title: CLL with unmutated IgV gene uCLL_2

description: batch 3


title: CLL with unmutated IgV gene uCLL_3

status: Public on Sep 27 2012

type: RNA

city: Essen

first: Marc

middle: JS

last: Seifert

state: NRW

address: Virchowstraße 173

department: IFZ

country: Germany

institute: University Hospital Essen

description: batch 3

hyb_protocol: Following fragmentation, cRNA was hybridized on GPL570 Arrays with the Affymetrix GeneChip Hybridization, Wash and Stain kit, according to manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G and GeneChip Command Console 3.2 software.

data_processing: Data were normalized according to vsn and imported into Gene Spring GX 7.3.1 and filtered according to a minimum amount of 4 present calls (according to GC-RMA normalization and flagging by MAS5) within at least one condition (cell type) and raw signal above 50. Remaining probe sets were exported, processed with ComBat software to compell batch effects and reimported into Gene Spring for further analysis.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human peripheral blood

label_protocol: Two rounded in vitro transcription protocol with Ambion MessageAmpII kit and MessageAmp Biotin Enhanced-Kit according to manufacturer's instructions.

growth_protocol: cell sorting, see sample title

extract_protocol: 10,000 cell samples sorted into Trizol lysis buffer, hydrous phase mixed with equal volume of 70% EtOH and loaded onto Qiagen RNeasy micro colum. Further processing according to manufacturer's instruction.

tag: tumor stage

value: tumor

tag: cell type

value: CLL cell with unmutated IgV gene


title: AML [ ID_01 ]

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

institute: Charité Universitätsmedizin Berlin

description: AML [ ID_01 ], ID01_ULM_00127.CEL

hyb_protocol: Hybridization, washing, and staining protocols were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: The samples were scanned on Affymetrix GeneChip Scanner GCS3000 system using default settings and the software GCOS version 1.2 or newer.

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed.

source_name: cytogenetically normal AML (CN-AML), CEBPA: mut, FLT3-ITD: wt, FLT3-TKD: wt, NPM1: wt

label_protocol: Total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

extract_protocol: The total RNA was purified with a TRIzol-based protocol.

treatment_protocol: Diagnostic samples were collected from untreated patients (de novo AML).

tag: diagnosis

value: Acute myeloid leukemia (AML)

value: mononuclear

tag: cell source

value: bone marrow


title: CLL with unmutated IgV gene uCLL_1

description: batch 3


title: CLL with mutated IgV gene mCLL_5

description: batch 3

value: CLL cell with mutated IgV gene


title: CLL with mutated IgV gene mCLL_4

description: batch 3


title: tissue type name: Skin - developmental stage name: R2 - rep2

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

description: tissue type name=Skin|developmental stage name=R2 rep 2 (May still include original submitter created erros/discrepancies)

hyb_protocol: CNB Grapegen Affymetrix hybridization

scan_protocol: CNB Grapegen Affymetrix scanning

data_processing: RMA normalization was performed for Affymetrix Platforms: Using APT (apt-1.12.0: apt-probeset-summarize.cpp,v 1.178).

organism: Vitis vinifera

source_name: Exocarp (tissue type name: Skin - developmental stage name: R2)

label_protocol: CNB Grapegen Affymetrix labeling

extract_protocol: Optimized grapevine RNA isolation

tag: cultivar

value: Muscat Hamburg cv.

tag: tissue

value: exocarp

tag: development stage

value: Ripe 2

tag: growth media

value: field soil


title: CLL with mutated IgV gene mCLL_3

description: batch 3


title: CLL with mutated IgV gene mCLL_2

description: batch 3


title: tissue type name: Skin - developmental stage name: R2 - rep3

description: tissue type name=Skin|developmental stage name=R2 rep 3 (May still include original submitter created erros/discrepancies)


title: tissue type name: Skin - developmental stage name: R2 - rep5

description: tissue type name=Skin|developmental stage name=R2 rep 5 (May still include original submitter created erros/discrepancies)


title: tissue type name: Skin - developmental stage name: R2 - rep4

description: tissue type name=Skin|developmental stage name=R2 rep 4 (May still include original submitter created erros/discrepancies)


title: tissue type name: Skin - developmental stage name: R2 - rep6

description: tissue type name=Skin|developmental stage name=R2 rep 6 (May still include original submitter created erros/discrepancies)


title: tissue type name: Skin - developmental stage name: R1 - rep5

description: tissue type name=Skin|developmental stage name=R1 rep 5 (May still include original submitter created erros/discrepancies)

source_name: Exocarp (tissue type name: Skin - developmental stage name: R1)

value: Ripe 1


title: tissue type name: Skin - developmental stage name: R1 - rep6

description: tissue type name=Skin|developmental stage name=R1 rep 6 (May still include original submitter created erros/discrepancies)


title: tissue type name: Skin - developmental stage name: R1 - rep3

description: tissue type name=Skin|developmental stage name=R1 rep 3 (May still include original submitter created erros/discrepancies)


title: tissue type name: Skin - developmental stage name: R2 - rep1

description: tissue type name=Skin|developmental stage name=R2 rep 1 (May still include original submitter created erros/discrepancies)


title: Tumor 1_22C @ 120 mins

city: INDIANAPOLIS

first: Nick

last: Liu

state: Indiana

address: 535 Barnhill Drive Suite 420

department: Department of Urology

institute: Indiana University Hospital

description: Gene expression data from tumor 1 at ischemic conditions

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 plus 2.0 olgionucleotide array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Each array was  washed, stained and scanned by the Affymetrix GeneChip 3000 Scanner. Raw intensities for each probe were stored as .DAT and .CEL files by the GeneChip Operating Software v1.4 (Affymetrix Inc, Santa Clara, CA USA).

data_processing:
Complete analyses of array data were carried out in BRB-Array Tools v3.7 (http://linus.nci.nih.gov/BRB-ArrayTools.html)
Processed/Filtered and Log2_transformed array intensities

source_name: Tumor 1_22C @ 120 mins

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA using GeneChip Two-Cycle cDNA Target Synthesis Kit (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: 10 renal tumors were divided and treated under the above listed conditions and snap frozen at 5, 30, 60, 120 and 240 minutes after surgical resection

value: VHL Clear Cell Renal Cell Carcinoma

tag: patient

value: Tumor 1

tag: treatment


title: CLL with mutated IgV gene mCLL_1

description: batch 3


title: IgD+CD27- PB B cells naive_7

description: batch 3

value: non-tumor

value: IgD+CD27- PB B cells


title: IgD+CD27- PB B cells naive_5

description: batch 1


title: IgD+CD27- PB B cells naive_3

description: batch 2


title: tissue type name: Skin - developmental stage name: R1 - rep4

description: tissue type name=Skin|developmental stage name=R1 rep 4 (May still include original submitter created erros/discrepancies)


title: tissue type name: Skin - developmental stage name: R1 - rep2

description: tissue type name=Skin|developmental stage name=R1 rep 2 (May still include original submitter created erros/discrepancies)


title: tissue type name: Skin - developmental stage name: V2 - rep5

description: tissue type name=Skin|developmental stage name=V2 rep 5 (May still include original submitter created erros/discrepancies)

source_name: Exocarp (tissue type name: Skin - developmental stage name: V2)

value: 100% véraison


title: IgD+CD27- PB B cells naive_4

description: batch 1


title: IgM+CD27+CD21high splenic B cells MGZ_4

description: batch 1

source_name: human splenic tissue

value: IgM+CD27+CD21high splenic B cells


title: IgM+CD27+CD21high splenic B cells MGZ_5

description: batch 1


title: tissue type name: Skin - developmental stage name: V2 - rep4

description: tissue type name=Skin|developmental stage name=V2 rep 4 (May still include original submitter created erros/discrepancies)


title: IgD+CD27- PB B cells naive_6

description: batch 3


title: AML [ ID_51 ]

description: AML [ ID_51 ], ID51_MB_080806_05KM1583-2.CEL

source_name: cytogenetically normal AML (CN-AML), CEBPA: mut, FLT3-ITD: mut, FLT3-TKD: wt, NPM1: wt


title: IgD+CD27- PB B cells naive_1

description: batch 2


title: tissue type name: Skin - developmental stage name: R1 - rep1

description: tissue type name=Skin|developmental stage name=R1 rep 1 (May still include original submitter created erros/discrepancies)


title: tissue type name: Skin - developmental stage name: V2 - rep6

description: tissue type name=Skin|developmental stage name=V2 rep 6 (May still include original submitter created erros/discrepancies)


title: IgM+CD27+CD21high splenic B cells MGZ_3

description: batch 2


title: tissue type name: Skin - developmental stage name: V2 - rep2

description: tissue type name=Skin|developmental stage name=V2 rep 2 (May still include original submitter created erros/discrepancies)


title: IgD+CD27- PB B cells naive_2

description: batch 2


title: tissue type name: Skin - developmental stage name: V2 - rep1

description: tissue type name=Skin|developmental stage name=V2 rep 1 (May still include original submitter created erros/discrepancies)


title: IgM+CD27+CD21high splenic B cells MGZ_2

description: batch 2


title: SC F3-Vin biological rep1

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
Gene expression data from Sertoli cell from 20 days old ovary of F3 vinclozolin lineage rat
Three pools of P20 Sertoli cells were produced per treatment, with each pool containing cells from 2 to 6 animals.

hyb_protocol: Following fragmentation, ssDNA were hybridized  on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the   Affymetrix Fluidics Station 4500.

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

data_processing: The data were analyzed with Partek Genomic Suite 6.5 beta software  (Partek Inc., St. Louis, MO) using RMA, GC-content adjusted algorithm background correction, quintile normalization, median polish methods for probesets summarization, and log values of probes signals using base 2.  Sertoli cell preparation date batch effect was removed.

organism: Rattus norvegicus

source_name: Sertoli cell from 20 days old F3 vinclozolin lineage rat testis

label_protocol: Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).

growth_protocol: Sertoli cell were isolated from 20 days old male rats of F3 generation of vinclozolin and control lineages as described previously [Muir T, Sadler-Riggleman I, Skinner MK (2005) Role of the basic helix-loop-helix transcription factor, scleraxis, in the regulation of Sertoli cell function and differentiation. Mol Endocrinol 19: 2164-2174].    In brief, decapsulated testes were minced with razor blades and then tissue fragments were digested with trypsin (1.5 mg/ml, Life Technologies, Gaithersburg, MD) to remove the interstitial cells. This was followed by incubation with collagenase (1 mg/ml type I, Sigma) for removal of peritubular cells and then hyaluronidase (1 mg/ml, Sigma) for removal of germ cells. The purity of the Sertoli cell preparations were determined to be >98%.

extract_protocol: RNA was isolated from Sertoli cells after lysis in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.

treatment_protocol: Gestating outbred Sprague-Dawley mother rats were given intraperitoneal injections of Vinclozolin (100mg/kg/day) or vehicle (DMSO, Control) from embryonic day 8-14 (E8-E14) of gestation (i.e. F0 generation) [Cupp AS, et al., 2003].  Subsequent  F2 and F3 generations wee obtained from F1 rats.

