buffy coats were obtained from the National Blood Centre. Circulating myeloid DCs were isolated from buffy coats by adherence and culture in IL-4 and granulocyte-macrophage colony-stimulating factor (GM-CSF). DC preparations analyzed were more than 98% pure.


title: DC_Unstimulated_Rep1


title: K562 Transcriptome map

source_name: K562 cells

growth_protocol: K562 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

tag: lymphoblastoid cells


title: lung_E18_wildtype

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: signal intensity values for each probe set derived from the Affymetrix Microarray Analysis Suite (v5.0) software; target value normalized to 150

source_name: whole lung E18 normal

label_protocol: Affymetrix

extract_protocol: trizol followed by RNeasy Qiagen kit

tag: normal lung


title: lung_E18_nmyc9a

source_name: whole lung E18 nmyc9a hypomorphic allele homozygote

tag: pooled whole E18 lungs from animals homozygous for the nmyc 9a hypomorphic allele


title: BALB/c_PBS Replicate 3

city: Abbott Park

first: Xin

last: Lu

state: IL

address: 100 Abbott Park Rd

department: Cancer Research

institute: Abbott Laboratories

description: gene expression from allergen stimulated mouse lung

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on rat RAE-230A microrray gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: GCRMA

source_name: mouse whole lung

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: RNA was isolated using TRIZOL reagent (Gibco-BRL Life Technologies) according to the manufacturers protocol

tag: 8 wk old BALB/c (or BALB-RAG) mice were sensitized to ovalbumin (or PBS)]on days 1 and 7, and challenged with aerosolized ovalbumin (or PBS) on days 15-21, and samples harvested on day 22


title: BALB/c_OVA Replicate 4


title: BALB/c_OVA Replicate 3


title: BALB-RAG_OVA Replicate 3


title: BALB-RAG_PBS Replicate 4


title: HeLa Transcriptome maps

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

tag: cervix carcinoma cells


title: BALB-RAG_OVA Replicate 1


title: BALB/c_OVA Replicate 1


title: BALB-RAG_OVA Replicate 2


title: BALB-RAG_PBS Replicate 1


title: BALB/c_OVA Replicate 2


title: BALB/c_PBS Replicate 2


title: SH-EP Transcriptome map

source_name: SH-EP2 cells

growth_protocol: SH-EP cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

tag: human neuroblastoma cells


title: BALB/c_PBS Replicate 4


title: BALB-RAG_OVA Replicate 4


title: BALB-RAG_PBS Replicate 2


title: BALB-RAG_PBS Replicate 3


title: BALB/c_PBS Replicate 1


title: Drosophila_stwlbam_rep2

status: Public on Apr 15 2007

city: Dallas

first: Dennis

last: McKearin

state: TX

address: 6000 Harry Hines Blvd., NA5.214

department: Molecular Biology

institute: UT Southwestern Med. Ctr.

description: Drosophila ovaries, stwl bam double mutant

hyb_protocol: Full protocol at: http://microarray.swmed.edu/AffyHybProtocol.htm

scan_protocol: Standard Affymetrix scanning protocol

data_processing:
Affymetrix GCOS
GeneSpring

organism: Drosophila melanogaster

label_protocol: Standard labeling protocol

growth_protocol: Standard cornmeal molasses + dry yeast

extract_protocol: Total RNA extracted with TRIzol reagent

tag: Genotype

value: stwl bam double mutants

tag: Aged 3-5 days


title: Drosophila_bam86_rep3

description: Drosophila ovaries, bam mutant

source_name: Drosophila ovaries, bam mutant

value: bam[delta86] mutant


title: HSC_Zfx-flox_Replicate2

status: Public on Apr 20 2007

city: New York

first: Jose

middle: M

last: Galan

state: NY

address: 701 W 168th St Room 609

institute: Columbia University Medical Center

description: Murine Zfx-flox HSC Replicate2

hyb_protocol: Hybridization performed on a Affymetrix FS450/250 Fluidics Station using the FS450_0002 script.

