title: StrainPERA_M_6C_Rep2


title: StrainPERA_F_HF_Rep1

status: Public on Dec 10 2008

type: RNA

city: Bar Harbor

first: Keith

last: Shockley

state: ME

address: 600 Main Street

department: Computational and Systems Biology

country: USA

institute: The Jackson Laboratory

description: One group of mice was fed an atherogenic high-fat (30% fat) diet containing cholic acid to increase fat uptake and another was fed a low-fat (6% fat) regular chow diet.  Males and females from both diets were studied for mouse strains 129S1/SvImJ, A/J, BALB/cJ, C3H/HeJ, C57BL/6J, CAST/EiJ, DBA/2J, I/LnJ, MRL/MpJ-Tnfrsf6lpr/J, NZB/BINJ, PERA/Ei, and SM/J. All strains were sacrificed between 11- and 13 weeks of age except for CAST and PERA, which were harvested after 50 weeks of age. CAST and PERA were subsequently removed from our analysis based on discrepant harvest age, but can be found in our database (see below). Three replicate animals were used for each combination of diet, strain, and sex, resulting in a total of 120 mice surveyed for gene expression.

hyb_protocol: Fifteen micrograms of biotin-labeled and fragmented cRNA was then hybridized onto MOE430v2.0 GeneChip® arrays for 16 hours at 45°C. Post-hybridization staining and washing were performed according to the manufacturer’s protocols using the Fluidics Station 450 instrument (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 laser confocal slide scanner. Images were quantified using GeneChip Operating Software (GCOS) v1.2 (Affymetrix).

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

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Strain PERA, Females, HF Diet

label_protocol: The cDNA was linearly amplified with biotinylated nucleotides (Enzo Diagnostics, Farmingdale, NY) through an in vitro transcription reaction with T7 RNA polymerase.

extract_protocol: Liver samples were extracted from each mouse as described previously (Shockley and Churchill, 2006). Total RNA was reverse transcribed with oligo(dT)-T7 primers. before double-stranded cDNA was generated with the Superscript double-stranded cDNA synthesis custom kit (Invitrogen).

tag: Strain

value: PERA

tag: Sex

value: Female

tag: Diet

value: 30% fat

tag: Biological Replicate


title: StrainPERA_F_HF_Rep2


title: StrainSM_F_HF_Rep2

source_name: Strain SM, Females, HF Diet

value: SM


title: StrainSM_M_HF_Rep3

source_name: Strain SM, Males, HF Diet

value: Male


title: StrainSM_M_HF_Rep2


title: StrainPERA_F_6C_Rep2

source_name: Strain PERA, Females, 6C Diet

value: 6% fat (regular chow)


title: StrainPERA_F_6C_Rep3


title: StrainPERA_F_HF_Rep3


title: StrainPERA_F_6C_Rep1


title: StrainSM_F_6C_Rep3

source_name: Strain SM, Females, 6C Diet


title: StrainNZB_M_6C_Rep2

source_name: Strain NZB, Males, 6C Diet

value: NZB


title: StrainNZB_F_HF_Rep2

source_name: Strain NZB, Females, HF Diet


title: StrainMRL_M_HF_Rep3

source_name: Strain MRL, Males, HF Diet

value: MRL


title: StrainMRL_M_6C_Rep2

source_name: Strain MRL, Males, 6C Diet


title: StrainMRL_M_HF_Rep1


title: StrainNZB_F_6C_Rep1

source_name: Strain NZB, Females, 6C Diet


title: StrainNZB_F_6C_Rep3


title: StrainNZB_F_HF_Rep3


title: StrainNZB_F_6C_Rep2


title: StrainNZB_M_HF_Rep1

source_name: Strain NZB, Males, HF Diet


title: StrainMRL_M_6C_Rep3


title: StrainNZB_M_6C_Rep1


title: StrainMRL_M_6C_Rep1


title: StrainMRL_F_6C_Rep2

source_name: Strain MRL, Females, 6C Diet


title: StrainI_M_HF_Rep3

source_name: Strain I, Males, HF Diet

value: I


title: StrainNZB_M_6C_Rep3


title: StrainNZB_M_HF_Rep2


title: StrainNZB_M_HF_Rep3


title: StrainI_M_6C_Rep2

source_name: Strain I, Males, 6C Diet


title: StrainMRL_M_HF_Rep2


title: StrainMRL_F_HF_Rep3

source_name: Strain MRL, Females, HF Diet


title: StrainI_M_HF_Rep1


title: StrainI_M_6C_Rep3


title: StrainMRL_F_HF_Rep2


title: StrainI_M_HF_Rep2


title: StrainMRL_F_6C_Rep1


title: StrainI_M_6C_Rep1


title: StrainDBA_M_6C_Rep3

source_name: Strain DBA, Males, 6C Diet

value: DBA


title: StrainDBA_M_HF_Rep3

source_name: Strain DBA, Males, HF Diet


title: StrainI_F_6C_Rep3

source_name: Strain I, Females, 6C Diet


title: StrainI_F_6C_Rep2


title: StrainDBA_M_HF_Rep1


title: StrainI_F_6C_Rep1


title: StrainI_F_HF_Rep1

source_name: Strain I, Females, HF Diet


title: StrainDBA_M_6C_Rep2


title: StrainCAST_M_6C_Rep2

source_name: Strain CAST, Males, 6C Diet

value: CAST


title: StrainCAST_F_HF_Rep2

source_name: Strain CAST, Females, HF Diet


title: StrainCAST_M_HF_Rep2

source_name: Strain CAST, Males, HF Diet


title: StrainCAST_M_HF_Rep3


title: StrainDBA_F_HF_Rep2

source_name: Strain DBA, Females, HF Diet


title: StrainNZB_F_HF_Rep1

source_name: Strain NZB, Females, HF Diet


title: StrainDBA_F_6C_Rep3

source_name: Strain DBA, Females, 6C Diet


title: StrainI_F_HF_Rep2


title: StrainDBA_M_HF_Rep2


title: StrainCAST_F_HF_Rep3


title: StrainCAST_M_6C_Rep1


title: StrainCAST_M_6C_Rep3


title: StrainDBA_M_6C_Rep1


title: StrainCAST_F_6C_Rep2

source_name: Strain CAST, Females, 6C Diet


title: StrainDBA_F_HF_Rep1


title: StrainCAST_M_HF_Rep1


title: StrainCAST_F_HF_Rep1


title: StrainC3H_M_HF_Rep3

source_name: Strain C3H, Males, HF Diet


title: StrainCAST_F_6C_Rep3


title: StrainC3H_M_HF_Rep2


title: StrainDBA_F_6C_Rep2


title: StrainC3H_M_HF_Rep1


title: StrainDBA_F_6C_Rep1


title: StrainC3H_M_6C_Rep2

source_name: Strain C3H, Males, 6C Diet


title: StrainMRL_F_HF_Rep1


title: StrainI_F_HF_Rep3


title: StrainC3H_M_6C_Rep3


title: StrainMRL_F_6C_Rep3

source_name: Strain MRL, Females, 6C Diet


title: StrainC3H_M_6C_Rep1


title: StrainC3H_F_6C_Rep1

source_name: Strain C3H, Females, 6C Diet


title: StrainC3H_F_HF_Rep3

source_name: Strain C3H, Females, HF Diet


title: StrainC3H_F_6C_Rep3


title: StrainC3H_F_HF_Rep2


title: StrainC3H_F_6C_Rep2


title: StrainC3H_F_HF_Rep1


title: StrainBALB_F_HF_Rep3

source_name: Strain BALB, Females, HF Diet

value: BALB


title: StrainBALB_M_HF_Rep2

source_name: Strain BALB, Males, HF Diet


title: StrainDBA_F_HF_Rep3


title: StrainBALB_M_6C_Rep3

source_name: Strain BALB, Males, 6C Diet


title: StrainBALB_F_HF_Rep2


title: StrainB6_M_HF_Rep2

source_name: Strain B6, Males, HF Diet


title: StrainB6_F_HF_Rep3

source_name: Strain B6, Females, HF Diet


title: StrainBALB_M_6C_Rep2


title: StrainB6_F_HF_Rep1


title: StrainB6_F_6C_Rep2

source_name: Strain B6, Females, 6C Diet


title: StrainB6_M_6C_Rep1

source_name: Strain B6, Males, 6C Diet


title: StrainB6_F_HF_Rep2


title: StrainBALB_F_6C_Rep1

source_name: Strain BALB, Females, 6C Diet


title: StrainB6_M_6C_Rep3


title: StrainA_M_HF_Rep3

source_name: Strain A, Males, HF Diet

value: A


title: StrainB6_F_6C_Rep3


title: StrainBALB_F_HF_Rep1


title: StrainB6_M_HF_Rep3


title: StrainB6_M_6C_Rep2


title: StrainBALB_F_6C_Rep2


title: StrainBALB_M_6C_Rep1


title: StrainB6_M_HF_Rep1


title: StrainB6_F_6C_Rep1


title: StrainBALB_F_6C_Rep3


title: StrainA_M_HF_Rep1


title: StrainA_M_HF_Rep2


title: StrainA_M_6C_Rep2

source_name: Strain A, Males, 6C Diet


title: StrainCAST_F_6C_Rep1


title: StrainA_M_6C_Rep3


title: StrainA_F_HF_Rep1

source_name: Strain A, Females, HF Diet


title: StrainA_F_6C_Rep1

source_name: Strain A, Females, 6C Diet


title: StrainA_F_6C_Rep3


title: Strain129_F_6C_Rep2

source_name: Strain 129, Females, 6C Diet


title: Strain129_F_HF_Rep2

source_name: Strain 129, Females, HF Diet


title: Strain129_F_HF_Rep3


title: Strain129_F_HF_Rep1


title: Strain129_M_HF_Rep1

source_name: Strain 129, Males, HF Diet


title: Strain129_M_HF_Rep2


title: StrainA_F_6C_Rep2


title: Strain129_M_HF_Rep3


title: StrainA_F_HF_Rep2


title: Strain129_F_6C_Rep3


title: StrainA_F_HF_Rep3


title: Strain129_M_6C_Rep2

source_name: Strain 129, Males, 6C Diet


title: Strain129_M_6C_Rep3


title: Strain129_F_6C_Rep1


title: StrainA_M_6C_Rep1


title: Strain129_M_6C_Rep1


title: StrainBALB_M_HF_Rep3


title: TPA_DOX_CONTROL_REP1

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

description: HEL cells carrying control plasmid vector. The cells were treated with doxycycline and incubated for 24 hours with TPA. TPA enhances the differentiation of HEL cells into megakaryocyte-like polyploid cells.

hyb_protocol: cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: RMA probe summarization and quantile normalization of the expression data was carried out using the affy software package for the R programming environment.