tag: cell preparation date batch

tag: strain

value: Sprague-Dawley rat

tag: gender

value: Male

value: Sertoli cell

tag: age

value: 20 days old rat

value: vinclozolin lineage


title: tissue type name: Skin - developmental stage name: V1 - rep5

description: tissue type name=Skin|developmental stage name=V1 rep 5 (May still include original submitter created erros/discrepancies)

source_name: Exocarp (tissue type name: Skin - developmental stage name: V1)

value: 50% véraison


title: tissue type name: Skin - developmental stage name: V2 - rep3

description: tissue type name=Skin|developmental stage name=V2 rep 3 (May still include original submitter created erros/discrepancies)

value: Muscat Hamburg cv.


title: SC F3-Vin biological rep3


title: tissue type name: Skin - developmental stage name: V1 - rep6

description: tissue type name=Skin|developmental stage name=V1 rep 6 (May still include original submitter created erros/discrepancies)

value: exocarp


title: IgM+CD27+CD21high splenic B cells MGZ_1

description: batch 2


title: tissue type name: Skin - developmental stage name: V1 - rep4

description: tissue type name=Skin|developmental stage name=V1 rep 4 (May still include original submitter created erros/discrepancies)


title: SC F3-Vin biological rep2


title: IgM+IgD+CD27+ PB B cells MD27_5

description: batch 2

value: IgM+IgD+CD27+ PB B cells


title: IgM+IgD+CD27+ PB B cells MD27_3

description: batch 1


title: tissue type name: Skin - developmental stage name: V1 - rep3

description: tissue type name=Skin|developmental stage name=V1 rep 3 (May still include original submitter created erros/discrepancies)

value: field soil


title: IgM+IgD+CD27+ PB B cells MD27_2

description: batch 1


title: SC F3-Control biological rep2

description:
Gene expression data from Sertoli cell from 20 days old ovary of F3 control lineage rat
Three pools of P20 Sertoli cells were produced per treatment, with each pool containing cells from 2 to 6 animals.

source_name: Sertoli cell from 20 days old F3 control lineage rat testis

value: control lineage


title: SC F3-Control biological rep3


title: tissue type name: Skin - developmental stage name: V1 - rep1

description: tissue type name=Skin|developmental stage name=V1 rep 1 (May still include original submitter created erros/discrepancies)


title: IgM+IgDlowCD27+ PB B cells IgM-only_5

description: batch 1

value: IgM+IgDlowCD27+ PB B cells


title: SC F3-Control biological rep1


title: IgM+IgD+CD27+ PB B cells MD27_4

description: batch 2


title: IgM+IgD+CD27+ PB B cells MD27_1

description: batch 1


title: tissue type name: Skin - developmental stage name: V1 - rep2

description: tissue type name=Skin|developmental stage name=V1 rep 2 (May still include original submitter created erros/discrepancies)


title: tissue type name: Skin - developmental stage name: P - rep5

description: tissue type name=Skin|developmental stage name=P rep 5 (May still include original submitter created erros/discrepancies)

source_name: Exocarp (tissue type name: Skin - developmental stage name: P)

value: Pre-véraison


title: tissue type name: Skin - developmental stage name: P - rep6

description: tissue type name=Skin|developmental stage name=P rep 6 (May still include original submitter created erros/discrepancies)


title: IgM+IgDlowCD27+ PB B cells IgM-only_3

description: batch 2

value: non-tumor


title: tissue type name: Skin - developmental stage name: P - rep4

description: tissue type name=Skin|developmental stage name=P rep 4 (May still include original submitter created erros/discrepancies)


title: IgM+IgDlowCD27+ PB B cells IgM-only_2

description: batch 2


title: ulcerative colitis mucosa 12b (Nimblegen)

type: genomic

city: Kiel

first: Zhe

last: Feng

address: Schittenhelmstr. 12

institute: Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany

hyb_protocol: Labelling was performed using the Nimblegen Dual-Color DNA Labeling Kits and hybridization kit together with buffers.

scan_protocol: Scanning of the arrays were performed on a 2-m, high-resolution NimbleGen MS 200 Microarray Scanner.

data_processing: Initial data analysis of the the data was done using NimbleScan software. To quantify DNA methylation from the Nimblegen data the BATMAN algorithm was applied (Down et al 2008). This algorithm uses the CpG density of each probe in combination with the hybridization intensity data to normalize the DNA methylation probe scores.

molecule: genomic DNA

source_name: endoscopic biopsies

extract_protocol: DNA wa extracted using commercial kit (Done in Kiel)DNA methylated sequences was enriched by MeDIP protocol identical to (Weber et al 2005 Nature genetics)

value: Intestinal mucosa

tag: discordant twins id (a&b twins)

value: inflammatory mucosa


title: IgM+IgDlowCD27+ PB B cells IgM-only_4

description: batch 1


title: ulcerative colitis mucosa 09b (Nimblegen)

label_protocol: Labelling was performed using the Nimblegen Dual-Color DNA Labeling Kits and hybridization kit together with buffers.


title: tissue type name: Skin - developmental stage name: P - rep3

description: tissue type name=Skin|developmental stage name=P rep 3 (May still include original submitter created erros/discrepancies)


title: IgM+IgDlowCD27+ PB B cells IgM-only_1

description: batch 2


title: tissue type name: Skin - developmental stage name: P - rep1

description: tissue type name=Skin|developmental stage name=P rep 1 (May still include original submitter created erros/discrepancies)


title: ulcerative colitis mucosa 10b (Nimblegen)


title: FBP1 expressing-Hs578T

city: Lexington

first: Binhua

middle: P

last: Zhou

state: KY

address: 789 South Limestone

department: Markey Cancer Center/Biochemistry

description: SAMPLE 4

hyb_protocol: Hyb protocol was performed at the microarry core facility at the University of Kentucky School of Medicine.

scan_protocol: Scan protocol was performed at the microarry core facility at the University of Kentucky School of Medicine.

data_processing: Data was processed at the microarry core facility in Univ. of Kentucky School of Medicine; program-name = Affymetrix Expression Console (v. 1.1.2800.28061), affymetrix-algorithm-name = rma-gene-default (v. 1.0), affymetrix-algorithm-param-apt-opt-analysis-spec = rma-bg, quant-norm.sketch=-1

label_protocol: Label protocol was performed at the microarry core facility at the University of Kentucky School of Medicine.

growth_protocol: Cells were grown in DMEM/F12 plus 10%FBS in 5%CO2 at 37C.

extract_protocol: Total RNA was extract from cells using Qiagene RNA purification kit following manfacturer's protocol

treatment_protocol: Cells were trypinized and harvested when in log-growth phase.

tag: cell line

value: basal-like breast cancer

tag: genotype/variation

value: expressing FBP1


title: Control cells-MDA-MB231

institute: University of Kentucky School of Medicine

description: SAMPLE 1


title: tissue type name: Flesh - developmental stage name: R2 - rep6

description: tissue type name=Flesh|developmental stage name=R2 rep 6 (May still include original submitter created erros/discrepancies)

source_name: Mesocarp (tissue type name: Flesh - developmental stage name: R2)

value: mesocarp

value: Ripe 2


title: FBP1 expressing-MDA-MB231

description: SAMPLE 2


title: ulcerative colitis mucosa 08b (Nimblegen)


title: IgG+CD27+ and IgA+CD27+ PB B cells class switched_7

description: batch 3

tag: tumor stage

value: IgG+CD27+ and IgA+CD27+ PB B cells


title: tissue type name: Skin - developmental stage name: P - rep2

description: tissue type name=Skin|developmental stage name=P rep 2 (May still include original submitter created erros/discrepancies)


title: Control cells-Hs578T

description: SAMPLE 3

tag: cell type


title: CLL with unmutated IgV gene umCLL_5

description: CD43 positive

hyb_protocol: cRNA was hybridized to GPL6244 Arrays with the Affymetrix GeneChip Hybridization, Wash and Stain kit, according to manufacturer's instructions.

data_processing: Data were normalized according to vsn and imported into Gene Spring GX 11.5.1 for further analysis.

label_protocol: Samples were processed with WT Ovation PICO RNA Amplification System, the WT Ovation Exon module and fragmented and labeled with the Encore Biotin module according to manufacturer's instructions.

value: tumor

value: CLL cell with unmutated IgV gene


title: tissue type name: Flesh - developmental stage name: R2 - rep5

description: tissue type name=Flesh|developmental stage name=R2 rep 5 (May still include original submitter created erros/discrepancies)

value: Muscat Hamburg cv.


title: CLL with unmutated IgV gene umCLL_4

description: CD43 positive


title: IgM+IgD+CD27+ PB B cells MD27_7

description: batch 3


title: IgM+IgD+CD27+ PB B cells MD27_6

description: batch 3


title: IgG+CD27+ and IgA+CD27+ PB B cells class switched_6

description: batch 3


title: IgG+CD27+ and IgA+CD27+ PB B cells class switched_5

description: batch 2


title: ulcerative colitis mucosa 06b (Nimblegen)

tag: diagnosis


title: CLL with unmutated IgV gene umCLL_3

description: CD43 positive


title: tissue type name: Flesh - developmental stage name: R2 - rep4

description: tissue type name=Flesh|developmental stage name=R2 rep 4 (May still include original submitter created erros/discrepancies)


title: ulcerative colitis mucosa 04b (Nimblegen)


title: tissue type name: Flesh - developmental stage name: R2 - rep3

description: tissue type name=Flesh|developmental stage name=R2 rep 3 (May still include original submitter created erros/discrepancies)


title: CLL with unmutated IgV gene umCLL_2

description: CD43 positive


title: ulcerative colitis mucosa 07b (Nimblegen)


title: IgG+CD27+ and IgA+CD27+ PB B cells class switched_4

description: batch 2


title: CLL with mutated IgV gene mutCLL_5

description: CD43 positive

value: CLL cell with mutated IgV gene


title: CLL with unmutated IgV gene umCLL_1

description: CD43 positive


title: tissue type name: Flesh - developmental stage name: R2 - rep1

description: tissue type name=Flesh|developmental stage name=R2 rep 1 (May still include original submitter created erros/discrepancies)


title: CLL with mutated IgV gene mutCLL_2

description: CD43 positive


title: tissue type name: Flesh - developmental stage name: R2 - rep2

description: tissue type name=Flesh|developmental stage name=R2 rep 2 (May still include original submitter created erros/discrepancies)


title: IgG+CD27+ and IgA+CD27+ PB B cells class switched_1

description: batch 1


title: tissue type name: Flesh - developmental stage name: R1 - rep6

description: tissue type name=Flesh|developmental stage name=R1 rep 6 (May still include original submitter created erros/discrepancies)

source_name: Mesocarp (tissue type name: Flesh - developmental stage name: R1)

value: Ripe 1


title: IgG+CD27+ and IgA+CD27+ PB B cells class switched_3

description: batch 1


title: CLL with mutated IgV gene mutCLL_3

description: CD43 positive


title: Healthy mucosa 12a (Nimblegen)

value: healthy mucosa


title: mature CD5+ PB B cells CD5_5

description: batch 3

value: mature CD5+ PB B cells


title: CLL with mutated IgV gene mutCLL_1

description: CD43 positive


title: ulcerative colitis mucosa 03b (Nimblegen)


title: ulcerative colitis mucosa 01b (Nimblegen)


title: Healthy mucosa 10a (Nimblegen)


title: tissue type name: Flesh - developmental stage name: R1 - rep3

description: tissue type name=Flesh|developmental stage name=R1 rep 3 (May still include original submitter created erros/discrepancies)

value: field soil


title: tissue type name: Flesh - developmental stage name: R1 - rep4

description: tissue type name=Flesh|developmental stage name=R1 rep 4 (May still include original submitter created erros/discrepancies)


title: IgG+CD27+ and IgA+CD27+ PB B cells class switched_2

description: batch 1


title: ulcerative colitis mucosa 02b (Nimblegen)


title: tissue type name: Flesh - developmental stage name: R1 - rep5

description: tissue type name=Flesh|developmental stage name=R1 rep 5 (May still include original submitter created erros/discrepancies)


title: tissue type name: Flesh - developmental stage name: V2 - rep6

description: tissue type name=Flesh|developmental stage name=V2 rep 6 (May still include original submitter created erros/discrepancies)

source_name: Mesocarp (tissue type name: Flesh - developmental stage name: V2)

value: 100% véraison


title: In vivo Praziquantel GX for adult S. japonicum 18

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

description: GX, S. japonicum drug treatment

hyb_protocol: Then, the samples were combined with 2× Gene Expression  hybridization Buffer HI-RPM, mixed and applied to a gasket slide that was pre-positioned in a hybridisation chamber (Agilent). The microarray slide was placed probe side towards the target. The chamber was assembled and placed in a hybridisation oven and incubated for 17 h at  65°C. After hybridisation the chamber was opened and the microarray slides were washed using the standard Agilent protocol (Agilent Technologies, USA)

scan_protocol: The images from the DNA Microarray Scanner were extracted using Feature Extraction (v10.5).

