title: A549 cells_12h SIS3_biological rep1

status: Public on Jun 24 2011

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

state: PA

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

description: Cultured A549 cells treated with 10uM SIS3 30 min prior to stimulation with 2ng/ml TGF-b

hyb_protocol: Labeled RNA was hybridized for 17 hr at 60C on Agilent 4X44K gene expression array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K array slides

data_processing: Agilent Feature Extraction v9.5.2, default parameters

source_name: A549 cells, 12h SIS3, biological rep1

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 500ng total RNA

growth_protocol: Cells grown in F12-K culture medium supplemented with 10% fetal bovine serum

extract_protocol: Total RNA extracted using Trizol according to the manufacturer's instructions.

treatment_protocol: Cultured A549 cells treated with DMSO 30 min prior to stimulation with 2ng/ml TGF-b

value: lung epithelial cells


title: A549 cells_0h SIS3_biological rep3

type: RNA

country: USA

molecule: total RNA

organism: Homo sapiens

source_name: A549 cells, 0h SIS3, biological rep3

tag: tissue

tag: gender

value: male

tag: age


title: A549 cells_24h control_biological rep3

description: Cultured A549 cells treated with DMSO 30 min prior to stimulation with 2ng/ml TGF-b

source_name: A549 cells, 24h control, biological rep3


title: A549 cells_2h control_biological rep3

source_name: A549 cells, 2h control, biological rep3


title: A549 cells_12h control_biological rep1

source_name: A549 cells, 12h control, biological rep1


title: E. coli virF vs virFdel rep 2

status: Public on Jun 25 2011

city: Rome

first: Gianni

last: Prosseda

address: via dei sardi 70

department: Biology and Biotechology C. Darwin

country: Italy

institute: Saoienza , University of Rome

hyb_protocol: The labeled cDNA (Cy3 sample and Cy5 sample mixed) were added to 50 µl of hybridization buffer containing 50% formamide, 10X SSC, 0.2% SDS. After hybridization, slides were washed sequential

scan_protocol: Scanned on an PerkinElmer ScanArray Lite scanner. Images were quantified using ScanArray Express and GenePix Pro 6.1 software

data_processing: Global Lowess normalized, with J-Express software. We filtered the data to exclude artifacts, and low signal spots

organism: Escherichia coli

source_name: E. coli MG1655 pMYSH6504 (virF)

label_protocol: 80 µg of total RNA was labeled with Cy3 or Cy5 using LabelStar Array Kit (Qiagen)

growth_protocol: Bactera were grown in Luria Broth medium (LB) and allowed to growth to OD600 = 0,6-0,8.

extract_protocol: Total RNA was isolated by hot phenol extraction. Than RNA was treated with DNAse I for 30 minutes at 37°C

tag: strain

source_name: E. coli MG1655 pMY6504R


title: A549 cells_12h SIS3_biological rep2

source_name: A549 cells, 12h SIS3, biological rep2


title: A549 cells_24h control_biological rep1

source_name: A549 cells, 24h control, biological rep1


title: A549 cells_0h control_biological rep2

source_name: A549 cells, 0h control, biological rep2


title: R2

city: Kurume

first: Yoshizo

last: Kimura

department: Pathology

country: Japan

institute: Kurume university

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi package in R.

label: biotin

source_name: normal mantle zone B-lymphocytes

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA from whole tissue was extracted with Trizol reagent. RNA, which was laser-microdissected from tissue, was isolated according to Ambion RNAqueous-Micro protocal for LCM. Quality control was performed with Experion BIO-RAD automated electrophoresis system.

value: lymph node

tag: diagnosis

value: benign lymphadenitis

value: female

tag: sample type

value: laser microdissection


title: mkk1CR_run3

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression data were obtained from SK-MEL-28 melanoma cells.

hyb_protocol: Agilent hybridization protocol 65C 10rpm 17 h.

scan_protocol: Agilent arrays were scanned using the Agilent Scanner G2565BA.

data_processing:
The data was first processed by background correction and then quantile normalization.
Agilent Feature Extraction software v.10.7.3

label: Agilent  part #5190-0442 Quick-Amp Labeling kit 1-color.

source_name: SK-MEL-28 melanoma cells +/- cleavage resistant (CR) MKK1/MKK2

label_protocol: 300 ng of Qiagen-purified total RNA

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

tag: cell line

value: melanoma cell line SK-MEL-28

tag: subtype


title: lacZ_run3

value: lacZ


title: lf_run3

value: lethal factor (anthrax toxin)


title: A549 cells_24h SIS3_biological rep3

source_name: A549 cells, 24h SIS3, biological rep3


title: mkk2CR_run2


title: A549 cells_0h SIS3_biological rep2

source_name: A549 cells, 0h SIS3, biological rep2


title: A549 cells_0h SIS3_biological rep1

source_name: A549 cells, 0h SIS3, biological rep1


title: A549 cells_12h control_biological rep2

source_name: A549 cells, 12h control, biological rep2


title: lf_run2


title: mkk2CR_run3


title: A549 cells_24h SIS3_biological rep1

source_name: A549 cells, 24h SIS3, biological rep1


title: A549 cells_2h control_biological rep2

source_name: A549 cells, 2h control, biological rep2


title: A549 cells_24h control_biological rep2

source_name: A549 cells, 24h control, biological rep2


title: lacZ_run2


title: A549 cells_0h control_biological rep1

source_name: A549 cells, 0h control, biological rep1


title: A549 cells_0h control_biological rep3

source_name: A549 cells, 0h control, biological rep3


title: mkk1CR_run2


title: mkk2CR_run1


title: A549 cells_24h SIS3_biological rep2

source_name: A549 cells, 24h SIS3, biological rep2


title: A549 cells_2h control_biological rep1

source_name: A549 cells, 2h control, biological rep1


title: lacZ_run1


title: MPI-827_tissue

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

hyb_protocol: Affymetrix hybridization was carried on U133A GeneChips according to the manufacturer's recommendations. In brief, 15 microgram of Biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter

scan_protocol: After hybridization of night (16 hours, 45° C) the hybridization mixture was removed from the GeneChip and washing and staining of the GeneChips was performed in a fluidics station (Affymetrix). The detection of the Biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500)

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

source_name: tumor

label_protocol: For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the INVITROGEN Superscript kit. After removal of small molecular components (Affymetrix Clean-up Module), Biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop) and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation

extract_protocol: RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)

value: ABC

value: non-mBL

value: Test

value: FISH data not available

value: FALSE


title: MPI-840_tissue

value: unclassified


title: lf_run1


title: MPI-818_tissue


title: MPI-835_tissue

value: GCB

value: intermediate


title: MPI-823_tissue

value: break

value: TRUE


title: MPI-834_tissue

value: male


title: MPI-817_tissue


title: MPI-839_tissue


title: mkk1CR_run1


title: MPI-832_tissue


title: MPI-842_tissue


title: MPI-821_tissue


title: MPI-814_tissue


title: MPI-841_tissue


title: MPI-820_tissue


title: MPI-830_tissue


title: MPI-813_tissue


title: MPI-822_tissue


title: MPI-816_tissue


title: MPI-843_tissue


title: MPI-812_tissue


title: Subject53825

type: genomic

city: Las Vegas

first: Patricia

last: Bray-Ward

state: NV

address: 1707 W Charleston Blvd, 110B

department: Pediatrics

institute: University of Nevada School of Medicine

description:
hybridized to 6.0 Chip
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files , CHP and txt files were generated using Affymetrix software per Affymetrix instructions. Data results were compared to those found using Partek software.
affymetrix-algorithm-name: birdseed-v2
affymetrix-algorithm-version: 2.4
affymetrix-array-type: GenomeWideSNP_6
program-name: Genotyping Console
program-version: Genotyping Console-4.0.3566.17393

label: Biotin

molecule: genomic DNA

source_name: Individual (53825) with mild dysmorphia, severe language disorder, mild intellectual disability, attention deficit hyperactivity disorder (ADHD), and a mood disorder.

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from EBV-transformed cell lines derived from peripheral blood using the Puregene DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: patient