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: RNeasy Mini Kit (Qiagen)


title: NOTPA_DOX_MKL_REP1

description: MKL1/HEL cells with 24 hours of doxycycline induced MKL1 overexpression without TPA.  TPA enhances the differentiation of HEL cells into megakaryocyte-like polyploid cells.


title: TPA_NODOX_CONTROL_REP1

description: HEL cells carrying control plasmid vector. The cells were treated with TPA and incubated for 24 hours without doxycycline. TPA enhances the differentiation of HEL cells into megakaryocyte-like polyploid cells.


title: NOTPA_NODOX_CONTROL_REP1

description: HEL cells carrying control plasmid vector. The cells were incubated for 24 hours without doxycycline or TPA. TPA enhances the differentiation of HEL cells into megakaryocyte-like polyploid cells.


title: TPA_DOX_MKL_REP2

description: MKL1/HEL cells under 24 hr TPA-stimulated differentiation with dox induced MKL1 overexpression

tag: MKL1/HEL cells under-TPA stimulated differentiation with dox induced MKL1 overexpression


title: CD44+ stromal cells_control_replicate 3

city: Montréal

first: Caroline

last: Lemieux

state: Québec

address: 5000, Bélanger Est

department: Centre de recherche

country: Canada

institute: Institut de Cardiologie de Montréal

description: bone marrow cultured CD44+ stromal cells, control

hyb_protocol: After fragmentation, 10ug of the biotin-labeled cRNA was hybridized on the GeneChip Mouse Genome 430 2.0 array for 16 hours at 45C in the GeneChip Hybridization oven. Following hybridization, the sample volumes were removed from the arrays. They were then washed with high and low-stringency buffers and stained with R-Phycoerythrin streptavidin in the Affymetrix Fluidics station 450.

scan_protocol: Genechips were then scanned with the GeneChip Scanner 3000 (Affimetrix)

data_processing: Robust Multi-array Average (RMA) expression values and Gene Ontology annotations (www.geneontology.org) were obtained with R software from Bioconductor (www.bioconductor.org)

label_protocol: Each double stranded cDNA was synthesized from 50 ηg of total RNA, and in vitro transcription was performed to produce biotin-labeled cRNA using Affymetrix Two-Cycle Target Labeling and Control Reagent Kit (Affimetrix, Santa Clara, CA) according to the manufacturer’s instructions

extract_protocol: c-kit+ stem cells and CD44+ stromal cells total RNAs were extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions

treatment_protocol: Primary whole bone marrow cultures were treated with a physiological dose of 17βE (10-9M) for a one week period

tag: Gender

value: female

tag: Age

value: 6 weeks


title: NOTPA_DOX_CONTROL_REP1

description: HEL cells carrying control plasmid vector.  The cells were treated with doxycycline and incubated for 24 hours without TPA.  TPA enhances the differentiation of HEL cells into megakaryocyte-like polyploid cells.


title: NOTPA_NODOX_MKL_REP1

description: MKL1/HEL cells with 24 hours of incubation without TPA and doxycycline induced MKL1 overexpression. TPA enhances the differentiation of HEL cells into megakaryocyte-like polyploid cells.


title: c-kit+ stem cells_control_replicate 2

description: bone marrow cultured c-kit+ stem cells, control


title: c-kit+ stem cells_control_replicate 3

source_name: bone marrow cultured c-kit+ stem cells, control


title: CD44+ stromal cells_17βE_replicate 3

description: bone marrow cultured CD44+ stromal cells, 17βE treated


title: c-kit+ stem cells_17βE_replicate 3

description: bone marrow cultured c-kit+ stem cells, 17βE treated


title: TPA_NODOX_MKL_REP2

description: MKL1/HEL cells under 24 hr TPA-stimulated differentiation without dox induced MKL1 overexpression

tag: MKL1/HEL cells under-TPA stimulated differentiation without dox induced MKL1 overexpression


title: c-kit+ stem cells_control_replicate 1


title: c-kit+ stem cells_17βE_replicate 1

source_name: bone marrow cultured c-kit+ stem cells, 17βE treated


title: CD44+ stromal cells_17βE_replicate 2

source_name: bone marrow cultured CD44+ stromal cells, 17βE treated


title: TPA_DOX_MKL_REP1


title: CD44+ stromal cells_control_replicate 1

source_name: bone marrow cultured CD44+ stromal cells, control


title: CD44+ stromal cells_17βE_replicate 1


title: CD44+ stromal cells_control_replicate 2


title: TPA_NODOX_MKL_REP1


title: 293-tet-On-EWS/NOR1 without doxycycline

city: Tokyo

first: Naganari

last: Ohkura

address: 5-1-1, Tsukiji, Chuo-ku

department: Tumor Endocrinology Project

country: Japan

institute: National Cancer Center Research Institute

description: To identify genes affected by EWS/NOR1 overexpression, we compared expression profiles between EWS/NOR1-induced 293-tet-On cells and its control cells.

hyb_protocol: Labeled cRNA was hybridized with the array in the hybridization buffer for 16 hours.

scan_protocol: GCOS (GeneChip operating software)

data_processing: GCOS (GeneChip operating software)

source_name: 293-tet-On-EWS/NOR1 cells, doxycycline untreated

label_protocol: in vitro transcription, Affymetrix protocol

growth_protocol: DMEM supplemented with 10% FCS

extract_protocol: Qiagen RNeasy mini column

treatment_protocol: without doxycycline

tag: 293-tet-On-EWS/NOR1 cells were cultured without doxycycline for 24 hours.


title: c-kit+ stem cells_17βE_replicate 2


title: 293-tet-On-NOR1 with doxycycline

description: To identify genes affected by NOR1 overexpression, we compared expression profiles between NOR1-induced 293-tet-On cells and its control cells.

source_name: 293-tet-On-NOR1 cells, doxycycline treated

treatment_protocol: with doxycycline

tag: 293-tet-On-NOR1 cells were cultured with doxycycline for 24 hours.


title: 293-tet-On-NOR1 without doxycycline

source_name: 293-tet-On-NOR1 cells, doxycycline untreated

tag: 293-tet-On-NOR1 cells were cultured without doxycycline for 24 hours.


title: TconvLN, rep3

status: Public on Dec 09 2008

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Per Joslin Diabetes Center microarray core facility.

data_processing: RMA

label: Biotin

source_name: Tconv cells isolated from LN

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

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

tag: Genetic background

tag: Number of mice per chip

tag: Tissue

value: LN (cervical, inguinal, mesenteric)

tag: Sort


title: TregLN, rep3

scan_protocol: Per Joslin Diabetes Center microarray core facility.

source_name: Treg cells isolated from LN


title: TconvLN, rep2


title: 3PPS07042003_DU145_cell_monolayer

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: gcRMA, scaled to a median intensity of 100

label_protocol: 50 ng total RNA was used in a standard Affymetrix double amplification protocol.

extract_protocol: Total RNA was isolated from cell pellets using the RNeasy kit (Qiagen, Valencia, CA, USA).

treatment_protocol: For flow cytometry, cell were dissociated with Accutase (Innovative Cell Tech Inc., San Diego, CA, USA) and washed 2 times in the staining solution containing Ca2+ and Mg2+-free PBS with 1mM ethylenediaminetetraacetic acid (EDTA), 25mM Hepes (pH 7.0) (Gibco BRL), 0.5% FBS. Cells were stained live in the staining solution containing conjugated anti-CD44 and anti-CD133 antibody (50 min at 4oC). Samples were analyzed on BD LSR II flow cytometer (Beckton Dickinson Immunocytometry Systems, San Jose, CA).  A minimum of (or At least) 500,000 viable cells were measured per sample. For FACS, 2x107 cells were processed for double CD44 and CD133 staining along with appropriate negative controls and single color positive controls. The CD44+/CD133+ and CD44-/CD133- populations were sorted out on a BD FACS Diva cell sorter (Beckton Dickinson Immunocytometry Systems, San Jose, CA).


title: TregLN, rep2


title: TconvThy, rep3

source_name: Tconv cells isolated from the thymus

value: 4-6 wks

value: Thymus

value: (pre-sort depletion of CD8a by MACS) B220-, CD11b-, CD8a-, CD4+, CD25-


title: TregThy, rep3

source_name: Treg cells isolated from the thymus

value: (pre-sort depletion of CD8a by MACS) B220-, CD11b-, CD8a-, CD4+, CD25+


title: 3PPS07042004_DU145_cell_spheres


title: TconvThy, rep2


title: Larval Feeding Salivary Gland rep2

status: Public on Dec 08 2008

city: Glasgow

first: Jing

last: Wang or Venkat Chintapalli

state: Scotland

address: Dumbarton Road

department: Molecular Genetics

country: United Kingdom

institute: University of Glasgow

description:
The larval salivary glands, dissected from third-instar feeding larvae.
amplification: 1-round

hyb_protocol: Following fragmentation, 10 ug of cRNA (or according to the affy IVT protocol)  were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Drosophila melanogaster

source_name: Larval Feeding Salivary Gland

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

growth_protocol: Wild-type Drosophila melanogaster (Canton S strain) were raised on standard medium on a 12:12 h L:D cycle, at 23C, and at 55% r.h. To facilitate the collection of accurately staged adults, a laying population of around 12 males and 12 females were transferred to fresh vials daily. When adults subsequently emerged, they were transferred to fresh vials on the day of emergence, and used 7 days later. Where larvae were used, these were third instar.

extract_protocol: Total RNA was extracted using RNeasy Micro kit (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Flies were anaesthetised briefly by chilling on ice, then immediately dissected.

tag: tissue

value: Canton-S, 100 feeding third instar larvae


title: Adult Female Spermatheca Mated rep3

description:
The female spermatheca surrounded by fatbody
amplification: 2-round

source_name: Adult Female Spermatheca Mated

value: Canton-S, 60 female spermatheca, 7 days old


title: Adult Female Spermatheca Virgin rep4

source_name: Adult Female Spermatheca Virgin


title: Larval Feeding Mid Gut rep1

description:
The midgut, extending from behind the proventriculus to just in front of the insertion of the Malpighian tubules, dissected from third-instar feeding larvae.
amplification: 1-round

source_name: Larval Feeding Mid Gut

value: Canton-S, 30 feeding third instar larvae


title: Adult Female Spermatheca Mated rep2


title: Larval Feeding Salivary Gland rep1


title: Adult Female Spermatheca Virgin rep2


title: Adult Female Spermatheca Virgin rep1


title: TregThy, rep2


title: Adult Female Spermatheca Mated rep1


title: Larval Feeding Mid Gut rep4


title: Adult Female Spermatheca Mated rep4


title: Adult Female Spermatheca Virgin rep3


title: Larval Feeding Salivary Gland rep4


title: Larval Feeding Hind Gut rep3

description:
The hindgut, from just behind the insertion of the Malpighian tubules, and including the rectum, severing at the anus , dissected from third-instar feeding larvae.
amplification: 1-round

source_name: Larval Feeding Hind Gut


title: Larval Feeding Hind Gut rep2


title: Larval Feeding Salivary Gland rep3


title: Larval Feeding Mid Gut rep2


title: Larval Feeding Hind Gut rep4


title: Larval Feeding Hind Gut rep1


title: Adult Thoracoabdominal ganglion rep2

description:
The ventral nerve cord or thoracoabdominal ganglion
amplification: 1-round

source_name: Adult Thoracoabdominal ganglion

value: Canton-S, 100 female and  100 male flies, 7 days old


title: Adult Carcass biological rep4

description:
The abdominal cuticle
amplification: 1-round

source_name: Adult Carcass

value: Canton-S, 25 female and  25 male flies, 7 days old


title: Larval Feeding Mid Gut rep3


title: Adult Thoracoabdominal ganglion rep1


title: Adult Thoracoabdominal ganglion rep3


title: Adult Carcass biological rep3


title: Adult Thoracoabdominal ganglion rep4


title: Adult Carcass biological rep1


title: Adult Carcass biological rep2


title: 475H_KO

status: Public on Dec 07 2008

first: Jun

last: Lu

address: 10 Amistad St

department: Yale Stem Cell Center and Department of Genetics

description: Lin-Sca+Kit+ hematopoietic stem cells (HSCs) purified from an ADAR1 -/- mouse.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: RMA normalization

source_name: Hematopoieitc stem cells purified from an ADAR1 -/- mouse

label_protocol: Nugen kit

extract_protocol: Qiagen RNA kit

tag: Source

value: fetal liver


title: 476H_KO

tag: Strain


title: 473H_HT

description: Lin-Sca+Kit+ hematopoietic stem cells (HSCs) purified from an ADAR1 +/- mouse.