data_processing:
Automatic outliner flagging was used and the resulting list filtered on the basis of p-value generated. Feature-extracted data was analyzed and visualized using GENESPRING (version 11; Agilent Technologies). Microarray data were normalised using a normalisation scenario for ‘Agilent FE one-color’, ProcessedSignal values were determined using Feature Extraction software and GeneSpring microarray software, including aspects of the signal to noise ratio, spot morphology and homogeneity. ProcessedSignal represents the signal after localized background subtraction and includes corrections for surface trends. Features were deemed ‘Absent’ when the processed signal intensity was less than twice the value of the processed signal error value. Features were deemed ‘Marginal’ when the measured intensity was at a saturated value or if there was a substantial amount of variation in the signal intensity within the pixels of a particular feature. Features that were neither absent nor marginal were deemed ‘Present’.
Data points were included only if they were present or marginal, and probes or Contigs were retained if at least half of the data points were ‘Present’. Differential probe hybridisation was statistically evaluated as a p-value, and a cut-off value of ≤0.05 in at least 10 of 20 hybridisations used as the confidence level. Samples were normalised to untreated parasites at time point equals 0, and expressed as a relative fold change on a log2 scale. Microarray data was analysed using GeneSpring p-values calculated were used to filter data (≤0.05), carefully considering false-positive results. Multiple testing techniques available via GeneSpring used include the Benjamini and Hochberg False Discovery Rate

organism: Schistosoma japonicum

source_name: Adult Female 4hrs post dosage

label_protocol: Once the concentration had been determined, 1.65 μg aliquots of CY3c were placed in a fresh tube together with the fragmentation mix (Agilent Technologies, Santa Clara, USA) and incubated for 30 min at 60°C.

growth_protocol: 30 cercariae of S. japonicum (Anhui Strain) were used to infect mice (BALB/c females, 6 weeks old).

extract_protocol: Total RNA of schsitosomes was isolated by using TRIZOL Reagent (Invitrogen) and RNeasy Micro Kit (Qiagen). DNA was removed from RNA preparations using RNase-free DNase I (Promega).

treatment_protocol: Six weeks after infection mice were treated with a single oral dose (300 mg/kg in PBS) of PZQ. Control infected mice received the carrier without PZQ and parasites were isolated, with each group containing 5 mice. Schistosomes were obtained from mice at four time points after administration of PZQ - 30 min, 4 hrs, 12 hrs and 24 hrs by portal perfusion of euthanized mice using 37 ºC RPMI 1640 medium

value: Female

value: 4hrs post dosage of praziquantel


title: mature CD5+ PB B cells CD5_4

description: batch 3

source_name: human peripheral blood

value: non-tumor


title: mature CD5+ PB B cells CD5_2

description: batch 3


title: Healthy mucosa 09a (Nimblegen)

value: Intestinal mucosa


title: tissue type name: Flesh - developmental stage name: R1 - rep1

description: tissue type name=Flesh|developmental stage name=R1 rep 1 (May still include original submitter created erros/discrepancies)


title: mature CD5+ PB B cells CD5_3

description: batch 3


title: In vivo Praziquantel GX for adult S. japonicum 20

description: GX, S. japonicum drug treatment

source_name: Adult Female 24hrs post dosage

value: 24hrs post dosage of praziquantel


title: mature CD5+ PB B cells CD5_1

description: batch 3


title: In vivo Praziquantel GX for adult S. japonicum 19

description: GX, S. japonicum drug treatment

source_name: Adult Female 12hrs post dosage

value: 12hrs post dosage of praziquantel


title: tissue type name: Flesh - developmental stage name: R1 - rep2

description: tissue type name=Flesh|developmental stage name=R1 rep 2 (May still include original submitter created erros/discrepancies)

value: mesocarp


title: Healthy mucosa 07a (Nimblegen)


title: tissue type name: Flesh - developmental stage name: V2 - rep5

description: tissue type name=Flesh|developmental stage name=V2 rep 5 (May still include original submitter created erros/discrepancies)


title: A549 cont vs. A549 M PHMG-5

city: Cheonan

first: Yong-Sik

last: Kim

address: Soonchunhyang-2gil 8

department: Microbiology

country: South Korea

institute: College of Medicine, Soonchunhyang University

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: A549 cells were cultured in standard DMEM/Ham’s F-12 medium supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS) and 1% (v/v) antibiotic/antimycotic cocktail (100 U/ml penicillin, 100 μg/ml streptomycin, and 0.25 μg/ml amphotericin B; Invitrogen, Carlsbad, CA, USA) at 37oC under saturating humidity in 5% CO2/95% air.

extract_protocol: Total RNA extracted using Rneasy kit (Qiagen) following manufacturer's instructions

treatment_protocol: A549 cells were treated 5 ug/ml PHMG for 24 h.

value: 5 ug/ml PHMG


title: tissue type name: Flesh - developmental stage name: V2 - rep3

description: tissue type name=Flesh|developmental stage name=V2 rep 3 (May still include original submitter created erros/discrepancies)


title: Healthy mucosa 04a (Nimblegen)


title: In vivo Praziquantel GX for adult S. japonicum 17

description: GX, S. japonicum drug treatment

source_name: Adult Female 30min post dosage

value: 30min post dosage of praziquantel


title: tissue type name: Flesh - developmental stage name: V2 - rep4

description: tissue type name=Flesh|developmental stage name=V2 rep 4 (May still include original submitter created erros/discrepancies)


title: AT-II 3 DAY4

city: Chapel Hill

first: Lyndon

last: Cooper

state: NC

address: 330 Brauer Hall, CB#7450

department: Prosthodontics

institute: UNC School of Dentistry

hyb_protocol: 4440537 Ambion(r) WT Expression Kit for High-Throughput Robotics/Affymetrix Rat gene 1.1 ST Array

scan_protocol: Affymetrix GeneChip Scanner 3000 7G Plus with Autoloader

data_processing: RMA normalization performed with Expression Console. GeneSpring software v.11.5.1 used for analysis.

source_name: implant adherent cells-rat tibia-microrough surface implant-day4

label_protocol: Samples were processed and hybridized to the Affymetrix Rat gene 1.1 ST Array at the UNC core facility following the manufacturer’s recommended protocols and reagents (Affymetrix, San Clara,CA).

growth_protocol: Eight male Sprague Dawley rats (326-350 g) were purchased from Harlan laboratories and acclimated for 7 days prior to initiation of studies. Anesthesia was achieved using Ketamine/Xylazine (80-100mg/kg and 10 mg/kg respectively) along with supplemental local anesthesia (Lidocaine 2% with epinephrine (1:100,000) .The dorsal/medial aspect of the tibiae was identified, shaved, and disinfected using betadine and 70% ethanol scrub. Using aseptic technique, a full thickness myocutaneous flap was made and carefully retracted to reveal the medial aspect of the tibia bone. With sterilized stainless steel burs, two osteotomies were created with copious irrigation. The osteotomies were made approximately 5 mm apart .

extract_protocol: At 2 and 4 days following surgery, animals were euthanized. Immediately thereafter, the tibia sites were isolated and the implant site was exposed using sterile technique and the entire tibias were harvested and the implants were explanted by fracture of the tibia. For evaluation of mRNA expression in cells adherent to explanted endosseous implant surfaces, the implants were rinsed in cold PBS immediately following retrieval and then placed into 1000 μl of Tri-reagent. Total RNA was isolated from the lysates using the standard Tri-reagent protocol and collected by ethanol precipitation. This was followed by purification using RNeasy MinElute Clean up kit (Qiagen, Valencia, CA, USA).  RNA was assessed for quality and quantity using a bioanalyzer (Agilent, Santa Clara, CA, USA) and nanodrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE) respectively.

treatment_protocol: Two implants (cp titanium) were placed in each tibia to provide sufficient RNA for each experimental sample. For every time point (day2 and 4), 4 rats were used per time point. Each animal received two AT-I implants in one tibia and two AT-II implants in the contralateral tibia (randomly distributed). The periosteum was adapted over the site using interrupted 4-0 chromic gut sutures for subcuticular closure. The skin was then closed using vicryl sutures. Animals were monitored continuously following surgery. Ambulation was the defined criteria for immediate recovery. A postoperative analgesic was provided for 48 hours after surgery, by means of subcutaneous ketoprofen injections (5mg/kg) once daily. At the time of sacrifice, each animal was placed in a CO2—saturated chamber.  Death was assured by thoracotomy and severance of the inferior vena cava for exsanguination.

value: Sprague Dawley

value: Male

value: tibial


title: In vivo Praziquantel GX for adult S. japonicum 16

description: GX, S. japonicum drug treatment

source_name: Adult Female untreated

value: untreated


title: AT-II 4 DAY4


title: AT-II 1 DAY4


title: Healthy mucosa 03a (Nimblegen)

value: healthy mucosa


title: tissue type name: Flesh - developmental stage name: V2 - rep2

description: tissue type name=Flesh|developmental stage name=V2 rep 2 (May still include original submitter created erros/discrepancies)

value: Muscat Hamburg cv.