scan_protocol: Array scanning and raw data processing were done using GCOS 1.4 software (Affymetrix)

source_name: Bone Marrow sorted Zfx-flox HSC (Lin-, Sca1+, c-Kit+)

label_protocol:
Ambion MessageAmp II aRNA protocol
Two-round amplification and labeling

extract_protocol: RNA was isolated and quantified using the Quant-IT RNA Assay Kit (Invitrogen)

tag: 5 x 10^4 Zfx-flox LSK (Lin-, Sca1+, c-Kit+) cells were sorted directly into Trizol Reagent (Invitrogen) form pooled bone marrow cells from Zfx-flox mice.


title: HSC_Zfx-flox_Replicate1

description: Murine Zfx-flox HSC Replicate1

data_processing:
Array scanning and raw data processing were done using
GCOS 1.4 software (Affymetrix)


title: Drosophila_stwlbam_rep1

description: Drosophila ovary, stwl bam double mutant

value: stwl bam double mutant


title: ESC_Zfx-null_Replicate1

description: Murine Zfx-null ESC Replicate1

source_name: ESC Cultured in 15% KO + LIF without feeders

label_protocol:
Ambion MessageAmp II aRNA protocol
Single-round amplification and labeling

extract_protocol: QIAGEN RNeasy protocol

tag: Zfx-null TC1 ESC


title: ESC_Zfx-flox_Replicate1

description: Murine Zfx-flox ESC Replicate1

tag: Zfx-flox TC1 ESC

tag: Cultured in 15% KO + LIF without feeders


title: ESC_Zfx-null_Replicate2

description: Murine Zfx-null ESC Replicate2


title: Drosophila_stwlbam_rep3

source_name: Drosophila ovaries, stwl bam double mutant


title: HSC_Zfx-cko_Replicate1

description: Murine Zfx-cko HSC Replicate1

source_name: Bone Marrow sorted Zfx-cko HSC (Lin-, Sca1+, c-Kit+)

tag: 5 x 10^4 Zfx-cko LSK (Lin-, Sca1+, c-Kit+) cells were sorted directly into Trizol Reagent (Invitrogen) form pooled bone marrow cells from Zfx-cko mice.


title: ESC_Zfx-flox_Replicate2

description: Murine Zfx-flox ESC Replicate2


title: HSC_Zfx-cko_Replicate2

description: Murine Zfx-cko HSC Replicate2


title: Jurkat-KD1

status: Public on Apr 13 2007

city: Philadelphia

first: Gary

middle: P

last: Wang

state: PA

address: 405 Johnson Pavilion, 3610 Hamilton Walk

department: Microbiology

institute: University of Pennsylvania School of Medicine

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Affymetrix U133 v2 microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.

label: phycoerythrin

source_name: Jurkat cells with LEDGF transcript knockdown (PSIP1 gene)

label_protocol: total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

extract_protocol: total RNA was extracted from Jurkat cells using the RNeasy mini kit (Qiagen, Valencia, CA).

tag: Jurkat cells stably transfected with shRNA constructs (si1340) against LEDGF transcript (PSIP1 gene), derived from Jurkat si1340JK Cl-2 which was established and described in LLano et al. (2004). J. Virol. 78 (17):9524-9537.


title: Drosophila_bam86_rep2

description: Drosophila ovaries, bam mutant

hyb_protocol: Full protocol at http://microarray.swmed.edu/AffyHybProtocol.htm

tag: Gentoype


title: Jurkat-KD2


title: Jurkat-J3

source_name: wild type Jurkat cells

tag: wild type Jurkat cells


title: Jurkat-KD3


title: Jurkat-J2


title: Jurkat-J1d

tag: wild-type Jurkat cells


title: DC_double_matched_rep2

status: Public on Apr 12 2007

city: Houston

first: William

middle: K

last: Decker

address: 1515 Holcombe Blvd.