source_name: Hematopoieitc stem cells purified from an ADAR1 +/- mouse


title: 472H_HT

tag: strain

tag: source


title: 470H_HT


title: 477H_WT

description: Lin-Sca+Kit+ hematopoietic stem cells (HSCs) purified from a WT control mouse.

source_name: Hematopoieitc stem cells purified from a WT control mouse


title: 469H_WT


title: 471H_KO


title: FBB1.11-2

status: Public on Dec 05 2008

first: Vijay

middle: G.

last: Sankaran

address: 300 Longwood Avenue

department: Department of Medicine

institute: Children's Hospital Boston

description: Microarray expression analysis from parental control mouse erythroleukemia (MEL) cells containing the BirA enzyme (MelBirA cells) and cells containing tagged versions (FLAG-Biotag) of BCL11A.

hyb_protocol: The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.  The fragmented cRNA is added to a hybridization solution containing  several biotinylated control oligonucleotides (for quality control), and  hybridized to a microarray chip overnight at 45°C.  The chips are then transferred to a fluidics instrument that performs  washes to remove cRNA that has not hybridized to its complementary  oligonucleotide probe. The bound cRNA is then fluorescently labeled using  phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then  added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using  a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of  subsequent biostatistical analysis.

data_processing: dChip normalization

label: SAPE

source_name: Mel-BirA Cell Line Stably Expressing FLAG-Biotag-BCL11A

extract_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer   in the synthesis of the first cDNA strand; second strand cDNA synthesis is  then carried out.  The double-stranded cDNA is used as the template in an in vitro  transcription (IVT) reaction catalyzed by T7 polymerase and containing  biotinylated CTP and UTP in addition to the four unmodified ribonucleoside  triphosphates.  The biotinylated complementary RNA (cRNA) is purified from the IVT  reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified  spectrophotometrically and purity of the cRNA is also assessed by  spectrophometric measurements. Those cRNA's that fall outside of an  acceptable range will not be carried forward in the analysis. Should this  occur, investigators would be notified and asked to provide a new RNA  sample.

tag: Expressing Clone


title: MelBirA2

source_name: Parental Mel-BirA Cell Line

label_protocol: The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE

tag: Control


title: FBB1.7-2


title: Melanocyte-Control-rep2

city: Las Vegas

first: Byungwoo

last: Ryu

state: NV

address: 1 Breakthrough Way

institute: Nevada Cancer Institute

description: gene expression data from GFP expressing lentivirus

hyb_protocol: Following fragmentation, 15ug cRNA and incubated at 95ºC for 35 minutes to fragment the cRNA.  The samples are ice quenched and combined with hybridization cocktail (prepared as per manufacturer’s protocol, Affymetrix, eukaryotic expression array protocol).  After 10 minutes of pre-hybridizing Human U133 Plus 2.0 Genome array at 45ºC, 60rpm, 200uL of cocktail is loaded onto each array and the arrays are hybridized for 16 hours at 45ºC, 60rpm.  The cocktail is removed and the arrays are stained and washed using the Affymetrix GeneChip Fluidics Station 450 and FS450_004 fluidics script.

scan_protocol: All arrays are scanned in the Affymetrix GeneChip Scanner 3000

data_processing: Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4 and the data was normalized using RMA

source_name: Primary melanocytes transduced with GFP expressing lentivirus

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

growth_protocol: Melanocytes are maintained in melanocyte growth medium (Cell Application Inc. San Diego CA)

extract_protocol: Total RNA was extracted and purified by combination of Trizol extraction followed by RNeasy column purification in order to remove melanin.

treatment_protocol: Melanocytes are treated by polybrane (6.0 ug/ml) and immediately infected by lentivirus with MOI 10. After infection, cell were mainteined 5 days before subjected to RNA extraction.

tag: Short-term cultured human primary melanocytes (passage #

tag: Pooled from five donors

tag: Primary human melanocytes were isolated from neonatal foreskins


title: Melanocyte-BRAF-rep1

description: gene expression data from BRAFV600E expressing lentivirus

source_name: Primary melanocytes transduced with oncogenic BRAF expressing lentivirus


title: Melanocyte-BRAF-rep2


title: B5

description: Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.

source_name: BCL11A siRNA treated erythroid progenitors

growth_protocol: human cell culture

treatment_protocol: siRNA treated

tag: Gene Knockdown


title: FBB1.7-1


title: FBB1.11-1


title: B6


title: B4


title: Melanocyte-Control-rep1


title: MelBirA1


title: FBB1.5-2


title: FBB1.10-2


title: B2


title: B3


title: FBB1.5-1


title: B1


title: FBB1.10-1


title: N5

source_name: non-targeting siRNA treated erythroid progenitors


title: N6


title: N4


title: N1


title: PBMC cells 2

status: Public on Dec 04 2008

city: Taipei

first: Wen-Hung

last: Chung

address: 199, Tung-Hwa North Road

department: Dermatology

country: Taiwan

institute: Chang Gung Memorial Hospital

description: PBMC cells from SJS patient

data_processing: Affymetrix Microarray Suite version 5.0

source_name: PBMC cells

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the PBMC cell lysate using an TRI Reagent (Ambion).

treatment_protocol: direct extract RNA from PBMC cells

tag: PBMC cells from SJS patient


title: PBMC cells 6

description: PBMC cells from SJS patient


title: Breast cancer her2+ 16

status: Public on Dec 03 2008

city: Paris

first: Thierry

last: Dubois

address: 26 rue d'Ulm

department: Département de Transfert

country: France

institute: Institut Curie

description: All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification

hyb_protocol: 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin

scan_protocol: Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)

data_processing:
Background correction method: GC Robust Mult-array Average (GC-RMA).
Normalization: quantile
Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
Signal intensities were log2-transformed

source_name: Breast sample

label_protocol: Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented

extract_protocol: RNA extraction was done using RNAeasy minikit (Qiagen)

tag: Gender

tag: subtype

tag: Grade

value: III


title: PBMC cells 1

description: PBMC cells from SJS patient


title: SJS blister cell 5

description: SJS blister cells in active stage

source_name: SJS blister cells

extract_protocol: Total RNA was extracted from the SJS blister cell lysate using an TRI Reagent (Ambion).

treatment_protocol: direct extract RNA from SJS blister cells

tag: SJS blister cells in active stage


title: Breast cancer her2+ 25


title: Breast cancer her2+ 24


title: N3


title: SJS blister cell 3

description: SJS blister cells in active stage


title: SJS blister cell 2

description: SJS blister cells in active stage


title: Breast cancer her2+ 19


title: N2


title: Breast cancer her2+ 17


title: Breast cancer her2+ 23


title: SJS blister cell 4

description: SJS blister cells in active stage


title: Breast cancer her2+ 6


title: Breast cancer her2+ 13


title: Breast cancer her2+ 15


title: SJS blister cell 1

description: SJS blister cells in active stage

growth_protocol: non


title: Breast cancer her2+ 5


title: Breast cancer her2+ 3


title: PBMC cells 4

description: PBMC cells from SJS patient


title: Breast cancer basal 20

value: basal-like


title: Breast cancer basal 18


title: Breast cancer basal 12


title: Breast cancer basal 11


title: Breast cancer basal 21


title: Breast cancer basal 9


title: Breast cancer basal 8


title: Breast cancer basal 10


title: Breast cancer basal 2


title: Breast cancer basal 7


title: Breast cancer basal 4


title: Breast cancer basal 1


title: PBMC cells 5

description: PBMC cells from SJS patient


title: HCT116_rep2

status: Public on Dec 01 2008

city: Edinburgh

first: Kathryn

middle: Clare

last: Connolly

address: Crewe Road South

department: Cancer Research Centre

institute: University of Edinburgh

description: Clone HCT116C

hyb_protocol: affymetrix hybridization

scan_protocol: affymetrix scan

data_processing: Affymetrix CEL files were processed using RMA

label: affymetrix labelling

source_name: HCT116 cells, parental

label_protocol: affymetrix labelling

extract_protocol: QIagen RNeasy plus

tag: Cells

value: HCT116 colon cancer cell line


title: HLF 3-4 (Cr)

status: Public on Dec 02 2008

city: Washington

first: DONG-SOON

last: BAE

state: DC

address: 2300 I Street, NW

department: Pharmacology & Physiology

institute: George Washinton Uni.

description: no additional information

hyb_protocol: Hybridization, washing and staining were carried out according to the Affymetrix’s instructions.

scan_protocol: GeneChip Human Genome U133 Plus 2.0 Arrays were scanned with an Agilent laser scanner.

data_processing:
Default normalization steps recommended by GeneSpring software were used:
(1) data transformation: set measurements less than 0.01 to 0.01
(2) per chip: normalize to 50th percentile
(3) per gene: normalize to median

source_name: Human lung fibroblasts

label_protocol: Total RNA (10 ug) was labeled by One-Cycle Target Labeling Kit as specified by Affymetrix.

growth_protocol: Cells were seeded at 2 million/150mm dish and incubated with Ham's F-12 nutrient mixture, supplemented with 15% FBS, 50 units/ml penicilin and 50 ug/ml streptomycin for 24h, total RNA was isolated after incubation with 1uM Cr(VI) for 24hr.

extract_protocol: Following 24hr treatment with 1uM Cr(VI), RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9.

treatment_protocol: Sodium chromate [Cr(VI)] for 24hr

tag: Normal diploid human lung fibroblast cell line, LL24, was originally isolated from normal autopsy tissue of an 11-year-old male.


title: L_p8_rep1

description: Clone L8

source_name: HCT116 cells, luciferase shRNA, late passage


title: L_p8_rep4

description: Clone L24


title: X_p8_rep2

description: Clone X10

source_name: HCT116 cells, XIAP shRNA, late passage


title: L_p8_rep2

description: Clone L15


title: HLF 4-3 (SOV+Cr)

description: no additional information

growth_protocol: Cells were seeded at 2 million/150mm dish and incubated with Ham's F-12 nutrient mixture, supplemented with 15% FBS, 50 units/ml penicilin and 50 ug/ml streptomycin for 24h, total RNA was isolated after incubation with 1uM Cr(VI) + 10uM SOV for 24hr. The SOV was added 30 min prior to Cr(VI) addition.

extract_protocol: Following 24hr treatment with 1uM Cr(VI) + 10uM SOV, RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9.