tag: cell type

value: lymphoblast line


title: MPI-815_tissue


title: MPI-808_tissue


title: MPI-811_tissue


title: MPI-807_tissue

value: female


title: MPI-810_tissue


title: MPI-802_tissue


title: MPI-806_tissue


title: MPI-798_tissue


title: MPI-796_tissue


title: MPI-800_tissue


title: MPI-791_tissue


title: MPI-789_tissue


title: MPI-799_tissue


title: MPI-790_tissue


title: MPI-792_tissue


title: MPI-783_tissue


title: MPI-794_tissue


title: MPI-766_tissue


title: MPI-782_tissue


title: MPI-788_tissue


title: MPI-801_tissue


title: MPI-765_tissue


title: MPI-797_tissue


title: MPI-767_tissue


title: MPI-795_tissue


title: MPI-781_tissue


title: MPI-761_tissue


title: MPI-769_tissue


title: MPI-755_tissue


title: MPI-780_tissue


title: MPI-762_tissue


title: MPI-746_tissue


title: MPI-756_tissue


title: MPI-757_tissue


title: MPI-744_tissue


title: MPI-748_tissue


title: MPI-737_tissue


title: MPI-734_tissue


title: MPI-730_tissue


title: MPI-749_tissue


title: MPI-745_tissue


title: MPI-732_tissue


title: MPI-735_tissue


title: MPI-724_tissue


title: MPI-713_tissue


title: MPI-733_tissue


title: MPI-731_tissue


title: MPI-705_tissue


title: MPI-716_tissue


title: MPI-723_tissue


title: MPI-702_tissue


title: MPI-706_tissue


title: MPI-760_tissue


title: MPI-708_tissue


title: MPI-703_tissue


title: MPI-684_tissue


title: MPI-691_tissue


title: MPI-693_tissue


title: MPI-695_tissue


title: MPI-679_tissue


title: MPI-699_tissue


title: MPI-692_tissue


title: MPI-664_tissue


title: MPI-661_tissue


title: MPI-686_tissue


title: MPI-704_tissue


title: MPI-694_tissue


title: MPI-688_tissue


title: MPI-667_tissue


title: MPI-660_tissue


title: MPI-665_tissue


title: MPI-689_tissue


title: MPI-696_tissue


title: MPI-656_tissue


title: MPI-654_tissue


title: MPI-657_tissue


title: MPI-663_tissue


title: MPI-650_tissue


title: MPI-655_tissue


title: MPI-647_tissue


title: MPI-651_tissue


title: MPI-635_tissue


title: MPI-646_tissue


title: MPI-634_tissue


title: MPI-630_tissue


title: MPI-649_tissue


title: MPI-582_tissue


title: MPI-637_tissue


title: MPI-557_tissue


title: MPI-648_tissue


title: MPI-558_tissue


title: MPI-624_tissue

value: Train

value: negative


title: MPI-556_tissue


title: MPI-599_tissue


title: MPI-553_tissue


title: MPI-559_tissue


title: MPI-550_tissue


title: MPI-543_tissue


title: MPI-644_tissue


title: MPI-626_tissue


title: MPI-566_tissue


title: MPI-638_tissue


title: MPI-548_tissue


title: MPI-547_tissue


title: MPI-552_tissue


title: MPI-554_tissue


title: MPI-546_tissue


title: MPI-541_tissue


title: MPI-628_tissue


title: MPI-440_tissue


title: MPI-503_tissue


title: MPI-438_tissue


title: MPI-427_tissue


title: MPI-514_tissue


title: MPI-441_tissue


title: MPI-416_tissue


title: MPI-539_tissue


title: MPI-410_tissue


title: MPI-435_tissue


title: MPI-418_tissue


title: MPI-443_tissue


title: MPI-434_tissue


title: MPI-412_tissue


title: MPI-406_tissue


title: MPI-436_tissue


title: MPI-513_tissue


title: MPI-453_tissue


title: MPI-404_tissue


title: MPI-413_tissue


title: MPI-419_tissue


title: MPI-403_tissue


title: MPI-400_tissue


title: MPI-439_tissue


title: MPI-424_tissue


title: MPI-411_tissue


title: MPI-401_tissue


title: MPI-402_tissue


title: MPI-399_tissue


title: MPI-397_tissue


title: MPI-398_tissue


title: MPI-390_tissue


title: MPI-394_tissue


title: MPI-391_tissue


title: MPI-395_tissue


title: MPI-381_tissue


title: MPI-384_tissue


title: MPI-373_tissue


title: MPI-379_tissue


title: MPI-372_tissue


title: MPI-377_tissue


title: MPI-385_tissue


title: MPI-393_tissue


title: MPI-374_tissue


title: MPI-383_tissue


title: MPI-369_tissue


title: MPI-370_tissue


title: MPI-378_tissue


title: MPI-386_tissue


title: MPI-368_tissue


title: MPI-362_tissue


title: MPI-366_tissue


title: MPI-363_tissue


title: MPI-359_tissue


title: MPI-365_tissue


title: MPI-360_tissue


title: MPI-371_tissue


title: MPI-367_tissue


title: MPI-352_tissue


title: MPI-357_tissue


title: MPI-358_tissue


title: MPI-347_tissue


title: MPI-353_tissue


title: MPI-349_tissue


title: MPI-345_tissue


title: MPI-346_tissue


title: MPI-351_tissue


title: MPI-355_tissue


title: MPI-364_tissue


title: MPI-350_tissue


title: MPI-344_tissue


title: MPI-348_tissue


title: MPI-339_tissue


title: MPI-340_tissue


title: MPI-342_tissue


title: MPI-338_tissue


title: MPI-343_tissue


title: MPI-341_tissue


title: MPI-335_tissue


title: MPI-336_tissue


title: MPI-330_tissue


title: MPI-337_tissue


title: MPI-329_tissue


title: MPI-332_tissue


title: MPI-326_tissue


title: MPI-321_tissue


title: MPI-314_tissue


title: MPI-315_tissue


title: MPI-327_tissue


title: MPI-312_tissue


title: MPI-319_tissue


title: MPI-318_tissue


title: MPI-311_tissue


title: MPI-324_tissue


title: MPI-308_tissue


title: MPI-316_tissue


title: MPI-309_tissue


title: MPI-317_tissue


title: MPI-310_tissue


title: MPI-306_tissue


title: MPI-299_tissue


title: MPI-292_tissue


title: MPI-294_tissue


title: MPI-285_tissue


title: MPI-288_tissue


title: MPI-278_tissue


title: MPI-290_tissue


title: MPI-286_tissue


title: MPI-282_tissue


title: MPI-295_tissue


title: MPI-293_tissue


title: MPI-279_tissue


title: MPI-289_tissue


title: MPI-274_tissue


title: MPI-261_tissue


title: MPI-281_tissue


title: MPI-276_tissue


title: MPI-277_tissue


title: MPI-272_tissue


title: MPI-270_tissue


title: 25 MAP

city: Durham

first: Holly

middle: Kloos

last: Dressman

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University Medical Center

hyb_protocol: Affymetrix suggested protocol for Affymetrix GeneChip hybridization oven 645 and Fluidics Station 450

scan_protocol: Affymetrix suggested protocol for Affymetrix GeneChip Scanner 7G

data_processing: Generated MAS5 data using the Affymetrix Expression Console version 1.1 software

source_name: FFPE xenograft, human melanoma cells into Mus musculus, MAP

label_protocol: MessageAmp™ Premier RNA Amplification Kit

extract_protocol: RecoverAll-MagMAX Custom Kit and protocol (Applied Biosystems)


title: 4hm MAP

source_name: FFPE human melanoma, MAP

value: FFPE human melanoma


title: MPI-269_tissue


title: MPI-262_tissue


title: 5hm MAP


title: 1hm MAP


title: 2hm MAP


title: MPI-273_tissue


title: 24 MAP

value: FFPE xenograft, human melanoma cells into Mus musculus


title: 3hm MAP


title: 21 MAP


title: 6hm MAP


title: 22 MAP


title: 20 MAP


title: 17 MAP


title: 18 MAP


title: 15 MAP


title: 19 MAP


title: 14 MAP


title: 16 MAP


title: 12 MAP


title: 23 MAP


title: 13 MAP


title: 9 MAP


title: 7 MAP


title: 10 MAP


title: 6 MAP


title: 5 MAP


title: 3 MAP


title: 2 MAP


title: 8 MAP


title: 24tl MAP

source_name: Fresh-frozen xenograft, human melanoma cells into Mus musculus, MAP

extract_protocol: RNeasy kit (Qiagen)

value: fresh-frozen xenograft, human melanoma cells into Mus musculus


title: 11 MAP


title: 25tl MAP


title: 18tl MAP


title: 11tl MAP


title: 22tl MAP


title: 4 MAP


title: 10tl MAP


title: 12tl MAP


title: 1 MAP


title: 19tl MAP


title: 14tl MAP


title: 13tl MAP


title: 21tl MAP


title: 20tl MAP


title: 6tl MAP


title: 9tl MAP


title: 17tl MAP


title: 2tl MAP


title: 23tl MAP


title: m8 MAP

source_name: HMEC, MYC, MAP

value: HMECs infected with adenovirus expressing MYC


title: 7tl MAP


title: MPI-325_tissue

value: Test


title: 15tl MAP


title: 8tl MAP


title: 16tl MAP


title: 1tl MAP


title: m5 MAP


title: 4tl MAP


title: r9 MAP

source_name: HMEC, RAS, MAP

value: HMECs infected with adenovirus expressing RAS


title: m6 MAP


title: m4 MAP


title: 3tl MAP


title: m3 MAP


title: 5tl MAP


title: r3 MAP


title: r2 MAP


title: r8 MAP


title: r1 MAP


title: r7 MAP


title: r6 MAP


title: g8 MAP

source_name: HMEC, GFP, MAP

value: HMECs infected with adenovirus expressing GFP


title: m7 MAP


title: g9 MAP


title: g6 MAP


title: r5 MAP


title: g5 MAP


title: g4 MAP


title: g7 MAP


title: g3 MAP


title: 25tl One-Cycle

source_name: Fresh-frozen xenograft, human melanoma cells into Mus musculus, One-Cycle

label_protocol: Affymetrix one cycle IVT labeling procedure


title: 16tl One-Cycle


title: 23tl One-Cycle


title: 18tl One-Cycle


title: 17tl One-Cycle


title: 3tl One-Cycle


title: 24tl One-Cycle


title: 12tl One-Cycle


title: 19tl One-Cycle


title: 4tl One-Cycle


title: 11tl One-Cycle


title: 10tl One-Cycle


title: g2 MAP


title: 5tl One-Cycle


title: 6tl One-Cycle


title: 13tl One-Cycle


title: 20tl One-Cycle


title: 9tl One-Cycle


title: 2tl One-Cycle


title: 15tl One-Cycle


title: 8tl One-Cycle


title: 22tl One-Cycle


title: m4 One-Cycle

source_name: HMEC, MYC, One-Cycle


title: m7 One-Cycle


title: 21tl One-Cycle


title: m5 One-Cycle


title: m8 One-Cycle


title: 7tl One-Cycle


title: 14tl One-Cycle


title: r7 One-Cycle

source_name: HMEC, RAS, One-Cycle


title: r3 One-Cycle


title: r9 One-Cycle


title: 1tl One-Cycle


title: r6 One-Cycle


title: g8 One-Cycle

source_name: HMEC, GFP, One-Cycle


title: r5 One-Cycle


title: r8 One-Cycle


title: m6 One-Cycle


title: r1 One-Cycle


title: g7 One-Cycle


title: m3 One-Cycle


title: g3 One-Cycle


title: g9 One-Cycle


title: g5 One-Cycle


title: r2 One-Cycle


title: g2 One-Cycle


title: g4 One-Cycle


title: U251ctrl_2

city: Richmond

first: William

middle: C

last: Broaddus

state: VA

address: 417 North 11th Street, Sixth floor

department: Neurosurgery

institute: VCU

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

source_name: Glioma U251 cells treated with Oligofectamine

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Human glioma U251 cells were plated in 6-well plates at a density of 200K cells/well, in triplicates per condition, and grown in 10% DMEM with Pen-Strep.