department: Stem Cell Transplantation and Cellular Therapy

institute: University of Texas MD Anderson Cancer Center

description: doubly-loaded matched dendritic cells

hyb_protocol: Used the GeneChip® Eukaryotic Hybridization Control Kit (Affymetrix P/N 900299 or 900362). Set up reaction based on following the Human U133 Plus 2.0 chart in a 49 format array. Incubated at 99 degrees for 5 minutes then 45 degrees for 5 minutes. Pre-fill array with 250 uL of 1X hybridization Buffer and rotate in hyb oven for 10 minutes @ 45 degrees C. 1X Hybridization buffer consisted of: 8.3mL of 12X MES (Morhpolinoethanesulfonic Acid) 17.7mL of 5M NaCl 4.0mL of 0.5M EDTA 0.1mL of 10% Tween-20 19.9mL of water 50.0 mL Total Remove 1 X pre-hyb buffer from array and inject 200 uL of Hyb cocktail mix. Rotate in hyb-oven 16-18 hours at 45 degrees C. Add 200 uL Wash Buffer A Wash Buffer A 300 ml of 20X SSPE 1.0 ml of 10% Tween-20 699 ml of water 1000 ml Total Prepared SAPE solution and then prepared Antibody Solution Mix. Used Fluidics script EukGE-WS2v5_450 to run the fluidics station (Affymetrix Fluidics 450). Used Affymetrix GeneChip® Operating Software (GCOS) to run the fluidics script. Washing and Staining: Wash Buffer B 83.3 mL of 12X MES Stock Buffer 5.2 mL of 5M NaCl 1.0 mL of 10% Tween-20 910.5 mL of water 1000 mL Total 2X Stain Buffer 41.6 mL 12X MES Stock Buffer 92.5 mL 5 M NaCl 2.5 mL 10% Tween 20 113.3 mL Water 250 mL Total EukGE-WS2v5 wash cycle (used for Human U133 Plus 2.0 array) was used.

scan_protocol: GCS3000 scanner

data_processing: The software used in scanning to create the images and perform basic analysis is the Affymetrix GCOS (GeneChip® Operating Software). All the normalizations and algorithms are set within the software.

source_name: dendritic cells loaded with matched mRNA/lysate replicate2

label_protocol: Used the GeneChip IVT Labeling Kit (Affymetrix P/N 900449) for synthesis of Biotin-labeled cRNA. Prepared each sample reaction using all of template cDNA and incubated for 16 hours at 37 degrees C. Cleaned up and Quantified the biotin-labeled cRNA by using GeneChip® Sample Cleanup Module (Affymetrix P/N 900371). Used the NanoDrop ND-1000 spectrophotometer to quantified the cRNA and then calculated adjusted yield.

extract_protocol: Total RNA was extracted uzing the Trizol method

tag: Mature dendritic cells pooled from 7 different normal donors, loaded with both mRNA and cell lysates derived from 1 of 3 different AML tumor products.  Here, mRNA and lysate were derived from the same source (tumor product).


title: DC_double_matched_rep1

description: doubly-loaded matched dendritic cells

source_name: dendritic cells loaded with matched lysate/mRNA replicate1

tag: Mature dendritic cells pooled from 7 different normal donors, loaded with both mRNA and cell lysate derived from exogenous tumor products.  Here, mRNA and lysates were derived from the same source (same tumor).


title: Drosophila_bam86_rep1

description: Drosophila ovary, bam mutant

hyb_protocol: Full protocol at: http://microarray.swmed.edu/AffyHybProtocol.htm Eukaryotic Target fragmentation and Hybridization 1. Calculate the necessary amount of cRNA 20ug (cRNA concentration at least 0.625ug/ul ) Place in 0.5ml tubes. Adjust volume to 32ul with nuclease free water. 2.Add 8ul of 5x Fragmentation buffer to each sample. Vortex, spin briefly. 3. Incubate at 94?ムfor 35 minutes in the heat block. 4.While cRNA is fragmenting, take out Gene Chips and place them at room temperature. 5. . Incubate the probe array filled with 1X Hybridization Buffer at 45?ムfor 10 minutes with rotation. Place Chips at 45?ムin Hybridization oven, rotating at 60 rpm. for 10 minutes. 6. When 35 min is up remove samples from heat block and spin down . 7.Add the following reagents 5ul  of Oligo B2 15 ul of 20x Eukaryotic Controls (It is imperative that frozen stocks of 20X GeneChip Eukaryotic Hybridization Controls are heated to 65?ムfor 5 minutes to completely resuspend the cRNA before aliquotting) 3ul  of herring Sperm DNA 3ul of BSA 84 ul  of Nuclease free water 150 ul of  2x Hybridization Buffer Vortex,Spin briefly.. 8.. Heat the hybridization cocktail to 99?ムfor 5 minutes in a heat block. 9. Transfer the hybridization cocktail that has been heated at 99?レ to a 45?ーoven for 5 minutes. 10. Spin hybridization cocktail(s) at maximum speed in a microcentrifuge for 5 minutes to remove any insoluble material from the hybridization mixture. 11.Remove the buffer solution from the probe array cartridge and fill with appropriate volume (Table 2.2.2) of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube. 12.Place probe array into the Hybridization Oven, set to 45?ヮ Avoid stress to the motor; load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm. 13.Hybridize for 16-18 hours.