treatment_protocol: Sodium chromate [Cr(VI)] in the presence of SOV for 24hr


title: HCT116_rep1

description: Clone HCT116B


title: HLF 4-2 (SOV+Cr)

description: no additional information


title: X_p8_rep4

description: Clone X23


title: L_p8_rep3

description: Clone L23


title: X_p4_rep4

description: Clone X23

source_name: HCT116 cells, XIAP shRNA, early passage


title: HLF 3-1 (Cr)

description: no additional information


title: HLF 3-3 (Cr)

description: no additional information


title: HLF 1-4 (No)

description: no additional information

growth_protocol: Cells were seeded at 2 million/150mm dish and incubated with Ham's F-12 nutrient mixture, supplemented with 15% FBS, 50 units/ml penicilin and 50 ug/ml streptomycin for 24h, total RNA was isolated after incubation with F12 medium for 24hr.

extract_protocol: Following 24hr treatment with culture medium, RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9.

treatment_protocol: culture medium for 24hr


title: HLF 4-4 (SOV+Cr)

description: no additional information


title: X_p4_rep2

description: Clone X10


title: HLF 4-1 (SOV+Cr)

description: no additional information


title: HLF 1-2 (No)

description: no additional information

source_name: Human lung fibroblats


title: X_p8_rep1

description: Clone X6


title: X_p8_rep3

description: Clone X16


title: HLF 3-2 (Cr)

description: no additional information


title: X_p4_rep1

description: Clone X6


title: X_p4_rep3

description: Clone X16


title: HLF 1-1 (No)

description: no additional information


title: L_p4_rep4

description: Clone L24

source_name: HCT116 cells, luciferase shRNA, early passage


title: L_p4_rep3

description: Clone L23


title: HLF 1-3 (No)

description: no additional information


title: L_p4_rep2

description: Clone L15


title: L_p4_rep1

description: Clone L8


title: Replicate 1 for MB231control72h breast cell line

city: X

first: Alex

middle: T.

last: Adai

state: X

address: X

department: Oncology Diagnostics

institute: Genentech

description: Cell line, RPMI1640, 10 %FBS, 2mM L-glutamine, 10mM HEPES

hyb_protocol: Affymetrix standard protocols.  See Clin Cancer Res 2005;11(24) December 15, 2005

data_processing: gcRMA (justGCRMA in R/Bioconductor)

source_name: Human cell line


title: Replicate 3 for MB231untreated72h breast cell line

scan_protocol: Affymetrix standard protocols.  See Clin Cancer Res 2005;11(24) December 15, 2005


title: Replicate 3 for MCF7siRNAESR1_72h breast cell line

label_protocol: Affymetrix standard protocols.  See Clin Cancer Res 2005;11(24) December 15, 2005


title: Replicate 3 for MB231inhibitor72h breast cell line

extract_protocol: Affymetrix standard protocols.  See Clin Cancer Res 2005;11(24) December 15, 2005


title: Replicate 3 for MCF7untreated72h breast cell line


title: Replicate 2 for MCF7siRNActr72h breast cell line


title: Replicate 1 for MCF7mimic72h breast cell line


title: Replicate 1 for MCF7siRNActr72h breast cell line


title: Replicate 2 for MCF7mimic72h breast cell line


title: Replicate 3 for MCF7siRNActr72h breast cell line


title: Replicate 2 for MB231untreated72h breast cell line


title: Replicate 3 for MCF7siRNActr breast cell line

tag: MCF7 siRNA against ESR1 control at 18h


title: Replicate 3 for MCF7mimic72h breast cell line


title: Replicate 1 for MCF7siRNAESR1 breast cell line

tag: MCF7 siRNA against ESR1 at 18h


title: Replicate 1 for MB231untreated72h breast cell line


title: Replicate 2 for MB231inhibitor72h breast cell line


title: Replicate 2 for MCF7siRNAESR1_72h breast cell line


title: Replicate 2 for BT474 breast cell line

tag: No treatment. See ATCC/DSMZ for cell line details.


title: Replicate 2 for MB231control72h breast cell line


title: Replicate 3 for BT474 breast cell line


title: Replicate 1 for MB231inhibitor72h breast cell line


title: Replicate 2 for MCF7untreated72h breast cell line


title: Replicate 3 for MCF7control72h breast cell line


title: Replicate 2 for MCF7siRNAESR1 breast cell line


title: Replicate 1 for MCF7control72h breast cell line


title: Replicate 1 for MCF7untreated72h breast cell line


title: Replicate 2 for MCF7siRNActr breast cell line


title: Replicate 2 for MCF7control72h breast cell line


title: Replicate 3 for MB231control72h breast cell line


title: Replicate 3 for MCF7untreated breast cell line

tag: MCF7 untreated cell line to compare to older profiled MCF7 sample. See ATCC/DSMZ for cell line details.


title: Replicate 2 for MCF7mimic breast cell line

tag: MCF7 mir-221/222 mimic at 18h


title: Replicate 1 for MCF7mimic breast cell line


title: Replicate 3 for MCF7mimic breast cell line


title: Replicate 1 for MCF7siRNActr breast cell line


title: Replicate 3 for MCF7control breast cell line

tag: MCF7 mir-221/222 mimic control at 18h


title: Replicate 2 for MCF7untreated breast cell line


title: Replicate 1 for JIMT1 breast cell line


title: Replicate 1 for MCF7control breast cell line


title: Replicate 1 for HCC1569 breast cell line


title: Replicate 2 for MCF7control breast cell line


title: Replicate 1 for UACC893 breast cell line


title: Replicate 1 for MCF7untreated breast cell line


title: Replicate 1 for UACC812 breast cell line


title: Replicate 1 for MDAMB361.1 breast cell line


title: Replicate 1 for HCC38 breast cell line


title: Replicate 1 for BT474.tb breast cell line


title: Replicate 3 for MB231inhibitor breast cell line

tag: MB231 mir-221/222 inhibitor at 18h


title: Replicate 3 for MB231control breast cell line

tag: MB231 mir-221/222 inhibitor control at 18h


title: Replicate 2 for MB231inhibitor breast cell line


title: Replicate 1 for MB231control breast cell line


title: Replicate 3 for MB231untreated breast cell line

tag: MB231 untreated cell line to compare to older profiled MB231 sample. See ATCC/DSMZ for cell line details.


