title: APOE_KO_RAGE_KO_DM_9W_11

city: New York

first: Ann

middle: Marie

last: Schmidt

state: NY

department: Department of Surgery

institute: Columbia University

description: Aorta of ApoE-/- RAGE -/- diabetic mouse.

hyb_protocol: 1 μg of RNA was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the two-cycle protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the RMA algorithm.

source_name: Aorta from ApoE-/- RAGE -/- mouse with diabetes sacrificed at 9 weeks.

label_protocol: After purification, cDNA was in vitro transcribed into biotin labeled antisense cRNA using an Affymetrix kit according to the standard kit protocol.

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a pathogen-free environment with free access to rodent chow and water.

extract_protocol: Total aortic RNA was isolated from the indicated mice by using TRIzol (Invitrogen) and RNeasy MinElute Cleanup (QIAGEN Inc.) including a DNase step. Total RNA concentration and quality were assessed on a 2100 Bioanalyzer system (Agilent Technologies). All of our samples had an RNA integrity score >8, and there was no indication of RNA degradation or contamination with DNA.

treatment_protocol: Mouse was rendered diabetic at six weeks by administration of 5 daily intraperitoneal injections of streptozotocin, 65 mg/kg in citrate buffer (0.05 mol/L; pH 4.5) (Sigma Aldrich).

value: ApoE-/- RAGE-/-

tag: mouse provider

value: Ann Marie Schmidt laboratory, Columbia University

value: Male

value: 9 weeks

value: Total aorta from root to bifurcation.

tag: disease state

value: diabetic


title: APOE_KO_RAGE_KO_DM_9W_12

status: Public on Mar 01 2010

type: RNA

country: USA

label: Biotin

molecule: total RNA

organism: Mus musculus

tag: genotype/variation

tag: strain

tag: gender

tag: age

tag: tissue


title: APOE_KO_RAGE_KO_DM_9W_9


title: APOE_KO_RAGE_KO_NODM_9W_14

description: Aorta of ApoE-/- RAGE-/- non diabetic mouse.

source_name: Aorta from ApoE-/-  RAGE-/- mouse without diabetes sacrificed at 9 weeks.

treatment_protocol: At 6 weeks mouse was treated by administration of 5 daily intraperitoneal injections of citrate buffer control (0.05 mol/L; pH 4.5) (Sigma Aldrich).

value: non-diabetic


title: APOE_KO_RAGE_KO_NODM_9W_13


title: APOE_KO_RAGE_KO_DM_9W_10


title: APOE_KO_RAGE_KO_NODM_9W_15


title: APOE_KO_DM_9W_4

description: Aorta of ApoE-/- diabetic mouse.

source_name: aorta from ApoE-/- mouse with diabetes sacrificed at 9 weeks.

value: ApoE-/-

value: Jackson labs (backcrossed >10 generations against C57BL/6 background).


title: APOE_KO_NODM_9W_7

description: Aorta of ApoE-/- nondiabetic mouse.

source_name: Aorta from ApoE-/- mouse without diabetes sacrificed at 9 weeks.


title: APOE_KO_NODM_9W_6

description: Aorta of ApoE-/- nondiabetic mouse.


title: APOE_KO_NODM_9W_5

description: Aorta of ApoE-/- nondiabetic mouse.


title: APOE_KO_NODM_9W_8

description: Aorta of ApoE-/- non diabetic mouse.


title: APOE_KO_DM_9W_3

description: Aorta of ApoE-/- diabetic mouse.

source_name: Aorta from ApoE-/- mouse with diabetes sacrificed at 9 weeks.


title: Ler KAR1 24 h seed batch C

city: Crawley

first: David

middle: C

last: Nelson

state: WA

address: The University of Western Australia - M316

department: Plant Energy Biology

country: Australia

institute: University of Western Australia

description:
Gene expression data from wildtype Ler seed imbibed 24 h on KAR1.
Ler K24C

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with GeneChip® Hybridization Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner and Affymetrix GCOS software.

data_processing: The data were analyzed with Avadis software using standard GC-RMA normalization.

label: biotin

organism: Arabidopsis thaliana

source_name: Landsberg erecta seed, imbibed 24 h on KAR1

label_protocol: Biotinylated cRNA was prepared using Affymetrix Gene Expression 3' Amplification one cycle target labeling kit with 7 ug total RNA using manufacturer's protocol.

growth_protocol: Primary dormant seed was collected from plants grown in continuous light (100 uE) and stored at -80C to preserve dormancy. Distinct seed batches were harvested and assayed.

extract_protocol: Total RNA was extracted from seed using Ambion RNAqueous kit with Plant RNA Isolation Aid. Before column purification, solubilized seed mixture was extracted with chloroform:isoamyl alcohol (24:1) to further remove polysaccharide and phenolic contaminants. RNA quality was confirmed using Agilent BioAnalyzer RNA 6000 Nano chips.

treatment_protocol: Seed was imbibed 24 h on 0.8% water-agar with or without 1 uM KAR1 at 20C under 100 uE white light.

value: seed

tag: ecotype

value: Landsberg erecta (Ler)

tag: genotype

value: wildtype

tag: treatment

tag: batch

value: C


title: ga1 KAR1 24 h seed batch C

description:
Gene expression data from ga1-3 mutant seed imbibed 24 h on KAR1.
ga1 K24C

source_name: ga1-3 seed imbibed 24 h on KAR1


title: Ler KAR1 24 h seed batch A

description:
Gene expression data from wildtype Ler seed imbibed 24 h on KAR1.
Ler K24A

value: A


title: APOE_KO_DM_9W_2

description: Aorta of ApoE-/- diabetic mouse

treatment_protocol: Mouse was rendered diabetic at six weeks by administration of 5 daily intraperitoneal injections of streptozotocin, 65 mg/kg in citrate buffer (0.05 mol/L; pH 4.5) (Sigma Aldrich). Serum glucose was measured from tail vein blood using a glucometer. Mice with a glucose concentration greater than 250 mg/ml were considered diabetic. All nondiabetic mice had a glucose concentration well below 200 mg/ml. Beginning at age 9 weeks, certain diabetic and nondiabetic mice were euthanized. Serum glucose was measured again before euthanization. Total Aortic segments from root to bifurcation) were snap-frozen for further analysis. Aortic roots were embedded into OCT (Tissue-Tek) and further sectioned for histological and immuohistochemical analysis.


title: Ler WATER 24 h seed batch C

description:
Gene expression data from wildtype Ler seed imbibed 24 h on water.
Ler W24C

source_name: Landsberg erecta seed, imbibed 24 h on water

value: water


title: ga1 KAR1 24 h seed batch B

description:
Gene expression data from ga1-3 mutant seed imbibed 24 h on KAR1.
ga1 K24B

value: B


title: Ler WATER 24 h seed batch B

description:
Gene expression data from wildtype Ler seed imbibed 24 h on water.
Ler W24B


title: ga1 WATER 24 h seed batch B

description:
Gene expression data from ga1-3 mutant seed imbibed 24 h on water.
ga1 W24B

source_name: ga1-3 seed imbibed 24 h on water


title: ga1 WATER 24 h seed batch A

description:
Gene expression data from ga1-3 mutant seed imbibed 24 h on water.
ga1 W24A


title: Ler KAR1 24 h seed batch D

description:
Gene expression data from wildtype Ler seed imbibed 24 h on KAR1.
Ler K24D

value: D


title: Ler KAR1 24 h seed batch B

description:
Gene expression data from wildtype Ler seed imbibed 24 h on KAR1.
Ler K24B


title: ga1 WATER 24 h seed batch C

description:
Gene expression data from ga1-3 mutant seed imbibed 24 h on water.
ga1 W24C


title: ga1 KAR1 24 h seed batch A

description:
Gene expression data from ga1-3 mutant seed imbibed 24 h on KAR1.
ga1 K24A


title: Ler WATER 24 h seed batch D

description:
Gene expression data from wildtype Ler seed imbibed 24 h on water.
Ler W24D


title: Ler WATER 24 h seed batch A

description:
Gene expression data from wildtype Ler seed imbibed 24 h on water.
Ler W24A


title: Wt1-null MEFs-1

city: Stanford

last: Sweet-Cordero

state: CA

address: CCSR-1215B, 269 Campus Dr

department: Pediatrics

institute: Stanford University

hyb_protocol: Standard Affymetrix protocols were used.

data_processing: Microarray data was normalized with Expression Console software (Affymetrix, Santa Clara) using RMA algorithms for normalization.

extract_protocol: RNA was isolated using Trizol 7 days after infection.  RNA was further prepared by passage over an RNeasy column.  cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430_2 was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).

treatment_protocol: Wt1f/f MEFs were infected with adenoviral Cre to knockout Wt1.

tag: cell type

value: Mouse embryonic fibroblasts (MEFs)

tag: genome/variation


title: mKras-MEFs-2

scan_protocol: Standard Affymetrix protocols were used.

source_name: mutant Kras mouse embryonic fibroblasts

treatment_protocol: K-rasLSL-G12D MEFs were infected with adenoviral Cre to activate K-ras.

value: K-ras mut


title: APOE_KO_DM_9W_1

description: aorta of ApoE-/- diabetic mouse.

data_processing: Data was normalized using the RMA algorithm

source_name: aorta from ApoE-/- mouse with diabetes sacrificed at 9 weeks

treatment_protocol:
Mouse was rendered diabetic at six weeks by administration of 5 daily intraperitoneal injections of streptozotocin, 65 mg/kg in citrate buffer (0.05 mol/L; pH 4.5) (Sigma Aldrich).
Serum glucose was measured from tail vein blood using a glucometer. Mice with a glucose concentration greater than 250 mg/ml were considered diabetic. All nondiabetic mice had a glucose concentration well below 200 mg/ml. Beginning at age 9 weeks, certain diabetic and nondiabetic mice were euthanized. Serum glucose was measured again before euthanization. Total Aortic segments from root to bifurcation) were snap-frozen for further analysis. Aortic roots were embedded into OCT (Tissue-Tek) and further sectioned for histological and immuohistochemical analysis.

value: Male


title: mKras-MEFs-1

description: K-rasLSL-G12D MEFs were infected with adenoviral Cre to activate K-ras

label_protocol: Standard Affymetrix protocols were used.


title: NF1-C2S transfected cells, rep2

status: Public on Feb 27 2010

city: Gothenburg

first: Jeanette

last: Nilsson

address: Box 462

department: Cell and Molecular Biology

country: Sweden

institute: Gothenburg University

hyb_protocol: Done by the SCIBLU Micoarray Resourse Center (MARC), Lund University, Sweden.

data_processing: RMA normalization, done by the SCIBLU Micoarray Resourse Center (MARC), Lund University, Sweden.

organism: Homo sapiens

source_name: breast tumor cells, MDA-MB-436, transfected with NF1-C2S

growth_protocol: The  MDA-MB-436 cells were grown at 37°C in a 5% CO2/95% air atmosphere in RPMI-1640 medium supplemented with 10% FCS, 1% PEST and 5 μg/ml insulin.