title: Healthy mucosa 06a (Nimblegen)


title: In vivo Praziquantel GX for adult S. japonicum 14

description: GX, S. japonicum drug treatment

source_name: Adult Male 12hrs post dosage


title: In vivo Praziquantel GX for adult S. japonicum 15

description: GX, S. japonicum drug treatment

source_name: Adult Male 24hrs post dosage


title: Healthy mucosa 01a (Nimblegen)


title: AT-I 4 DAY4

source_name: implant adherent cells-rat tibia-nanosurface implant-day4


title: tissue type name: Flesh - developmental stage name: V2 - rep1

description: tissue type name=Flesh|developmental stage name=V2 rep 1 (May still include original submitter created erros/discrepancies)

value: field soil


title: In vivo Praziquantel GX for adult S. japonicum 13

description: GX, S. japonicum drug treatment

source_name: Adult Male 4hrs post dosage


title: tissue type name: Flesh - developmental stage name: V1 - rep5

description: tissue type name=Flesh|developmental stage name=V1 rep 5 (May still include original submitter created erros/discrepancies)

source_name: Mesocarp (tissue type name: Flesh - developmental stage name: V1)

value: 50% véraison


title: In vivo Praziquantel GX for adult S. japonicum 12

description: GX, S. japonicum drug treatment

source_name: Adult Male 30min post dosage


title: AT-I 2 DAY4


title: tissue type name: Flesh - developmental stage name: V1 - rep6

description: tissue type name=Flesh|developmental stage name=V1 rep 6 (May still include original submitter created erros/discrepancies)


title: tissue type name: Flesh - developmental stage name: V1 - rep4

description: tissue type name=Flesh|developmental stage name=V1 rep 4 (May still include original submitter created erros/discrepancies)


title: Healthy mucosa 02a (Nimblegen)

source_name: endoscopic biopsies


title: AT-I 1 DAY4


title: Healthy mucosa 08a (Nimblegen)


title: caloric restriction, biological rep3

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

country: Japan

institute: Akita Prefectural University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
PM data of CEL file was parametrically normalized, and expression levels at each gene was estimated by trimmed means of the normalized PM data (Konishi (2008), Statistical Applications in Genetics and Molecular Biology: Vol. 7: Iss. 1, Article 25.) The normalized probe-level PM data is available as a supplementary txt file for each Sample, where the columns of data represent the probes 1-12 in same order to that of the chip's CDF file.
A pseudo data was then derived in a form of antilog of the z-scores; the center of the pseudo data was 256. The pseudo data, ABS_CALL, and the normalized data (z-scores) are presented in the matrix form.

source_name: wild Wistar rats, caloric restriction to 70% of the energy intake

label_protocol: standard Affymetrix protocol

growth_protocol: From six weeks of age, (-/-) rats were divided into two groups: ad libitum (AL) and CR (70% of the energy intake). AL, CR and Tg rats were sacrificed at 24 weeks of age.

extract_protocol: Total RNA was isolated from the epididymal WAT using TRIZOL (Life Technologies).

treatment_protocol: All rats were provided food 30 minutes prior to turning off the lights in the evening and were sacrificed after turning on the lights in the following morning.

value: white adipose tissue

tag: genotype

value: Jcl:Wistar (-/-) rat

value: 24 weeks


title: In vivo Praziquantel GX for adult S. japonicum 10

description: GX, S. japonicum drug treatment

value: Female


title: tissue type name: Flesh - developmental stage name: V1 - rep3

description: tissue type name=Flesh|developmental stage name=V1 rep 3 (May still include original submitter created erros/discrepancies)

tag: cultivar


title: AT-I 3 DAY4


title: In vivo Praziquantel GX for adult S. japonicum 11

description: GX, S. japonicum drug treatment

source_name: Adult Male untreated


title: AT-II 4 DAY2

source_name: implant adherent cells-rat tibia-microrough surface implant-day2


title: caloric restriction, biological rep1

tag: tissue


title: In vivo Praziquantel GX for adult S. japonicum 9

description: GX, S. japonicum drug treatment


title: caloric restriction, biological rep2


title: caloric restriction, biological rep4


title: AT-II 3 DAY2


title: tissue type name: Flesh - developmental stage name: V1 - rep1

description: tissue type name=Flesh|developmental stage name=V1 rep 1 (May still include original submitter created erros/discrepancies)

tag: development stage


title: tissue type name: Flesh - developmental stage name: V1 - rep2

description: tissue type name=Flesh|developmental stage name=V1 rep 2 (May still include original submitter created erros/discrepancies)

tag: growth media


title: In vivo Praziquantel GX for adult S. japonicum 8

description: GX, S. japonicum drug treatment

source_name: Adult Female 4hrs post dosage

value: 4hrs post dosage of praziquantel


title: In vivo Praziquantel GX for adult S. japonicum 6

description: GX, S. japonicum drug treatment


title: tissue type name: Flesh - developmental stage name: P - rep5

description: tissue type name=Flesh|developmental stage name=P rep 5 (May still include original submitter created erros/discrepancies)

source_name: Mesocarp (tissue type name: Flesh - developmental stage name: P)

value: Pre-véraison


title: In vivo Praziquantel GX for adult S. japonicum 5

description: GX, S. japonicum drug treatment

value: 24hrs post dosage of praziquantel


title: anti-sense GH transgene, biological rep4

source_name: heterozygous transgenic dwarf rats bearing an anti-sense GH transgene fed ad libitum


title: ad libitum, biological rep2

source_name: wild Wistar rats fed ad libitum


title: tissue type name: Flesh - developmental stage name: P - rep6

description: tissue type name=Flesh|developmental stage name=P rep 6 (May still include original submitter created erros/discrepancies)

value: mesocarp


title: In vivo Praziquantel GX for adult S. japonicum 4

description: GX, S. japonicum drug treatment

value: 12hrs post dosage of praziquantel


title: In vivo Praziquantel GX for adult S. japonicum 7

description: GX, S. japonicum drug treatment

source_name: Adult Female 30min post dosage

value: 30min post dosage of praziquantel


title: ad libitum, biological rep4


title: AT-II 2 DAY2

value: Sprague Dawley

value: Male


title: ad libitum, biological rep3


title: In vivo Praziquantel GX for adult S. japonicum 2

description: GX, S. japonicum drug treatment


title: AT-I 4 DAY2

source_name: implant adherent cells-rat tibia-nanosurface implant-day2

value: tibial


title: In vivo Praziquantel GX for adult S. japonicum 3

description: GX, S. japonicum drug treatment


title: tissue type name: Flesh - developmental stage name: P - rep4

description: tissue type name=Flesh|developmental stage name=P rep 4 (May still include original submitter created erros/discrepancies)


title: anti-sense GH transgene, biological rep3


title: tissue type name: Flesh - developmental stage name: P - rep2

description: tissue type name=Flesh|developmental stage name=P rep 2 (May still include original submitter created erros/discrepancies)


title: anti-sense GH transgene, biological rep2


title: AT-II 1 DAY2


title: AT-I 3 DAY2


title: AT-I 2 DAY2


title: moroberekan, fraction of transpirable soil water (FTSW) 1, biological rep 2

status: Public on Sep 26 2012

city: Metro Manila

first: Andrew

last: Cal

address: DAPO BOX 7777

country: Philippines

institute: International Rice Research Institute

hyb_protocol: Hybridization was processed at 45°C, with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640). The arrays were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix Gene Chip Scanner 3000. The microarray hybridization and scanning were conducted in the DNA microarray core laboratory of the Institute of Plant and Microbial Biology, Academia Sinica (IPMB).

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

data_processing: CEL files were preprocessed with RMA and analysed using the PUMA package in R [31]. A transcript-consistent alternate cdf file  (http://gauss.dbb.georgetown.edu/liblab/affyprobeminer/[32]) was used to eliminate probe sets that map to the same gene in the affymetrix cdf. GoSlim assignments were downloaded from the MSU Rice Genome Annotation Project (and full GO assignments were integrated from RAP and Gramene annotations. Gene IDs were converted with RAP ID converter (http://rapdb.dna.affrc.go.jp/tools/converter)

organism: Oryza sativa

source_name: rice elongation zone at FTSW 1.0

label_protocol: Preparation of labeled material for array hybridization was carried out according to manufacturer's instructions (Affymetrix, Santa Clara, CA). Briefly, 2μg of total RNA was used for synthesizing ds cDNA. Biotin-tagged cRNA was generated from an in vitro transcription reaction using MessageAmp™II aRNA Amplification Kit and then fragmented into 35-200 bases in length.

growth_protocol: IRRI phytotron in October/November 2007. Trays (25cm X 40 cm X 15cm) were filled with two kg dried, sieved soil. 60 pre-germinated seedlings per tray were sown in pairs; after seven days one seedling per pair was removed, leaving six rows each containing five plants. Genotypes were sown in alternating rows within the same tray.

extract_protocol: Sampled leaf tissues were ground in liquid nitrogen and RNA was extracted using the TRIZOL reagent (Sigma Chemical Co., USA) according to the manufacturer's instructions, and crude RNA preparations were treated with DNase (Invitrogen, USA), following extraction.

treatment_protocol: Trays assigned to the drought treatments were drained overnight after the emergence of the 6th leaf and allowed to dry until target FTSW. Trays were weighed and re-watered four times daily to maintain target FTSW. Sampling for RNA was conducted co-incidentally for all treatments at the 7th leaf stage between 9 and 11 AM. Approximately three cm of the leaf elongation zone was excised from elongating leaves; all samples of the same genotype from a given tray were bulked for RNA extraction.

value: moroberekan

value: FTSW 1.0

value: leaf elongation zone


title: moroberekan, fraction of transpirable soil water (FTSW) 0.5, biological rep 2

source_name: rice elongation zone at FTSW 0.5

value: FTSW 0.5


title: tissue type name: Flesh - developmental stage name: P - rep1

description: Flesh from Muscat Hamburg pre-véraison berries (May still include original submitter created erros/discrepancies)

value: Muscat Hamburg cv.

value: field soil


title: moroberekan, fraction of transpirable soil water (FTSW) 0.5, biological rep 3


title: anti-sense GH transgene, biological rep1

value: white adipose tissue

value: Jcl:Wistar (-/-) rat

value: 24 weeks


title: moroberekan, fraction of transpirable soil water (FTSW) 1, biological rep 1


title: moroberekan, fraction of transpirable soil water (FTSW) 1, biological rep 3


title: AT-I 1 DAY2


title: In vivo Praziquantel GX for adult S. japonicum 1

description: GX, S. japonicum drug treatment

value: untreated


title: ir64, fraction of transpirable soil water (FTSW) 0.5, biological rep 3


title: ir64, fraction of transpirable soil water (FTSW) 1, biological rep 2


title: ir64, fraction of transpirable soil water (FTSW) 1, biological rep 1


title: ir64, fraction of transpirable soil water (FTSW) 0.2, biological rep 3

source_name: rice elongation zone at FTSW 0.2

value: FTSW 0.2


title: ir64, fraction of transpirable soil water (FTSW) 1, biological rep 3


title: moroberekan, fraction of transpirable soil water (FTSW) 0.2, biological rep 3


title: moroberekan, fraction of transpirable soil water (FTSW) 0.2, biological rep 1


title: moroberekan, fraction of transpirable soil water (FTSW) 0.2, biological rep 2


title: moroberekan, fraction of transpirable soil water (FTSW) 0.5, biological rep 1


title: Empty control #1

city: New Brunswick

first: John

last: Langenfeld

state: NJ

address: One Robert Wood Johnson Place

department: Surgery

institute: Rutgers-RWJMS

description: Gene expression data from LNCap cells transfected with MED1 expression vector

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: LNCaP-control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA  (Affymetrix).

growth_protocol: LNCaP cells were cultured in RPMI-1640 containing 10% FBS

extract_protocol: Total RNA was extracted using RNAeasy kit (Qiagen).

treatment_protocol: Cells were transiently transfected with MED1 expression vector or empty vector control using Lipofectamine.