title: Replicate 1 for SW527 breast cell line


title: Replicate 1 for MB231inhibitor breast cell line


title: Replicate 1 for CAL148 breast cell line


title: Replicate 1 for MB231untreated breast cell line


title: Replicate 1 for MCF7siRNAESR1_72h breast cell line


title: Replicate 2 for MB231untreated breast cell line


title: Replicate 2 for MB231control breast cell line


title: Replicate 1 for HCC1806 breast cell line


title: Replicate 1 for ZR75 breast cell line


title: Replicate 1 for HDQP1 breast cell line


title: Replicate 1 for T47D1 breast cell line


title: Replicate 1 for ZR751 breast cell line


title: Replicate 1 for HCC2218 breast cell line


title: Replicate 1 for HCC1395 breast cell line


title: Replicate 1 for MFM223 breast cell line


title: Replicate 1 for HCC1500 breast cell line


title: Replicate 1 for HCC1428 breast cell line


title: Replicate 1 for HCC1954 breast cell line


title: Replicate 1 for HCC1143 breast cell line


title: Replicate 1 for CAL1201 breast cell line


title: Replicate 1 for SKBR31 breast cell line


title: Replicate 1 for EFM19 breast cell line


title: Replicate 1 for HCC1419 breast cell line


title: Replicate 1 for BT5491 breast cell line


title: Replicate 1 for HCC70 breast cell line


title: Replicate 1 for MDAMB468 breast cell line


title: Replicate 1 for CAMA1 breast cell line


title: Replicate 3 for BT474EI breast cell line


title: Replicate 1 for BT474EI breast cell line


title: Replicate 1 for DU4475 breast cell line


title: Replicate 1 for BT474 breast cell line


title: Replicate 1 for MDA361 breast cell line


title: Replicate 2 for MCF10A breast cell line


title: Replicate 1 for MDAMB415 breast cell line


title: Replicate 2 for BT474EI breast cell line


title: Replicate 1 for MT3 breast cell line


title: Replicate 1 for MDAMB453 breast cell line


title: Replicate 1 for AU565 breast cell line


title: Replicate 1 for HCC1937 breast cell line


title: Replicate 1 for MDA468 breast cell line


title: Replicate 1 for EVSA1 breast cell line


title: Replicate 2 for T47D breast cell line


title: Replicate 1 for MDA231 breast cell line


title: Replicate 1 for MCF10A breast cell line


title: Replicate 1 for T47D breast cell line


title: Replicate 1 for MDA435 breast cell line


title: Replicate 1 for MDA436 breast cell line


title: Replicate 2 for KPL1 breast cell line


title: Replicate 1 for CAL120 breast cell line


title: Replicate 1 for SKBR3 breast cell line


title: Replicate 1 for KPL1 breast cell line


title: Replicate 1 for CAL51 breast cell line


title: Replicate 1 for BT483 breast cell line


title: Replicate 1 for MCF7 breast cell line


title: Replicate 2 for CAL51 breast cell line


title: Replicate 1 for HS578T breast cell line


title: Replicate 1 for CAL851 breast cell line


title: Replicate 1 for MDA175 breast cell line


title: Replicate 1 for SUDHL4 cell line


title: Replicate 1 for EFM192A breast cell line


title: Replicate 2 for H596 cell line


title: Replicate 2 for H1650 cell line


title: Replicate 1 for BT549 breast cell line


title: Replicate 1 for SC1 cell line


title: Replicate 2 for H1781 cell line


title: Replicate 1 for HT cell line


title: Replicate 1 for DB cell line


title: Replicate 2 for H650 cell line


title: Replicate 2 for H838 cell line


title: Replicate 2 for LXFL529 cell line


title: Replicate 2 for H226 cell line


title: Replicate 2 for SKMES1 cell line


title: Replicate 2 for H1435 cell line


title: Replicate 1 for HOP62 cell line


title: Replicate 2 for HLFA cell line


title: Replicate 1 for H2009 cell line


title: Replicate 2 for H1793 cell line


title: Replicate 1 for H2405 cell line


title: Replicate 1 for HOP18 cell line


title: Replicate 1 for SW1573 cell line


title: Replicate 1 for H23 cell line


title: Replicate 1 for H1666 cell line


title: Replicate 1 for H1568 cell line


title: Replicate 1 for H647 cell line


title: Replicate 1 for HOP92 cell line


title: Replicate 2 for EKVX cell line


title: Replicate 1 for H520 cell line


title: Replicate 2 for SKCO1 cell line


title: Replicate 1 for CL40 cell line


title: Replicate 1 for H2126 cell line


title: Replicate 1 for H1155 cell line


title: Replicate 2 for SW620 cell line


title: Replicate 1 for H1651 cell line


title: Replicate 2 for RKO cell line


title: Replicate 2 for HCT15 cell line


title: Replicate 2 for CX1 cell line


title: Replicate 2 for RKOAS451 cell line


title: Replicate 1 for SW480 cell line


title: Replicate 2 for H322T cell line


title: Replicate 1 for H661 cell line


title: Replicate 1 for A427 cell line


title: Replicate 2 for H522 cell line


title: Replicate 1 for H2122 cell line


title: Replicate 2 for H1299 cell line


title: Replicate 2 for H292 cell line


title: Replicate 2 for H1838 cell line


title: Replicate 2 for H2030 cell line


title: Replicate 1 for A549 cell line


title: Replicate 1 for H460 cell line


title: Replicate 1 for H1703 cell line


title: Replicate 1 for GRANTA519 cell line


title: Replicate 3 for HCT116 cell line


title: Replicate 2 for HCT116 cell line


title: Replicate 3 for COLO205 cell line


title: Replicate 1 for HCT8 cell line


title: Replicate 2 for H441 cell line


title: Replicate 1 for CALU1 cell line


title: Replicate 3 for COLO201 cell line


title: Replicate 1 for H358 cell line


title: Replicate 1 for SW403 cell line


title: Replicate 2 for CACO2 cell line


title: Replicate 2 for COLO205 cell line


title: Replicate 1 for OV90 cell line


title: Replicate 1 for WSUDLCL2 cell line


title: Replicate 3 for LOVO cell line


title: Replicate 3 for CACO2 cell line


title: Replicate 1 for H1993 cell line


title: Replicate 1 for OVCAR3 cell line


title: Replicate 1 for FUOV1 cell line


title: Replicate 3 for DLD1 cell line


title: Replicate 1 for LOVO cell line


title: Replicate 1 for COLO201 cell line


title: Replicate 1 for CAOV3 cell line


title: Replicate 1 for DLD1 cell line


title: Replicate 3 for HCT8 cell line


title: Replicate 1 for SKOV3 cell line


title: Replicate 1 for COLO704 cell line


title: Replicate 1 for ES2 cell line


title: Replicate 1 for EFO21 cell line


title: Replicate 1 for TOV112D cell line


title: Replicate 1 for RERFLCKJ cell line


title: Replicate 1 for RERFLCAD1 cell line


title: Replicate 1 for KNS62 cell line


title: Replicate 1 for EBC1 cell line


title: Replicate 1 for ABC1 cell line


title: Replicate 1 for RERFLCOK cell line


title: Replicate 1 for VMRCLCD cell line


title: Replicate 1 for RERFLCMS cell line


title: cortex_HtrA2_KO_rep2

city: London

first: Kristina

last: Klupsch

address: 44 Lincoln's Inn Fields

department: London Research Institute

institute: Cancer Research UK

description: Gene expression data from HtrA2 KO mouse cortex tissue at post-natal day 29

hyb_protocol: The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.

data_processing: Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.

source_name: HtrA2 KO mouse cortex, P29

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf

growth_protocol: Wild type and HtrA2 knockout littermate mice.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).

treatment_protocol: Mice at post-natal day 29 (P29).

tag: Genotype

value: HtrA2 knockout


title: cortex_WT_rep2

description: Gene expression data from WT mouse cortex tissue at post-natal day 29

source_name: WT mouse cortex, P29

value: HtrA2 wild type


title: MCF10A cells cocultured with breast cancer associated fibroblasts that extracted from breast cancer sample No 4

city: Columbus

first: Sandya

last: Liyanarachchi

state: OH

address: Rm 830, 460, W 12th Avenue

department: Human Genetics

institute: OSU

description: gene expression data from MCF10A cells cocultured with breast fibroblasts

data_processing: Robust Multichip Averages

source_name: MCF10A cells

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

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

tag: cell line, normal mammary epithelium, immortalized


title: MCF10A cells cocultured with breast cancer associated fibroblasts that extracted from breast cancer sample No 15


title: Megakaryoblastic sample 2

city: Montreal

first: Eric

last: Rassart

state: Quebec

address: C.P. 8888 Succursale Centre-Ville

department: Biology

institute: UQAM

description: inoculation of Graffi GV-1.4 virus in NFS mice

hyb_protocol: Affymetrix S.O.P (one cycle)

scan_protocol: Affymetrix GeneChip® Scanner 3000

data_processing: The data were  normalized using RMA and Flexarray software

source_name: megakaryoblastic leukemia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The quality was assessed using the Agilent Bioanalyzer.

treatment_protocol: Inoculation of the Graffi GV-1.4 retrovirus in NFS mice


title: (Tam+G) treated MCF-7 wt xenograft, biological rep2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: Gene expression data from MCF-7 xenograft tumors that acquired resistance to E2 withdrawal plus tamoxifen.

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized on Human Genome U133 Plus 2.0 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-ws2v5 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Affymetrix).

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10%. of intensity values

source_name: MCF7 xenografts

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 carried out using EZ1 RNA universal tissue kit with BioRobot EZ1 workstation according to the manufacturer's instructions.

tag: (Tam+G) treatment


title: MCF10A cells cocultured with breast cancer associated fibroblasts that extracted from breast cancer sample No 12


title: cortex_WT_rep3


title: (Tam+G) treated MCF-7 wt xenograft, biological rep3


title: cortex_HtrA2_KO_rep1


title: Megakaryoblastic sample 3


title: T-cell control sample

description: non-infected NFS mice (n=12)

source_name: thymus


title: ED treated MCF7 wt xenograft, biological rep3

tag: E2 deprivation (ED) treatment


title: (Tam+G) treated MCF-7 wt xenograft, biological rep1


title: cortex_WT_rep1


title: B-cell control sample

description: non-infected NFS mice (n=12)

source_name: spleen


title: Myeloid sample 1

source_name: myeloid leukemia


title: Megakaryoblastic sample 1


title: (Tam+G) treated MCF-7 wt xenograft, biological rep4


title: Erythroid sample 3

source_name: erythroid leukemia


title: ED treated MCF7 wt xenograft, biological rep1


title: (E2+G) treated MCF7 wt xenograft, biological rep2

tag: (E2+G) treatment


title: ED treated MCF7 wt xenograft, biological rep2


title: Eythroblasts control sample

description: non-infected NFS mice (n=12)

source_name: bone marrow


title: MCF10A cells cocultured with normal breast fibroblasts that extracted from normal breast tissue sample No 16


title: MCF10A cells cocultured with normal breast fibroblasts that extracted from normal breast tissue sample No 23


title: MCF10A cells cocultured without any breast fibroblasts and this sample is served as experimental control


title: Erythroid sample 2


title: cortex_HtrA2_KO_rep3


title: ED treated MCF7 wt xenograft, biological rep4


title: Erythroid sample 1


title: (E2+G) treated MCF7 wt xenograft, biological rep1


title: B-cell sample 3

source_name: B-cell leukemia


title: B-cell sample 1


title: T-cell sample 1

source_name: T-cell leukemia


title: T-cell sample 2


title: Fulv treated MCF7 wt xenograft, biological rep4

tag: Fulv treatment


title: E2 + Tam MCF7/HER2-18 xenograft, biological rep3

source_name: MCF7/HER2-18 xenografts

tag: E2+Tam treatment


title: TAM R (Big) MCF7/HER2-18 xenograft, biological rep4

tag: Tam treatment, late tumor


title: Fulv treated MCF7 wt xenograft, biological rep2

description: Gene expression data from MCF-7 xenograft tumors supplemented with estrogen (E2).


title: Fulv treated MCF7 wt xenograft, biological rep1


title: Fulv treated MCF7 wt xenograft, biological rep3


title: T-cell sample 3


title: E2 + Tam MCF7/HER2-18 xenograft, biological rep2


title: E2 + Tam MCF7/HER2-18 xenograft, biological rep4


title: E2 + Tam MCF7/HER2-18 xenograft, biological rep1


title: TAM R (Big) MCF7/HER2-18 xenograft, biological rep2


title: mouse colon_hnf4mutant_rep2

city: Sherbrooke

first: Francois

last: Boudreau

address: 3001 12e ave Nord

department: Anatomy and Cell Biology

institute: University of Sherbrooke

description: Monitor the effect of HNF4alpha lost in mouse colonic epithelium

hyb_protocol: The hybridization mixture was prepared by mixing 15 mg biotinylated probe with control oligonucleotide B2 (final concentration 50 pM; Affymetrix), herring sperm DNA (final concentration 0.1 mg/ml; Research Genetics), acetylated bovine serum albumin (final concentration 0.5 mg/ml; Gibco BRL Life Technologies) in a final volume of 300 ml of 13 MES hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20; all reagents from Sigma). The hybridization mixture was denatured for 10 minutes at 99 C, incubated for 5 minutes at 45 C, and spun for 5 minutes in a benchtop microcentrifuge. The microarray was warmed to room temperature and prehybridized in hybridization buffer for 10–20 minutes at 45 C. The prehybridization solution was removed and 150 ml of the hybridization mix was added to the array. The array and probe fragments were incubated at 45 C overnight (16–20 hours).  After hybridization, nonspecifically bound probe was removed by washing with the GeneChip Fluidics station 400 (Affymetrix). In total, 10 low-stringency washes (63 SSPE, 0.01% Tween-20, 0.005% Antifoam) and 4 high-stringency washes (100 mM MES, 0.1 M NaCl, 0.01% Tween-20, 50 C) were performed (all reagents from Sigma).

scan_protocol: Specifically bound probe was detected by incubating the arrays with SAPE (Molecular Probes) and scanning the chips with a Hewlett-Packard GeneArray scanner (Affymetrix). A second scan was performed after signal enhancement with biotinylated anti-streptavidin antibody Vector Laboratories). The scanned images were analyzed using the GeneChip Analysis Suite 3.3 (Affymetrix) to identify genes differentially expressed among the RNA samples.

data_processing: RMA algorithm

source_name: adult male mouse colon, Hnf4a mutant

label_protocol: Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.

growth_protocol: Mice were maintained in pathogen free environnement.

extract_protocol: Extraction with the ambion Totally RNA kit

treatment_protocol: Injection of Ketamine/xylazine (300mg/kg; 40mg/kg) before sacrifice

tag: strain:C57BL/6; VillinCRE-HNF4loxp; male; tissue colon; mutant


title: (Tam+G) Sen  MCF7/HER2-18 xenograft, biological rep3

tag: Tam+G treatment, sensitive tumor


title: TAM R (Big) MCF7/HER2-18 xenograft, biological rep1


title: (Tam+G) Sen  MCF7/HER2-18 xenograft, biological rep4


title: 438BP-24-CpGA 12 hr

city: Atlanta

first: Weiping

last: Cao

state: GA

address: 954 Gatewood Road

department: Emory Vaccine Center

institute: Emory University

description: No

hyb_protocol: Affymetrix Murine Genome 430 2.0 microarray chips (Affymetrix)

scan_protocol: GeneArray scanner (Affymetrix)

data_processing: GeneSpring software (Silicon Genetics)

label_protocol: Ovation Biotin System (Nugen)

extract_protocol: sorted plasmacytoid dendritic cell

treatment_protocol: CpGA stimulation for 4 hr

tag: Strain

tag: Gender

value: Female

tag: Tissue

value: Spleen


title: (Tam+G) Sen  MCF7/HER2-18 xenograft, biological rep2


title: 438BP-22-Medium

description: No

source_name: spleen plasmacytoid dendritic cell

treatment_protocol: Medium


title: 438BP-25-CpGA-Rapamycin 4 hr

description: No

treatment_protocol: CpGA stimulation for 4 hr after rapamycin pretreatment for 3 hr


title: mouse colon_hnf4mutant_rep3


title: 438BP-23-CpGA 4hr

description: No

value: spleen


title: mouse colon_hnf4control_rep1

source_name: adult female mouse colon, wildtype

tag: strain:C57BL/6; VillinCRE-HNF4loxp; female; tissue colon; control


title: mouse colon_hnf4control_rep3


title: (Tam+G) Sen  MCF7/HER2-18 xenograft, biological rep1


title: mouse colon_hnf4control_rep2


title: mouse colon_hnf4mutant_rep1

source_name: adult female mouse colon, Hnf4a mutant

tag: strain:C57BL/6; VillinCRE-HNF4loxp; female; tissue colon; mutant


title: (Tam+G) Res  MCF7/HER2-18 xenograft, biological rep4

tag: Tam+G treatment, resistant tumor


title: 438BP-26-CpGA-Rapamycin 12 hr

description: No

treatment_protocol: CpGA stimulation for 12 hr after rapamycin pretreatment for 3 hr

tag: strain


title: (Tam+G) Res  MCF7/HER2-18 xenograft, biological rep3


title: (Tam+G) Res  MCF7/HER2-18 xenograft, biological rep2


title: (Tam) Small  MCF7/HER2-18 xenograft, biological rep3

tag: Tam treatment, early tumor


title: (Tam) Small  MCF7/HER2-18 xenograft, biological rep2


title: (Tam+G) Res  MCF7/HER2-18 xenograft, biological rep1


title: (Tam) Small  MCF7/HER2-18 xenograft, biological rep4


title: (Tam) Small  MCF7/HER2-18 xenograft, biological rep5


title: (Tam) Small  MCF7/HER2-18 xenograft, biological rep1


title: liver_Gnmt k-o male_tumor adj.

first: Yi-Ming

middle: Arthur

last: Chen

state: Taiwan

address: 155, Li-Noun St., Sec. 2

department: AIDS Prevention and Research Center

institute: National Yang-Ming University

description: Gene expression data from HCC adjacent tissues of a male Gnmt -/- mouse

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

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

source_name: Liver tumor adjacent tissues

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).