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

tag: cell line

value: breast tumor epithelial cells

tag: condition

value: overexpressing NF-C2


title: NF1-C2S transfected cells, rep3

scan_protocol: Done by the SCIBLU Micoarray Resourse Center (MARC), Lund University, Sweden.


title: case 12 mRNA

status: Public on Feb 26 2010

city: Taipei

first: Yu Hsuan

last: Wu

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang-Ming University

description: Gene expression data from CNS GCT patient

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

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

data_processing: RMA through R based affymetrix module

source_name: GCT patient case

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: primary intracranial pediatric germ cell tumor (GCT)

tag: diagnosis

value: immature teratoma predominant + embryonal carcinoma + yolk sac tumor

value: 7.7 years


title: case 9 mRNA

value: immature teratoma

value: 10 days


title: case 6 mRNA

value: germinoma

value: 14 years


title: NF1-C2S transfected cells, rep1

label_protocol: Done by the SCIBLU Micoarray Resourse Center (MARC), Lund University, Sweden.


title: case 7 mRNA

value: germinoma 20% + mature teratoma 80%

value: 9.7 years


title: case 1 mRNA

value: 15.9 years


title: case 5 mRNA

value: 11.5 years


title: case 13 mRNA

value: yolk sac tumor + germinoma

value: 14.5 years


title: case 4 mRNA

value: 10.4 years


title: patient_24 (melphalan)

city: Durham

first: Christina

last: Augustine

state: NC

address: VAMC RmE4001 508 Fulton St.

department: Surgery

institute: Duke University Medical Center

hyb_protocol: labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols

scan_protocol: Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000

data_processing: Expression values across 54675 probe sets were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS).  A statistical p-value, suggesting the level of confidence in each of the qualitative measurements, as well as a present/absent call (based on the p-value) are included.

source_name: melanoma

label_protocol: one-cycle cDNA synthesis of 1µg total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA

extract_protocol: Tissue was homogenized and RNA isolated using Qiagen Rneasy kit.  A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue.  Each RNA isolation included treatment with DNase to minimize genomic DNA.

treatment_protocol: 4mm punch biopsies were obtained prior to isolated-limb-infusion with melphalan following a protocol approved by the Duke University institutional review board.  Biopsies were snap frozen and stored at -130.

tag: disease type

value: in-transit melanoma

tag: stage

tag: chemotherapy response

value: CR - complete response

tag: mutation

value: unknown


title: patient_25 (melphalan)


title: case 10 mRNA

value: primary intracranial pediatric germ cell tumor (GCT)

value: germinoma + immature teratoma

value: 10.25 years


title: case 8 mRNA

value: immature teratoma predominant + germinoma

value: 4.3 years


title: case 11 mRNA

value: yolk sac tumor predominant + immature teratoma

value: 10.6 years


title: patient_23 (melphalan)

value: SD - stable disease


title: patient_9 (melphalan)

value: PD - progressive disease


title: patient_21 (melphalan)

value: PR - partial response


title: wild type cells, rep3

source_name: breast tumor cells, MDA-MB-436

value: breast tumor epithelial cells

value: wildtype


title: case 2 mRNA

value: germinoma


title: patient_8 (melphalan)


title: patient_27 (melphalan)


title: patient_28 (melphalan)


title: patient_29 (melphalan)


title: patient_26 (melphalan)


title: patient_22 (melphalan)


title: case 3 mRNA

value: 14.2 years


title: patient_7 (melphalan)

value: in-transit melanoma


title: patient_16_b (melphalan)

value: CR - complete response


title: patient_20_a (melphalan)


title: patient_11_c (melphalan)


title: patient_19_b (melphalan)


title: patient_13_b (melphalan)


title: patient_11_b (melphalan)


title: patient_14_b (melphalan)


title: patient_13_c (melphalan)


title: patient_11_a (melphalan)


title: patient_18_a (melphalan)


title: patient_15_a (melphalan)


title: patient_17_b (melphalan)


title: patient_17_a (melphalan)


title: patient_18_b (melphalan)


title: patient_16_c (melphalan)


title: patient_20_b (melphalan)


title: patient_12_c (melphalan)


title: patient_16_a (melphalan)


title: patient_10_a (melphalan)


title: patient_13_a (melphalan)


title: patient_15_b (melphalan)


title: patient_15_c (melphalan)


title: patient_14_a (melphalan)


title: patient_12_a (melphalan)


title: patient_19_a (melphalan)


title: patient_6_a (melphalan)


title: patient_5_c (melphalan)


title: patient_5_a (melphalan)


title: patient_6_b (melphalan)


title: patient_4_c (melphalan)


title: patient_4_a (melphalan)


title: patient_5_b (melphalan)


title: patient_4_d (melphalan)


title: patient_3_c (melphalan)


title: patient_10_b (melphalan)


title: patient_3_a (melphalan)


title: patient_3_b (melphalan)


title: patient_2_b (melphalan)


title: patient_4_b (melphalan)


title: endometrial NK cells sample 1

status: Public on Feb 25 2010

city: Boston

first: Hernan

last: Kopcow

state: MA

address: 330 Brookline Ave RN359

department: Medicine

institute: Beth Israel  Deaconess  Medical Center

description: RNA was subjected to 2 rounds amplification with Acturus RiboAmp OA kit

hyb_protocol: Following fragmentation, 15 ug  of cRNA were hybridized for 16  hr at 45 C on GeneChip HGU133Plus2  Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000

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

source_name: NK cells from cycling endometrtium

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

extract_protocol: Total RNA was isolated with TRIzol  following manufacturer's instructions, with addition of 5 µg linear polyacrylamide (Genelute LPA; Sigma Aldrich) to aid visualization of RNA pellets. RNA was cleaned-up (Rneasy, QIAGEN) and  amplified with ( Acturus RiboAmp OA)  all according to kit manufacturers instructions.

treatment_protocol: Tissues were collected and processed as described ( Koopman et al J Exp Med. 2003, 198(8):1201-12). Briefly samples were washed in PBS, minced, digested with 0.1% collagenase type IV and 0.01% DNase I (both from Sigma-Aldrich) in RPMI 1640 medium for 30 min at 37 C. Disgestion was stoped by addition of RPMI 1640 medium containing 10% fetal calf serum.  Adherent cells were allowed to adhere  in tissue culture plates for  2 hours at 37C in humidified incubators. Non adherent lymphocytes  were then isolated by density gradient centrifugtion (Ficoll-Hypaque; Amersham Biosciences), washed and stained for FACS sorting. dNK cells were isolated as CD3-. CD16-, CD56+ cells. eNK cells were isolated as CD45+, CD3-, CD56+ cells. After sorting cells were extesively wahed with PBS and cell pellets frozen a at -80C until prcessing for RNA extraction.

tag: cycle phase/ gestational age

value: cycling endometrium secretory phase

value: eNK cell


title: P493_NoMyc_1a

city: Baltimore

first: Chi

middle: V.

last: Dang

state: MD

address: 720 Rutland Ave, Ross 1032

institute: Johns Hopkins University, School of Medicine

hyb_protocol: Standard Protocol from Affymetrix Inc. at JHMI Microarray Core

data_processing: Quality of the microarray experiment was assessed with affyPLM and Affy, two bioconductor packages for statistical analysis of microarray data.  To estimate the gene expression signals, data analysis was conducted on the chips’ CEL file probe signal values at the Affymetrix probe pair (perfect match (PM) probe and mismatch (MM) probe) level, using the statistical algorithm RMA (Robust Multi-array expression measure) (Irizarry, 2003) with Affy. This probe level data processing includes a normalization procedure utilizing quantile normalization method (Bolstad, 2003) to reduce the obscuring variation between microarrays, which might be introduced during the processes of sample preparation, manufacture, fluorescence labeling, hybridization and/or scanning.

extract_protocol: Qiagen RNeasy

value: B lymphocyte cells

value: no Myc expression


title: P493_NoMyc_2a

scan_protocol: Standard Protocol from Affymetrix Inc. at JHMI Microarray Core


title: P493_LowMyc_3a

label_protocol: Standard Protocol from Affymetrix Inc. at JHMI Microarray Core

value: low Myc expression


title: P493_LowMyc_2a


title: endometrial NK cells sample 6

value: cycling endometrium proliferative phase


title: endometrial NK cells sample 5


title: endometrial NK cells sample 9


title: patient_2_a (melphalan)


title: wild type cells, rep1


title: decidual NK cells sample 2

source_name: decidual NK cells

value: first trimester

value: dNK cell


title: wild type cells, rep2


title: endometrial NK cells sample 13


title: decidual NK cells sample 1


title: decidual NK cells sample 4


title: decidual NK cells sample 3


title: P493_HighMyc_4a

value: high Myc expression


title: P493_HighMyc_3a


title: P493_HighMyc_1a


title: P493_LowMyc_1a


title: P493_HighMyc_2a


title: Donor 3, S2 stimulation, 48 h

status: Public on Feb 24 2010

city: Bethesda

first: Amrita

last: Ghosh

address: 49 Convent Drive, 3B-07

department: Genetics and Molecular Biology

institute: National Human Genome Research Institute (NHGRI), NIH

description:
Gene expression data from donor 3 human CD34+ bone marrow-derived cells after stimulation with S2 for 48 h.
Don 3 S2-48

hyb_protocol: Fifteen micrograms of fragmented, biotinylated cRNA was hybridized to HG U133 Plus 2.0 microarrays (Affymetrix) for 16 hours at 45 deg C. Genechips were hybridized, washed, and stained on an Affymetrix fluidics station.

scan_protocol: Microarray chips were scanned with a 532-nm emission laser and underwent detection at 570 nm.

data_processing: GeneChip images were quantified using GeneChip Operating Software (GCOS, Affymetrix) and normalized by RMA (Genesifter.net).

source_name: Bone marrow donor 3, CD34+ cells stimulated in S2 after 48 h

label_protocol: One-hundred ng of total RNA was subjected to one round amplification using the Riboamp RNA amplification kit (Molecular Devices) according to the manufacturer's instructions.

growth_protocol: Bone marrow-derived CD34+ cells were isolated from three human donors.

extract_protocol: Total RNA was extracted using the Picopure RNA Isolation kit (Molecular Devices, Sunnyvale, CA) from unstimulated cells and from cells cultured in S1 or S2 conditions for 48, 72, or 96 h.  Quality of RNA was assessed by Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol:
Cells were stimulated according to S1 or S2 conditions. Cells from each time point (0 h, 48 h, 72 h, 96 h) were collected and washed with PBS.

S1 conditions: X-vivo 10, 4% fetal calf serum, 300 ng/ml SCF, 100 ng/ml TPO, 60 ng/ml IL3, and 300 ng/ml FL.