value: prostate cancer cell

value: LNCaP

tag: transfection

value: empty vector


title: MED1 overexpression #2

source_name: LNCaP-MED1 overexpressed

value: MED1 expression vector


title: ir64, fraction of transpirable soil water (FTSW) 0.5, biological rep 1

tag: treatment


title: ir64, fraction of transpirable soil water (FTSW) 0.2, biological rep 2


title: ir64, fraction of transpirable soil water (FTSW) 0.5, biological rep 2


title: Empty control #2


title: ir64, fraction of transpirable soil water (FTSW) 0.2, biological rep 1


title: MED1 overexpression #1


title: BEAS2B_unexposed passaged_6month_rep3

city: Morgantown

first: Todd

middle: A

last: Stueckle

state: WV

address: 1095 Willowdale Road

department: Health Effects Laboratory Division

institute: National Institute for Occupational Safety and Health

description:
Genome expression after 6 month unexposed passage
Raw data file: B-Control-3.txt

hyb_protocol: Microarray hybridization was performed at 65°C for 17 hours on Agilent 4x44K Whole Human Genome Oligonucleotide Microarray (#014850) in Agilent SureHyb Hybridization Chambers.

scan_protocol: After washing processed slides were scanned with an Agilent G2505B DNA scanner.

data_processing: Agilent Feature Extraction Software (ver. 10.5.1.1) gene expression text files were imported into GeneSpring GX (ver. 10.0) for normalization using Agilent FE one-color scenarios.  Only genes marked marginal or present in all samples were used (n=20,232).  Normalization was performed by taking the average intensity across replicate samples.

source_name: BEAS-2B human immortalized lung epithelial cell, unexposed, 6 month passage, replicate 3

label_protocol: Samples were amplified, Cy3 labeled using Agilent Quick Amp Labeling Kit following manufactorer's protocol. Microarray hybridization was performed at 65°C for 17 hours in Agilent’s SureHyb Hybridization Chambers. After being washed in an ozone-free environment, the slides were scanned using the Agilent DNA microarray scanner (part number G2505B).

growth_protocol: Cells were maintained in DMEM medium with 5% fetal bovine serum, 2 mM L-glutamine and 100 U/mL penicillin and streptomycin.  Cell cultures were held in a humid, 37o C and 5% CO2 cell culture incubator.

extract_protocol: B-As  and B-Control cell RNA replicate samples were collected with TRIzol (Invitrogen) post-exposure using manufactorer's protocol.  RNA quality was assessed in house using gel electrophoresis and 260/280 nm absorbance ratio.  Samples stored at -80o C were shipped to ArrayStar (Rockville, MD).  At ArrayStar, samples were treated with DNase digestion and analyzed for RNA quality using Nanodrop ND-100 and Bioanalyser 2100.

treatment_protocol: As2O3 spiking solutions in sterile PBS were diluted in fresh media and added to culture plates.  Unexposed BEAS-2B cells (2x105 cells/well) were seeded to 6-well plates.  After 24 hours, cell cultures were either exposed 2.5 μM As2O3 or unexposed for the following 6 months.  Spiked media was changed every 3 to 4 days while cells were split once every 7 days.

value: immortalized lung epithelial cells (BEAS-2B)

tag: stress

value: control


title: BEAS2B_unexposed passaged_6month_rep4

description:
Genome expression after 6 month unexposed passage
Raw data file: B-Control-4.txt

source_name: BEAS-2B human immortalized lung epithelial cell, unexposed, 6 month passage, replicate 4


title: Control_180

city: Cincinnati

first: Ashish

last: Kumar

state: OH

address: 3333 Burnet Ave

department: Bone Marrow Transplant and Immune Deficiency

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Stadard Affymetric protocols

scan_protocol: Stadard Affymetric protocols

data_processing: Expression console

label: Biotin

organism: Mus musculus

source_name: Lineage neg bone marrow

label_protocol: Labeling was performed using the Ambion WT Expression kit.

growth_protocol: Lineage negative cells were harvested and cultured in liquid media containing cytokines (SCF, G-CSF, TPO) and 4-OHT.

extract_protocol: Total RNA was extracted using Rneasy mini kit (Qiagen).

value: Control, wildtype

tag: strain


title: Meis1-deleted_176


title: BEAS2B_unexposed passaged_6month_rep2

description:
Genome expression after 6 month unexposed passage
Raw data file: B-Control-2.txt

source_name: BEAS-2B human immortalized lung epithelial cell, unexposed, 6 month passage, replicate 2


title: Bl6_VN62_3

city: Seattle

first: Aderem

last: Lab

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Microarrays were normalized at the gene level using the BrainArray custom CDF (Entrez Gene, Version 14) for probeset definitions and RMA as implemented in the justRMA function of the Bioconductor package affy for background adjustment, quantile normalization and summarization
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: primary tracheal cells from wild-type Bl6 mice

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Collect trachea from euthanized animal in cold HBSS. Rinse trachea in ice-cold PBS containing 5 mM DTT, followed by ice-cold PBS alone. Incubate 4°C overnight in Protease. Next day, scrape off epithelial cells from mucosal side using a scalpel blade. Collect cells in a tube and dislodge cells by vigorous agitation and pipetting. Inactivate protease with 2.5% FCS. Centrifuge at 500 x g for 5 min. Resuspend pellet in 1:1 ratio of DMEM:Ham’s F12 containing 5% FCS and antibiotics/Amphotericin B. Wash cells with DMEM:Ham’s F12 containing 5% FCS and antibiotics/Amphotericin B. Collect the non-adherent cells and disperse again by pipetting. Centrifuge and resuspend cells in seeding media. Seed 150 ul cells on to tissue culture one inserts.  Maintain cells in media for 48 hrs and carefully replace the media with growth media. When cells are confluent, the media is changed with differentiating media, and cells are brought to air-liquid interface (ALI) by removing the media from the top chamber. Continue to grow the cells by changing media every other day.

extract_protocol: Harvest apical and basolateral supernatants and cells. 30 min prior to time point add 250 ul DM to apical side. At experimental time point, remove 250 ul DM from aical side and replace with additional 250 ul DM. Remove the second 250 ul DM from apical side, and pool with the first 250 ul apical supernatant for a total volume of 500 ul. Remove all 1mL basolateral medium. 250 ul Trizol added to apical side. Cells scraped with P1000 pipet tip to help with removal. Further rise with additional 250 ul Trizol, for total volume of cell collection of 500 ul.

treatment_protocol: Wash apical side of cultures with pre-warmed HBSS, and moved to a new 24 well plates per infection setup. Replace the basolateral side with 1 ml of pre-warmed Differentiation Medium (DM). Add 200 ul virus in DM to apical side only. Incubate at 37°C for 1 hr. Depending on particular experiment, inoculums are either collected or disposed of after 1 hr incubation. Wash apical sides with 200 ul pre-warmed 1x HBSS, then allowed to remain dry for further steps. Cultures kept in 37°C until harvest.

tag: time

value: 12 hrs

tag: infection (influenza strain)

tag: virus concentration

value: MOI 3.0

value: primary tracheal epithelial cells


title: Bl6_X31_3


title: Bl6_X31_2


title: Bl6_VN62_1


title: Bl6_PR8_3


title: Bl6_X31_1


title: Control_124


title: Bl6_VN62_2


title: BEAS2B_unexposed passaged_6month_rep1

description:
Genome expression after 6 month unexposed passage
Raw data file: B-Control-1.txt

source_name: BEAS-2B human immortalized lung epithelial cell, unexposed, 6 month passage, replicate 1

tag: cell line


title: non-infected susceptible line S S0:0 65839805

city: Rehovot

first: Dagan

last: Sade

address: Hertzel

country: Israel

institute: Hebrew University of Jerusalem

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc. Reykjavik, Iceland following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Reykjavik, Iceland, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Solanum lycopersicum

source_name: non-infected susceptible line

label_protocol: Labeling was performed by NimbleGen Systems Inc., Reykjavik, Iceland, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Plants were grown in an insect-proof greenhouse kept at 18 ºC – 24 0C, with 8 h/16 h dark/light regimen.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: Five days after LeHT1 silencing, groups of twenty silenced and twenty non-silenced plants of the same age were inoculated with TYLCV by caging plants with viruliferous whiteflies for a 3-day long inoculation access period, (approximately 30 insects per plant), in insect-proof wooden cages kept at 24-27 ºC in an insect-proof growth chamber.

value: TYLCV susceptible line S

tag: infection

value: non-infected

value: whole plant


title: Bl6_Mock_2

value: Mock


title: TYLCV infected susceptible line S Si:0 65839905

source_name: TYLCV infected susceptible line

value: TYLCV infected


title: non-infected resistant line R R0:0 65839705

source_name: non-infected resistance line

value: TYLCV resistant line R


title: Bl6_Mock_3


title: TYLCV infected resistant line R Ri:0 65840005

source_name: TYLCV infected resistance line


title: BEAS2B_2.5 μM arsenic trioxide_6month_rep3

description:
Genome expression after 6 month arsenic trioxide 2.5 μM in vitro exposure
Raw data file: B-As-3.txt

source_name: BEAS-2B human immortalized lung epithelial cell, 2.5 μM arsenic trioxide, 6 month exposed, replicate 3

value: arsenic


title: Bl6_PR8_2


title: BEAS2B_2.5 μM arsenic trioxide_6month_rep2

description:
Genome expression after 6 month arsenic trioxide 2.5 μM in vitro exposure
Raw data file: B-As-2.txt

source_name: BEAS-2B human immortalized lung epithelial cell, 2.5 μM arsenic trioxide, 6 month exposed, replicate 2


title: Meis1-deleted_120


title: BEAS2B_2.5 μM arsenic trioxide_6month_rep1

description:
Genome expression after 6 month arsenic trioxide 2.5 μM in vitro exposure
Raw data file: B-As-1.txt

source_name: BEAS-2B human immortalized lung epithelial cell, 2.5 μM arsenic trioxide, 6 month exposed, replicate 1


title: Bl6_PR8_1


title: 5023 CY4 GN

city: Modena

first: Enrico

last: Tagliafico

state: MO

address: Via Campi 287

department: Center for Genome Research

country: Italy

institute: University of Modena and Reggio Emilia

description: miRNA expression profiles of in granulocytes in patients with polycythemia vera (PV) and essential thrombocythemia (ET) receiving INCB018424

hyb_protocol: Total labeled RNA was hybridized to the Affymetrix Genechip miRNA array 1.0 using manufacturer's protocols.

scan_protocol: Image files from scanning (.dat and .cel files) were generated with Affymetrix Expression Console package.

data_processing: Partek GS was then used to generate signals using RMA procedure.

source_name: Peripheral Blood Granulocytes

label_protocol: Total RNA (500ng for samples) was labeled using the FlashTag® Biotin HSR kit (Genisphere)

extract_protocol: Total cellular RNA, including small RNAs, was extracted using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

treatment_protocol: Patients with polycythemia vera and essential thrombocythemia received the JAK1 and JAK2 inhibitor INCB018424; garnulocytes were isolated from peripheral blood and assayed for array. No further in vitro treatment was performed.

tag: disease

value: polycythemia vera

value: YES


title: 5018 CY4 GN


title: non-infected resistant line R R0:0 66450005


title: Bl6_VN62_20090430_07

tag: cell type


title: 5019 CY4 GN

value: essential thrombocythemia


title: 5021 CY4 GN


title: Bl6_Mock_1


title: non-infected susceptible line S S0:0 65974605


title: TYLCV infected resistant line R Ri:0 65974705


title: Bl6_VN62_20090430_06


title: Bl6_X31_20090430_04


title: 5022 CY4 GN


title: Bl6_X31_20090430_05


title: Bl6_PR8_20090430_02


title: TYLCV infected LeHT1-silenced resistant line R Ri: TRV HEX 65974505

description: Resistance plants where LeHT1 has been silenced using Tobacco rattle virus-induced gene silencing (TRV VIGS).