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

value: male

tag: Genotype

value: Gnmt knockout

tag: Age

value: 18 months

value: liver tumor adjacent


title: liver_Gnmt k-o female_tumor

description: Gene expression data from HCC tissues of a female Gnmt -/- mouse

source_name: Liver tumor tissues

value: female

value: 14 months

value: liver tumor


title: (ED+G) Sens MCF7/HER2-18 xenograft

tag: ED+G treatment, sensitive tumor


title: (ED+G) Res  MCF7/HER2-18 xenograft, biological rep4

tag: ED+G treatment, resistant tumor


title: (ED+G) Res  MCF7/HER2-18 xenograft, biological rep3


title: liver_Gnmt k-o female_tumor adj.

description: Gene expression data from HCC adjacent tissues of a female Gnmt -/- mouse


title: (E2+G) Res  MCF7/HER2-18 xenograft, biological rep5

tag: E2+G treatment, late tumor


title: (ED+G) Res  MCF7/HER2-18 xenograft, biological rep5


title: liver_Gnmt k-o male_tumor

description: Gene expression data from HCC tissues of a male Gnmt -/- mouse


title: (ED+G) Res  MCF7/HER2-18 xenograft, biological rep1


title: liver_Gnmt k-o female_dysplasia nodules

description: Gene expression data from liver dysplasia nodules tissues of a female Gnmt -/- mouse

source_name: Liver dysplasia nodules tissues

value: 21 months

value: liver dysplasia nodules


title: liver_wt female_11 wk

description: Gene expression data from 3 wild-type female mice liver tissues at 11 weeks old

source_name: Liver tissue from 3 mice at 11 weeks old

value: wild-type

value: 11 weeks

value: liver


title: (E2+G) Res  MCF7/HER2-18 xenograft, biological rep3


title: liver_Gnmt k-o female_11 wk

description: Gene expression data from 3 Gnmt -/- female mice liver tissues at 11 weeks old


title: liver_wt male_11 wk

description: Gene expression data from 3 wild-type male mice liver tissues at 11 weeks old


title: liver_Gnmt k-o male_11 wk

description: Gene expression data from 3 Gnmt -/- male mice liver tissues at 11 weeks old


title: liver_Gnmt k-o female_dysplasia nodules adj.

description: Gene expression data from liver dysplasia nodules adjacent tissues of a female Gnmt -/- mouse

source_name: Liver dysplasia nodules adjacent tissues

value: liver dysplasia nodules adjacent


title: (E2+G) Res  MCF7/HER2-18 xenograft, biological rep4


title: (E2+G) Res  MCF7/HER2-18 xenograft, biological rep2


title: (E2+G) Res  MCF7/HER2-18 xenograft, biological rep1


title: (ED+G) Res  MCF7/HER2-18 xenograft, biological rep2


title: (E2+G) Small MCF7/HER2-18 xenograft, biological rep4

tag: E2+G treatment, early tumor


title: (E2+G) Small MCF7/HER2-18 xenograft, biological rep1


title: (E2+G) Small MCF7/HER2-18 xenograft, biological rep3


title: ED Sens  MCF7/HER2-18 xenograft, biological rep4

tag: E2 deprivation (ED) treatment, sensitive tumor


title: TAM R (Big) MCF7/HER2-18 xenograft, biological rep3

tag: Tam treatment, late tumor


title: ED R  MCF7/HER2-18 xenograft, biological rep4

tag: E2 deprivation (ED) treatment, resistant tumor


title: (E2+G) Small MCF7/HER2-18 xenograft, biological rep2


title: ED Sens  MCF7/HER2-18 xenograft, biological rep1


title: B-cell sample 2


title: ED R  MCF7/HER2-18 xenograft, biological rep3


title: ED R  MCF7/HER2-18 xenograft, biological rep2


title: (+) E2 Small Group MCF7/HER2-18 xenograft, biological rep2

tag: E2 treatment, early tumor


title: (+) E2 Small Group MCF7/HER2-18 xenograft, biological rep3


title: ED Sens  MCF7/HER2-18 xenograft, biological rep2


title: (+) E2 Small Group MCF7/HER2-18 xenograft, biological rep4


title: (+) E2 Small Group MCF7/HER2-18 xenograft, biological rep1


title: ED R  MCF7/HER2-18 xenograft, biological rep1


title: (+) E2 Big Group MCF7/HER2-18 xenograft, biological rep3

tag: E2 treatment, late tumor


title: ED Sens  MCF7/HER2-18 xenograft, biological rep3


title: (+) E2 Big Group MCF7/HER2-18 xenograft, biological rep2


title: (+) E2 Big Group MCF7/HER2-18 xenograft, biological rep1


title: spleen akr2

status: Public on Nov 30 2008

city: Bethesda

first: Kent

last: Hunter

state: MD

address: 37/4048 37 Convent Drive

department: Center for Cancer Research

institute: National Cancer Institute

description: gene expression from tissue

hyb_protocol: Hybridization was performed following Affymetrix standard protocols .GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Microarrays were scanned using an Agilent GeneArray Scanner

data_processing: The data was processed using Affymetrix Microarray Suite version 5.0.0.032.  RMA normalization was performed using BRB Array Tools version 3.7.0

source_name: (AKR/J x FVB/NJ)F1 female

label_protocol: Labeling was performed following the standard Affymetrix protocol

extract_protocol: RNA was extracted by Trizol following the manufacturers suggested protocol.

treatment_protocol: animals were euthanized by cervical dislocation under Avertin anesthesia.  Tissue was snap frozen in LN2 prior to RNA extraction

tag: highly metastatic


title: lung akr2

description: gene expression from tissue


title: spleen dba2

description: gene expression from tissue

source_name: (DBA/2J x FVB/NJ)F1 female

tag: low metastatic


title: lung dba2

description: gene expression from tissue


title: lung akr3

description: gene expression from tissue


title: spleen dba1

description: gene expression from tissue


title: spleen dba3

description: gene expression from tissue


title: thymus akr2

description: gene expression from tissue


title: spleen akr3

description: gene expression from tissue


title: thymus dba2

description: gene expression from tissue


title: spleen akr1

description: gene expression from tissue


title: thymus akr1

description: gene expression from tissue


title: thymus dba3

description: gene expression from tissue


title: lung akr1

description: gene expression from tissue


title: lung dba3

description: gene expression from tissue


title: bone_marrow_dba2

description: gene expression from tissue


title: lung dba1

description: gene expression from tissue


title: thymus dba1

description: gene expression from tissue


title: bone_marrow_akr3

description: gene expression from tissue


title: bone_marrow_dba1

description: gene expression from tissue


title: thymus akr3

description: gene expression from tissue


title: blood_dba3

description: gene expression from whole blood

label_protocol: RNA was amplified using the Affymetrix 2-cycle kit.  Labeling was performed following the standard Affymetrix protocol

treatment_protocol: animals were euthanized by cervical dislocation under Avertin anesthesia.  Blood was collected by cardiac puncture


title: bone_marrow_dba3

description: gene expression from tissue


title: bone_marrow_akr2

description: gene expression from tissue


title: bone_marrow_akr1

description: gene expression from tissue


title: OPM1 control 2

city: Salamanca

first: Enrique

middle: M

last: Ocio

address: Pº San Vicente, 58-182

country: Spain

institute: Hospital Universitario de Salamanca

hyb_protocol: Hybridizations were performed according to protocols from Affymetrix. Labeled RNA was hybridized to Human Genome U133A microarray Affymetrix), after quality checking on GeneChips Test 3 Arrays.

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix Inc.).

data_processing: Expression value for each probe set was calculated using D-Chip program that uses Li and Wong algorithm.

source_name: OPM1 cell line

label_protocol: Labeling were performed according to protocols from Affymetrix. Briefly,100 ng of total RNA was amplified and labeled using the GeneChip two-cycle cDNA synthesis kit and GeneChip IVT labeling kit (Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: Total RNA was extracted from purified cell populations using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. The RNA integrity was assessed using Agilent 2100 bioanalyzer (Agilent,Palo Alto, CA, USA).

tag: Untreated OPM1 cells


title: OPM1 Zalypsis 1

tag: OPM1 cells treated with Zalypsis 5 nM for 19h


title: OPM1 Control 1


title: MM1S Zalypsis 1

source_name: MM1S cell line

tag: MM1S treated with Zalypsis 5 nM for 9 hours


title: blood_dba2

description: gene expression from whole blood


title: MM1S Zalypsis 2


title: MM1S Control 2

tag: Untreated MM1S


title: OPM1 Zalypsis 2


title: blood_dba1

description: gene expression from whole blood


title: blood_akr1

description: gene expression from whole blood


title: blood_akr2

description: gene expression from whole blood


title: B6_Mock_3

status: Public on Nov 29 2008

city: Munich

first: Reinhard

last: Hoffmann

address: Trogerstr. 30

country: Germany

institute: Institute for medical microbiology

description: IL-2 differentiated NK cells from C57BL/6 mice

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard on 7G scanner

data_processing: GC-RMA

source_name: Mouse NK cells

label_protocol: Ambion MessageAmp kit acording to manufacturers recommendations

extract_protocol: Qiagen Rneasy Micro kit according to manufacturer's recommendations

tag: IL-2 grown NK cells


title: B6_IL1218_3

description: IL-2 differentiated NK cells from C57BL/6 mice were treated with IL-12+IL-18

tag: IL-2 grown NK cells were treated will IL-12 + IL-18


title: IGROV - Mock -1

first: Hagen

last: Kulbe

address: Charterhouse Square

department: Centre for Cancer and Inflammation

institute: Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry

description: IGROV transfected with scrambled RNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human U133plus2.0 expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Three Affymetrix data sets were obtained from triplicate samples of IGROV-1, IGROV-Mock and shCXCR4 I and II cells. Data were analysed using Bioconductor 1.9 (http://bioconductor.org) running on R 2.6.0. Probeset expression measures were calculated using the Affymetrix package's Robust Multichip Average (RMA) default method.

source_name: human ovarian cancer cell line IGROV-1

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

growth_protocol: The human ovarian cancer cell line IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g/l NaHCO3 and 10 % FCS.