treatment_protocol: The siRNA sequences (scrambled and WT1) were obtained from Dharmacon (Cat. Nos.: D-001206-14-05 and M-009101-01-0005 respectively ), and were applied to the cells at a concentration of 100nM per well. Following transfection, the plates were kept on a rocker at 370C for 4 hours, after which period, 500 ul of 3X-Opti-MEM (containing) was added.

tag: treatment

value: Oligofectamine


title: U251si_2

source_name: Glioma U251 cells treated with Oligofectamine+ si-WT1 siRNA

value: Oligofectamine + si-WT1 siRNA


title: g6 One-Cycle


title: U251scr_1

source_name: Glioma U251 cells treated with Oligofectamine + non-targeting siRNA control


title: U251ctrl_3


title: U251scr_2

value: Oligofectamine + non-targeting siRNA control


title: U251ctrl_1


title: U251scr_3


title: U251si_3


title: seedling of RIL241, biological rep2

city: Wuhan

first: Jia

last: Wang

state: Hubei

address: Shizishan Street #1

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University (HZAU)

description: expression variations in rice shoot at early seedling stage

hyb_protocol: Microarray hybridization were conducted by the CapitalBio Corporation (Beijing, China) according to the Affymetrix standard protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The probe intensity files (.cel files) for expression variations were read into R. Background correction, quantile normalization and summarization were performed using the RMA method in Bioconductor affy package.

organism: Oryza sativa Indica Group

source_name: shoots, 72h after germination, dark, RIL241

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: The seeds of 110 RILs and the parents Zhenshan 97 and Minghui 63 were first soaked in water for 48 h in a chamber (Conviron S10H, Controlled Environment Limited, Winnipeg, Canada) set at 25°C/85% relative humidity/dark, and transferred to another chamber (Conviron PVG36, Controlled Environment Limited, Winnipeg, Canada) for pre-germination (35°C, 85% relative humidity, dark). Germination of the seeds was checked every 2 h and germinated seeds were transferred to a growth chamber (Conviron S10H) and incubated for 72 h (25°C, 85% relative humidity, dark).

extract_protocol: Total RNA extraction was performed using Trizol, according to the manufacturer's instructions.

treatment_protocol: Untreated.