source_name: TYLCV infected LeHT1-silenced resistance line


title: 5017 CY4 GN


title: Bl6_Mock_20090430_01


title: 5014 CY4 GN


title: non-infected LeHT1-silenced resistant line R R0: TRV HEX 65838905

source_name: non-infected LeHT1-silenced resistance line

value: LeHT1 has been silenced using Tobacco rattle virus-induced gene silencing


title: Bl6_PR8_20090430_03


title: Bl6_VN62_20090219_05


title: TYLCV infected resistant line R Ri:0 65839005


title: 5015 CY4 GN


title: 5016 CY4 GN


title: ad libitum, biological rep1

source_name: wild Wistar rats fed ad libitum

value: white adipose tissue

value: Jcl:Wistar (-/-) rat

tag: age

value: 24 weeks


title: tissue type name: Flesh - developmental stage name: P - rep3

description: tissue type name=Flesh|developmental stage name=P rep 3 (May still include original submitter created erros/discrepancies)

hyb_protocol: CNB Grapegen Affymetrix hybridization

data_processing: RMA normalization was performed for Affymetrix Platforms: Using APT (apt-1.12.0: apt-probeset-summarize.cpp,v 1.178).

source_name: Mesocarp (tissue type name: Flesh - developmental stage name: P)

label_protocol: CNB Grapegen Affymetrix labeling

value: Muscat Hamburg cv.

value: mesocarp

value: Pre-véraison

value: field soil


title: non-infected resistant line R R0:0 65839105

tag: genotype

value: non-infected


title: TYLCV infected susceptible line S Si:0 65838805

value: TYLCV susceptible line S

value: whole plant


title: non-infected LeHT1-silenced resistant line R R0: TRV HEX 65646002


title: 5012 CY4 GN


title: 5013 CY4 GN


title: non-infected resistant line R R0:0 65645802


title: Bl6_PR8_20090219_03

value: 12 hrs

value: primary tracheal epithelial cells


title: TYLCV infected LeHT1-silenced resistant line R Ri: TRV HEX 65645902

value: TYLCV resistant line R

value: TYLCV infected


title: TYLCV infected resistant line R Ri:0 65645702


title: 5010 CY4 GN

value: YES


title: Bl6_Mock_20090219_01

value: Mock


title: Bl6_Mock_InVivo_0000_Lung_3

description: Lung tissue after stimulation with either PR8, VN, X31 or Mock for 12 hours

source_name: wild-type Bl6 mice lung tissue

extract_protocol: Mice sacrificed by CO2 inhalation. Hole clipped in trachea, and bronchoalveolar fluid (BALF) taken. Lungs perfused. Whole lungs removed and homogenized (with hand held homogenizer) in 1 ml Trizol. Samples snap frozen in liquid nitrogen.

treatment_protocol: Virus aliquots stored at -80C; quick thaw to RT and immediate dilution. Viruses diluted to 1x10^5 PFU/30ul (3.33x10^6 PFU/ml) in ice-cold 1x PBS in polystyrene tubes. Virus dilution maintained at 4C until use. Mice are all female C57BL/6J from Jackson Labs (order #000664). Mouse sedation: Approximately 350ul of Avertin (2, 2, 2-Tribromoethanol) is administered intraperitoneally.  About 10 minutes is needed for full effect. Mouse infection:30ul of virus dilution is administered intranasally to mice. Mice are kept on a heating pad until the Avertin wears off.

value: lung


title: 5007 CY4 GN

value: essential thrombocythemia


title: Bl6_Mock_InVivo_0000_Lung_5


title: 5022 SC GN

value: polycythemia vera

value: NO


title: 5021 SC GN


title: 5008 CY4 GN


title: Bl6_X31_InVivo_0720_Lung_4


title: Bl6_X31_20090219_04


title: 5009 CY4 GN


title: Bl6_Mock_InVivo_0000_Lung_2


title: 5019 SC GN


title: Bl6_Mock_InVivo_0000_Lung_1


title: Bl6_X31_InVivo_0720_Lung_3


title: 5023 SC GN


title: 5006 CY4 GN


title: 5016 SC GN


title: Bl6_VN62_InVivo_0720_Lung_4


title: Bl6_X31_InVivo_0720_Lung_5


title: Bl6_X31_InVivo_0720_Lung_1


title: Bl6_Mock_20090219_02


title: Bl6_X31_InVivo_0720_Lung_2


title: 5018 SC GN


title: 5017 SC GN


title: Bl6_VN62_InVivo_0720_Lung_3


title: Bl6_VN62_InVivo_0720_Lung_5


title: 5014 SC GN


title: GS000000527-ASM

city: South San Francisco

first: Peter

last: Haverty

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

hyb_protocol: Hybridization was performed under contract by Illumina, Inc. per manufacturer's protocol.

scan_protocol: Scanning were performed under contract by Illumina, Inc. per manufacturer's protocol.

data_processing:
Genotype and normalized signal intensity were computed by Illumina's Genome Studio, V2011.1. A modified version of the PICNIC (PMID 19837654) algorithm computed total copy number and LOH as described previously (PMID 22895193). http://www.illumina.com/documents/products/technotes/technote_topbot.pdf
Segmented_Absolute_Copy_Number; Segmented copy number for this SNP, where 2 is normal. PICNIC segmentation of data in the Absolute_Copy_Number column.
Genotype; Genotype as called by GenomeStudio
GC_SCORE; GenCall Score, genotyping quality from GenomeStudio
Absolute_Copy_Number; Copy number for this SNP, where 2 is normal. Scaling from tumor/normal ratio to absolute copy number takes into account the overall sample ploidy, as estimated by the PICNIC algorithm.
Segmented_Lesser_Parental_Copy_Number; PICNIC determines the copy number state for both parental alleles. For a normal autosome, one would expect one copy from each parent and the Segmented_Lesser_Parental_Copy_Number would then be 1. A value of zero represents LOH and values > 1 represent gain of both alleles.
Raw data file column X; Signal intensity for X allele, as provided by GenomeStudio. Scaled to the same mean across array strips/sections.
Raw data file column Y; Signal intensity for Y allele, as provided by GenomeStudio. Scaled to the same mean across array strips/sections.

source_name: Cell line_adenocarcinoma_smoker

label_protocol: Labeling was performed under contract by Illumina, Inc. per manufacturer's protocol.

growth_protocol: Cells were grown in RPMI medium supplemented with 10% fetal calf serum. All cells were grown at 37°c and 5% CO2.

extract_protocol: Extraction was performed under contract by Illumina, Inc. per manufacturer's protocol.

treatment_protocol: No treatments were performed prior to these assays.

tag: cell line name

tag: other name

tag: atcc #

tag: disease state

value: non-small cell lung cancer

tag: tissue diagnosis

value: adenocarcinoma

tag: gender

value: female

tag: race

value: Caucasian

tag: smoking history

value: smoker

tag: pack years

tag: cell line initiation date

tag: source of speciment

value: lymph node

tag: stage at initial evaluation

tag: initial diagnosis date


title: 5013 SC GN

tag: disease

tag: treatment


title: 5015 SC GN


title: 5012 SC GN


title: Bl6_VN62_InVivo_0720_Lung_2

tag: strain

tag: time

tag: infection (influenza strain)

tag: virus concentration

tag: tissue


title: Bl6_PR8_InVivo_0720_Lung_3


title: 5010 SC GN


title: Bl6_VN62_InVivo_0720_Lung_1


title: 5009 SC GN


title: Bl6_PR8_InVivo_0720_Lung_5


title: 5008 SC GN


title: Bl6_PR8_InVivo_0720_Lung_4


title: Bl6_PR8_InVivo_0720_Lung_2


title: 5007 SC GN


title: AT-II 2 DAY4

source_name: implant adherent cells-rat tibia-microrough surface implant-day4

value: Sprague Dawley

value: Male

tag: cell type

value: tibial


title: 5006 SC GN


title: GS000000572-ASM

tag: cell line name

tag: other name

tag: atcc #

tag: disease state

tag: tissue diagnosis

value: male

tag: age

tag: death date


title: WT_DTT_rep3

status: Public on Sep 25 2012

city: Singapore

first: Guillaume

last: Thibault

address: 1 Research Link, National University of Singapore

department: Cell Stress and Homeostasis

country: Singapore

institute: Temasek Life Sciences Laboratory

hyb_protocol: Hybridized on Custom Microarray Agilent GE 4x44K array

scan_protocol: Arrays were scanned using High-resolution DNA Microarray Scanner model: G2505C (Agilent Technologies)

data_processing:
Data was analyzed using GeneSpring GX software (Agilent Technologies).   Normalization: Percentile shift to 75th percentile (per chip normalization); Baseline to Median of Individual batch data (per gene normalization).
For additional data processing details (eg, settings, filtering, etc.), please see the supplementary file linked to the Series record.

organism: Saccharomyces cerevisiae

source_name: WT treated 1h with 2 mM DTT, replica 3

label_protocol: Labeling System with 100 ng of total RNA as starting material following manufacturer instruction: One-Color Microarray-Based Gene Expression Analysis Protocol version 6.5 (Agilent Technologies)

growth_protocol: Culture were grown to an OD600 of 0.25 at 30oC in selective synthetic complete media.

extract_protocol: Total RNA was extracted by the hot acid phenol method as previously described (Spellman et al., 1998). Total RNA was subsequently cleaned up using Rnease Mini Kit (Qiagen)

treatment_protocol: The UPR was induced by the addition of 2 mM DTT or 1 µg/ml Tm for one hour prior to harvest the cells

tag: strain background

value: W303, mat alpha

tag: genotype/variation

value: Wild type

tag: agent

value: DTT


title: WT_DTT_rep1

source_name: WT treated 1h with 2 mM DTT, replica 1


title: Δopi3_rep2

source_name: Δopi3, replica 2


title: WT_DTT_rep2

source_name: WT treated 1h with 2 mM DTT, replica 2


title: GS000000516-ASM

source_name: Cell line_adenocarcinoma

tag: gender

tag: cell line initiation date

tag: source of speciment

value: pleural effusion

tag: stage at initial evaluation

tag: initial diagnosis date


title: GS000000521-ASM

source_name: Cell line_carcinoma large cell neuroendocrine_smoker

value: carcinoma large cell neuroendocrine

tag: race

tag: smoking history

tag: pack years

value: lung


title: Embryo at E10.5, diabetic, biological rep1

city: Baton Rouge

first: Claudia

last: Kappen

state: LA

address: 6400 Perkins Road

department: Developmental Biology

institute: Pennington Biomedical Research Center

hyb_protocol: GeneChip arrays (Mouse 430A2.0) were hybridized overnight in the Affymetrix hybridization oven at 42 degrees Celsius. Washing and scanning was performed using the Affymetrix GeneChip Fluidics Station 450.