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

treatment_protocol: IGROV-1 cells were transfected with SUPER RNAi™ plasmids containing two different shRNA sequences targeting CXCR4, or a control plasmid containg scrambled RNA (IGROV-Mock). Cells were transfected using Lipofectamin 2000 (Invitrogen, UK) following the manufauctures's instruction. Antibiotic selection for stable cell lines started 48 hours in 4 µg/ml puromycin (Sigma, UK) for 30 days. IGROV-Mock were a pool of clones whereas individual clones of shCXCR4 cells were selected.

tag: IGROV transfected with scrambled RNA


title: shCXCR4 (II) -1

description: IGROV transfected with shCXCR4 II

tag: IGROV transfected with shCXCR4 II


title: B6_IL1218_4


title: B6_Mock_4


title: IGROV- 1

description: Parental IGROV

tag: Parental IGROV


title: shCXCR4 (II) -2

description: IGROV transfected with shCXCR4 II


title: B6_IL1218_WAP_3

description: IL-2 differentiated NK cells from C57BL/6 mice were treated with IL-12+IL-18 and infected with Y. enterocolitica strain WA(pYV)

tag: IL-2 grown NK cells were treated will IL-12 + IL-18 and infected with Y. enterocolitica WA(pYV)


title: IGROV - Mock -3

description: IGROV transfected with scrambled RNA


title: IGROV - Mock -2

description: IGROV transfected with scrambled RNA


title: B6_IL1218_WAP_4


title: B6_Mock_5


title: IGROV- 3

description: Parental IGROV


title: shCXCR4 (I) -2

description: IGROV transfected with shCXCR4 I

tag: IGROV transfected with shCXCR4 I


title: IGROV- 2

description: Parental IGROV


title: shCXCR4 (II) -3

description: IGROV transfected with shCXCR4 II


title: shCXCR4 (I) -1

description: IGROV transfected with shCXCR4 I


title: B6_IL1218_5


title: B6_IL1218_WAP_5


title: shCXCR4 (I) -3

description: IGROV transfected with shCXCR4 I


title: 2270 - mAdbID:93188

status: Public on Nov 28 2008

first: Louis

middle: M.