source_name: Drosophila ovary, bam mutant

tag: Drosophila females


title: DC_unloaded_rep2

description: Unloaded dendritic cells

source_name: Unloaded dendritic cells replicate2

tag: Mature DC from 9 different normal donors, unoladed with exogenous antigenic material


title: Backskin_Get1_e18_KO2

city: Irvine

first: Kevin

last: Lin

state: CA

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California, Irvine

description: Get1, grainyhead epithelial transactivator 1. Also known as grainyhead-like 3 (Grhl3)

hyb_protocol: Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Genome 430 2.0 array.

scan_protocol: The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip Scanner 3000. The results were quantified and analyzed using GCOS 1.1.1 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA  present in the isolated total RNA (10 ug total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY).  15ug of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

extract_protocol: Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA). In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up. Eluted total RNAs were quantified with a portion of the recovered total RNA adjusted to a final concentration of 1 ug/ul. All starting total RNA samples were quality assessed prior to beginning target preparation/processing steps by running out a small amount of each sample (typically 25-250 ng/well) onto a RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) that was evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

tag: Strain C57BL/6

tag: Tissue

value: Backskin

tag: Age


title: DC_double_mismatched_rep1

description: doubly-loaded mismatched dendritic cells

source_name: dendritic cells loaded with unmatched mRNA/lysate replicate1

tag: Mature dendritic cells pooled from 7 different normal donors, loaded with exogenously-derived mRNA and cell lysate.  Here mRNA and lysate were derived from different (mismatched) sources.


title: MDA Mb231 Treated 1 Treated

status: Public on Apr 09 2007

city: San Diego

first: Richard

middle: B

last: Roth

address: 12790 El Camino Real

department: Molecular Medicine

institute: Neurocrine Biosciences, Inc.

description: Treated

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with robust multi-array (RMA) for background correction, normalization and polishing.

source_name: Male/Female; Normal/Diseased

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

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

treatment_protocol: Not treated

tag: Tissue/Cell Line [C]

value: MDA-MB231 cells

tag: Disease/Normal or Treatment [C]

value: treated

tag: Gender

value: F

tag: Disease type

value: Normal


title: Backskin_Get1_e18_KO3


title: Backskin_Get1_e18_KO1


title: MDA Mb231 Treated 2 Treated

description: Treated


title: renal_vesicle_Lim1_mutant_4

status: Public on Apr 10 2007

city: Cincinnati

first: Steven

last: Potter

state: OH

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Children's hospital Medical Center

description: Laser capture of E12.5 Lim1 mutant renal vesicles

hyb_protocol: Standard Affymetrix procedures, using 5 micrograms of target.

scan_protocol: standard Affymetrix scan procedures

data_processing: GCOS used to generate expression values, with all probe sets, signal set to 1500.