value: shoot

value: 72 h after germination

tag: line

tag: variety

value: Minghui 63/Zhenshan 97 RILs


title: seedling of RIL238, biological rep2

source_name: shoots, 72h after germination, dark, RIL238


title: seedling of Minghui 63, biological rep3

source_name: shoots, 72h after germination, dark, Minghui 63

value: Minghui 63

value: Parent Minghui 63


title: seedling of Zhenshan 97, biological rep2

source_name: shoots, 72h after germination, dark, Zhenshan 97

value: Zhenshan 97

value: Parent Zhenshan 97


title: seedling of RIL236, biological rep2

source_name: shoots, 72h after germination, dark, RIL236


title: seedling of Zhenshan 97, biological rep1


title: seedling of RIL210, biological rep2

source_name: shoots, 72h after germination, dark, RIL210


title: U251si_1


title: seedling of Zhenshan 97, biological rep3


title: seedling of RIL232, biological rep2

source_name: shoots, 72h after germination, dark, RIL232


title: seedling of RIL215, biological rep2

source_name: shoots, 72h after germination, dark, RIL215


title: seedling of Minghui 63, biological rep1


title: seedling of RIL219, biological rep2

source_name: shoots, 72h after germination, dark, RIL219


title: seedling of RIL216, biological rep2

source_name: shoots, 72h after germination, dark, RIL216


title: seedling of Minghui 63, biological rep2


title: seedling of RIL206, biological rep2

source_name: shoots, 72h after germination, dark, RIL206


title: seedling of RIL209, biological rep2

source_name: shoots, 72h after germination, dark, RIL209


title: seedling of RIL204, biological rep2

source_name: shoots, 72h after germination, dark, RIL204


title: seedling of RIL199, biological rep2

source_name: shoots, 72h after germination, dark, RIL199


title: seedling of RIL193, biological rep2

source_name: shoots, 72h after germination, dark, RIL193


title: seedling of RIL205, biological rep2

source_name: shoots, 72h after germination, dark, RIL205


title: seedling of RIL197, biological rep2

source_name: shoots, 72h after germination, dark, RIL197


title: seedling of RIL195, biological rep2

source_name: shoots, 72h after germination, dark, RIL195


title: seedling of RIL191, biological rep2

source_name: shoots, 72h after germination, dark, RIL191


title: seedling of RIL192, biological rep2

source_name: shoots, 72h after germination, dark, RIL192


title: seedling of RIL180, biological rep2

source_name: shoots, 72h after germination, dark, RIL180


title: seedling of RIL185, biological rep2

source_name: shoots, 72h after germination, dark, RIL185


title: seedling of RIL184, biological rep2

source_name: shoots, 72h after germination, dark, RIL184


title: seedling of RIL175, biological rep2

source_name: shoots, 72h after germination, dark, RIL175


title: seedling of RIL187, biological rep2

source_name: shoots, 72h after germination, dark, RIL187


title: seedling of RIL183, biological rep2

source_name: shoots, 72h after germination, dark, RIL183


title: seedling of RIL178, biological rep2

source_name: shoots, 72h after germination, dark, RIL178


title: seedling of RIL169, biological rep2

source_name: shoots, 72h after germination, dark, RIL169


title: seedling of RIL165, biological rep2

source_name: shoots, 72h after germination, dark, RIL165


title: seedling of RIL163, biological rep2

source_name: shoots, 72h after germination, dark, RIL163


title: seedling of RIL164, biological rep2

source_name: shoots, 72h after germination, dark, RIL164


title: seedling of RIL161, biological rep2

source_name: shoots, 72h after germination, dark, RIL161


title: seedling of RIL167, biological rep2

source_name: shoots, 72h after germination, dark, RIL167


title: seedling of RIL162, biological rep2

source_name: shoots, 72h after germination, dark, RIL162


title: seedling of RIL173, biological rep2

source_name: shoots, 72h after germination, dark, RIL173


title: seedling of RIL159, biological rep2

source_name: shoots, 72h after germination, dark, RIL159


title: seedling of RIL155, biological rep2

source_name: shoots, 72h after germination, dark, RIL155


title: seedling of RIL160, biological rep2

source_name: shoots, 72h after germination, dark, RIL160


title: seedling of RIL156, biological rep2

source_name: shoots, 72h after germination, dark, RIL156


title: seedling of RIL152, biological rep2

source_name: shoots, 72h after germination, dark, RIL152


title: seedling of RIL149, biological rep2

source_name: shoots, 72h after germination, dark, RIL149


title: seedling of RIL139, biological rep2

source_name: shoots, 72h after germination, dark, RIL139


title: seedling of RIL133, biological rep2

source_name: shoots, 72h after germination, dark, RIL133


title: seedling of RIL150, biological rep2

source_name: shoots, 72h after germination, dark, RIL150


title: seedling of RIL154, biological rep2

source_name: shoots, 72h after germination, dark, RIL154


title: seedling of RIL141, biological rep2

source_name: shoots, 72h after germination, dark, RIL141


title: seedling of RIL134, biological rep2

source_name: shoots, 72h after germination, dark, RIL134


title: seedling of RIL129, biological rep2

source_name: shoots, 72h after germination, dark, RIL129


title: seedling of RIL145, biological rep2

source_name: shoots, 72h after germination, dark, RIL145


title: seedling of RIL151, biological rep2

source_name: shoots, 72h after germination, dark, RIL151


title: seedling of RIL147, biological rep2

source_name: shoots, 72h after germination, dark, RIL147


title: seedling of RIL137, biological rep2

source_name: shoots, 72h after germination, dark, RIL137


title: seedling of RIL131, biological rep2

source_name: shoots, 72h after germination, dark, RIL131


title: seedling of RIL118, biological rep2

source_name: shoots, 72h after germination, dark, RIL118


title: seedling of RIL125, biological rep2

source_name: shoots, 72h after germination, dark, RIL125


title: seedling of RIL123, biological rep2

source_name: shoots, 72h after germination, dark, RIL123


title: seedling of RIL106, biological rep2

source_name: shoots, 72h after germination, dark, RIL106


title: seedling of RIL112, biological rep2

source_name: shoots, 72h after germination, dark, RIL112


title: seedling of RIL111, biological rep2

source_name: shoots, 72h after germination, dark, RIL111


title: seedling of RIL140, biological rep2

source_name: shoots, 72h after germination, dark, RIL140


title: seedling of RIL114, biological rep2

source_name: shoots, 72h after germination, dark, RIL114


title: seedling of RIL101, biological rep2

source_name: shoots, 72h after germination, dark, RIL101


title: seedling of RIL109, biological rep2

source_name: shoots, 72h after germination, dark, RIL109


title: seedling of RIL105, biological rep2

source_name: shoots, 72h after germination, dark, RIL105


title: seedling of RIL095, biological rep2

source_name: shoots, 72h after germination, dark, RIL095


title: seedling of RIL084, biological rep2

source_name: shoots, 72h after germination, dark, RIL084


title: seedling of RIL086, biological rep2

source_name: shoots, 72h after germination, dark, RIL086


title: seedling of RIL099, biological rep2

source_name: shoots, 72h after germination, dark, RIL099


title: seedling of RIL081, biological rep2

source_name: shoots, 72h after germination, dark, RIL081


title: seedling of RIL083, biological rep2

source_name: shoots, 72h after germination, dark, RIL083


title: seedling of RIL103, biological rep2

source_name: shoots, 72h after germination, dark, RIL103


title: seedling of RIL080, biological rep2

source_name: shoots, 72h after germination, dark, RIL080


title: seedling of RIL077, biological rep2

source_name: shoots, 72h after germination, dark, RIL077


title: seedling of RIL087, biological rep2

source_name: shoots, 72h after germination, dark, RIL087


title: seedling of RIL089, biological rep2

source_name: shoots, 72h after germination, dark, RIL089


title: seedling of RIL090, biological rep2

source_name: shoots, 72h after germination, dark, RIL090


title: seedling of RIL072, biological rep2

source_name: shoots, 72h after germination, dark, RIL072


title: seedling of RIL071, biological rep2

source_name: shoots, 72h after germination, dark, RIL071


title: seedling of RIL186, biological rep2

source_name: shoots, 72h after germination, dark, RIL186


title: seedling of RIL066, biological rep2

source_name: shoots, 72h after germination, dark, RIL066


title: seedling of RIL059, biological rep2

source_name: shoots, 72h after germination, dark, RIL059


title: seedling of RIL068, biological rep2

source_name: shoots, 72h after germination, dark, RIL068


title: seedling of RIL198, biological rep2

source_name: shoots, 72h after germination, dark, RIL198


title: seedling of RIL062, biological rep2

source_name: shoots, 72h after germination, dark, RIL062


title: seedling of RIL027, biological rep2

source_name: shoots, 72h after germination, dark, RIL027


title: seedling of RIL026, biological rep2

source_name: shoots, 72h after germination, dark, RIL026


title: seedling of RIL054, biological rep2

source_name: shoots, 72h after germination, dark, RIL054


title: seedling of RIL030, biological rep2

source_name: shoots, 72h after germination, dark, RIL030


title: seedling of RIL016, biological rep2

source_name: shoots, 72h after germination, dark, RIL016


title: seedling of RIL022, biological rep2

source_name: shoots, 72h after germination, dark, RIL022


title: seedling of RIL019, biological rep2

source_name: shoots, 72h after germination, dark, RIL019


title: seedling of RIL023, biological rep2

source_name: shoots, 72h after germination, dark, RIL023


title: seedling of RIL042, biological rep2

source_name: shoots, 72h after germination, dark, RIL042


title: seedling of RIL047, biological rep2

source_name: shoots, 72h after germination, dark, RIL047


title: seedling of RIL039, biological rep2

source_name: shoots, 72h after germination, dark, RIL039


title: seedling of RIL017, biological rep2

source_name: shoots, 72h after germination, dark, RIL017


title: seedling of RIL020, biological rep2

source_name: shoots, 72h after germination, dark, RIL020


title: seedling of RIL053, biological rep2

source_name: shoots, 72h after germination, dark, RIL053


title: seedling of RIL048, biological rep2

source_name: shoots, 72h after germination, dark, RIL048


title: seedling of RIL203, biological rep2

source_name: shoots, 72h after germination, dark, RIL203


title: seedling of RIL018, biological rep2

source_name: shoots, 72h after germination, dark, RIL018


title: seedling of RIL014, biological rep2

source_name: shoots, 72h after germination, dark, RIL014


title: seedling of RIL015, biological rep2

source_name: shoots, 72h after germination, dark, RIL015


title: seedling of RIL013, biological rep2

source_name: shoots, 72h after germination, dark, RIL013


title: seedling of RIL012, biological rep2

source_name: shoots, 72h after germination, dark, RIL012


title: seedling of RIL009, biological rep2

source_name: shoots, 72h after germination, dark, RIL009


title: seedling of RIL007, biological rep2

source_name: shoots, 72h after germination, dark, RIL007


title: seedling of RIL005, biological rep2

source_name: shoots, 72h after germination, dark, RIL005


title: seedling of RIL006, biological rep2

source_name: shoots, 72h after germination, dark, RIL006


title: seedling of RIL238, biological rep1

source_name: shoots, 72h after germination, dark, RIL238


title: seedling of RIL216, biological rep1

source_name: shoots, 72h after germination, dark, RIL216


title: seedling of RIL241, biological rep1

source_name: shoots, 72h after germination, dark, RIL241


title: seedling of RIL236, biological rep1

source_name: shoots, 72h after germination, dark, RIL236


title: seedling of RIL001, biological rep2

source_name: shoots, 72h after germination, dark, RIL001


title: seedling of RIL209, biological rep1

source_name: shoots, 72h after germination, dark, RIL209


title: seedling of RIL004, biological rep2

source_name: shoots, 72h after germination, dark, RIL004


title: seedling of RIL219, biological rep1

source_name: shoots, 72h after germination, dark, RIL219


title: seedling of RIL206, biological rep1

source_name: shoots, 72h after germination, dark, RIL206


title: seedling of RIL204, biological rep1

source_name: shoots, 72h after germination, dark, RIL204


title: seedling of RIL203, biological rep1

source_name: shoots, 72h after germination, dark, RIL203


title: seedling of RIL210, biological rep1

source_name: shoots, 72h after germination, dark, RIL210


title: seedling of RIL215, biological rep1

source_name: shoots, 72h after germination, dark, RIL215


title: seedling of RIL232, biological rep1

source_name: shoots, 72h after germination, dark, RIL232


title: seedling of RIL197, biological rep1

source_name: shoots, 72h after germination, dark, RIL197


title: seedling of RIL205, biological rep1

source_name: shoots, 72h after germination, dark, RIL205


title: seedling of RIL198, biological rep1

source_name: shoots, 72h after germination, dark, RIL198


title: seedling of RIL186, biological rep1

source_name: shoots, 72h after germination, dark, RIL186


title: seedling of RIL199, biological rep1

source_name: shoots, 72h after germination, dark, RIL199


title: seedling of RIL187, biological rep1

source_name: shoots, 72h after germination, dark, RIL187


title: seedling of RIL193, biological rep1

source_name: shoots, 72h after germination, dark, RIL193


title: seedling of RIL195, biological rep1

source_name: shoots, 72h after germination, dark, RIL195


title: seedling of RIL184, biological rep1

source_name: shoots, 72h after germination, dark, RIL184


title: seedling of RIL185, biological rep1

source_name: shoots, 72h after germination, dark, RIL185


title: seedling of RIL183, biological rep1

source_name: shoots, 72h after germination, dark, RIL183


title: seedling of RIL178, biological rep1

source_name: shoots, 72h after germination, dark, RIL178


title: seedling of RIL180, biological rep1

source_name: shoots, 72h after germination, dark, RIL180


title: seedling of RIL192, biological rep1

source_name: shoots, 72h after germination, dark, RIL192


title: seedling of RIL191, biological rep1

source_name: shoots, 72h after germination, dark, RIL191


title: seedling of RIL173, biological rep1

source_name: shoots, 72h after germination, dark, RIL173


title: seedling of RIL082, biological rep2

source_name: shoots, 72h after germination, dark, RIL082


title: seedling of RIL169, biological rep1

source_name: shoots, 72h after germination, dark, RIL169


title: seedling of RIL163, biological rep1

source_name: shoots, 72h after germination, dark, RIL163


title: seedling of RIL160, biological rep1

source_name: shoots, 72h after germination, dark, RIL160


title: seedling of RIL156, biological rep1

source_name: shoots, 72h after germination, dark, RIL156


title: seedling of RIL159, biological rep1

source_name: shoots, 72h after germination, dark, RIL159


title: seedling of RIL151, biological rep1

source_name: shoots, 72h after germination, dark, RIL151


title: seedling of RIL150, biological rep1

source_name: shoots, 72h after germination, dark, RIL150


title: seedling of RIL167, biological rep1

source_name: shoots, 72h after germination, dark, RIL167


title: seedling of RIL152, biological rep1

source_name: shoots, 72h after germination, dark, RIL152


title: seedling of RIL145, biological rep1

source_name: shoots, 72h after germination, dark, RIL145


title: seedling of RIL149, biological rep1

source_name: shoots, 72h after germination, dark, RIL149


title: seedling of RIL161, biological rep1

source_name: shoots, 72h after germination, dark, RIL161


title: seedling of RIL165, biological rep1

source_name: shoots, 72h after germination, dark, RIL165


title: seedling of RIL162, biological rep1

source_name: shoots, 72h after germination, dark, RIL162


title: seedling of RIL175, biological rep1

source_name: shoots, 72h after germination, dark, RIL175


title: seedling of RIL155, biological rep1

source_name: shoots, 72h after germination, dark, RIL155


title: seedling of RIL164, biological rep1

source_name: shoots, 72h after germination, dark, RIL164


title: seedling of RIL147, biological rep1

source_name: shoots, 72h after germination, dark, RIL147


title: seedling of RIL139, biological rep1

source_name: shoots, 72h after germination, dark, RIL139


title: seedling of RIL140, biological rep1

source_name: shoots, 72h after germination, dark, RIL140


title: seedling of RIL141, biological rep1

source_name: shoots, 72h after germination, dark, RIL141


title: seedling of RIL129, biological rep1

source_name: shoots, 72h after germination, dark, RIL129


title: LV sham-Control vs. LV following banding of the descending thoracic aorta (AOB-LV)