S2 conditions: X-vivo 10, 1% human serum albumin, 300 ng/ml SCF, 100 ng/ml TPO, 20 ng/ml IL3, and 300 ng/ml FL.

value: bone marrow-derived CD34+ cells

value: S2 stimulation (British trial conditions)

tag: treatment time

value: 48 hr

tag: donor


title: Donor 2, S2 stimulation, 96 h

description:
Gene expression data from donor 2 human CD34+ bone marrow-derived cells after stimulation with S2 for 96 h.
Don 2 S2-96

source_name: Bone marrow donor 2, CD34+ cells stimulated in S2 after 96 h

value: 96 hr


title: Donor 3, S1 stimulation, 96 h

description:
Gene expression data from donor 3 human CD34+ bone marrow-derived cells after stimulation with S1 for 96 h.
Don 3 S1-96

source_name: Bone marrow donor 3, CD34+ cells stimulated in S1 after 96 h

value: S1 stimulation (French trial conditions)


title: Donor 3, S2 stimulation, 96 h

description:
Gene expression data from donor 3 human CD34+ bone marrow-derived cells after stimulation with S2 for 96 h.
Don 3 S2-96

source_name: Bone marrow donor 3, CD34+ cells stimulated in S2 after 96 h


title: Donor 3, 0 h

description:
Gene expression data from donor 3 human CD34+ bone marrow-derived cells before stimulation.
Don 3 0 h

source_name: Bone marrow donor 3, CD34+ cells before stimulation

value: 0 hr


title: Donor 2, S1 stimulation, 72 h

description:
Gene expression data from donor 2 human CD34+ bone marrow-derived cells after stimulation with S1 for 72 h.
Don 2 S1-72

source_name: Bone marrow donor 2, CD34+ cells stimulated in S1 after 72 h

value: 72 hr


title: Donor 3, S1 stimulation, 72 h

description:
Gene expression data from donor 3 human CD34+ bone marrow-derived cells after stimulation with S1 for 72 h.
Don 3 S1-72

source_name: Bone marrow donor 3, CD34+ cells stimulated in S1 after 72 h


title: Donor 2, S2 stimulation, 72 h

description:
Gene expression data from donor 2 human CD34+ bone marrow-derived cells after stimulation with S2 for 72 h.
Don 2 S2-72

source_name: Bone marrow donor 2, CD34+ cells stimulated in S2 after 72 h


title: Donor 1, S2 stimulation, 72 h

description:
Gene expression data from donor 1 human CD34+ bone marrow-derived cells after stimulation with S2 for 72 h.
Don 1 S2-72

source_name: Bone marrow donor 1, CD34+ cells stimulated in S2 after 72 h


title: Donor 2, S1 stimulation, 48 h

description:
Gene expression data from donor 2 human CD34+ bone marrow-derived cells after stimulation with S1 for 48 h.
Don 2 S1-48

source_name: Bone marrow donor 2, CD34+ cells stimulated in S1 after 48 h


title: Donor 1, S2 stimulation, 48 h

description:
Gene expression data from donor 1 human CD34+ bone marrow-derived cells after stimulation with S2 for 48 h.
Don 1 S2-48

source_name: Bone marrow donor 1, CD34+ cells stimulated in S2 after 48 h


title: Donor 2, 0 h

description:
Gene expression data from donor 2 human CD34+ bone marrow-derived cells before stimulation.
Don 2 0 h

source_name: Bone marrow donor 2, CD34+ cells before stimulation


title: Donor 2, S2 stimulation, 48 h

description:
Gene expression data from donor 2 human CD34+ bone marrow-derived cells after stimulation with S2 for 48 h.
Don 2 S2-48

source_name: Bone marrow donor 2, CD34+ cells stimulated in S2 after 48 h


title: Donor 2, S1 stimulation, 96 h

description:
Gene expression data from donor 2 human CD34+ bone marrow-derived cells after stimulation with S1 for 96 h.
Don 2 S1-96

source_name: Bone marrow donor 2, CD34+ cells stimulated in S1 after 96 h


title: Donor 1, S1 stimulation, 48 h

description:
Gene expression data from donor 1 human CD34+ bone marrow-derived cells after stimulation with S1 for 48 h.
Don 1 S1-48

source_name: Bone marrow donor 1, CD34+ cells stimulated in S1 after 48 h


title: Donor 1, S2 stimulation, 96 h

description:
Gene expression data from donor 1 human CD34+ bone marrow-derived cells after stimulation with S2 for 96 h.
Don 1 S2-96

source_name: Bone marrow donor 1, CD34+ cells stimulated in S2 after 96 h


title: Donor 3, S2 stimulation, 72 h

description:
Gene expression data from donor 3 human CD34+ bone marrow-derived cells after stimulation with S2 for 72 h.
Don 3 S2-72

source_name: Bone marrow donor 3, CD34+ cells stimulated in S2 after 72 h


title: Donor 1, S1 stimulation, 72 h

description:
Gene expression data from donor 1 human CD34+ bone marrow-derived cells after stimulation with S1 for 72 h.
Don 1 S1-72

source_name: Bone marrow donor 1, CD34+ cells stimulated in S1 after 72 h


title: Donor 3, S1 stimulation, 48 h

description:
Gene expression data from donor 3 human CD34+ bone marrow-derived cells after stimulation with S1 for 48 h.
Don 3 S1-48

source_name: Bone marrow donor 3, CD34+ cells stimulated in S1 after 48 h


title: Donor 1, S1 stimulation, 96 h

description:
Gene expression data from donor 1 human CD34+ bone marrow-derived cells after stimulation with S1 for 96 h.
Don 1 S1-96

source_name: Bone marrow donor 1, CD34+ cells stimulated in S1 after 96 h


title: Donor 1, 0 h

description:
Gene expression data from donor 1 human CD34+ bone marrow-derived cells before stimulation.
Don 1 0 h

source_name: Bone marrow donor 1, CD34+ cells before stimulation


title: hES_SA01_2

city: Evry

first: Genevieve

last: PIETU

address: 1 rue de l'Internationale

country: France

institute: INSERM

description: gene expression data from undifferentiated hES cells line SA01

hyb_protocol: Hybridisation, washing and staining procedures of the Affymetrix GeneChip® Human Genome U133 Plus 2.0 were carried out as described in the Affymetrix technical manual (see manufacturer's web site)

scan_protocol: Scanning procedures of the Affymetrix GeneChip® Human Genome U133 Plus 2.0 were carried out as described in the Affymetrix technical manual (see manufacturer's web site)

data_processing: The statistical treatment of the expression data was achieved using the Array Assist 4.1 software (Stratagene). Normalization was performed using the GC-RMA algorithm.

source_name: human embryonic stem (hES) cells line SA01, biological replicate  2

label_protocol: 100 ng of total RNA was used to generate biotinylated cRNA using the GeneChip® Two-Cycle Target Labeling and Control Reagents from Affymetrix according to the manufactures protocol

growth_protocol: The hES cell lines were maintained on a feeder layer of mitomycin C-inactivated murine embryonic fibroblast (MEF) cells. The culture media (DMEM/F12 supllemented with 20% KRS and 4ng/ml bFGF) was changed daily and routine passages were performed by mechanical cutting of hES cells on a fresh feeder layer every 4-5 days.

extract_protocol: Total RNA was extracted from the cells using the RNeasy Mini kit (Qiagen) according to the manufacturer protocol

tag: human ES cells line from Cellartis, Sweden; commercial line derived from normal embryos

tag: Karyotype

value: X,Y


title: hES_VUB03_DM1_1

description: gene expression data from undifferentiated hES cells line VUB03_DM1

source_name: human embryonic stem (hES) cells line VUB03_DM1, biological replicate  1

tag: human ES cells line from AZ-VUB laboratory, Belgium; derived from a blastocyst obtained after an in vitro fertilization carried out during a PGD procedure for DM1

value: X,X


title: hES_VUB01_2

description: gene expression data from undifferentiated hES cells line VUB01

source_name: human embryonic stem (hES) cells line VUB01, biological replicate  2

tag: human ES cells line from AZ-VUB laboratory, Belgium; derived from normal embryos


title: hES_VUB01_3

source_name: human embryonic stem (hES) cells line VUB01, biological replicate  3


title: hES_VUB03_DM1_3

source_name: human embryonic stem (hES) cells line VUB03_DM1, biological replicate  3


title: hES_VUB03_DM1_2

source_name: human embryonic stem (hES) cells line VUB03_DM1, biological replicate  2


title: hES_SA01_1

source_name: human embryonic stem (hES) cells line SA01, biological replicate  1


title: NPC_VUB03_DM1_1

description: gene expression data for VUB03_DM1 hES cells line-derived NPC

source_name: Neural precursor cells derived from hES cells line VUB03_DM1, biological replicate  1

growth_protocol: Neural precursor cells (NPC) were purified from neural rosettes derived from hES cells (Perrier et al, 2004)  by cell sorting using the pan neuronal marker NCAM ( Neural Cell Adhesion molecule or CD56).

tag: Differentiation of hES cells line VUB03_DM1 towards neural rosettes

tag: Neural precursor phenotype


title: hES_SA01_3

source_name: human embryonic stem (hES) cells line SA01, biological replicate  3


title: NPC_VUB03_DM1_2

source_name: Neural precursor cells derived from hES cells line VUB03_DM1, biological replicate  2


title: hES_VUB01_1

source_name: human embryonic stem (hES) cells line VUB01, biological replicate  1


title: NPC_VUB03_DM1_3

source_name: Neural precursor cells derived from hES cells line VUB03_DM1, biological replicate  3


title: NPC_SA01_3

description: gene expression data for SA01 hES cells line-derived NPC

source_name: Neural precursor cells derived from hES cells line SA01, biological replicate  3

tag: Differentiation of hES cells line SA01 towards neural rosettes


title: NPC_SA01_1

source_name: Neural precursor cells derived from hES cells line SA01, biological replicate  1


title: MSC_VUB03_DM1_1

description: gene expression data for VUB03_DM1 hES cell line-derived MPC

source_name: Mesodermal Precursor Cells derived from hES cells line VUB03_DM1, biological replicate 1

growth_protocol: Mesodermal Precursor Cells (MPC) were derived from hES by plating cells on 0,1% Gelatin coated dishes in KO-DMEM medium supplemented with 20% FBS.

tag: Differentiation of hES cells line VUB03_DM1 towards MPC-like cells

tag: Mesenchymal stem cells phenotype


title: MSC_VUB03_DM1_3

source_name: Mesodermal Precursor Cells derived from hES cells line VUB03_DM1, biological replicate 3


title: MSC_VUB01_2

description: gene expression data for VUB01 hES cell line-derived MPC

source_name: Mesodermal Precursor Cells derived from hES cells line VUB01, biological replicate 2

tag: Differentiation of hES cells line VUB01 towards MPC-like cells


title: NPC_VUB01_3

description: gene expression data for VUB01 hES cells line-derived NPC

source_name: Neural precursor cells derived from hES cells line VUB01, biological replicate  3

tag: Differentiation of hES cells line VUB01 towards neural rosettes


title: MSC_VUB01_1

source_name: Mesodermal Precursor Cells derived from hES cells line VUB01, biological replicate 1


title: NPC_VUB01_2

source_name: Neural precursor cells derived from hES cells line VUB01, biological replicate  2


title: NPC_VUB01_1

source_name: Neural precursor cells derived from hES cells line VUB01, biological replicate  1


title: NPC_SA01_2

source_name: Neural precursor cells derived from hES cells line SA01, biological replicate  2


title: MSC_SA01_3

description: gene expression data for SA01 hES cell line-derived MPC

source_name: Mesodermal Precursor Cells derived from hES cells line SA01, biological replicate 3

tag: Differentiation of hES cells line SA01 towards MPC-like cells


title: MSC_VUB01_3

source_name: Mesodermal Precursor Cells derived from hES cells line VUB01, biological replicate 3


title: MSC_SA01_1

source_name: Mesodermal Precursor Cells derived from hES cells line SA01, biological replicate 1


title: MSC_SA01_2

source_name: Mesodermal Precursor Cells derived from hES cells line SA01, biological replicate 2


title: MSC_VUB03_DM1_2

source_name: Mesodermal Precursor Cells derived from hES cells line VUB03_DM1, biological replicate 2


title: Pre-operation cyanotic CC4A

status: Public on Feb 23 2010

city: Bristol

first: Mohamed

middle: T.