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

data_processing:
Images were analyzed using Affymetrix GCOS imaging software. Statistical analyses were performed using GeneSpring7 and CyberT.
MAS 5.0

source_name: diabetic pregnancy pool D1 E10.5

label_protocol: Five ug of total RNA was reverse transcribed and biotin-labeled samples were generated using the Affymetrix Eukaryotic One-Cycle Target Labeling Assay.

growth_protocol: Diabetes was induced in femal FVB mice by two intraperitoneal injections of 100mg/kg body weight Streptozotocin in 50mM sodium citrate buffer within a one week interval. Mice with a blood glucose level higher than 250mg/dL were considered diabetic and used for mating. The morning with presence of a vaginal plug was counted as 0.5 days of gestation, after which pregnant dams were single-housed.

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

treatment_protocol: Embryos were dissected at 10.5 days of gestation and stored in Trizol at minus 80 degrees Celsius.

tag: strain

value: FVB

tag: tissue

value: whole embryo

value: diabetic pregnancy


title: WT_Tm_rep1

source_name: WT treated 1h with 1 µg/ml Tunicamycin, replica 1

value: Tunicamycin


title: Δcho2_rep3

source_name: Δcho2, replica 3


title: Δcho2_rep2

source_name: Δcho2, replica 2


title: Embryo at E10.5, diabetic, biological rep3

source_name: diabetic pregnancy pool D3 E10.5

tag: disease state


title: GS000000523-ASM

source_name: Cell line_carcinoma squamous cell_smoker

tag: cell line name

tag: other name

tag: atcc #

value: non-small cell lung cancer

tag: tissue diagnosis

value: carcinoma squamous cell

value: Caucasian


title: Embryo at E10.5, diabetic, biological rep2

source_name: diabetic pregnancy pool D2 E10.5

tag: age


title: Δopi3_rep3

source_name: Δopi3, replica 3

tag: strain background

tag: genotype/variation

tag: agent


title: Δpah1_rep2

source_name: Δpah1, replica 2


title: Δpah1_rep3

source_name: Δpah1, replica 3


title: Δcho2_rep1

source_name: Δcho2, replica 1


title: Embryo at E10.5, control, biological rep3

source_name: control pregnancy pool C3 E10.5

value: control pregnancy


title: Bl6_PR8_InVivo_0720_Lung_1

source_name: wild-type Bl6 mice lung tissue

tag: time

value: 12 hrs

tag: infection (influenza strain)

tag: virus concentration


title: Δpah1_rep1

source_name: Δpah1, replica 1


title: GS000000514-ASM

value: adenocarcinoma

tag: gender

tag: cell line initiation date


title: Embryo at E10.5, control, biological rep1

source_name: control pregnancy pool C1 E10.5


title: Δopi3_rep1

source_name: Δopi3, replica 1


title: GS000000515-ASM

source_name: Cell line_carcinoma large cell_smoker

value: carcinoma large cell

value: male

tag: race

tag: smoking history

value: smoker

tag: pack years

tag: source of speciment

tag: stage at initial evaluation

tag: death date

tag: initial diagnosis date


title: GS000000519-ASM

source_name: Cell line_carcinoma non-small cell

tag: cell line name

tag: other name

tag: atcc #

tag: disease state

tag: tissue diagnosis

value: carcinoma non-small cell


title: GS000000697-ASM

value: carcinoma mucoepidermoid

value: female

tag: age

value: African American

value: never-smoker

value: lymph node


title: GS000000528-ASM

value: pleural effusion


title: WT_rep2

source_name: Wild type, replica 2

tag: strain background

value: W303, mat alpha

tag: genotype/variation

value: Wild type

tag: agent


title: WT_rep1

source_name: Wild type, replica 1


title: Embryo at E10.5, control, biological rep2

source_name: control pregnancy pool C2 E10.5

tag: strain

value: FVB

tag: tissue

value: whole embryo


title: WT_rep3

source_name: Wild type, replica 3


title: lung from GS10 group, rep3

city: yangzhou

first: Jiao

last: Hu

address: E. Wenhui Road 12

country: China

institute: yangzhou university

description: Gene expression data of lung from GS10-infected mouse

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies) in Hybridization Oven (Agilent) according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent) with default settings. Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Feature Extraction software 10.7 was used to analyzed data and raw data were normalized by Quantile algorithm Gene Spring Software 11.0.

source_name: lung from GS10-infected mouse, day 1 post infection

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit,One-Color (Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (QIAGEN).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Qualified total RNA was further purified by Rneasy mini kit (QIAGEN,GmBH, Germany) and RNase-Free DNase Set (QIAGEN).

treatment_protocol: Lungs were collected from mice and immediately froze in liquid nitrogen and then stored at -70℃.

value: BALB/c

tag: infection

value: lung


title: GS000000593-ASM

value: non-small cell lung cancer

tag: gender


title: lung from control group, rep1

description: Gene expression data of lung from mock-infected mouse

source_name: lung from mock-infected mouse

value: control


title: lung from control group, rep3


title: GS000000520-ASM

source_name: Cell line_adenocarcinoma_smoker

value: adenocarcinoma

value: male

tag: race

value: Caucasian

tag: smoking history

tag: pack years

tag: cell line initiation date

tag: source of speciment

value: soft tissue


title: A549_48hr_CNT-2

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression after 48hr in CNT-2-exposed human alveolar epithelial cell

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v1_Sep09 and Grid: 026652_D_F_20110819). Background detrend: On (Feat NCRange, LoPass). Multiplicative detrend: True. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalized data is the average of n=4. VALUE: Normalized signal intensity (log2)

source_name: Alveolar epithelial cell, 48hr, CNT-2, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Tokyo, Japan). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Human alveolar epithelial cell line A549 were seeded into each well of a 96-well plate (Becton, Dickinson and Company, Franklin Lakes, NJ) and grown in the DMEM with 10% heat-inactivated fetal bovine serum medium for 24 hours.

extract_protocol: Total RNA was extracted from the cells using the QIAcube instrument (Qiagen, Tokyo, Japan) following the manufactures instructions. RNA was quantified using a NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Each medium were replaced by three kinds of single-wall carbon nanotubes (SWCNTs), CNT-1, CNT-2 or CNT-3 in a 10-fold dilution series. Cell concentrations at this point were approximately 1.3 x 10^5 cells/mL. The cultures were incubated for 24 or 48 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell type

value: Alveolar epithelial cell

tag: cell line

tag: treatment

tag: time


title: GS000000518-ASM

source_name: Cell line_adenocarcinoma

tag: cell line name

tag: other name

tag: atcc #

tag: disease state

tag: tissue diagnosis


title: A549_48hr_control for CNT-3

description: Gene expression after 48hr in human alveolar epithelial cell  as cotrol for CNT-3

source_name: Alveolar epithelial cell, 48hr, control for CNT-3, replicate 4

value: untreatment, control for CNT-3


title: A549_48hr_control for CNT-2

description: Gene expression after 48hr in human alveolar epithelial cell  as cotrol for CNT-2

source_name: Alveolar epithelial cell, 48hr, control for CNT-2, replicate 4

value: untreatment, control for CNT-2


title: A549_48hr_CNT-3

description: Gene expression after 48hr in CNT-3-exposed human alveolar epithelial cell

source_name: Alveolar epithelial cell, 48hr, CNT-3, replicate 4


title: lung from GS10 group, rep1

tag: strain

tag: tissue


title: lung from control group, rep2

tag: infection


title: GS000000513-ASM

tag: gender

tag: age

tag: race

value: smoker

tag: stage at initial evaluation

tag: death date

tag: initial diagnosis date


title: GS00255-DNA_D03-ASM

value: female

tag: smoking history

tag: pack years

tag: cell line initiation date

tag: source of speciment


title: hTF P28

city: Greifswald

first: Joerg

last: Mostertz

address: F.-L.-Jahnstr 15

department: Competence Center Functional Genomics

institute: Greifswald University

hyb_protocol: Biotinylated sense-strand DNA was then hybridized on to the Affymetrix GeneChip® Human Gene 1.0 ST arrays, for 16 h. --> folllowed the protocols of the manufacturer

scan_protocol: The arrays were washed and stained using the Fluidics Station 450 and scanning was performed by Scanner 3000 7G (Affymetrix, High Wycombe, UK).--> folllowed the protocols of the manufacturer

data_processing:
Microarray data analysis was carried out by using the Rosetta Resolver® system for gene expression data analysis (Rosetta Biosoftware, Seattle, WA, USA). In brief, the raw signals of the probes were summarized using RMA thereby generating probe set specific signal intensities. Chips were normalized by using quantile normalization.
To compare RNA expression levels of genes in hCF, hSF and hTF, normalized expression signals of genes from corresponding samples were averaged and fold changes were calculated. To assess differences in mean signal intensities between experimental groups, ANOVA (analysis of variance, with Benjamini Hochberg test correction) and a post-hoc Scheffe test was performed. Rosetta Resolver ratio built statistics to correct for possible signal intensity bias were also considered. Only genes (1) an absolute fold change of ≥ 1.5 together with a Scheffe test p value ≤ 0.05 in at least one of the three pairwise comparisons hCF vs. hTF, hSF vs. hTF and hCF vs. hSF, resp., as well as (2) a ratio built p value ≤ 0.05 were deemed differentially expressed genes (DEG) and considered for further evaluation.

source_name: Tenon’s space fibroblasts (hTF)

label_protocol: For each sample, total RNA (200 ng) was reverse transcribed into cDNA,  subsequently amplified and in-vitro transcribed to cRNA. Sense-strand cDNA was generated from 10µg of purified cRNA using random primers, followed by subsequent fragmentation and labeling. Biotinylated sense-strand DNA was then hybridized on to the Affymetrix GeneChip® Human Gene 1.0 ST arrays, for 16 h. The arrays were washed and stained using the Fluidics Station 450 and scanning was performed by Scanner 3000 7G (Affymetrix, High Wycombe, UK). --> folllowed the protocols of the manufacturer

growth_protocol: Each tissue was cut into pieces of approximately 1 mm2 in size, placed in a 12 well cell culture plate in DMEM (Applichem, Darmstadt, Germany) with 50 U/ml of penicillin, 50 μg/ml streptomycin and 10% FCS (PAA, Cölbe, Germany), and incubated at 37° C under 5% CO2 at 95 % humidity. Growth medium was changed three times a week. When outgrowing primary fibroblasts reached a confluent monolayer, cells were trypsinized in 0.25% trypsin/EDTA (PAA, Cölbe, Germany) solution in phosphate buffered saline (PBS) and transferred to a 25 cm2 cell culture flasks (Greiner bio one, Frickenhausen, Germany).

extract_protocol: To the cells harvested in TRIzol®, chloroform (Baker, Deventer, Netherlands) was added (10 %), and cells were vigorously vortexed. The resulting homogenate was centrifuged at 10,000 g for 2 min and the aqueous supernatant was reextracted with TRIzol®/chloroform and centrifuged as above. The aqueous supernatant was adjusted to 35 % enthanol and applied onto an RNeasy column (QIAGEN, Hilden, Germany). After washing the column residual DNA was digested with DNase I (QIAGEN, Hilden, Germany) and after three wash steps total RNA was eluted with 100 µL of RNase free water followed by purification using the RNA Clean-Up and Concentration Micro Kit (Norgen Biotek Corp., Thorold, ON, Canada). RNA quantity and purity was measured at 260/280/230 nm with a Nanodrop photospectrometer (Thermo Scientific, Waltham, MA, USA) and RNA integrity was assessed by using the Bioanalyzer 2100 (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: no differing treatment  in terms of 'control-treatment' settings

tag: cell type

value: Tenon’s space fibroblasts (hTF)


title: NoL_control07

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

country: Spain

institute: Cancer Research Center (CiC-IBMCC)

description:
Gene expression data from human clinical samples
xc07_NoL_Exp_U133p2

hyb_protocol: Hybridized to the Human Genome U133 Plus 2.0 microarray, after quality checking on GeneChips Test Arrays.