city: Boston

first: James

middle: D

last: McCully

state: MA

address: 77 Avenue Louis Pasteur

department: Cardiothoracic Surgery

institute: BIDMC/Harvard Medical School

description: Rabbit Heart left ventricle (LV) sham-Control vs. Rabbit Heart left ventricle (LV) following banding of the descending thoracic aorta (AOB-LV)

hyb_protocol: Microarray slides were pre-hybridized in a solution containing 3.5 x SSC, 0.1% SDS and 1% BSA at 50C for at least 60 min. and then rinsed 2x in ddH2O; once in isopropanol and then spun dry at 1,000 rpm for 1 min and then immediately used for hybridization. Control heart samples were labeled with Cy3-dUTP and  experimental hearts samples (AOB-LV and PAB-RV) were  labeled with Cy5-dUTP and then  combined with 30 uL hybridization solution (stock solution containing 100 uL DIG EasyHyb hybridization solution (Roche), 5 uL yeast tRNA (10 mg/mL), 5 uL human COT1 DNA, 5 uL Poly-dA, and 5 uL salmon sperm DNA (10 mg/mL).  Dye swaps also performed. The probe solution was hybridized to the arrayed slide at 37 C overnight.  The following day, slides were  washed first with 1x SSC to remove the cover slip (Hybri-Slips, Sigma) , then 3 successive washes of 1x SSC / 0.1% SDS for 15 minutes each at 50 oC, followed by a rinse with 1x SSC.  The slides were dried in individual 50 mL conical tubes and centrifuged at 500 rpm to remove excess fluid.

scan_protocol: Scanning of the slides was performed using the GMS 418 scanner (Affymetrix) at 532 nm (Cy3) and 635 nm (Cy5).

data_processing:
Local background was subtracted from the fluorescent value Cluster Analysis. All treatments were compared to Control to account for constitutive gene expression. Raw scanned images of Cy3 and Cy5 fluorescence were processed using Axon 4000A microarray scanner with GenePix analysis software using Rosetta Resolver (Molecular Devices Corp, Sunnyvale CA.). Dye swap was treated as technical replicates to account for dye effect error. Fold change criteria was used together with p-values to identify gene expression changes. p values were calculated based on dye swap results. Computational biology was performed using Spotfire Decision Site 8.1 (Spotfire, Somerville, MA).  Functional annotation cluster analysis was performed using DAVID 2007 functional annotation bioiformatics microarray analysis (http://david.abcc.ncifcrf.gov/).
Lowess normalization.

organism: Oryctolagus cuniculus

source_name: Left venticluar heart tissue (male, 15-20 weeks; 3 to 4 kg)

label_protocol: 4uL first strand buffer; 2uL 0.1M DTT;  2uL 10X low dTTP–dNTP (5 mM dATP, dCTP, dGTP, and 2 mM dTTP); 2uL CyanineX-dUTP (1 mM ; Cyanine3; Cy3 for control; green and Cyanine5; Cy5 for experimental; Amersham, Pharmacia Biotech); 1uL RNasin and 1uL of Superscript II (GIBCO) and incubated at 42 oC  for 30 min. then and another 1uL Superscript II added and the reaction allowed to continue a further 40 min. at 42 oC. The reaction was stopped with the addition of  2.5 uL 500 mM EDTA and heating to 65 oC for 1 min. The RNA template was hydrolyzed with the addition of 5 uL 1M NaOH and incubation at 65 oC for 10 min. and then neutralized by adding 12.5 uL 1M Tris pH 7.5 immediately to neutralize the pH. The labeled cDNA probes were purified by gel exclusion chromatography (ProbeQuant G-50, Amersham) and the volume reduced to 5-10 uL using a Speedvac.

extract_protocol: Cardiac ventricular RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Newborn New Zealand White rabbits were sedated and anesthetized and a mini thoracotomy was performed. LV-POH was achieved by banding the descending thoracic aorta (n=6), RV-POH was achieved by banding the pulmonary artery (n=6). Sham–Control animals (SC; n=6 each) were sham-manipulated. Following 4 (LV-POH) and 6 weeks (RV-POH) recovery the hearts were removed and matched sample RNA and proteins were isolated for microarray and proteomic analysis.

value: control

value: male

value: 15-20 weeks

tag: weight

value: 3 to 4 kg

value: Left ventricular heart

value: LV sham-Control

value: test


title: seedling of RIL133, biological rep1

source_name: shoots, 72h after germination, dark, RIL133


title: seedling of RIL154, biological rep1

source_name: shoots, 72h after germination, dark, RIL154


title: seedling of RIL134, biological rep1

source_name: shoots, 72h after germination, dark, RIL134


title: LV following banding of the descending thoracic aorta (AOB-LV) vs. LV sham-Control

description: Rabbit Heart left ventricle (LV) following banding of the descending thoracic aorta (AOB-LV) vs. Rabbit Heart left ventricle (LV) sham-Control


title: LV following banding the pulmonary artery (PAB-LV) vs. RV following banding the pulmonary artery (PAB-RV)

description: Rabbit Hear tleft ventricle (LV) following banding the pulmonary artery (PAB-LV) vs. Rabbit Heart right ventricle (RV) following banding the pulmonary artery (PAB-RV)

source_name: Right venticluar heart tissue (male, 15-20 weeks; 3 to 4 kg)

value: Right ventricular heart


title: seedling of RIL125, biological rep1

source_name: shoots, 72h after germination, dark, RIL125


title: seedling of RIL114, biological rep1

source_name: shoots, 72h after germination, dark, RIL114


title: RV following banding the pulmonary artery (PAB-RV) vs. LV following banding the pulmonary artery (PAB-LV)

description: Rabbit Heart right ventricle (RV) following banding the pulmonary artery (PAB-RV) vs. Rabbit Hearlleft ventricle (LV) following banding the pulmonary artery (PAB-LV)


title: seedling of RIL131, biological rep1

source_name: shoots, 72h after germination, dark, RIL131


title: seedling of RIL103, biological rep1

source_name: shoots, 72h after germination, dark, RIL103


title: RV following banding the pulmonary artery (PAB-RV) vs. RV sham-Control

description: Rabbit Heart right ventricle (RV) following banding the pulmonary artery (PAB-RV) vs. Rabbit Heart right ventricle (RV) sham-Control

source_name: Right ventricular heart tissue (male,15-20 weeks; 3 to 4 kg)

value: RV sham-Control


title: RV sham-Control vs. RV following banding the pulmonary artery (PAB-RV)

description: Rabbit Heart right ventricle (RV) sham-Control vs. Rabbit Heart right ventricle (RV) following banding the pulmonary artery (PAB-RV)


title: seedling of RIL118, biological rep1

source_name: shoots, 72h after germination, dark, RIL118


title: seedling of RIL105, biological rep1

source_name: shoots, 72h after germination, dark, RIL105


title: seedling of RIL099, biological rep1

source_name: shoots, 72h after germination, dark, RIL099


title: seedling of RIL111, biological rep1

source_name: shoots, 72h after germination, dark, RIL111


title: seedling of RIL112, biological rep1

source_name: shoots, 72h after germination, dark, RIL112


title: Brucella suis strain VTRS1 infected macrophages at 48 hour post infection), #3

city: Ann Arbor

first: Yongqun

last: He

address: 018 ARF, 1150 W. Medical Center Dr.

institute: University of Michigan

description: This is a macrophage sample that was at 48 h post infection with B. suis rough strain VTRS1.

hyb_protocol: Total RNA (20 µg) per sample was used for hybridization with Affymetrix mouse GeneChip 430 2.0 array at the Core Laboratory Facility at the Virginia Bioinformatics Institute (VBI).

scan_protocol: Follow standard Affymetrix protocol.

data_processing: The data was processed using RMA.

organism: Mus musculus

source_name: Murine J774.A1 macrophages, 48 hour infection with Brucella suis strain VTRS1

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

extract_protocol: Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 48 h post infection. This is replicate #3.

value: Murine J774.A1 macrophages


title: seedling of RIL106, biological rep1

source_name: shoots, 72h after germination, dark, RIL106

value: shoot


title: Brucella suis strain VTRS1 infected macrophages at 48 hour post infection), #2

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 48 h post infection. This is replicate #2.

value: 48 hour infection with Brucella suis strain VTRS1


title: seedling of RIL137, biological rep1

source_name: shoots, 72h after germination, dark, RIL137

value: 72 h after germination

value: Minghui 63/Zhenshan 97 RILs


title: seedling of RIL089, biological rep1

source_name: shoots, 72h after germination, dark, RIL089


title: seedling of RIL101, biological rep1

source_name: shoots, 72h after germination, dark, RIL101


title: seedling of RIL087, biological rep1

source_name: shoots, 72h after germination, dark, RIL087


title: seedling of RIL084, biological rep1

source_name: shoots, 72h after germination, dark, RIL084


title: seedling of RIL086, biological rep1

source_name: shoots, 72h after germination, dark, RIL086


title: Brucella suis strain VTRS1 infected macrophages at 24 hour post infection), #3

description: This is a macrophage sample that was at 24 h post infection with B. suis rough strain VTRS1.

source_name: Murine J774.A1 macrophages, 24 hour infection with Brucella suis strain VTRS1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 24 h post infection. This is replicate #3.


title: seedling of RIL109, biological rep1

source_name: shoots, 72h after germination, dark, RIL109


title: seedling of RIL095, biological rep1

source_name: shoots, 72h after germination, dark, RIL095


title: seedling of RIL090, biological rep1

source_name: shoots, 72h after germination, dark, RIL090


title: Brucella suis strain VTRS1 infected macrophages at 48 hour post infection), #1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 48 h post infection. This is replicate #1.


title: Brucella suis strain VTRS1 infected macrophages at 24 hour post infection), #2