last: Ghorbel

address: Level 7, BRI, Marlborough street

department: Bristol Heart Institute

country: United Kingdom

institute: University of Bristol

description: Patients with a diagnosis of cyanotic Tetralogy of Fallot congenital heart disease undergoing corrective surgery

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: RMA normalized

source_name: Right ventricle biopsy

label_protocol: One microgram of total RNA was processed to produce biotinylated cRNA targets using the Affymetrix protocol

extract_protocol: Five to ten milligrams of frozen right ventricle biopsy was homogenized and total RNA extracted using the Qiagen MiniElute protocol (Qiagen, UK).

tag: tissue

value: Pre-operative human heart


title: Pre-operation cyanotic CC9A


title: Pre-operation cyanotic CC1A


title: Pre-operation acyanotic AC3A

description: Patients with a diagnosis of acyanotic Tetralogy of Fallot congenital heart disease undergoing corrective surgery


title: Pre-operation cyanotic CC6A


title: Pre-operation acyanotic AC7A


title: Pre-operation cyanotic CC3A


title: Pre-operation acyanotic AC6A


title: Flow sorted normal Pro-Myelocytes, 1

status: Public on Feb 21 2010

city: Lund

first: Thoas

middle: Anna

address: Lund University Hospital

institute: Dept of Clinical Genetics

description: CD34-/CD117low/CD33+/CD13+/CD11blow/CD2-

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: Data were analyzed using Bioconductor and normalization was performed using gcRMA within Biocinductor

source_name: Normal Pro-Myelocytes

label_protocol: RNA was amplified using the MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification (Ambion)

extract_protocol: Flow sorted cells from adult bone marrow. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: normal flow sorted bone marrow

tag: cell type

value: Normal Pro-Myelocytes


title: Flow sorted normal Pro-B cells, 1

source_name: Normal Pro-B cells

value: Normal Pro-B cells


title: Pre-operation cyanotic CC7A


title: Pre-operation cyanotic CC2A


title: Flow sorted normal Pro-Myelocytes, 2


title: Flow sorted normal GMP cells, 1

source_name: Normal GMP cells

value: Normal GMP cells


title: Flow sorted normal Myelocytes, 2

description: CD34-/CD117-/CD33+/CD13low/CD11b++/CD14-/CD2-

source_name: Normal Myelocytes

value: Normal Myelocytes


title: Flow sorted normal Pre-B cells, 2

source_name: Normal Pre-B cells

value: Normal Pre-B cells


title: Flow sorted normal CMP cells, 2

source_name: Normal CMP cells

value: Normal CMP cells


title: Flow sorted normal immature B-cells, 1

source_name: Normal immature B-cells

value: Normal immature B-cells


title: Flow sorted normal CMP cells, 1


title: Flow sorted normal Pre-B cells, 1


title: Flow sorted normal Pro-B cells, 2


title: Flow sorted normal immature B-cells, 2


title: Flow sorted normal Myelocytes, 1


title: Pre-operation acyanotic AC4A


title: Flow sorted normal GMP cells, 2


title: human blastocyst, biological rep 3

status: Public on Feb 20 2010

city: Urbana

first: Dan

last: Xie

state: IL

address: 3215 Digital Computer Lab, MC-278, 1304 W. Springfield Ave

department: Bioengineering

institute: University of Illinois at Urbana and Champaign

description: Gene expression data from blastocyst

hyb_protocol: Following a 16-hour hybridization the chip was washed and stained utilizing an Affymetrix GeneChipâ Fluidics Station 450 and Affymetrix GeneChipâ Command Console Software.   Initial staining utilized streptavidin-conjugated phycoerythrin dye (Invitrogen Corporation, Carlsbad, CA).  This stain was enhanced with biotinylated goat anti-streptavidin antibody (Vector Laboratories, Burlingame, CA), then counterstained with the conjugated phycoerythrin.

scan_protocol: The chip was scanned with an Affymetrix GeneChipâ Scanner model 3000 7G Plus.  Files of the fluorescence intensities were utilized to generate corresponding probe expression levels utilizing Affymetrix Expression Console version 1.1, and quality control values were checked.

data_processing: The data were analyzed with dChip. Normalization was under default settings.

source_name: Human blastocyst

label_protocol: RNA was prepared utilizing three rounds of amplification and hybridized to Affymetrix GeneChipâ Bovine Genome Expression Arrays (Affymetrix, Inc., Santa Clara, CA)  utilizing Ambion’s MessageAmp TM II aRNA Amplification and MessageAmpTM II-Biotin Enhanced Kits (Applied Biosystems, Foster City, CA) according to the manufacturers’ instructions.

extract_protocol: Total RNA extraction was carried out using the mirVana RNA extraction kit according to the manufacturers protocols (Applied Biosciences/Ambion, Austin, TX ).

treatment_protocol: Human embryos: Supernumerary human embryos were obtained from patients at the Boston IVF Clinic through informed consent with the approval of the Internal Review Board of Harvard University.  Embryos thus obtained were cultured in a two-step culture system (Sage/Biopharma, CT) in micro-drops at 37? C and 5% CO2 under oil (Sage, CT) as described previously.  Embryos from each stage were segregated into three groups.  Each group was considered to be a biologic replicate: embryos within each replicate were pooled for further analysis.  The blastocyst embryos were graded according to the Gardner scale. Mouse embryos: Briefly, female mice were impregnated, and embryos were flushed from the oviducts.  Individual embryos were morphologically staged by light microscopy.  Bovine embryos: Ovaries were washed and 2-6 mm follicles were aspirated.  Only oocytes surrounded by several cell layers of dense cumulus were selected for culture.  Oocytes were washed three times in TL-HEPES (0.22mM sodium pyruvate, 3mg/ml BSA, pH 7.4), and we placed maturation media that had been equilibrated in 5% carbon dioxide and air (39°C, high humidity).  The maturation medium consisted of TC199 supplemented with 3ml of bovine LH and FSH (Sioux Biochemical), 0.25mM sodium pyruvate, and 10% fetal calf serum.  After 20 hours of incubation in maturation media, oocytes were removed, washed in TL-HEPES and  placed in groups of 10 oocytes each into 44 μl microdrops of IVF-Talp (Biowhittaker, Walkersburg, MD) supplemented with 0.22mM sodium pyruvate, and 6 mg/ml essentially fatty acid-free BSA. Live sperm were separated by centrifugation in a percoll gradient (Sigma, P1985).  Eggs were fertilized by adding one million/ml of sperm,  2.0μg heparin (Sigma H-3125), pencillamine, hypotaurine and epinephrine (Sigma-P-4875, H-1384, E-4250) to each drop of fertilization media. Oocytes were removed from the fertilization media after 18-22 hours, washed in TL-HEPES, placed in a 1.5 ml tube, and vortexed for 2 min to remove cumulus cells. Twenty-five cumulus-free oocytes were placed in each 50μl drop of SOF culture medium, supplemented with 8 mg/ml of fatty acid-free BSA, nonessential and essential amino acids and pyruvate. The IVF conditions were optimized for each species. To minimize the influence of IVF conditions to cross-species comparison, we subsequently based the comparisons on either relative expression changes or co-expression patterns.

tag: development stage

value: blastocyst


title: human blastocyst, biological rep 2

description: Gene expression data from blastocyst


title: human embryo at morula stage, biological rep 3

description: Gene expression data from morula

source_name: Human morula

value: morula


title: human blastocyst, biological rep 1

description: Gene expression data from blastocyst


title: human embryo at morula stage, biological rep 1

description: Gene expression data from morula


title: human embryo at 4 cell stage, biological rep 3

description: Gene expression data from zygote before divide

source_name: Human embryo at four cell stage

value: embryo at four cell stage


title: human embryo at morula stage, biological rep 2

description: Gene expression data from morula


title: human embryo at 8 cell stage, biological rep 1

source_name: Human embryo at eight cell stage

value: embryo at eight cell stage


title: human embryo at 4 cell stage, biological rep 1


title: human embryo at 2 cell stage, biological rep 1

source_name: Human embryo at two cell stage

value: embryo at two cell stage


title: human embryo at 1 cell stage, biological rep 2

source_name: Human embryo at one cell stage

value: embryo at one cell stage


title: human embryo at 2 cell stage, biological rep 3


title: human embryo at 2 cell stage, biological rep 2


title: human embryo at 1 cell stage, biological rep 1


title: human embryo at 8 cell stage, biological rep 2


title: human embryo at 8 cell stage, biological rep 3


title: human embryo at 1 cell stage, biological rep 3


title: human embryo at 4 cell stage, biological rep 2


title: Pre-operation acyanotic AC5A


title: SKGT4_REST_24Hr_1

city: Dublin

first: Shane

middle: P

last: Duggan

address: TCD Health Sciences Building, St James Hospital,

department: Clinical Medicine

country: Ireland

institute: Institute of Molecular Medicine

description: RNA samples were taken at 4, 8, 12 and 24 hours from DCA (DCA) exposed and resting (REST) timepoint controls.

hyb_protocol: as per instructions by affymetrix.

scan_protocol: as per instructions by affymetrix.

data_processing: Value as determined at a target intensity of 100 in MAS5.0

source_name: SKGT4 cells in untreated media for 24 hours

label_protocol: as per instructions by affymetrix.

growth_protocol: SKGT4 cells are grown in RPMI1640 with 10% fetal calf serum and penn-step-glutamine supplementation.

extract_protocol: Total RNA was extracted using Machery-Nagel RNA extraction spin columns.

treatment_protocol: These cells have not been treated and are used as a biological time point control for experiments involving exposure of these cells to carcinogens over time.

tag: The SKGT4 cell line is derived from the Barrett's associated adenocarcinoma of the lower esophageal epithelium and used in these experiments at passage 4.


title: SKGT4_REST_24Hr_2


title: SKGT4_DCA_4Hr_2

source_name: SKGT4 cells exposed to DCA (300um) media for 4 hours

treatment_protocol: These cells have been exposed to deoxycholic acid (DCA) 300um for the time detailed above, in RPMI media without supplementation or fetal calf serum.


title: SKGT4_DCA_8Hr_1

source_name: SKGT4 cells exposed to DCA (300um) media for 8 hours


title: SKGT4_DCA_4Hr_1


title: SJGT4_REST_12Hr_2

source_name: SKGT4 cells in untreated media for 12 hours


title: SKGT4_REST_12Hr_1


title: SKGT4_REST_4Hr_2

source_name: SKGT4 cells in untreated media for 4 hours


title: SKGT4_DCA_8Hr_2


title: SKGT4_REST_8Hr_1

source_name: SKGT4 cells in untreated media for 8 hours


title: SKGT4_DCA_24Hr_1

source_name: SKGT4 cells exposed to DCA (300um) media for 24 hours


title: SKGT4_REST_8Hr_2


title: SKGT4_DCA_12Hr_2

source_name: SKGT4 cells exposed to DCA (300um) media for 12 hours


title: SKGT4_DCA_12Hr_1


title: SKGT4_DCA_24Hr_2


title: SKGT4_REST_4Hr_1


title: HET-1A_DCA_8Hr_1

description: HET-1A cells were exposed to 300um DCA over 24 hours in duplicate experiments including matched timepoint controls

data_processing: Value data was derived through transformations in GCOS/MAS5 at a target intensity of 100

source_name: HET-1A cells exposed to 300um DCA for 8 hours

growth_protocol: HET-1A cells are grown in bronchial epithelial base medium (BEBM) with supplementation as described by the American Tissue Culture Collection (ATCC).