source_name: renal vesicle from E12.5 Lim1 mutant kidney

label_protocol: Target was prepared with Epicentre two round IVT kit as per Potter GUDMAP.org protocol

growth_protocol: Mice were grown normally

extract_protocol: RNA was purified with QIagen RNeasy Micro kit, as describe in Potter Protocols GUDMAP.org

treatment_protocol: Samples were prepared for laser capture microdissection as per Potter GUDMAP.org protocols

tag: from Lim1 mutant mice E 12.5 renal vesicle


title: MDA Mb231 6h + 75 nM Cxcl12 2 Treated

description: Treated


title: DC_lysate_rep1

description: lysate-loaded dendritic cells

source_name: lysate-loaded dendritic cells replicate1

tag: Mature dendritic cells pooled from 11 different normal donors, loaded with exogenous cell lysates, lysates were derived from 1 of 3 different AML tumor products


title: MDA Mb231 6h 6 Control

description: Control

value: control


title: MDA Mb231 3 Control

description: Control


title: MDA Mb231 Treated 3 Treated

description: Treated


title: DC_lysate_rep2

description: lysate-loaded dendritic cells

source_name: lysate-loaded dendritic cells replicate2


title: renal_vesicle_Lim1_mutant_3

description: No other informatin required.

hyb_protocol: Standard Affymetrix hybridization protocols, using five micrograms of target

scan_protocol: Standard Affymetrix scan protocols.

data_processing: Expression values generated with GCOS affymetrix software using all probe sets scaling factor 1500

label_protocol: Used two round Epicentre kit, as per Potter GUDMAP.ORG protocols

extract_protocol: According to GUDMAP  Potter laboratory protocols (GUDMAP.ORG)

treatment_protocol: Was prepared according to GUDMAP Potter protocols (GUDMAP.ORG)

tag: E12.5 Lim1 mutant renal vesicles isolated by laser capture microdissection.


title: DC_unloaded_rep1

description: Unloaded dendritic cells

source_name: Unloaded dendritic cells, replicate1

tag: Mature DC pooled from 9 different normal donors, not loaded with exogenous antigenic material


title: DC_mRNA_rep1

description: mRNA loaded dendritic cells

source_name: mRNA-loaded dendritic cells replicate1

tag: Mature DC pooled from 10 different normal donors, loaded with exogenous mRNA only; exogenous mRNA was derived from 1 of 3 different AML tumor products


title: MDA Mb231 2 Control

description: Control


title: MDA Mb231 1 Control

description: Control


title: MDA Mb231 6h + 75 nM Cxcl12 3 Treated

description: Treated


title: renal_vesicle_Lim1_mutant_2

description: No other informatin required.

tag: Renal vesicles from Lim1 mutant E12.5 embryos isolated by laser capture microdissection.


title: DC_mRNA_rep2

description: mRNA loaded dendritic cells

source_name: mRNA-loaded dendritic cells replicate2

tag: Mature denritic cells pooled from 10 different normal donors, loaded with exogenously-derived mRNA, mRNA was derived from 1 of 3 different AML tumor products


title: DC_double_mismatched_rep2

source_name: dendritic cells loaded with mismatched mRNA/lysate replicate2


title: renal_vesicle_Lim1_mutant_1

description: No other informatin required.

tag: E12.5 Lim1 mutant embryo renal vesicles isolated by laser capture microdissection