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 24 h post infection. This is replicate #2.

value: 24 hour infection with Brucella suis strain VTRS1


title: seedling of RIL068, biological rep1

source_name: shoots, 72h after germination, dark, RIL068


title: seedling of RIL077, biological rep1

source_name: shoots, 72h after germination, dark, RIL077


title: seedling of RIL048, biological rep1

source_name: shoots, 72h after germination, dark, RIL048


title: seedling of RIL054, biological rep1

source_name: shoots, 72h after germination, dark, RIL054


title: Brucella suis strain VTRS1 infected macrophages at 24 hour post infection), #1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 24 h post infection. This is replicate #1.


title: Brucella suis strain VTRS1 infected macrophages at 2 hour post infection), #2

description: This is a macrophage sample that was at 2 h post infection with B. suis rough strain VTRS1.

source_name: Murine J774.A1 macrophages, 2 hour infection with Brucella suis strain VTRS1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 2 h post infection. This is replicate #2.


title: seedling of RIL083, biological rep1

source_name: shoots, 72h after germination, dark, RIL083


title: seedling of RIL066, biological rep1

source_name: shoots, 72h after germination, dark, RIL066


title: seedling of RIL071, biological rep1

source_name: shoots, 72h after germination, dark, RIL071


title: seedling of RIL059, biological rep1

source_name: shoots, 72h after germination, dark, RIL059


title: seedling of RIL082, biological rep1

source_name: shoots, 72h after germination, dark, RIL082


title: Brucella suis strain VTRS1 infected macrophages at 4 hour post infection), #1

description: This is a macrophage sample that was at 4 h post infection with B. suis rough strain VTRS1.

source_name: Murine J774.A1 macrophages, 4 hour infection with Brucella suis strain VTRS1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 4 h post infection. This is replicate #1.


title: seedling of RIL042, biological rep1

source_name: shoots, 72h after germination, dark, RIL042


title: seedling of RIL072, biological rep1

source_name: shoots, 72h after germination, dark, RIL072


title: seedling of RIL062, biological rep1

source_name: shoots, 72h after germination, dark, RIL062


title: seedling of RIL027, biological rep1

source_name: shoots, 72h after germination, dark, RIL027


title: seedling of RIL039, biological rep1

source_name: shoots, 72h after germination, dark, RIL039


title: Brucella suis strain VTRS1 infected macrophages at 4 hour post infection), #2

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 4 h post infection. This is replicate #2.

value: 4 hour infection with Brucella suis strain VTRS1


title: seedling of RIL053, biological rep1

source_name: shoots, 72h after germination, dark, RIL053


title: Brucella suis strain VTRS1 infected macrophages at 8 hour post infection), #1

description: This is a macrophage sample that was at 8 h post infection with B. suis rough strain VTRS1.

source_name: Murine J774.A1 macrophages, 8 hour infection with Brucella suis strain VTRS1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 8 h post infection. This is replicate #1.


title: seedling of RIL030, biological rep1

source_name: shoots, 72h after germination, dark, RIL030


title: Brucella suis strain VTRS1 infected macrophages at 4 hour post infection), #3

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 4 h post infection. This is replicate #3.


title: Brucella suis strain VTRS1 infected macrophages at 8 hour post infection), #2

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 8 h post infection. This is replicate #2.

value: 8 hour infection with Brucella suis strain VTRS1


title: seedling of RIL080, biological rep1

source_name: shoots, 72h after germination, dark, RIL080


title: seedling of RIL026, biological rep1

source_name: shoots, 72h after germination, dark, RIL026


title: Brucella suis strain VTRS1 infected macrophages at 2 hour post infection), #3

source_name: Murine J774.A1 macrophages, 2 hour infection with Brucella suis strain VTRS1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 2 h post infection. This is replicate #3.


title: seedling of RIL047, biological rep1

source_name: shoots, 72h after germination, dark, RIL047


title: seedling of RIL123, biological rep1

source_name: shoots, 72h after germination, dark, RIL123


title: seedling of RIL023, biological rep1

source_name: shoots, 72h after germination, dark, RIL023


title: Brucella suis strain VTRS1 infected macrophages at 1 hour post infection), #3

description: This is a macrophage sample that was at 1 h post infection with B. suis rough strain VTRS1.

source_name: Murine J774.A1 macrophages, one hour infection with Brucella suis strain VTRS1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 1 h post infection. This is replicate #3.


title: Brucella suis strain VTRS1 infected macrophages at 2 hour post infection), #1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 2 h post infection. This is replicate #1.

value: 2 hour infection with Brucella suis strain VTRS1


title: Brucella suis strain VTRS1 infected macrophages at 1 hour post infection), #2

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 1 h post infection. This is replicate #2.

value: one hour infection with Brucella suis strain VTRS1


title: seedling of RIL019, biological rep1

source_name: shoots, 72h after germination, dark, RIL019

treatment_protocol: Untreated.


title: seedling of RIL015, biological rep1

source_name: shoots, 72h after germination, dark, RIL015


title: seedling of RIL016, biological rep1

source_name: shoots, 72h after germination, dark, RIL016


title: seedling of RIL006, biological rep1

source_name: shoots, 72h after germination, dark, RIL006


title: seedling of RIL014, biological rep1

source_name: shoots, 72h after germination, dark, RIL014


title: seedling of RIL018, biological rep1

source_name: shoots, 72h after germination, dark, RIL018


title: seedling of RIL020, biological rep1

source_name: shoots, 72h after germination, dark, RIL020


title: Macrophage control 3 treated with medium only

description: This is a macrophage sample without infection with B. suis rough strain VTRS1.

source_name: Murine J774.A1 macrophages, without infection

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA). No infection was applied to these cells. This is replicate #3.

value: without infection


title: seedling of RIL013, biological rep1

source_name: shoots, 72h after germination, dark, RIL013


title: seedling of RIL017, biological rep1

source_name: shoots, 72h after germination, dark, RIL017


title: seedling of RIL081, biological rep1

source_name: shoots, 72h after germination, dark, RIL081


title: seedling of RIL007, biological rep1

source_name: shoots, 72h after germination, dark, RIL007


title: Brucella suis strain 1330 (S1330) infected macrophages at 48 hour post infection), #3

description: This is a macrophage sample that was at 48 h post infection with B. suis strain 1330 (S1330).

source_name: Murine J774.A1 macrophages, at 48 h post infection with B. suis S1330

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 48 h post infection. This is replicate #3.

value: 48 h post infection with B. suis S1330


title: seedling of RIL012, biological rep1

source_name: shoots, 72h after germination, dark, RIL012


title: seedling of RIL005, biological rep1

source_name: shoots, 72h after germination, dark, RIL005


title: seedling of RIL009, biological rep1

source_name: shoots, 72h after germination, dark, RIL009


title: Brucella suis strain 1330 (S1330) infected macrophages at 48 hour post infection), #2

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 48 h post infection. This is replicate #2.


title: Macrophage control #1 treated with medium

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA). No infection was applied to these cells. This is replicate #1.


title: seedling of RIL004, biological rep1

source_name: shoots, 72h after germination, dark, RIL004


title: Brucella suis strain VTRS1 infected macrophages at 1 hour post infection), #1

source_name: Murine J774.A1 macrophages, one hour infection with Brucella suis strain VTRS1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 1 h post infection. This is replicate #1.


title: seedling of RIL001, biological rep1

source_name: shoots, 72h after germination, dark, RIL001


title: Brucella suis strain 1330 (S1330) infected macrophages at 48 hour post infection), #1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 48 h post infection. This is replicate #1.


title: Patient 14

city: Toronto

first: Bobby

last: Yanagawa

state: ONT

address: 306-25 The Esplanade

department: Cardiac Surgery

country: Canada

institute: University of Toronto

hyb_protocol: miRNA was hybridized to the Genosensor miRNA array according to the manufacturer's protocol.  For more details, see http://www.genosensorcorp.com/microRNA_chip.html.

scan_protocol: The array was scanned with the GenePix 4000b Biochip according to the manufacturer's protocol.  For more details, see http://www.genosensorcorp.com/microRNA_chip.html.

data_processing: Global signal intensity: Sum of all probe signal intensity.  Positive control average (PosAve): Average of all positive control probe signals without tRNA-M2.  Array background: Average of signal intensity of all negative controls and buffer. Background standard deviation: Standard deviation of all negative controls and buffer. Signal threshould: Threshold was determined by array background + 2x background SD (standard deviation)

source_name: Tricuspid

label_protocol: 2ug of miRNA sample was labeled with the GenoExplorer miRNA labeling kit as per the manufacturer's instructions

extract_protocol: MiRNA was isolated from a 50% of a human aortic valve leaflet using the miRNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer`s instructions

value: Aortic Valve Leaflet


title: Patient 16


title: Patient 21


title: Patient 22


title: Patient 9


title: Patient 8


title: Patient 28


title: Patient 39


title: Brucella suis strain 1330 (S1330) infected macrophages at 24 hour post infection), #2

description: This is a macrophage sample that was at 24 h post infection with B. suis strain 1330 (S1330).

source_name: Murine J774.A1 macrophages, at 24 h post infection with B. suis S1330

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 24 h post infection. This is replicate #2.

value: 24 h post infection with B. suis S1330


title: Brucella suis strain 1330 (S1330) infected macrophages at 24 hour post infection), #1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 24 h post infection. This is replicate #1.


title: Brucella suis strain 1330 (S1330) infected macrophages at 24 hour post infection), #3

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 24 h post infection. This is replicate #3.


title: Brucella suis strain 1330 (S1330) infected macrophages at 8 hour post infection), #2

description: This is a macrophage sample that was at 8 h post infection with B. suis strain 1330 (S1330).

source_name: Murine J774.A1 macrophages, at 8 h post infection with B. suis S1330