treatment_protocol: Cells were exposed to DCA 300um in media without supplementation.

tag: The HET-1A cell line is derived from the normal squamous esophageal epithelium and used in these experiments at passage 4.


title: HET-1A_DCA_8Hr_2


title: HET-1A_DCA_4Hr_2

source_name: HET-1A cells exposed to 300um DCA for 4 hours


title: HET-1A_DCA_24Hr_2

source_name: HET-1A cells exposed to 300um DCA for 24 hours


title: HET-1A_REST 24Hr_2

source_name: HET-1A cells in untreated media for 24 hours


title: HET-1A_DCA_12Hr_2

source_name: HET-1A cells exposed to 300um DCA for 12 hours


title: HET-1A_REST_8Hr_2

source_name: HET-1A cells in untreated media for 8 hours

label_protocol: Labelled as per instructions by affymetrix.


title: HET-1A_DCA_12Hr_1


title: HET-1A_REST_8HR_1


title: HET-1A_DCA_24Hr_1


title: HET-1A_REST 12Hr_2

source_name: HET-1A cells in untreated media for 12 hours


title: HET-1A_REST 4Hr_2

source_name: HET-1A cells in untreated media for 4 hours


title: HET-1A_REST 24Hr_1


title: HET-1A_REST 4Hr_1

hyb_protocol: Hybridised as per instructions by affymetrix.

scan_protocol: Scanned as per instructions by affymetrix at tgt 100.


title: HET-1A_REST 12Hr_1


title: Never smoker female study #95

status: Public on Feb 15 2010

first: Zeynep

middle: H.

last: Gumus

address: 1300 York Ave

department: Physiology and Biophysics

institute: Cornell University

description:
Gene expression data from buccal mucosa biopsy female never smoker
40 never smokers and 40 active smokers were recruited. Subjects were age- and gender- matched.

hyb_protocol: Following fragmentation 10 ug of cRNA were hybridized for 16 h at 45ºC on Gene Chip HGU133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Average (RMA) algorithm within GeneSpring 7.2 Software (Agilent Technologies). Data from each chip were normalized for inter-array comparisons by first setting measurements of <0.01 to 0.01 and then normalizing to 50% of measurements taken from that array.

source_name: Never smoker female buccal mucosa

label_protocol: Biontinylated cRNAs were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (www.affymetrix.com).

extract_protocol: Total RNA was isolated with an RNeasy Mini Kit (Qiagen Inc) and stored at 80ºC until analysis.

treatment_protocol: After topical anesthesia 5-mm punch biopsies were obtained from grossly normal appearing buccal mucosa.

value: buccal mucosa

tag: smoking status

value: Never Smoker

tag: gender

value: female


title: Smoker female study #93

description:
Gene expression data from buccal mucosa biopsy female smoker
40 never smokers and 40 active smokers were recruited. Subjects were age- and gender- matched.

source_name: Smoker female buccal mucosa

value: Smoker


title: HET-1A_DCA_4Hr_1


title: Never smoker female study #8


title: Smoker male study #96

description:
Gene expression data from buccal mucosa biopsy male smoker
40 never smokers and 40 active smokers were recruited. Subjects were age- and gender- matched.

source_name: Smoker male buccal mucosa

value: male


title: Never smoker male study #80

description:
Gene expression data from buccal mucosa biopsy male never smoker
40 never smokers and 40 active smokers were recruited. Subjects were age- and gender- matched.

source_name: Never smoker male buccal mucosa


title: Smoker male study #81


title: Never smoker male study #9


title: Never smoker female study #84


title: Smoker male study #98


title: Never smoker male study #91


title: Never smoker male study #66


title: Smoker female study #88


title: Smoker female study #71


title: Never smoker female study #74


title: Smoker male study #65


title: Smoker male study #9


title: Smoker female study #68


title: Smoker male study #6


title: Smoker male study #64


title: Never smoker male study #70


title: Never smoker female study #57


title: Smoker male study #61


title: Smoker female study #5


title: Smoker female study #55


title: Smoker female study #51


title: Never smoker male study #63


title: Never smoker male study #50


title: Never smoker female study #43


title: Smoker female study #53


title: Smoker female study #33


title: Smoker female study #77


title: Never smoker male study #38


title: Never smoker female study #3


title: Smoker female study #48


title: Smoker male study #49


title: Smoker male study #4


title: Never smoker female study #30


title: Never smoker male study #35


title: Never smoker male study #36

description:
Gene expression data from buccal mucosa biopsy never smoker
40 never smokers and 40 active smokers were recruited. Subjects were age- and gender- matched.


title: Smoker female study #41


title: Smoker male study #44


title: Never smoker female study #272


title: Smoker female study #2


title: Never smoker female study #32


title: Smoker female study #26


title: Smoker male study #31


title: Smoker male study #42

description:
Gene expression data from buccal mucosa biopsy
40 never smokers and 40 active smokers were recruited. Subjects were age- and gender- matched.


title: Never smoker female study #274


title: Never smoker female study #299


title: Smoker male study #40


title: Never smoker female study #269


title: Never smoker male study #267


title: Never smoker female study #265


title: Smoker male study #271


title: Never smoker male study #260


title: Never smoker male study #251


title: Never smoker female study #248


title: Smoker female study #205


title: Never smoker male study #1


title: Never smoker male study #17


title: Smoker female study #20


title: Smoker female study #210


title: Smoker male study #14


title: Never smoker male study #100


title: Smoker female study #107


title: Smoker female study #216


title: Smoker male study #203


title: Smoker male study #19


title: Never smoker female study #105


title: Smoker male study #113


title: Smoker male study #12


title: Never smoker female study #110


title: Never smoker male study #22


title: Never smoker female study #11


title: Never smoker male study #102


title: Never smoker female study #10


title: Never smoker male study #21


title: NM65  healthy control

city: Singapore

first: Yi

last: Hong

email: hong.yi@sgh.com.sg, fbap8570@yahoo.com

address: Outram Road

department: Colorectal Surgery

country: Singapore

institute: Singapore General Hospital

description: Gene expression data from healthy control

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45 °C on HG U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The baseline was arbitrarily set to 500.

source_name: mucosa collected and archived within 30mins after biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix)

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

tag: Sex:F, age:65


title: NM60  healthy control

tag: Sex:F, age:57


title: NM55  healthy control

tag: Sex:F, age:54


title: NM58  healthy control

tag: Sex:F, age:60


title: 4168T early stage CRC patient's tumor

description: Gene expression data from patients with metastasis

source_name: tumor collected and archived within 30mins after surgery

tag: Sex:F, age:68


title: NM59  healthy control

tag: Sex:M, age:54


title: NM66  healthy control

tag: Sex:M, age:59


title: 4040T early stage CRC patient's tumor

tag: Sex:F, age:52


title: 3931T early stage CRC patient's tumor

tag: Sex:F, age:51


title: 3959T early stage CRC patient's tumor

description: Gene expression data from patients without metastasis

tag: Sex:F, age:80


title: 3967T early stage CRC patient's tumor

tag: Sex:F, age:69


title: 4144T early stage CRC patient's tumor

tag: Sex:M, age:68


title: NM62  healthy control

tag: Sex:M, age:64


title: 3952T early stage CRC patient's tumor

tag: Sex:M, age:58


title: NM64  healthy control

tag: Sex:M, age:66


title: 3886T early stage CRC patient's tumor

tag: Sex:M, age:93


title: NM61  healthy control

tag: Sex:M, age:51


title: 4061T early stage CRC patient's tumor

tag: Sex:F, age:77


title: NM53  healthy control


title: 3860T early stage CRC patient's tumor

tag: Sex:F, age:79


title: 3842T early stage CRC patient's tumor

tag: Sex:F, age:61


title: 3865T early stage CRC patient's tumor

tag: Sex:M, age:56


title: 3872T early stage CRC patient's tumor


title: NM63  healthy control

tag: Sex:F, age:67


title: 3826T early stage CRC patient's tumor

tag: Sex:M, age:65


title: 3821T early stage CRC patient's tumor

tag: Sex:F, age:60


title: NM54  healthy control

tag: Sex:F, age:56


title: 3782T early stage CRC patient's tumor


title: 3757T early stage CRC patient's tumor

tag: Sex:M, age:73


title: 3765T early stage CRC patient's tumor

tag: Sex:F, age:62


title: 3685T early stage CRC patient's tumor

tag: Sex:M, age:52


title: 3775T early stage CRC patient's tumor

tag: Sex:M, age:71


title: 3684T early stage CRC patient's tumor

tag: Sex:M, age:74


title: 3626T early stage CRC patient's tumor

tag: Sex:M, age:57


title: 3750T early stage CRC patient's tumor

tag: Sex:F, age:59


title: 3616T early stage CRC patient's tumor

tag: Sex:M, age:61


title: 3644T early stage CRC patient's tumor

tag: Sex:M, age:59


title: 3735T early stage CRC patient's tumor

tag: Sex:M, age:67


title: 3667T early stage CRC patient's tumor


title: 3731T early stage CRC patient's tumor

tag: Sex:M, age:63


title: 3577T early stage CRC patient's tumor

tag: Sex:F, age:65


title: 3804T early stage CRC patient's tumor

tag: Sex:M, age:64


title: 3737T early stage CRC patient's tumor

tag: Sex:M, age:66


title: 3624T early stage CRC patient's tumor

tag: Sex:F, age:83


title: 3592T early stage CRC patient's tumor


title: 3679T early stage CRC patient's tumor


title: 3682T early stage CRC patient's tumor

tag: Sex:M, age:72


title: 3562T early stage CRC patient's tumor

tag: Sex:F, age:76


title: Never smoker male study #255

tag: tissue

tag: smoking status

tag: gender


title: 3602T early stage CRC patient's tumor

tag: Sex:M, age:75


title: 3599T early stage CRC patient's tumor


title: 3634T early stage CRC patient's tumor


title: 3557T early stage CRC patient's tumor

tag: Sex:F, age:64


title: 3604T early stage CRC patient's tumor

tag: Sex:M, age:70


title: 3717T early stage CRC patient's tumor

tag: Sex:M, age:83


title: 3567T early stage CRC patient's tumor

tag: Sex:F, age:82


title: Never smoker female study #72


title: 3515T early stage CRC patient's tumor

tag: Sex:F, age:69


title: 3423T early stage CRC patient's tumor

tag: Sex:F, age:71


title: 3501T early stage CRC patient's tumor

tag: Sex:F, age:66


title: 3438T early stage CRC patient's tumor

tag: Sex:M, age:65


title: 3530T early stage CRC patient's tumor

tag: Sex:M, age:58


title: 3459T early stage CRC patient's tumor

tag: Sex:M, age:76


title: 3357T early stage CRC patient's tumor


title: 3135T early stage CRC patient's tumor

tag: Sex:F, age:89


title: 3229T early stage CRC patient's tumor


title: 3431T early stage CRC patient's tumor

tag: Sex:M, age:74


title: 3382T early stage CRC patient's tumor

tag: Sex:M, age:71


title: 3395T early stage CRC patient's tumor

tag: Sex:M, age:62


title: 3441T early stage CRC patient's tumor

tag: Sex:M, age:68


title: 3373T early stage CRC patient's tumor

tag: Sex:F, age:83


title: 3094T early stage CRC patient's tumor


title: 3209T early stage CRC patient's tumor

tag: Sex:F, age:58


title: 3103T early stage CRC patient's tumor

tag: Sex:F, age:68


title: 3215T early stage CRC patient's tumor

tag: Sex:F, age:51


title: 3490T early stage CRC patient's tumor

tag: Sex:F, age:64


title: 3058T early stage CRC patient's tumor

tag: Sex:F, age:86


title: 3477T-R early stage CRC patient's tumor

tag: Sex:F, age:61


title: 3151T early stage CRC patient's tumor

tag: Sex:M, age:80


title: 3223T early stage CRC patient's tumor

tag: Sex:F, age:66


title: 3079T early stage CRC patient's tumor

tag: Sex:M, age:64


title: 3068T early stage CRC patient's tumor

tag: Sex:M, age:75


title: L428 (L9)