title: MDA Mb231 6h 4 Control

description: Control


title: MDA Mb231 6h + 10 nM Cxcl12 3 Treated

description: Treated


title: MDA Mb231 6h + 75 nM Cxcl12 1 Treated

description: Treated


title: MDA Mb231 6h + 10 nM Cxcl12 2 Treated

description: Treated


title: MDA Mb231 6h + 10 nM Cxcl12 1 Treated

description: Treated


title: MDA Mb231 6h 3 Control

description: Control


title: MDA Mb231 6h 5 Control

description: Control


title: MDA Mb231 6h 2 Control

description: Control


title: MDA Mb231 6h 1 Control

description: Control


title: MDA Mb231 1h + 10 nM Cxcl12 2 Treated

description: Treated


title: MDA Mb231 1h 3 Control

description: Control


title: MDA Mb231 1h 1 Control

description: Control


title: Substantia Nigra Reticulata 3 Disease

description: Disease

value: substantia nigra_reticulata

value: disease

value: M

value: Parkinson's disease


title: MDA Mb231 1h 2 Control

description: Control


title: Thalamus Lateral Nuclei 4 Normal

description: Normal

value: thalamus_lateral nuclei

value: normal


title: MDA Mb231 1h + 10 nM Cxcl12 3 Treated

description: Treated


title: MDA Mb231 1h + 10 nM Cxcl12 1 Treated

description: Treated


title: Thalamus Lateral Nuclei 1 Disease

description: Disease


title: Thalamus Lateral Nuclei 3 Normal

description: Normal


title: Thalamus Subthalamic Nucleus 2 Disease

description: Disease

value: thalamus_subthalamic nucleus


title: Thalamus Subthalamic Nucleus 3 Normal

description: Normal


title: Gloubus Pallidum Internal 7 Normal

description: Normal

value: gloubus pallidum_internal


title: Thalamus Lateral Nuclei 2 Disease

description: Disease


title: Gloubus Pallidum Internal 3 Disease

description: Disease


title: Thalamus Subthalamic Nucleus 1 Disease

description: Disease


title: Gloubus Pallidum Internal 4 Disease

description: Disease


title: Gloubus Pallidum External 5 Normal

description: Normal

value: gloubus pallidum_external


title: Gloubus Pallidum Internal 6 Normal

description: Normal


title: Gloubus Pallidum Internal 2 Disease

description: Disease


title: Gloubus Pallidum External 1 Disease

description: Disease


title: Thalamus Subthalamic Nucleus 4 Normal

description: Normal


title: Gloubus Pallidum External 6 Normal

description: Normal


title: Gloubus Pallidum External 3 Disease

description: Disease


title: Lymph Nodes 2 Normal

description: Normal


title: Gloubus Pallidum Internal 5 Normal

description: Normal


title: Urethra 4 Normal

description: Normal

value: urethra


title: Gloubus Pallidum Internal 1 Disease

description: Disease


title: Testes 2 Normal

description: Normal

value: testes


title: Urethra 2 Normal

description: Normal


title: Lymph Nodes 4 Normal

description: Normal


title: Thyroid Gland 3 Normal

description: Normal


title: Salivary Gland 3 Normal

description: Normal


title: Kidney Medulla 2 Normal

description: Normal


title: Thyroid Gland 2 Normal

description: Normal


title: Kidney Medulla 3 Normal

description: Normal


title: Kidney Medulla 4 Normal

description: Normal


title: Thyroid Gland 1 Normal

description: Normal


title: Lymph Nodes 1 Normal

description: Normal


title: Urethra 1 Normal

description: Normal


title: Lymph Nodes 3 Normal

description: Normal


title: Testes 1 Normal

description: Normal


title: Kidney Medulla 1 Normal

description: Normal


title: Salivary Gland 4 Normal

description: Normal


title: Thyroid Gland 4 Normal

description: Normal


title: Salivary Gland 2 Normal

description: Normal


title: Pituitary Gland 3 Normal

description: Normal


title: Pituitary Gland 4 Normal

description: Normal


title: Salivary Gland 1 Normal

description: Normal


title: Heart Atrium 1 Normal

description: Normal


title: Adrenal Gland Cortex 1 Normal

description: Normal


title: Pituitary Gland 2 Normal

description: Normal


title: Adrenal Gland Cortex 4 Normal

description: Normal


title: Substantia Nigra Pars Compacta 3 Disease

description: Disease

value: substantia nigra_pars compacta


title: Substantia Nigra Reticulata 2 Disease

description: Disease


title: Adrenal Gland Cortex 3 Normal

description: Normal


title: Adrenal Gland Cortex 2 Normal

description: Normal


title: Substantia Nigra Pars Compacta 6 Normal

description: Normal


title: Esophagus 3 Normal

description: Normal

value: esophagus


title: Substantia Nigra Reticulata 1 Disease

description: Disease


title: Substantia Nigra Reticulata 5 Normal

description: Normal


title: Substantia Nigra Pars Compacta 8 Normal

description: Normal


title: Substantia Nigra Reticulata 7 Normal

description: Normal


title: Esophagus 4 Normal

description: Normal


title: Substantia Nigra Pars Compacta 2 Disease

description: Disease


title: Substantia Nigra Pars Compacta 7 Normal

description: Normal


title: Substantia Nigra Pars Compacta 5 Normal

description: Normal


title: Substantia Nigra Reticulata 4 Normal

description: Normal


title: Substantia Nigra Pars Compacta 4 Normal

description: Normal


title: Substantia Nigra Reticulata 6 Normal

description: Normal


title: Esophagus 1 Normal

description: Normal


title: Substantia Nigra Pars Compacta 1 Disease

description: Disease


title: Esophagus 2 Normal

description: Normal


title: Gloubus Pallidum External 2 Disease

description: Disease


title: Oral Mucosa 4 Normal

description: Normal


title: Oral Mucosa 3 Normal

description: Normal


title: Oral Mucosa 2 Normal

description: Normal


title: Hypothalamus 4 Normal

description: Normal

value: hypothalamus


title: Putamen P5 Disease

description: Disease

value: putamen


title: Caudate P2 Disease

description: Disease

value: caudate

tag: Gender:


title: Caudate P5 Normal

description: Normal

value: Normal


title: Putamen P7 Normal

description: Normal


title: Putamen P9 Normal

description: Normal


title: Hypothalamus 3 Normal

description: Normal

value: F


title: Accumbens P9 Normal

description: Normal

value: accumbens


title: Caudate P1 Disease

description: Disease

value: disease

value: M


title: Accumbens P8 Normal

description: Normal


title: Hypothalamus 1 Normal

description: Normal


title: Putamen P2 Disease

description: Disease

value: Parkinson's disease


title: Accumbens P4 Disease

description: Disease


title: Accumbens P10 Normal

description: Normal

value: normal


title: Putamen P3 Disease

description: Disease


title: Caudate P4 Normal

description: Normal


title: Hypothalamus 2 Normal

description: Normal


title: Putamen P8 Normal

description: Normal


title: Gloubus Pallidum External 4 Disease

description: Disease


title: Oral Mucosa 1 Normal

description: Normal


title: Putamen P6 Normal

description: Normal


title: Accumbens P7 Normal

description: Normal


title: Accumbens P3 Disease

description: Disease


title: Caudate P3 Normal

description: Normal


title: Accumbens P6 Normal

description: Normal


title: Accumbens P2 Disease

description: Disease


title: Putamen P4 Disease

description: Disease


title: Caudate P6 Normal

description: Normal


title: Accumbens P1 Disease

description: Disease


title: Occipital Lobe 1 Normal

description: Normal


title: Nodose Nucleus 1 Normal

description: Normal


title: Putamen P1 Disease

description: Disease


title: Nodose Nucleus 4 Normal

description: Normal


title: Nodose Nucleus 3 Normal

description: Normal


title: Occipital Lobe 4 Normal

description: Normal


title: Accumbens P5 Normal

description: Normal


title: Occipital Lobe 2 Normal

description: Normal


title: Nodose Nucleus 2 Normal

description: Normal


title: Stomach Pyloric 4 Normal

description: Normal


title: Occipital Lobe 3 Normal

description: Normal


title: Cerebral Cortex 4 Normal

description: Normal


title: Liver 2 Normal

description: Normal

value: liver


title: Cerebral Cortex 3 Normal

description: Normal


title: Stomach Pyloric 3 Normal

description: Normal


title: Cerebral Cortex 1 Normal

description: Normal


title: Liver 1 Normal

description: Normal


title: Liver 4 Normal

description: Normal


title: Stomach Fundus 1 Normal

description: Normal


title: Stomach Fundus 3 Normal

description: Normal


title: Spleen 3 Normal

description: Normal

value: spleen


title: Spleen 1 Normal

description: Normal


title: Liver 3 Normal

description: Normal


title: Stomach Fundus 4 Normal

description: Normal


title: Stomach Pyloric 1 Normal

description: Normal


title: Spleen 2 Normal

description: Normal


title: Cerebral Cortex 2 Normal

description: Normal


title: Stomach Pyloric 2 Normal

description: Normal


title: Stomach Fundus 2 Normal

description: Normal


title: Kidney Cortex 3 Normal

description: Normal


title: Kidney Cortex 1 Normal

description: Normal


title: Ovary 3 Normal

description: Normal

value: ovary


title: Prostate Gland 2 Normal

description: Normal


title: Kidney Cortex 2 Normal

description: Normal


title: Endometrium 3 Normal

description: Normal

value: endometrium


title: Myometrium 3 Normal

description: Normal

value: myometrium


title: Prostate Gland 1 Normal

description: Normal


title: Kidney Cortex 4 Normal

description: Normal


title: Paravertebral Muscle 11 Disease

description: Disease

value: paravertebral muscle

value: Neuromuscular pain


title: Deltoid Muscle 6 Normal

description: Normal

value: deltoid muscle