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 8 h post infection. This is replicate #2.

value: 8 h post infection with B. suis S1330


title: SK_ctr for CTG infected_20 h_rep2

city: Baltimore

first: JC

last: xiao

state: MD

address: 600 N. Wolfe Street, Blalock 1109

institute: Johns Hopkins University

hyb_protocol: Biotinylated cRNAs were purified, fragmented, and subsequently hybridized to Affymetrix GeneChip human Exon 1.0 ST arrays.

scan_protocol: Array scanning was performed according to the manufacturer's instruction

data_processing:
Gene expression analysis was performed using the Affymetrix Human Exon 1.0 ST GeneChip. Data analysis began with raw GeneChip(r) data in the form of Affymetrix CEL files, produced and assigned quality control scores by Gene Expression Command Console software. Our analyses used the Affymetrix na 29 annotation release to align probes to genome build hg18. The probe-group file used was HuEx-1_0-st-v2.r2.pgf, and the meta-probeset file was HuEx-1_0-st-v2.na29.hg18.probeset_extended.mps.
These data were extracted and normalized with Partek(r) Genomics Suite(tm) software using the RMA (Robust Multichip Analysis) algorithm (Irrizary PMID: 12582260).
To ensure exploration of the broadest range of gene transcripts, we imported all Affymetrix "extended probes", yielding transcripts of which 76,206 currently have annotation with 43,004 at the gene- or mRNA-level.

source_name: Cells, uninfected

label_protocol: The RNAs was amplified into cRNAs and biotinylated by in vitro transcription using the Whole Transcript Sense Target Labeling protocol as described by Affymetrix with Affymetrix reagents.

growth_protocol: The human neuroepithelioma cell line SK-N-MC (ATCC, HTB-10) was propagated in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (D-MEM/F-12; Gibco) supplemented with 12.5% fetal bovine serum (FBS), 15 mmol/L HEPES, 4 mmol/L L-glutamine, 100 U/mL penicillin G, and 100 ug/mL streptomycin sulfate. Toxoplasma strains were maintained by passage in SK-N-MC monolayers cultured in DMEM supplemented with 3% FBS.

extract_protocol: Total RNA was harvested using the RNeasy reagent (QIAGEN, Valencia, CA)

treatment_protocol: SK-N-MC cells were plated in 6-well trays.  When reaching a confluence of 30–50%, cell cultures were synchronized by serum deprivation (0.5% FBS) for 2 days.  Parasites were released from intracellular vacuoles by syringe lysis and resuspended in Endo Buffer (44.7 mM K2SO4, 10 mM MgSO4, 106 mM sucrose, 5 mM glucose, 20 mM Tris–H2SO4, 3.5 mg/ml BSA, pH 8.2), this potassium buffer was used to synchronize invasion.  Briefly, at the time of infection, the synchronized cells infected with tachyzoites at a multiplicity of infection (MOI) of 3.  After adding parasites, the 6-well tray was centrifuged at 500 x g for 2 min and permitted to settle for 20 min at 37 ℃.  Endo buffer was then aspirated, replaced with 3% serum medium and incubated for 20 hr.

tag: infection

value: control (uninfected)

tag: toxoplasma strain

value: CTG


title: Brucella suis strain 1330 (S1330) infected macrophages at 4 hour post infection), #1

description: This is a macrophage sample that was at 2 h post infection with B. suis strain 1330 (S1330).

source_name: Murine J774.A1 macrophages, at 4 h post infection with B. suis S1330

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 4 h post infection. This is replicate #1.

value: 4 h post infection with B. suis S1330

value: Murine J774.A1 macrophages


title: Brucella suis strain 1330 (S1330) infected macrophages at 8 hour post infection), #1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 8 h post infection. This is replicate #1.


title: Brucella suis strain VTRS1 infected macrophages at 8 hour post infection), #3

source_name: Murine J774.A1 macrophages, 8 hour infection with Brucella suis strain VTRS1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis strain VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 8 h post infection. This is replicate #3.


title: Brucella suis strain 1330 (S1330) infected macrophages at 4 hour post infection), #2

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 4 h post infection. This is replicate #2.


title: Brucella suis strain 1330 (S1330) infected macrophages at 8 hour post infection), #3

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 8 h post infection. This is replicate #3.


title: SK_ctr for Pru infected_20 h_rep3

value: neuroepithelioma cell line SK-N-MC (ATCC, HTB-10)

value: Pru


title: Patient 43

source_name: Bicuspid


title: Patient 2


title: Brucella suis strain 1330 (S1330) infected macrophages at 4 hour post infection), #3

description: This is a macrophage sample that was at 4 h post infection with B. suis strain 1330 (S1330).

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 4 h post infection. This is replicate #3.


title: SK_CTG infected_20 h_rep1

source_name: Cells, infected by CTG

value: infected with Toxoplasma


title: SK_CTG infected_20 h_rep3


title: SK_ctr for CTG infected_20 h_rep3


title: SK_ctr for CTG infected_20 h_rep1


title: SK_CTG infected_20 h_rep2


title: SK_ctr for Pru infected_20 h_rep2


title: Patient 26


title: Patient 34


title: Patient 7


title: Patient 33


title: Brucella suis strain 1330 (S1330) infected macrophages at 2 hour post infection), #3

source_name: Murine J774.A1 macrophages, at 2 h post infection with B. suis S1330

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 2 h post infection. This is replicate #3.

value: 2 h post infection with B. suis S1330


title: SK_ctr for Pru infected_20 h_rep1


title: Patient 41


title: Brucella suis strain 1330 (S1330) infected macrophages at 2 hour post infection), #1

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 2 h post infection. This is replicate #1.


title: Brucella suis strain 1330 (S1330) infected macrophages at 2 hour post infection), #2

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 2 h post infection. This is replicate #2.


title: Brucella suis strain 1330 (S1330) infected macrophages (1 hour post infection), #2

description: This is a macrophage sample that was infected with B. suis strain 1330 (S1330) for one hour.

source_name: Murine J774.A1 macrophages, one hour infection with B. suis S1330

treatment_protocol: Macrophages were treated with Brucella suis strain 1330 (S1330) for one hour. This is replicate #2.

value: one hour infection with B. suis S1330


title: Brucella suis strain 1330 (S1330) infected macrophages (1 hour post infection), #1

treatment_protocol: Macrophages were treated with Brucella suis strain 1330 (S1330) for one hour. This is replicate #1.


title: Brucella suis strain 1330 (S1330) infected macrophages (1 hour post infection), #3

treatment_protocol: Macrophages were treated with Brucella suis strain 1330 (S1330) for one hour. This is replicate #3.


title: Macrophage control #3 treated with medium only

description: This is a control macrophage sample treated with only medium (no bacterial infection).

source_name: Murine J774.A1 macrophages, no infection

treatment_protocol: No specific treatment. This is a control (#3).

value: no infection


title: SK_Pru infected_20 h_rep2

source_name: Cells, infected by Pru


title: Patient 25


title: Patient 20


title: Patient 24


title: SK_Pru infected_20 h_rep3


title: SK_Pru infected_20 h_rep1


title: Macrophage control 2 treated with medium only

source_name: Murine J774.A1 macrophages, without infection

treatment_protocol: J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA). No infection was applied to these cells. This is replicate #2.


title: Macrophage control #2 treated with medium only

treatment_protocol: No specific treatment. This is a control (#2).


title: SK_ctr for 2F infected_20 h_rep3


title: SK_ctr for 2F infected_20 h_rep2


title: SK_2F infected_20 h_rep3

source_name: Cells, infected by 2F


title: Patient 3


title: Patient 12


title: SK_ctr for 2F infected_20 h_rep1


title: Macrophage control #1 treated with medium only

treatment_protocol: No specific treatment. This is a control for B. suis strain S1330-infected macrophage study.


title: SK_2F infected_20 h_rep1

treatment_protocol: SK-N-MC cells were plated in 6-well trays.  When reaching a confluence of 30–50%, cell cultures were synchronized by serum deprivation (0.5% FBS) for 2 days.  Parasites were released from intracellular vacuoles by syringe lysis and resuspended in Endo Buffer (44.7 mM K2SO4, 10 mM MgSO4, 106 mM sucrose, 5 mM glucose, 20 mM Tris–H2SO4, 3.5 mg/ml BSA, pH 8.2), this potassium buffer was used to synchronize invasion.  Briefly, at the time of infection, the synchronized cells infected with tachyzoites at a multiplicity of infection (MOI) of 3.  After adding parasites, the 6-well tray was centrifuged at 500 x g for 2 min and permitted to settle for 20 min at 37 ℃.  Endo buffer was then aspirated, replaced with 3% serum medium and incubated for 20 hr.


title: SK_2F infected_20 h_rep2


title: astroTIPeR, rep6

status: Public on Jun 23 2011

city: Philadelphia

first: Tae

middle: Kyung

last: Kim

address: 3620 Hamilton Walk

department: Pharmacology

institute: University of Pennsylvania

description: gene expression data from cardiomyocyte transcriptome TIPeRed astrocyte, single cell

hyb_protocol: Hybridization and scanning performed at Sidney Kimmel Nucleic Acid Facility at Thomas Jefferson University

data_processing: Data were analyzed using R/Bioconductor package and GeneSpring GX (version 11). Second highest intensity values were extracted from the probesets and informative probesets were selected by their ability to distinguish AVMs from fibroblasts. Individual t tests were performed for each probeset, contrasting AVM expression (n = 4) and fibroblast expression (n = 3) and retained the 3,257 probesets whose expression significantly differed between the two cell types (p < 0.05).

source_name: single cell

label_protocol: Illumina TotalPrep RNA Amplification Kit

growth_protocol: Isolated cells were cultured inDMEM media supplemented with 10% FBS

extract_protocol: Single cells were isolated using glass micro pipette and aRNAs were amplified using aRNA amplification procedure.