status: Public on Feb 13 2010

first: Chung-Wu

last: Lin

state: Taiwan

address: 7 South Chung-Shan Road

department: Pathology

institute: National Taiwan University

description: Array was performed as a control cell line to determine the effects of EBER in this Hodgkin lymphoma cell line. See also (accession number: GSM311203) for array of EBER1-expressing celll line LE.

hyb_protocol: Hybridization and washing of the arrays was done according to GeneChip Expression Analysis Technical Manual from Affymetrix.

scan_protocol: The arrays were scanned with GenePix 4000B (Molecular Devices, Sunnyvale, CA).

data_processing: The data were extracted with Affymetrix Microarray suite software (MAS).

label_protocol: The Affymetrix chip, Human Genome U133 plus 2.0, was used. First-strand cDNAs were synthesized from 10 ug total RNAs with a T7-ptomoter-oligo(dT) primer. After second-strand synthesis, biotin-labeled cRNAs were transcribed from the T7 promoter. The quality of cRNAs was checked by gel electrophoresis with an Agilent 6000 Bioanalyzer (Agilent Technologies, Foster City, CA). The cRNAs were fragmented into sizes from 35 to 200 nucleotides, and labeled with streptavidin-PE. The fragmented cRNAs were mixed with control RNAs (bioB, bioC, bioD, and cre) and hybridized with the membrane.

growth_protocol: They were cultured in RPMI1640 containing 10% fetal bovine serum, 100 ug/ml streptomycin, and 100U/ ml penicillin, at 37oC with 5% CO2.

extract_protocol: Total RNA sample was extracted by TRIzol® reagent (Invitrogen ).

treatment_protocol: 1x 106 L428 cells were transfected with 30 ug plasmid (empty vector) by electroporation with an ECM630 system (BTX, Holliston, MA). Stable clone expressing the fluorescent protein EGFP from a PCMV promoter, was selected in RPMI1640 and 10% fetal bovine serum containing 1mg/ml GENETICIN (Invitrogen, Carlsbad, CA).

tag: L428, Hodgkin lymphoma cell lines.


title: EBER+ KM-H2 (KE)

description: Array was performed to determine the effects of EBER in this Hodgkin lymphoma cell line. See also (accession number: GSM311194) for array of the control celll line KM-H2.

treatment_protocol: 1x 106 KMH2 cells were transfected with 30 ug plasmid by electroporation with an ECM630 system (BTX, Holliston, MA). Stable clone expressing the 167-nucleotide EBER1 transcribed from a H1 promoter in p9362 and the fluorescent protein EGFP from a PCMV promoter, was selected in RPMI1640 and 10% fetal bovine serum containing 1mg/ml GENETICIN (Invitrogen, Carlsbad, CA).

tag: KM-H2, Hodgkin lymphoma cell lines.


title: 3132T early stage CRC patient's tumor

tag: Sex:M, age:63


title: EBER+ L428 (LE)

description: Array was performed to determine the effects of EBER in this Hodgkin lymphoma cell line. See also (accession number: GSM311200) for array of the control celll line L428.

treatment_protocol: 1x 106 L428 cells were transfected with 30 ug plasmid by electroporation with an ECM630 system (BTX, Holliston, MA). Stable clone  expressing the 167-nucleotide EBER1 transcribed from a H1 promoter in p9362 and  the fluorescent protein EGFP from a PCMV promoter, was selected in RPMI1640 and 10% fetal bovine serum containing 1mg/ml GENETICIN (Invitrogen, Carlsbad, CA).

tag: L428, Hodgkin lymphoma cell line.


title: KM-H2 (K9)

description: Array was performed as a control cell line to determine the effects of EBER in this Hodgkin lymphoma cell line. See also (accession number: GSM311195) for array of EBER1-expressing celll line KE.

treatment_protocol: 1x 106 KMH2 cells were transfected with 30 ug control plasmid (empty vector with express EGFP) by electroporation with an ECM630 system (BTX, Holliston, MA). Stable clone expressing the fluorescent protein EGFP from a PCMV promoter, was selected in RPMI1640 and 10% fetal bovine serum containing 1mg/ml GENETICIN (Invitrogen, Carlsbad, CA).

tag: KMH2, Hodgkin lymphoma cell line.


title: Caov-3/CNTO328/IL-6

status: Public on Feb 11 2010

first: Zhenfeng

last: Duan

address: 100 Fruit St

institute: Massachusetts General Hospital

description: gene expression in Caov-3 cell line treated CNTO328 and IL-6

hyb_protocol: Hybridized to Affymetrix Genechip HG-U95Av2 arrays (Affymetrix, Santa Clara, CA) using standard protocols by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu).

scan_protocol: Processed according to standard protocols by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu).

data_processing: Affy Expression Console was used to analyze the raw data files (MAS5). The expression level of each mRNA is quantified by measuring its hybridization to these 23-mers in comparison to its hybridization to a one-base mismatch oligonucleotide. GeneSifter was used for statistical analysis (http://www.genesifter.net/web/). Fold change in expression between sensitive and resistant cell lines was evaluated using the Mann-Whitney test. A tenfold or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

source_name: Ovarian cancer cell line add CNTO328 and IL-6

growth_protocol: The SKOV-3 and Caov-3 ovarian cancer cell lines where seeded onto the 100mm cell culture plate for overnight.

extract_protocol: Total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer’s instructions. To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis.

treatment_protocol: The cells were then incubated with IL-6 (30ng/ml) alone for one hour or pre-treated with siltuximab for four hours and then treated with IL-6 for one hour.

tag: cell type

value: Ovarian cancer cell line

tag: cell line


title: Caov-3/IL-6

description: gene expression in Caov-3 cell line treated with IL-6

source_name: Ovarian cancer cell line add IL-6

label_protocol: Processed according to standard protocols by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu).


title: Healthy control saliva-bc6

city: Los Angeles

first: Lei

last: Zhang

address: 10833 Le Conte Ave., CHS 73-029

institute: UCLA Dental Research Institute

hyb_protocol: Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)

data_processing: The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.

source_name: saliva

label_protocol: Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).

extract_protocol: Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.

tag: biomaterial source

value: saliva

tag: disease status

value: Healthy Control


title: Caov-3

description: gene expression in Caov-3 cell line

source_name: Ovarian cancer cell line


title: Breast cancer saliva-8

scan_protocol: Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)

value: Breast Cancer


title: Healthy control saliva-bc2


title: Healthy control saliva-bc9


title: SKOV-3/CNTO328/IL-6

description: gene expression in SKOV-3 cell line treated with CNTO328 and IL-6


title: SKOV-3/IL-6

description: gene expression in SKOV-3 cell line treated with IL-6

source_name: Ovarain cancer cell line add IL-6


title: Healthy control saliva-bc7


title: Breast cancer saliva-10


title: Healthy control saliva-bc1


title: Breast cancer saliva-9


title: Breast cancer saliva-3


title: Healthy control saliva-bc8


title: Breast cancer saliva-5


title: Breast cancer saliva-7


title: Healthy control saliva-bc4


title: Healthy control saliva-bc5


title: SKOV-3

description: gene expression in SKOV-3 cell line

source_name: Ovarain cancer cell line


title: Healthy control saliva-bc10


title: Breast cancer saliva-4


title: Breast cancer saliva-2


title: Breast cancer saliva-6


title: Breast cancer saliva-1


title: Adult male, Hemiclone line P56, Repl. 3

status: Public on Feb 10 2010

city: Uppsala

first: Paolo

last: Innocenti

address: Norbyvägen 18D

department: Dept. of Animal Ecology

institute: Uppsala university

data_processing: The data were analyzed with RMA (Robust Multichip Average) as implemented by the affy package in R 2.9 (BioConductor 2.4) using default settings.

organism: Drosophila melanogaster

source_name: Adult male, Hemiclone line P56

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 base population of Drosophila melanogaster (LHM) has been maintained as a large, outbred population for over 400 non-overlapping generations. One hundred haplotypes were sampled from LHM and maintained as heterozygous stock hemiclonal lines using double-X clone-generator females [C(1)DX, y, f; T(2;3) rdgC st in ri pP bwD]. Each hemiclonal fly therefore shares one complete genomic haplotype in common, the other being a random sample from the base population.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by Qiagen purification.

treatment_protocol: Adult hemiclonal and LHM tester flies of both sexes (reared following the base population protocol) were then collected in groups of 16 on day-10. On day-12 each group of hemiclones was placed together with a group of tester flies of the opposite sex in yeasted vials. After 24 hours the tester flies were removed and after a further 20 hours groups of 6 flies were randomly chosen from each vial under brief CO2 anaesthesia. Four hours after sorting, the flies were frozen using liquid nitrogen prior to RNA extraction.

tag: tissue

value: whole fly

tag: genotype

value: LHm, hemiclone line

tag: age

value: Day 14 (4 days adult)


title: 3514T-R early stage CRC patient's tumor

tag: Sex:M, age:66


title: Adult male, Hemiclone line P50, Repl. 4

source_name: Adult male, Hemiclone line P50


title: Adult male, Hemiclone line P50, Repl. 3


title: human left atrial_control_4

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

country: Germany

institute: Universitätsmedizin Greifswald

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome 133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the protocol EukGe-Ws2v5.