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

data_processing: The justRMA function provided by the package Affy from R/Bioconductor was applied to the raw expression data. The probes were mapped to GENE LOCi by the CDF built by GATExplorer, which can be found at http://bioinfow.dep.usal.es/xgate/mapping/mapping.php.

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

extract_protocol: Total RNA from cells was extracted by homogenization in TRIZOL (Invitrogen, Carlsbad, CA, USA), following the manufacturer’s protocol, then treated with RQ1 RNAse-Free DNase (Promega, Madison, USA) to eliminate genomic DNA contamination, and finally purified with RNeasy Minikit (Qiagen)

treatment_protocol: Human samples obtained from patients and healthy donors

tag: disease type

tag: disease subtype

value: bone marrow mononuclear cells (BMNCs)


title: NoL_control05

description:
Gene expression data from human clinical samples
xc05_NoL_Exp_U133p2


title: GS000000524-ASM

source_name: Cell line_carcinoma squamous cell_never-smoker

tag: cell line name

tag: other name

tag: atcc #

tag: disease state

tag: tissue diagnosis

value: carcinoma squamous cell

value: never-smoker

value: pleural effusion


title: NoL_control06

description:
Gene expression data from human clinical samples
xc06_NoL_Exp_U133p2


title: hTF P17


title: hTF P14


title: lung from CK10 group, rep3

description: Gene expression data of lung from CK10-infected mouse

source_name: lung from CK10-infected mouse, day 1 post infection

tag: strain

value: BALB/c

tag: infection

tag: tissue

value: lung


title: lung from CK10 group, rep2


title: GS000000522-ASM

value: non-small cell lung cancer

tag: gender

tag: age

tag: race

value: African American

tag: death date


title: A549_24hr_CNT-3

description: Gene expression after 24hr in CNT-3-exposed human alveolar epithelial cell

source_name: Alveolar epithelial cell, 24hr, CNT-3, replicate 4

tag: cell line

tag: treatment

tag: time


title: A549_48hr_control for CNT-1

description: Gene expression after 48hr in human alveolar epithelial cell  as cotrol for CNT-1

source_name: Alveolar epithelial cell, 48hr, control for CNT-1, replicate 4

tag: cell type

value: untreatment, control for CNT-1


title: lung from GS10 group, rep2


title: NoL_control04

description:
Gene expression data from human clinical samples
xc04_NoL_Exp_U133p2

tag: disease type

tag: disease subtype


title: NoL_control03

description:
Gene expression data from human clinical samples
xc03_NoL_Exp_U133p2


title: A549_24hr_control for CNT-3

description: Gene expression after 24hr in human alveolar epithelial cell  as cotrol for CNT-3

source_name: Alveolar epithelial cell, 24hr, control for CNT-3, replicate 4


title: hSF P30

source_name: sclera fibroblasts (hSF)

value: sclera fibroblasts (hSF)


title: GS000000517-ASM

tag: cell line name

tag: other name

value: adenocarcinoma

value: Caucasian

tag: smoking history

tag: pack years

tag: cell line initiation date

tag: source of speciment

value: lymph node

tag: stage at initial evaluation

tag: initial diagnosis date


title: hTF P12


title: NoL_control02

description:
Gene expression data from human clinical samples
xc02_NoL_Exp_U133p2


title: MprU3h_MseU3h

city: Raleigh

first: Arpan

last: Mukherjee

address: 840 Main Campus Dr. Rm 3304

department: Chemical Engineering

institute: North Carolina State University

description:
Cells Mpr (DSMZ10039) and Mse(DSMZ5348) were grown at 70C in an orbital shaking oil bath at 90 rpm on DSMZ 88 medium (pH 2) with 0.2 wt% yeast extract
Mse and Mpr cells were grown upto mid log phase after which they were challenged with U shock and harvested at cell density of 1x108 cells/ml (mid log phase). Biological repeats were done for both experimental conditions. Mpr cDNA was hybdrized on Mse array as all genes in Mpr mapped to Mse genome.

hyb_protocol: Sample preparation steps for microarray hybridization: Prepare Prehyb buffer: 225mL water, 75mL 20X SSC, 0.3g SDS, 0.3g BSA. Preheat Prehyb buffer 45 min 42 degree C. Prehybidize slides at 42 degree C for 45 min. Wash slides by dipping 5 time in sterile dH2O at RT. Dip twice in isopropanol at RT. Dry slide in slide spinner. Add 1 ul COT1-DNA (20mg/ml) to samples. Heat probe mixture to 95oC in heat block for 2 min to denature DNA, do a quick spin. Add 30 ul of 2x hyb. buffer that has been preheated to 42oC to each tube. Hybridization buffer: 27.2uL water, 20uL 20X SSC, 8uL 50X Denhardts solution, 24uL formamide, 0.8uL 10% SDS. Apply hyb. mix to slide and cover with a 20x60 mm polyethylene hydrophobic coverslip. Place slide in water proof container, cover well with foil and place in 42 degree C bath for 18-20 hours. The following is a standard hybridization method that seems to work well for this procedure: 1 wash cycle at 42 degree C with 2X SSC w/ 0.2% SDS. 1 wash cycle at RT with 0.5X SSC w/ 0.2% SDS. 3 wash cycles at RT with 0.5X SSC

scan_protocol: Images were aquired with a GenePix 4000B scanner (Molecular Devices) using 532 nm and 635 nm lasers simultaneously. An automatic photomultiplier (PMT) gain adjustment was used to balance the 532 nm and 635 nm channels prior to scanning the whole slide. A pixel size of 10 microns was selected for the image resolution. Separate images were saved for the 532 and 635 nm scans, and analyzed together using  GenePix Pro (v6.0) software.

data_processing: Signals for each channel were obtained using GenePix Pro (v6.0) using circular features and were background substrated using the median local intensity around the spot. Once all the slides were quantitated, data from the dye-flip was analyzed with JMP Genomics 5.0 (SAS, NC), normalized using Lowess then ANOVA to estimate the global fixed effects of dye & treatment and the random effects array and block followed by using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001).

organism: Metallosphaera sedula DSM 5348

source_name: Cell Pellet

label_protocol: Producing cDNA: In a sterile PCR tube add 20 ug RNA with 6 ug random primers. Then add nuclease free water so the volume is 10 uL. Incubate at 70 degree C for 10 min. Place tube on ice for 1 min. Add 8 uL of RT Master Mix (recipe below) to each tube and swirl to mix. Quick spin before incubation. RT Master Mix: 4uL 5X strand buffer, 1uL 0.1M DTT, 1uL dNTP mix (see below), 2uL superscript III Invitrogen. dNTP mix: 3uL dATP (100mM), 3uL dGTP (100mM), 3uL dCTP(100mM), 1.8uL dTTP (100mM), 2.4uL aa-dUTP(50mM) Ambion, 6.8uL nuclease free water. Incubate at 46 degree C for at least 3 hours. Hydrolyze RNA by adding 10uL 1N NaOH to each tube. To stop reaction add 10 uL 0.5M EDTA to each tube. Mix and incubate at 65 degree C for 15 min. Add 10uL 1N HCl to each tube neutralize reaction mix. Transfer samples into labeled tubes of appropriate sizes. Add five volumes PB Buffer (Qiagen) to each tube and mix well. Add 300 ul of RT product to a labeled Qiagen PCR cleanup column. Spin at 1,000 rpm for 15 sec., empty collection tube, and repeat until all of the solution has passed through the column. Complete wash One, add 750 ul of phosphate wash buffer (recipe below) to column and spin at 13,000 rpm for 1 min., empty tube. Complete wash Two, add 750 ul of phosphate wash buffer to column and spin at 13,000 rpm for 1 min., empty tube. Phosphate wash buffer: 0.1mL 1M KPO4( pH 8.5), 3.05mL autoclaved dH2O and 16.85mL 95% EtOH. Spin an additional 1 min. with the same collection tube and discard the flow through. Transfer to new 1.5 mL tube, add 60uL phosphate elution buffer to the membrane and incubate at room temp. for 1 min. Spin at 13,000 rpm. Phosphate elution buffer: 4mM KPO4. Repeat phosphate elution into same tube using 60uL. Fluorescent Labeling: Dry all RT samples completely in speed vac. Resuspend each dried sample cDNA in 4.5 uL of 0.1M sodium carbonate buffer, pH 9.0. Mix up and down with pipette for good mixing. Dissolve and mix thoroughlythe Cy™ dye to be used with 20uL of DMSO. Tpically Cye dyes contain four applications in each vial. Mix 4.5 uL of dye with prepared cDNA sample. Incubate in the dark for 2 hour @ R.T. Mix RT-PCR products with 35uL 100mM NaOAc PH 5.2 and mix by vortexing. Mix with 250uL Qiagen Buffer PB and filter through spin columns (13,000 rpm). Wash spin column with 750 uL of Buffer PE (Qiagen). Spin an additional 1 min. with the same collection tube and discard the flow through. Elute labeled cDNA 2 times with 30 uL of EB Buffer (Qiagen). Combine different labeled probes Speed vacuum sample until dry (not too dry, i.e. don’t leave in speed vacuum for over 1 hour). Combine different labeled probes and speed vacuum sample until dry. Resuspend samples in 29uL sterilized dH2O

growth_protocol: Mpr and Mse cells were inoculated into DSMZ sulfolobus medium (with 0.2 wt% Yeast extract) and U shock at cell density of 1x108 cells/ml

extract_protocol: Cells were cooled to T < 10C using dry ice and ethanol mix and harvested by centrifugation (4800xg, 20 min at 4C) and pellets were stored at -80°C. Total RNA was isolated using a modified Trizol (Invitrogen) protocol in combination with an RNAeasy kit (Qiagen). RNA quality was determined by running it on 1% Agarose gel. The biological replicates were pooled prior to cDNA construction.

treatment_protocol: Harvest of cells occurred for both species at cell density of 1 x 108 cells/ml

tag: growth media

value: heterotrophic growth with 0.2 wt% yeast extract and U shock at mid log phase, harvested after 3hr

organism: Metallosphaera sedula

tag: strain


title: A549_24hr_CNT-2

description: Gene expression after 24hr in CNT-2-exposed human alveolar epithelial cell

source_name: Alveolar epithelial cell, 24hr, CNT-2, replicate 4

value: Alveolar epithelial cell


title: MDS_patient18_RARS

description:
Gene expression data from human clinical samples
p18_mdsRARS_Exp_U133p2

source_name: Low-risk MDS_BMNCs

value: Low-Risk Myelodysplastic Syndrome (MDS)


title: hSF P18


title: A549_48hr_CNT-1

description: Gene expression after 48hr in CNT-1-exposed human alveolar epithelial cell

source_name: Alveolar epithelial cell, 48hr, CNT-1, replicate 4


title: lung from CK10 group, rep1

tag: infection

tag: tissue


title: A549_24hr_CNT-1

description: Gene expression after 24hr in CNT-1-exposed human alveolar epithelial cell

source_name: Alveolar epithelial cell, 24hr, CNT-1, replicate 4

tag: cell line

tag: treatment