last: Staudt

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

department: Lymphoid Malignancies Branch

description: mAdb experiment ID: 93188

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

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

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

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

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

tag: Gender

tag: Age

tag: Tissue

value: lymph node

tag: Disease state

value: Lymphoma

tag: Individual

tag: Clinical info

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:1.59

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:2

value: LDH ratio:1.09

value: Number of extranodal sites:1


title: 2601 - mAdbID:93668

description: mAdb experiment ID: 93668

value: female

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:DEAD

value: Follow up years:1.21

value: ECOG performance status:1

value: LDH ratio:2.85


title: 2611 - mAdbID:93649

description: mAdb experiment ID: 93649

value: male

value: Follow up years:0.65

value: LDH ratio:NA

value: Number of extranodal sites:NA


title: 2274 - mAdbID:93186

description: mAdb experiment ID: 93186

value: lymph node

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:0.40

value: LDH ratio:0


title: MM1S Control 1

tag: Untreated MM1S cells


title: 2283 - mAdbID:93185

description: mAdb experiment ID: 93185

value: Follow up status:ALIVE

value: Follow up years:1.18

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:0


title: 2610 - mAdbID:93173

description: mAdb experiment ID: 93173

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:0.74

value: LDH ratio:2.44

value: Number of extranodal sites:1


title: 2291 - mAdbID:93696

description: mAdb experiment ID: 93696

value: male

value: Follow up status:DEAD

value: Follow up years:0.87

value: ECOG performance status:2

value: LDH ratio:1.05


title: 2614 - mAdbID:93172

description: mAdb experiment ID: 93172

value: lymph node

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.21

value: ECOG performance status:1

value: LDH ratio:1.32

value: Number of extranodal sites:0


title: 2612 - mAdbID:93674

description: mAdb experiment ID: 93674

value: female

value: Submitting diagnosis:DLBCL

value: Follow up years:1.16

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:2.51


title: 2311 - mAdbID:93177

description: mAdb experiment ID: 93177

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:0.80

value: LDH ratio:14.84

value: Number of extranodal sites:NA


title: 2321 - mAdbID:93175

description: mAdb experiment ID: 93175

value: lymph node

value: Follow up years:0.81

value: ECOG performance status:0

value: LDH ratio:NA


title: 2318 - mAdbID:93176

description: mAdb experiment ID: 93176

value: male

value: Lymphoma

value: Follow up years:0.98

value: LDH ratio:0.52


title: 2615 - mAdbID:93673

description: mAdb experiment ID: 93673

value: female

value: Submitting diagnosis:DLBCL

value: Follow up years:0.47

value: ECOG performance status:1

value: LDH ratio:1.12

value: Number of extranodal sites:1


title: 2271 - mAdbID:93187

description: mAdb experiment ID: 93187

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:ALIVE

value: Follow up years:1.60

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:0.93

value: Number of extranodal sites:0


title: 2306 - mAdbID:93181

description: mAdb experiment ID: 93181

value: lymph node

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.67

value: LDH ratio:2.73

value: Number of extranodal sites:NA


title: 2299 - mAdbID:93183

description: mAdb experiment ID: 93183

value: female

value: Lymphoma

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:0.93

value: ECOG performance status:0

value: LDH ratio:1.32


title: 1939 - mAdbID:93654

description: mAdb experiment ID: 93654

value: male

value: Submitting diagnosis:DLBCL

value: Follow up status:DEAD

value: Follow up years:0.46

value: ECOG performance status:1

value: LDH ratio:1.69

value: Number of extranodal sites:2


title: 2613 - mAdbID:92677

description: mAdb experiment ID: 92677

value: lymph node

value: Follow up status:ALIVE

value: Follow up years:1.65

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:1.15

value: Number of extranodal sites:0


title: 1618 - mAdbID:92679

description: mAdb experiment ID: 92679

value: female

value: Lymphoma

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:1.69

value: LDH ratio:0.79


title: 1297 - mAdbID:92682

description: mAdb experiment ID: 92682

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:4.23

value: LDH ratio:NA


title: 2415 - mAdbID:93170

description: mAdb experiment ID: 93170

value: Follow up years:0.62

value: ECOG performance status:2

value: LDH ratio:7.62

value: Number of extranodal sites:1


title: 2479 - mAdbID:93169

description: mAdb experiment ID: 93169

value: male

value: lymph node

value: Follow up status:ALIVE

value: Follow up years:0.50

value: ECOG performance status:0

value: LDH ratio:0.7


title: 1612 - mAdbID:92681

description: mAdb experiment ID: 92681

value: female

value: Lymphoma

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:5.37

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:0.81


title: 2309 - mAdbID:93178

description: mAdb experiment ID: 93178

value: Submitting diagnosis:DLBCL

value: Follow up years:0.42

value: ECOG performance status:3

value: LDH ratio:1.88

value: Number of extranodal sites:NA


title: 2814 - mAdbID:92650

description: mAdb experiment ID: 92650

value: lymph node

value: Follow up status:DEAD

value: Follow up years:0.80

value: ECOG performance status:NA

value: LDH ratio:2.22


title: 1294 - mAdbID:92683

description: mAdb experiment ID: 92683

value: female

value: Follow up years:0.53

value: ECOG performance status:2

value: LDH ratio:1.06

value: Number of extranodal sites:1


title: 2411 - mAdbID:93171

description: mAdb experiment ID: 93171

value: male

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:0.67

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:0

value: LDH ratio:0.93


title: 2813 - mAdbID:92651

description: mAdb experiment ID: 92651

value: lymph node

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:3.97

value: LDH ratio:NA


title: 1091 - mAdbID:92634

description: mAdb experiment ID: 92634

value: female

value: Follow up years:5.15

value: ECOG performance status:1

value: LDH ratio:0.72


title: 1093 - mAdbID:92633

description: mAdb experiment ID: 92633

value: male

value: Follow up status:DEAD

value: Follow up years:3.82

value: LDH ratio:0.51

value: Number of extranodal sites:1


title: 1175 - mAdbID:92618

description: mAdb experiment ID: 92618

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:1.05

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:2

value: LDH ratio:1.8


title: 1098 - mAdbID:92630

description: mAdb experiment ID: 92630

value: lymph node

value: Submitting diagnosis:DLBCL

value: Follow up status:ALIVE

value: Follow up years:3.52

value: LDH ratio:0.75

value: Number of extranodal sites:0


title: 1230 - mAdbID:92607

description: mAdb experiment ID: 92607

value: female

value: Follow up years:0.58

value: ECOG performance status:3

value: LDH ratio:5.56

value: Number of extranodal sites:2


title: 1109 - mAdbID:92626

description: mAdb experiment ID: 92626

value: Lymphoma

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:3.78

value: ECOG performance status:1

value: LDH ratio:0.9


title: 1096 - mAdbID:92631

description: mAdb experiment ID: 92631

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:4.01

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:0.8


title: 1168 - mAdbID:92621

description: mAdb experiment ID: 92621

value: male

value: lymph node

value: Submitting diagnosis:DLBCL

value: Follow up status:DEAD

value: Follow up years:0.41

value: LDH ratio:0.71


title: 1288 - mAdbID:92604

description: mAdb experiment ID: 92604

value: female

value: Follow up status:ALIVE

value: Follow up years:1.53

value: ECOG performance status:NA

value: LDH ratio:1.51

value: Number of extranodal sites:NA


title: 1195 - mAdbID:92616

description: mAdb experiment ID: 92616

value: Lymphoma

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:4.36

value: ECOG performance status:1

value: LDH ratio:1.07


title: 1867 - mAdbID:92572

description: mAdb experiment ID: 92572

value: male

value: Follow up years:1.16

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:2

value: LDH ratio:NA

value: Number of extranodal sites:2


title: 1231 - mAdbID:92606

description: mAdb experiment ID: 92606

value: female

value: lymph node

value: Submitting diagnosis:DLBCL

value: Follow up years:1.41

value: ECOG performance status:0

value: LDH ratio:0.77

value: Number of extranodal sites:0


title: 1747 - mAdbID:92581

description: mAdb experiment ID: 92581

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:1.47

value: LDH ratio:1.05


title: 23 - mAdbID:92562

description: mAdb experiment ID: 92562

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:2.51

value: ECOG performance status:1

value: LDH ratio:0.91


title: 2070 - mAdbID:92563

description: mAdb experiment ID: 92563

value: male

value: Follow up years:0.30

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:NA

value: LDH ratio:2.42

value: Number of extranodal sites:1


title: 1224 - mAdbID:92610

description: mAdb experiment ID: 92610

value: lymph node

value: Submitting diagnosis:DLBCL

value: Follow up years:3.22

value: ECOG performance status:0

value: LDH ratio:0.7


title: 2067 - mAdbID:92564

description: mAdb experiment ID: 92564

value: female

value: Lymphoma

value: Follow up status:ALIVE

value: Follow up years:2.17

value: LDH ratio:0.75


title: 1916 - mAdbID:92571

description: mAdb experiment ID: 92571

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:1.40

value: ECOG performance status:2

value: LDH ratio:2.69

value: Number of extranodal sites:2


title: 1623 - mAdbID:92582

description: mAdb experiment ID: 92582

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:2.80

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:1.12

value: Number of extranodal sites:3


title: 2445 - mAdbID:92559

description: mAdb experiment ID: 92559

value: lymph node

value: Submitting diagnosis:DLBCL

value: Follow up years:3.35

value: LDH ratio:0.97

value: Number of extranodal sites:1


title: 2482 - mAdbID:92554

description: mAdb experiment ID: 92554

value: male

value: Lymphoma

value: Follow up status:ALIVE

value: Follow up years:4.54

value: LDH ratio:0.9

value: Number of extranodal sites:0


title: 1861 - mAdbID:92578

description: mAdb experiment ID: 92578

value: female

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:DEAD

value: Follow up years:0.55

value: ECOG performance status:3

value: LDH ratio:NA

value: Number of extranodal sites:2


title: 2444 - mAdbID:92560

description: mAdb experiment ID: 92560

value: lymph node

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:3.99

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:2

value: LDH ratio:1.02


title: 1920 - mAdbID:92569

description: mAdb experiment ID: 92569

value: male

value: Lymphoma

value: Follow up status:ALIVE

value: Follow up years:1.31

value: ECOG performance status:1


title: 1928 - mAdbID:92566

description: mAdb experiment ID: 92566

value: female

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.72

value: Number of extranodal sites:0


title: 1927 - mAdbID:92567

description: mAdb experiment ID: 92567

value: Follow up years:1.53

value: LDH ratio:NA

value: Number of extranodal sites:1


title: 2483 - mAdbID:92553

description: mAdb experiment ID: 92553

value: lymph node

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:DEAD

value: Follow up years:3.88

value: LDH ratio:0.9


title: 2485 - mAdbID:92551

description: mAdb experiment ID: 92551

value: Lymphoma

value: Follow up years:4.42

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:NA


title: 2486 - mAdbID:92550

description: mAdb experiment ID: 92550

value: male

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:4.36


title: 2484 - mAdbID:92552

description: mAdb experiment ID: 92552

value: Follow up years:2.69

value: ECOG performance status:1

value: Number of extranodal sites:0


title: 2492 - mAdbID:92544

description: mAdb experiment ID: 92544

value: female

value: lymph node

value: Follow up years:3.96

value: LDH ratio:NA

value: Number of extranodal sites:1


title: 2488 - mAdbID:92548

description: mAdb experiment ID: 92548

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:4.20


title: 2487 - mAdbID:92549

description: mAdb experiment ID: 92549

value: Lymphoma

value: Follow up years:4.34

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:0.9


title: 2498 - mAdbID:92538

description: mAdb experiment ID: 92538

value: male

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:ALIVE

value: Follow up years:3.37


title: 2500 - mAdbID:92535

description: mAdb experiment ID: 92535

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:3.30

value: ECOG performance status:NA

value: Number of extranodal sites:0


title: 2501 - mAdbID:92534

description: mAdb experiment ID: 92534

value: female

value: lymph node

value: Follow up years:3.28

value: LDH ratio:NA


title: 2490 - mAdbID:92546

description: mAdb experiment ID: 92546

value: Submitting diagnosis:DLBCL

value: Follow up years:4.02

value: Number of extranodal sites:1


title: 2497 - mAdbID:92539

description: mAdb experiment ID: 92539

value: Lymphoma

value: Follow up years:3.44

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:1

value: Number of extranodal sites:NA


title: 2514 - mAdbID:92521

description: mAdb experiment ID: 92521

value: male

value: Follow up status:ALIVE

value: Follow up years:2.18

value: LDH ratio:0.9


title: 2508 - mAdbID:92527

description: mAdb experiment ID: 92527

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:2.58

value: ECOG performance status:NA

value: Number of extranodal sites:0


title: 2509 - mAdbID:92526

description: mAdb experiment ID: 92526

value: lymph node

value: Follow up status:DEAD

value: Follow up years:0.96

value: LDH ratio:NA


title: 2507 - mAdbID:92528

description: mAdb experiment ID: 92528

value: female

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:0.86

value: Number of extranodal sites:1


title: 2512 - mAdbID:92523

description: mAdb experiment ID: 92523

value: male

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:2.44

value: Chemotherapy:R-CHOP-Like Regimen

value: Number of extranodal sites:NA


title: 2505 - mAdbID:92530

description: mAdb experiment ID: 92530

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:ALIVE

value: Follow up years:2.75

value: ECOG performance status:1

value: LDH ratio:0.9


title: 2600 - mAdbID:92512

description: mAdb experiment ID: 92512

value: lymph node

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:DEAD

value: Follow up years:1.01

value: Number of extranodal sites:2


title: 2513 - mAdbID:92522

description: mAdb experiment ID: 92522

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:0.61

value: Number of extranodal sites:0


title: 2491 - mAdbID:92545

description: mAdb experiment ID: 92545

value: male

value: Follow up years:0.50

value: ECOG performance status:NA

value: LDH ratio:NA


title: 2511 - mAdbID:92524

description: mAdb experiment ID: 92524

value: Follow up years:1.55

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:3

value: LDH ratio:2


title: 2609 - mAdbID:92507

description: mAdb experiment ID: 92507

value: lymph node

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:ALIVE

value: Follow up years:8.89

value: ECOG performance status:1

value: LDH ratio:0.79

value: Number of extranodal sites:1


title: 2503 - mAdbID:92532

description: mAdb experiment ID: 92532

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:2.98

value: LDH ratio:0.9


title: 2599 - mAdbID:92514

description: mAdb experiment ID: 92514

value: male

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:4.05

value: LDH ratio:NA

value: Number of extranodal sites:0


title: 2604 - mAdbID:92508

description: mAdb experiment ID: 92508

value: lymph node

value: Follow up years:0.84

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:3.11

value: Number of extranodal sites:NA


title: 2504 - mAdbID:92531

description: mAdb experiment ID: 92531

value: female

value: Follow up status:ALIVE

value: Follow up years:2.77

value: ECOG performance status:NA


title: 2517 - mAdbID:92518

description: mAdb experiment ID: 92518

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:2.03

value: Number of extranodal sites:1


title: 2515 - mAdbID:92520

description: mAdb experiment ID: 92520

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:2.12

value: ECOG performance status:1

value: LDH ratio:0.9


title: 2639 - mAdbID:92506

description: mAdb experiment ID: 92506

value: male

value: lymph node

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:10.29

value: LDH ratio:0.7


title: 2516 - mAdbID:92519

description: mAdb experiment ID: 92519

value: Follow up status:ALIVE

value: Follow up years:2.06

value: Chemotherapy:R-CHOP-Like Regimen


title: 2584 - mAdbID:92516

description: mAdb experiment ID: 92516

value: female

value: Lymphoma

value: Follow up years:0.68

value: LDH ratio:0.82

value: Number of extranodal sites:0


title: 2603 - mAdbID:92509

description: mAdb experiment ID: 92509

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:4.42

value: ECOG performance status:2

value: LDH ratio:NA

value: Number of extranodal sites:NA


title: 2641 - mAdbID:92504

description: mAdb experiment ID: 92504

value: male

value: lymph node

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:1.37

value: ECOG performance status:1

value: LDH ratio:2.02


title: 2645 - mAdbID:92501

description: mAdb experiment ID: 92501

value: female

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:0.19

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:NA


title: 2650 - mAdbID:92496

description: mAdb experiment ID: 92496

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:2.42

value: LDH ratio:0.85


title: 2653 - mAdbID:92493

description: mAdb experiment ID: 92493

value: Follow up years:1.88

value: LDH ratio:1.1

value: Number of extranodal sites:2


title: 2646 - mAdbID:92500

description: mAdb experiment ID: 92500

value: male

value: lymph node

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:DEAD

value: Follow up years:0.17

value: LDH ratio:NA

value: Number of extranodal sites:1


title: 2651 - mAdbID:92495

description: mAdb experiment ID: 92495

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:1.61

value: ECOG performance status:1

value: Number of extranodal sites:0


title: 2652 - mAdbID:92494

description: mAdb experiment ID: 92494

value: female

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:1.83

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:0.99


title: 2642 - mAdbID:92503

description: mAdb experiment ID: 92503

value: lymph node

value: Follow up years:3.67

value: LDH ratio:1.82

value: Number of extranodal sites:NA


title: 28 - mAdbID:92491

description: mAdb experiment ID: 92491

value: Follow up years:3.96

value: ECOG performance status:3

value: LDH ratio:0.66


title: 2301 - mAdbID:91993

description: mAdb experiment ID: 91993

value: male

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:ALIVE

value: Follow up years:0.61

value: LDH ratio:NA


title: 2654 - mAdbID:92492

description: mAdb experiment ID: 92492

value: Lymphoma

value: Follow up years:1.42

value: ECOG performance status:1

value: LDH ratio:0.77

value: Number of extranodal sites:3


title: 1281 - mAdbID:91532

description: mAdb experiment ID: 91532

value: female

value: lymph node

value: Submitting diagnosis:DLBCL

value: Follow up years:3.36

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:NA

value: LDH ratio:0.93


title: 1220 - mAdbID:91259

description: mAdb experiment ID: 91259

value: male

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:DEAD

value: Follow up years:2.24

value: LDH ratio:0.9

value: Number of extranodal sites:1


title: 1216 - mAdbID:91260

description: mAdb experiment ID: 91260

value: Lymphoma

value: Follow up years:0.46

value: ECOG performance status:4

value: LDH ratio:7.65


title: 3 - mAdbID:92490

description: mAdb experiment ID: 92490

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:2.66

value: ECOG performance status:1

value: LDH ratio:1.08

value: Number of extranodal sites:0


title: 1087 - mAdbID:91267

description: mAdb experiment ID: 91267

value: lymph node

value: Submitting diagnosis:DLBCL

value: Follow up years:0.04

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:4.1


title: 5 - mAdbID:92487

description: mAdb experiment ID: 92487

value: male

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:DEAD

value: Follow up years:1.27

value: LDH ratio:0.88


title: 1092 - mAdbID:91265

description: mAdb experiment ID: 91265

value: Lymphoma

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:5.06

value: ECOG performance status:0

value: LDH ratio:0.51


title: 2002 - mAdbID:91251

description: mAdb experiment ID: 91251

value: Follow up status:ALIVE

value: Follow up years:1.29

value: LDH ratio:1.04


title: 48 - mAdbID:92488

description: mAdb experiment ID: 92488

value: female

value: lymph node

value: Submitting diagnosis:DLBCL

value: Follow up years:0.36

value: ECOG performance status:1

value: LDH ratio:0

value: Number of extranodal sites:0


title: 2649 - mAdbID:92497

description: mAdb experiment ID: 92497

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:2.12

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:NA

value: Number of extranodal sites:1


title: 1097 - mAdbID:91263

description: mAdb experiment ID: 91263

value: Lymphoma

value: Follow up status:DEAD

value: Follow up years:1.26

value: LDH ratio:0.68


title: 22 - mAdbID:91239

description: mAdb experiment ID: 91239

value: male

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:2.38

value: ECOG performance status:2

value: LDH ratio:0.77

value: Number of extranodal sites:2