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

data_processing: After probe set summarization using MAS5.0 algorithm in GCOS, expression raw data were transferred to GeneSpring GX software (7.3.1) to perform per Chip median normalization for signals which were flagged present or marginal.

source_name: human left atrial appendage - control

label_protocol: Probes for Affymetrix microarray analysis were prepared using 50ng total RNA with GeneChip Expression 3´Amplification Two Cycle Target labeling and Control Reagents Kits according to the manufacturer’s instructions (Affymetrix).

extract_protocol: Tissue was homogenized with Qiagen Shredder columns and digested with Proteinase K. For gene expression profiling RNA was prepared according to manufacturer´s Qiagen Mini Kit protocol. RNA integrity was checked using RNA 6000 Nano LabChip on a Bioanalyzer 2100 (Agilent)

treatment_protocol: Myocardial tissue was immediately frozen and stored at -80°C.

value: left atrial appendage


title: Adult female, Hemiclone line P50, Repl. 2

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

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

source_name: Adult female, Hemiclone line P50


title: Adult male, Hemiclone line P56, Repl. 4


title: Adult female, Hemiclone line P56, Repl. 2

source_name: Adult female, Hemiclone line P56


title: Adult female, Hemiclone line P50, Repl. 4


title: human left atrial_patient_2

source_name: human left atrial appendage - atrial fibrillation patient


title: human left atrial_control_5


title: Adult male, Hemiclone line P56, Repl. 2


title: Adult male, Hemiclone line P50, Repl. 2


title: Adult female, Hemiclone line P56, Repl. 3


title: human left atrial_patient_3


title: human left atrial_patient_4


title: Adult male, Hemiclone line P50, Repl. 1


title: human left atrial_control_2


title: Adult female, Hemiclone line P56, Repl. 4


title: Adult female, Hemiclone line P50, Repl. 3


title: Adult male, Hemiclone line P56, Repl. 1


title: human left atrial_control_1


title: human left atrial_patient_1


title: human left atrial_patient_5


title: Adult female, Hemiclone line P50, Repl. 1


title: human left atrial_control_3


title: Adult female, Hemiclone line P56, Repl. 1


title: Adult male, Hemiclone line P48, Repl. 4

source_name: Adult male, Hemiclone line P48


title: Adult male, Hemiclone line P48, Repl. 3


title: Adult male, Hemiclone line P26, Repl. 4

source_name: Adult male, Hemiclone line P26


title: Adult female, Hemiclone line P48, Repl. 1

source_name: Adult female, Hemiclone line P48


title: Adult male, Hemiclone line P22, Repl. 4

source_name: Adult male, Hemiclone line P22


title: Adult male, Hemiclone line P48, Repl. 2


title: Adult female, Hemiclone line P48, Repl. 2


title: Adult female, Hemiclone line P26, Repl. 1

source_name: Adult female, Hemiclone line P26


title: Adult female, Hemiclone line P26, Repl. 2


title: Adult female, Hemiclone line P26, Repl. 4


title: Adult female, Hemiclone line P48, Repl. 3


title: Adult male, Hemiclone line P26, Repl. 3


title: Adult female, Hemiclone line P48, Repl. 4


title: Adult female, Hemiclone line P26, Repl. 3


title: Adult male, Hemiclone line P26, Repl. 1


title: Adult male, Hemiclone line P22, Repl. 3


title: Adult male, Hemiclone line P48, Repl. 1


title: Adult male, Hemiclone line P22, Repl. 2


title: Adult male, Hemiclone line P22, Repl. 1


title: Adult female, Hemiclone line P22, Repl. 4

source_name: Adult female, Hemiclone line P22


title: Adult male, Hemiclone line P18, Repl. 1

source_name: Adult male, Hemiclone line P18


title: Adult female, Hemiclone line P18, Repl. 3

source_name: Adult female, Hemiclone line P18


title: Healthy control saliva-bc3

source_name: saliva


title: Adult female, Hemiclone line P22, Repl. 3


title: Adult female, Hemiclone line P22, Repl. 2


title: Adult female, Hemiclone line P18, Repl. 4


title: Adult male, Hemiclone line P26, Repl. 2


title: Adult male, Hemiclone line P18, Repl. 3


title: Adult female, Hemiclone line P22, Repl. 1


title: Adult male, Hemiclone line P18, Repl. 2


title: Adult male, Hemiclone line P18, Repl. 4


title: Adult female, Hemiclone line P15, Repl. 4

source_name: Adult female, Hemiclone line P15


title: Adult male, Hemiclone line P13, Repl. 1

source_name: Adult male, Hemiclone line P13


title: Adult male, Hemiclone line P13, Repl. 4


title: Adult female, Hemiclone line P15, Repl. 2


title: Adult female, Hemiclone line P13, Repl. 3

source_name: Adult female, Hemiclone line P13


title: Adult male, Hemiclone line P15, Repl. 2

source_name: Adult male, Hemiclone line P15


title: Adult female, Hemiclone line P13, Repl. 2


title: Adult female, Hemiclone line P15, Repl. 3


title: Adult male, Hemiclone line P13, Repl. 3


title: Adult female, Hemiclone line P13, Repl. 4


title: Adult male, Hemiclone line P15, Repl. 4


title: Adult female, Hemiclone line P13, Repl. 1


title: Adult male, Hemiclone line P15, Repl. 3


title: Adult female, Hemiclone line P18, Repl. 2


title: Adult male, Hemiclone line P13, Repl. 2


title: Adult male, Hemiclone line P15, Repl. 1


title: Adult female, Hemiclone line P15, Repl. 1


title: Adult male, Hemiclone line P07, Repl. 4

source_name: Adult male, Hemiclone line P07


title: Adult female, Hemiclone line P07, Repl. 3

source_name: Adult female, Hemiclone line P07


title: Adult male, Hemiclone line P07, Repl. 1


title: Adult male, Hemiclone line P07, Repl. 3


title: Adult female, Hemiclone line P07, Repl. 2


title: Adult female, Hemiclone line P07, Repl. 4


title: Adult male, Hemiclone line P07, Repl. 2


title: Adult female, Hemiclone line P07, Repl. 1


title: Adult male, Hemiclone line H14, Repl. 4

source_name: Adult male, Hemiclone line H14


title: Adult female, Hemiclone line P18, Repl. 1


title: Adult male, Hemiclone line H14, Repl. 2


title: Adult male, Hemiclone line H14, Repl. 3


title: Adult male, Hemiclone line H13, Repl. 3

source_name: Adult male, Hemiclone line H13


title: Adult female, Hemiclone line H14, Repl. 1

source_name: Adult female, Hemiclone line H14


title: Adult female, Hemiclone line H13, Repl. 1

source_name: Adult female, Hemiclone line H13


title: Adult male, Hemiclone line H12, Repl. 3

source_name: Adult male, Hemiclone line H12


title: Adult male, Hemiclone line H13, Repl. 2


title: Adult female, Hemiclone line H14, Repl. 4


title: Adult male, Hemiclone line H13, Repl. 4


title: Adult male, Hemiclone line H12, Repl. 4


title: Adult female, Hemiclone line H13, Repl. 3


title: Adult male, Hemiclone line H13, Repl. 1


title: Adult male, Hemiclone line H14, Repl. 1


title: Adult female, Hemiclone line H14, Repl. 2


title: Adult female, Hemiclone line H12, Repl. 4

source_name: Adult female, Hemiclone line H12


title: Adult female, Hemiclone line H13, Repl. 2


title: Adult male, Hemiclone line H12, Repl. 2


title: Adult female, Hemiclone line H14, Repl. 3


title: Adult female, Hemiclone line H13, Repl. 4


title: Adult female, Hemiclone line H12, Repl. 3


title: Adult female, Hemiclone line H10, Repl. 4

source_name: Adult female, Hemiclone line H10


title: Adult male, Hemiclone line H10, Repl. 1

source_name: Adult male, Hemiclone line H10


title: Adult female, Hemiclone line H12, Repl. 2


title: Adult male, Hemiclone line H12, Repl. 1


title: Adult male, Hemiclone line H10, Repl. 3


title: Adult male, Hemiclone line H10, Repl. 2


title: Adult female, Hemiclone line H10, Repl. 3


title: Adult male, Hemiclone line H10, Repl. 4


title: Adult female, Hemiclone line H12, Repl. 1


title: Adult female, Hemiclone line H10, Repl. 2


title: Adult male, Hemiclone line H09, Repl. 3

source_name: Adult male, Hemiclone line H09


title: Adult female, Hemiclone line H09, Repl. 4

source_name: Adult female, Hemiclone line H09


title: Adult male, Hemiclone line H07, Repl. 2

source_name: Adult male, Hemiclone line H07


title: Adult male, Hemiclone line H09, Repl. 2


title: Adult female, Hemiclone line H09, Repl. 2


title: Adult male, Hemiclone line H07, Repl. 1


title: Adult male, Hemiclone line H07, Repl. 3


title: Adult male, Hemiclone line H09, Repl. 1


title: Adult female, Hemiclone line H09, Repl. 3


title: Adult female, Hemiclone line H10, Repl. 1


title: Adult female, Hemiclone line H09, Repl. 1


title: Adult male, Hemiclone line H09, Repl. 4


title: Adult male, Hemiclone line H07, Repl. 4


title: Adult female, Hemiclone line H07, Repl. 1

source_name: Adult female, Hemiclone line H07


title: Adult female, Hemiclone line H07, Repl. 4


title: Adult female, Hemiclone line H07, Repl. 2


title: Adult female, Hemiclone line H07, Repl. 3


title: Arabidopsis_seedling_det2-light-dark_rep_1

city: Shang Hai

first: Li

last: Song

address: FengLin Road

country: China

institute: SIPPE

description: BR deficient mutant,14 days seedling grown in light to 8 hours dark response

hyb_protocol: Standand Affymetrix protocol

scan_protocol: Affy GeneChip Scanner 3000.

data_processing: The data normalized using MAS5.0 methods were analyzed parallel in order to improve the stability of Statistical Analysis (Smyth, 2004). Genes with absent for the detection value in the baseline data and decrease (or increase) for the change value were excluded from the list, only those regulated in both repeats were selected for further analysis. And linear statistical model in Limma package (Smyth et al., 2005) from Bioconductor was used to identify significant differently expressed genes between two groups.

source_name: det2_seedling_14 days

label_protocol: Standand Affymetrix protocol

extract_protocol: Triazol

value: 14 day seedling

tag: BR deficient mutant grown in light to 8 hours dark response


title: Arabidopsis_seedling_det2-light_rep_1

description: BR deficient mutant,7 days seedling grown in light

hyb_protocol: Standard Affymetrix Protocol

source_name: det2_seedling_7 days

label_protocol: Standard Affymetrix Protocol

extract_protocol: triazol

value: 7 days seedling

tag: BR deficient mutant grown in light


title: Arabidopsis_seedling_det2-_rep_2

description: BR deficient mutant, 7 days seedling grown in dark

value: 7 day seedling

tag: BR deficient mutant grown in dark


title: Arabidopsis_seedling_det2-light-dark_rep_2


title: Arabidopsis_seedling_det2-light_rep_2


title: Arabidopsis_seedling_det2-_rep_1


title: T-cell acute lymphoblastic leukemia, JURKAT

status: Public on Feb 08 2010

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

description:
Gene expression data from T-ALL cell line.
JURKAT

hyb_protocol: Following fragmentation, 20 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: Affymetrix Scanning Protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further analysis (e.g., clustering, classification) was carried using BRB-ArrayTools version (3.7.0).

source_name: T-ALL cell line

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

growth_protocol: All the tissues used in the study were fresh frozen and stored below -70 degree C.

extract_protocol: Total RNA was extracted with Trizol and further purified with RNeasy Mini Columns (Qiagen, Valencia, CA) before aliquots were run in agarose gel electrophoresis and measured by spectrophotometer at 260 and 280 nm to assess the quality of the RNA.