title: Paravertebral Muscle 7 Disease

description: Disease


title: Paravertebral Muscle 8 Disease

description: Disease


title: Paravertebral Muscle 9 Disease

description: Disease


title: Paravertebral Muscle 3 Disease

description: Disease


title: Deltoid Muscle 1 Normal

description: Normal


title: Deltoid Muscle 3 Normal

description: Normal


title: Paravertebral Muscle 1 Disease

description: Disease


title: Deltoid Muscle 2 Normal

description: Normal


title: Deltoid Muscle 5 Normal

description: Normal


title: Paravertebral Muscle 10 Disease

description: Disease


title: Paravertebral Muscle 6 Disease

description: Disease


title: Deltoid Muscle 4 Normal

description: Normal


title: Paravertebral Muscle 5 Disease

description: Disease


title: Paravertebral Muscle 4 Disease

description: Disease


title: HUVEC Cell Line 2 Normal

description: Normal

value: Huvec cells


title: Bone Marrow 10 Normal

description: Normal


title: Paravertebral Muscle 2 Disease

description: Disease


title: Frontal Cortex 1 Normal

description: Normal


title: Pituitary Gland 10 Normal

description: Normal


title: Synovial Membrane 11 Disease

description: Disease

value: synovial membrane

value: Rheumatoid arthritis


title: Synovial Membrane 5 Normal

description: Normal

value: Normal


title: HUVEC Cell Line 1 Normal

description: Normal


title: Pituitary Gland 8 Normal

description: Normal

value: F


title: CD4+ AntiCD3+AntiCD28 1 Activated

description: Activated

value: activated


title: CD8+ 1 Resting

description: Resting

value: resting

value: M


title: CD8+ AntiCD3+AntiCD28 1 Activated

description: Activated


title: PBMC Media 1 Resting

description: Resting


title: Synovial Membrane 9 Disease

description: Disease

value: disease


title: Synovial Membrane 10 Disease

description: Disease


title: Synovial Membrane 4 Normal

description: Normal

value: normal


title: Fallopian Tube AB2 Normal

description: Normal


title: Prostate Gland 4 Normal

description: Normal


title: Pituitary Gland 9 Normal

description: Normal


title: Prostate Gland 5 Normal

description: Normal


title: Penis 5 Normal

description: Normal

value: penis


title: Testes 6 Normal

description: Normal

value: testes


title: Prostate Gland 6 Normal

description: Normal


title: CD4+ 1 Resting

description: Resting


title: Urethra 6 Normal

description: Normal

value: urethra


title: Testes 4 Normal

description: Normal


title: Urethra 5 Normal

description: Normal


title: Penis 4 Normal

description: Normal


title: Synovial Membrane 6 Normal

description: Normal


title: PBMC PMA+Ionomycin 1 Activated

description: Activated


title: Spleen 4 Normal

description: Normal

value: spleen


title: Penis 6 Normal

description: Normal


title: Penis 2 Normal

description: Normal


title: Small Intestinejejunum 6 Normal

description: Normal


title: Joint Tissue Synovium 2 Normal

description: Normal


title: Small Intestine Jejunum 10 Normal

description: Normal


title: Joint Tissue Synovium 7 Normal

description: Normal


title: Penis 1 Normal

description: Normal


title: Myometrium 33 Disease

description: Disease

value: myometrium

value: Adenomyosis


title: Myometrium 24 Disease

description: Disease


title: Aorta 10 Normal

description: Normal

value: aorta


title: Skin 10 Normal

description: Normal

value: skin


title: Myometrium 15 Normal

description: Normal


title: Myometrium 32 Disease

description: Disease


title: Myometrium 31 Disease

description: Disease


title: Myometrium 14 Normal

description: Normal


title: Myometrium 11 Normal

description: Normal


title: Myometrium 27 Disease

description: Disease