treatment_protocol: The cryopreserved tissues from pre-treated biopsies obtained at the time of diagnosis had been stored in liquid nitrogen or -80 degree C before total RNA extraction.

value: T-ALL

tag: gender


title: T-cell line, Sezary syndrome

description:
Gene expression data from T-ALL cell line.
HUT78


title: T-cell prolymphocytic leukemia

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-93

source_name: Pre-treated fresh frozen biopsy, PTCL

value: PTCL


title: T-cell acute lymphoblastic leukemia, MOLT3

description:
Gene expression data from T-ALL cell line.
MOLT3


title: Angioimmunoblastic T-cell lymphoma 36_replicate

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-99


title: T-cell acute lymphoblastic leukemia, JURKAT_B

description:
Gene expression data from T-ALL cell line.
JURKAT_B


title: Angioimmunoblastic T-cell lymphoma 35

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-96


title: Anapalstic Large cell lymphoma ALK-NEG3_replicate

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-95


title: Angioimmunoblastic T-cell lymphoma 34

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-94


title: T-cell acute lymphoblastic leukemia, PEER

description:
Gene expression data from T-ALL cell line.
PEER


title: Angioimmunoblastic T-cell lymphoma 36

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-98


title: Angioimmunoblastic T-cell lymphoma 32

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-87

value: not available


title: Angioimmunoblastic T-cell lymphoma 33

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-92

value: female


title: Angioimmunoblastic T-cell lymphoma 31

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-84


title: Peripheral T-Cell lymphoma, unspecified 27

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-91


title: BEAS-2B_Control

status: Public on Feb 09 2010

city: ILLKIRCH

first: Thomas

last: Hussenet

address: 1 rue Laurent Fries

department: Cancer Biology Department

institute: IGBMC

description: Human immortalized and non tumorigenic lung squamous cell line, transduced with lentivirus for GFP and luciferase expression (Control).

hyb_protocol: Done by the Affymetrix core facility at IGBMC, following manufacturer instructions.

data_processing: RMA normalization using the “Remote Analysis Computation for gene Expression data” tool available online (RACE; Psarros et al., Nucleic Acids Research 2005).

source_name: Human lung squamous BEAS-2B Control cells

extract_protocol: Trizol extraction following manifacturer's instructions.

value: lung squamous BEAS-2B Control cells


title: Peripheral T-Cell lymphoma, unspecified 22

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-78

value: male


title: BEAS-2B_SOX2

description: Human immortalized and non tumorigenic lung squamous cell line, transduced with lentivirus for GFP and SOX2 expression.

scan_protocol: Done by the Affymetrix core facility at IGBMC, following manufacturer instructions.

source_name: Human lung squamous BEAS-2B SOX2 cells

value: lung squamous BEAS-2B SOX2 cells


title: Angioimmunoblastic T-cell lymphoma 29

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-77


title: Peripheral T-Cell lymphoma, unspecified 20

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-74


title: Peripheral T-Cell lymphoma, unspecified 23

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-81


title: Peripheral T-Cell lymphoma, unspecified 21

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-76


title: Angioimmunoblastic T-cell lymphoma 30

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-82


title: Adult T-cell leukemia/lymphoma-9

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-68


title: Peripheral T-Cell lymphoma, unspecified 19

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-72


title: Angioimmunoblastic T-cell lymphoma 28

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-75


title: Angioimmunoblastic T-cell lymphoma 26

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-67


title: Angioimmunoblastic T-cell lymphoma 24

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-62


title: Anapalstic Large cell lymphoma ALK-POS20

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-46


title: Anapalstic Large cell lymphoma ALK-POS6

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-48


title: Angioimmunoblastic T-cell lymphoma 22

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-58


title: Adult T-cell leukemia/lymphoma-5

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-61


title: Anapalstic Large cell lymphoma ALK-POS18

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-53


title: Angioimmunoblastic T-cell lymphoma 23

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-59


title: Anapalstic Large cell lymphoma ALK-POS15

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-44


title: Anapalstic Large cell lymphoma ALK-NEG3

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-42


title: Anapalstic Large cell lymphoma ALK-NEG9

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-40


title: Angioimmunoblastic T-cell lymphoma 25

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-63


title: Adult T-cell leukemia/lymphoma-3

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-43


title: Anapalstic Large cell lymphoma ALK-POS19

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-56


title: Anapalstic Large cell lymphoma ALK-POS14

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-41


title: Angioimmunoblastic T-cell lymphoma 27

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-70


title: Anapalstic Large cell lymphoma ALK-POS17

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-52


title: Adult T-cell leukemia/lymphoma-7

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-65


title: Anapalstic Large cell lymphoma ALK-POS4

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-36


title: Anapalstic Large cell lymphoma ALK-NEG2

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-34


title: Angioimmunoblastic T-cell lymphoma21

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-37


title: Angioimmunoblastic T-cell lymphoma 19

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-31


title: Anapalstic Large cell lymphoma ALK-POS3

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-28


title: Angioimmunoblastic T-cell lymphoma 17

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-27


title: Peripheral T-Cell lymphoma, unspecified 2_replicate

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-30


title: Anapalstic Large cell lymphoma ALK-POS1

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-26


title: Angioimmunoblastic T-cell lymphoma 18

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-29


title: Anapalstic Large cell lymphoma ALK-POS2

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-24


title: Angioimmunoblastic T-cell lymphoma 20

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-32


title: Anapalstic Large cell lymphoma ALK-NEG7

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-21


title: Peripheral T-Cell lymphoma, unspecified 10

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-16


title: Peripheral T-Cell lymphoma, unspecified 17

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-22


title: Peripheral T-Cell lymphoma, unspecified 13

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-154


title: Angioimmunoblastic T-cell lymphoma 15

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-19


title: Peripheral T-Cell lymphoma, unspecified 16_replicate

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-18


title: Angioimmunoblastic T-cell lymphoma 16

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-20


title: Peripheral T-Cell lymphoma, unspecified 16

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-17


title: Peripheral T-Cell lymphoma, unspecified 13_replicate

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-155


title: Angioimmunoblastic T-cell lymphoma 11

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-146


title: Angioimmunoblastic T-cell lymphoma 14

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-152


title: Peripheral T-Cell lymphoma, unspecified 14

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-158


title: Peripheral T-Cell lymphoma, unspecified 40

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-140


title: Angioimmunoblastic T-cell lymphoma 8

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-142


title: Peripheral T-Cell lymphoma, unspecified 12 replicate

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-14


title: Peripheral T-Cell lymphoma, unspecified 15

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-160


title: Peripheral T-Cell lymphoma, unspecified 1

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-15


title: Angioimmunoblastic T-cell lymphoma 9

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-143


title: Angioimmunoblastic T-cell lymphoma 13

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-149


title: Anapalstic Large cell lymphoma ALK-POS5

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-153


title: Peripheral T-Cell lymphoma, unspecified 2

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-159


title: Peripheral T-Cell lymphoma, unspecified 43

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-147


title: Angioimmunoblastic T-cell lymphoma 10

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-144


title: Peripheral T-Cell lymphoma, unspecified 12

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-13


title: Peripheral T-Cell lymphoma, unspecified 33

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-129


title: Peripheral T-Cell lymphoma, unspecified 39

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-131


title: Anapalstic Large cell lymphoma ALK-POS11

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-135


title: Angioimmunoblastic T-cell lymphoma 12

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-148


title: Peripheral T-Cell lymphoma, unspecified 34

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-130


title: Anapalstic Large cell lymphoma ALK-POS9

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-126


title: Peripheral T-Cell lymphoma, unspecified 28

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-120


title: Anapalstic Large cell lymphoma ALK-NEG6

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-125


title: Anapalstic Large cell lymphoma ALK-NEG5

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-121


title: Peripheral T-Cell lymphoma, unspecified 11

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-115


title: Adult T-cell leukemia/lymphoma-2

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-12


title: Peripheral T-Cell lymphoma, unspecified 9

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-114


title: Anapalstic Large cell lymphoma ALK-NEG4

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-111


title: Peripheral T-Cell lymphoma, unspecified 8

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-110


title: Angioimmunoblastic T-cell lymphoma 7

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-112


title: Peripheral T-Cell lymphoma, unspecified 29

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-118


title: Anapalstic Large cell lymphoma ALK-POS7

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-107


title: Peripheral T-Cell lymphoma, unspecified 5

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-103


title: Peripheral T-Cell lymphoma, unspecified 6

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-105


title: Peripheral T-Cell lymphoma, unspecified 18

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-102


title: Anapalstic Large cell lymphoma ALK-POS8

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-116


title: Angioimmunoblastic T-cell lymphoma 5

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-101


title: Angioimmunoblastic T-cell lymphoma 6

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-104


title: Peripheral T-Cell lymphoma, unspecified 4

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-100


title: Peripheral T-Cell lymphoma, unspecified 3_replicate

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-10


title: Adult T-cell leukemia/lymphoma-1_replicate

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-08


title: Peripheral T-Cell lymphoma, unspecified 3

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-09


title: Peripheral T-Cell lymphoma, unspecified 44

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-03


title: Adult T-cell leukemia/lymphoma-1

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-07


title: Peripheral T-Cell lymphoma, unspecified 41

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-02


title: Peripheral T-Cell lymphoma, unspecified 44_replicate

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-04


title: Angioimmunoblastic T-cell lymphoma 4

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-06


title: Activated CD8+ T-cells with anti-CD3, anti-CD28 and IL-12 and harvested after 2 hours incubation

description:
Gene expression data from resting CD8+ T-cells.
CD8-T2

source_name: Normal CD8+ T-cell subset

value: CD8+ T-cell


title: Anapalstic Large cell lymphoma ALK-NEG1

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-01


title: Activated CD8+ T-cells with anti-CD3, anti-CD28 and IL-12 and harvested after 8 hours incubation

description:
Gene expression data from resting CD8+ T-cells.
CD8-T8


title: Activated CD4+ T-cells with anti-CD3, anti-CD28 and IL-12 and harvested after 8 hours incubation

description:
Gene expression data from resting CD4+ T-cells.
CD4_T8

source_name: Normal CD4+ T-cell subset

value: CD4+ T-cell


title: Activated CD4+ T-cells with anti-CD3, anti-CD28 and IL-12 and harvested after 24 hours incubation

description:
Gene expression data from resting CD4+ T-cells.
CD4_T24


title: Activated CD4+ T-cells with anti-CD3, anti-CD28 and IL-12 and harvested after 2 hours incubation

description:
Gene expression data from resting CD4+ T-cells.
CD4_T2


title: Activated CD8+ T-cells with anti-CD3, anti-CD28 and IL-12 and harvested after 48 hours incubation

description:
Gene expression data from resting CD8+ T-cells.
CD8-T48


title: Activated CD4+ T-cells with anti-CD3, anti-CD28 and IL-12 and harvested after 48 hours incubation

description:
Gene expression data from resting CD4+ T-cells.
CD4_T48


title: Resting CD4+ T-cells (FACS sorted)

description:
Gene expression data from resting CD4+ T-cells.
CD4_T0


title: Activated CD8+ T-cells with anti-CD3, anti-CD28 and IL-12 and harvested after 24 hours incubation

description:
Gene expression data from resting CD8+ T-cells.
CD8-T24


title: Adult T-cell leukemia/lymphoma-4

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-60