treatment_protocol: poly-A RNAs were transfected using lipid reagent.

tag: transfected transcriptome

value: cardiomyoyte


title: astroTIPeR, rep4

scan_protocol: Hybridization and scanning performed at Sidney Kimmel Nucleic Acid Facility at Thomas Jefferson University

value: cardiomyocyte transcriptome TIPeRed astrocyte, single cell


title: astroTIPeR, rep1


title: astroControl, rep1

description: gene expression data from mock transfected astrocyte, single cell

value: mock transfected astrocyte, single cell

value: mock transfection


title: astroTIPeR, rep2


title: astroTIPeR, rep5


title: astroTIPeR, rep3


title: cardiomyocyte, rep3

description: gene expression data from cardiomyocyte, single cell

value: cardiomyocyte, single cell

value: No transfection


title: cardiomyocyte, rep4


title: fibroblast, rep3

description: gene expression data from fibroblast, single cell

value: fibroblast, single cell


title: seedling of RIL022, biological rep1

description: expression variations in rice shoot at early seedling stage

source_name: shoots, 72h after germination, dark, RIL022

treatment_protocol: Untreated.

tag: tissue

value: shoot

value: 72 h after germination

value: Minghui 63/Zhenshan 97 RILs


title: fibroblast, rep2


title: cardiomyocyte, rep1


title: fibroblast, rep1


title: astroControl, rep2


title: fibroControl, rep2

description: gene expression data from fibroblast transcriptome TIPeRed fibroblast, single cell

value: fibroblast


title: fibroControl, rep3

value: fibroblast transcriptome TIPeRed fibroblast, single cell


title: fibroTIPeR, rep4

description: gene expression data from cardiomyocyte transcriptome TIPeRed fibroblast, single cell

value: cadiomyocyte


title: fibroTIPeR, rep5

value: cardiomyocyte transcriptome TIPeRed fibroblast, single cell


title: Primary Effusion Lymphoma cell line JSC1 [AffyNsp250]

city: Chapel Hill

first: Dirk

last: Dittmer

address: 116 Manning Drive, CB# 7290

department: Microbiology & Immunology

institute: University of North Carolina at Chapel Hill

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
Raw .CEL and .CHP files were imported into Genomics Suite software available from Partek Incorp. and analyzed using the Copy Number workflows
Data provided in the GSE28684_500K_Genotype.txt and GSE28684_CopyNumber.txt include genotype calls across the SNP markers and copy number markers included in the 500K array, respectively.

source_name: PEL cell line JSC1

label_protocol: Standard Affymetrix protocol

extract_protocol: Genomic DNA was extracted from cell pellets using Promega Wizard DNA isolation kit

value: B-cell

value: PEL cell line JSC1


title: Normal Control Tonsil6 [AffyNsp250]

source_name: tonsil tissue from healthy donor

value: tonsil tissue from healthy donor


title: fibroTIPeR, rep1


title: 8wg16_Rpb2

city: madison

first: jeff

last: grass

state: wi

address: 1550 linden dr

department: biochemistry

institute: uw-madison

hyb_protocol: The amplified DNA was then labeled with Cy3 (input DNA) or Cy5 (IP DNA) dye, hybridized to a Nimblegen High Density 2.1 M promoter tiling array using a Maui hybridization apparatus (BioMicro Systems), and quantified using a Axon 4000B scanner (Molecular Devices) following the protocol from Nimblegen.

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.3 ChIP data extraction. Eight ChIP datasets were generated as log2(IP/input) fluorescence intensities using anti-FLAG IP of wild-type RPB2-FLAG cells in biological triplicate, anti-FLAG IP of ∆FL RPB2 FLAG cells in biological triplicate, and anti-RPB1 CTD, 8WG16 of both wild-type and ∆FL cells in biological duplicate. The two 8WG16- IP datasets were combined to measure the distribution of RPB1 signal. Data analysis was performed using the statistical program R (Bioconductor) and publicly available packages. To compare RNAPII distributions in wild-type and ∆FL RPB2 cells, replicate data sets were quantile normalized using the normalizeQuantiles function in the affyPLM package, averaged at each probe position to generate single values for each target, and then quantile normalized against each other to allow comparison.

source_name: 8wg16 ChIP DNA from wt Rpb2

label_protocol: The immunoprecipitated (IP) DNA sample and an input DNA sample (recovered after similar treatment but without immunoprecipitation) were amplified by linker-mediated PCR as described in the protocol from Nimblegen. The amplified DNA was then labeled with Cy3 (input DNA) or Cy5 (IP DNA) dye.

growth_protocol: Wt Rpb2-FLAG cells were grown as monolayers in DMEM supplemented with Tet free FBS and sodium bicarbonate (0.375%) and hygromycin (200 μg/mL).

extract_protocol: ChIP assays were performed essentially as described elsewhere. Cells were grown on 10 cm2 dishes, crosslinked by addition of formaldehyde to 1% and incubation at room temperature for 15 min, washed twice with PBS, scraped off the plates, and centrifuged in 15 ml conical tubes for 10 min at 1000 g. The pelleted cells were transferred to a 1.5 ml microfuge tube in 550 µl buffer A (50 mM Tris-HCl, pH 7.5, 10% glycerol, 1 mM EDTA, 1 mM EGTA, 150 mM NaCl and 1% Triton X-100) and sonicated (microtip sonicator, 60% output) 8 times on ice, pulsed for 30 s. Cell debris was removed by centrifugation at 20,800 g for 10 min at 4 oC, and the sample was then pre-cleared by addition of 30 µl Pansorbin (fixed Protein A-bearing S. aureus cells; Calbiochem) and incubation continued at 4 oC for 1 hour. RNAPII was immunoprecipitated with M2 anti-Flag antibody or with 8WG16 monoclonal antibody (45). Antibody (2-5 µg) was added to the pre-cleared sample and incubated overnight at 4 °C with mixing. Antibody complexes were recovered by binding to 30 µl Pansorbin and centrifugation for 4 min at 20,800 g, and then washed sequentially with buffer A, buffer B (50 mM Tris-HCl, pH 7.5, 750 mM KCl, 1 mM EDTA, 10% glycerol and 1% Triton X-100), and buffer C (20 mM Tris-HCl, pH 8.0, 100 mM KCl, 10 mM β−mercaptoethanol, 0.2 mM EDTA, 20% glycerol and 0.1% Triton X-100). Captured complexes were released by incubation for 20 min at room temperature in elution buffer (10% SDS, 100 mM NaHCO3), and recovery of supernatant after centrifugation at room temperature for 10 min at 20,800 g. The Pansorbin pellet was washed an additional time and the two washes were combined. Crosslinks were reversed by incubating at 65 °C overnight and the released DNA was then purified using a QIAquick PCR purification column.

treatment_protocol: Wt Rpb2-FLAG cells were treated with doxycycline (2 μg/mL).

tag: chip antibody

source_name: Input ChIP DNA from wt Rpb2

value: none, input DNA


title: fibroControl, rep1


title: Primary Effusion Lymphoma cell line VG1 [AffyNsp250]

source_name: PEL cell line VG1

value: PEL cell line VG1


title: Primary Effusion Lymphoma cell line BC5 [AffyNsp250]

source_name: PEL cell line BC5

value: PEL cell line BC5


title: fibroTIPeR, rep2


title: Normal Control Tonsil1 [AffyNsp250]


title: Primary Effusion Lymphoma cell line BCP1 [AffyNsp250]

source_name: PEL cell line BCP1

value: PEL cell line BCP1


title: Primary Effusion Lymphoma cell line TY1 [AffyNsp250]

source_name: PEL cell line TY1

value: PEL cell line TY1


title: fibroTIPeR, rep3


title: Primary Effusion Lymphoma cell line BC1 [AffyNsp250]

source_name: PEL cell line BC1

value: PEL cell line BC1


title: Primary Effusion Lymphoma cell line BC2 [AffyNsp250]

source_name: PEL cell line BC2

value: PEL cell line BC2


title: Burkitt's Lymphoma cell line BJAB [AffyNsp250]

source_name: Burkitt's Lymphoma cell line BJAB

value: Burkitt's Lymphoma cell line BJAB


title: Primary Effusion Lymphoma cell line BCBL [AffyNsp250]

source_name: PEL cell line BCBL

value: PEL cell line BCBL


title: WT_HSC_3

city: Houston

first: Megan

last: Baldridge

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

hyb_protocol: Manufacturer's (Affymetrix) standard protocol

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000.  Raw image and intensity files were generated using the GCOS 1.0 software (Affymetrix).

data_processing: Normalization and model-based expression measurements were performed in R with GC-RMA.

molecule: polyA RNA

source_name: Hematopoietic stem cells (HSCs) isolated from wild-type mice

label_protocol: RNA was labeled with biotin-conjugated UTP and CTP.

growth_protocol: Mice were maintained at a specific pathogen-free facility.

extract_protocol: RNA was extracted with the Ambion RNAqueous kit, treated with DNaseI, and linearly amplified using two rounds of T7-based in vitro transcription with the Ambion MessageAmp kit.

treatment_protocol: Whole bone marrow was extracted and HSCs were isolated by FACS using Hoechst 33342 staining to identify the side population, in addition to Sca-1, c-kit, and Lineage staining.

tag: C57BL/6, Age

value: 8-12 weeks, Tissue:hematopoietic stem cells from whole bone marrow


title: Primary Effusion Lymphoma cell line BC3 [AffyNsp250]

source_name: PEL cell line BC3

value: PEL cell line BC3


title: Primary Effusion Lymphoma cell line BCLM [AffyNsp250]

source_name: PEL cell line BCLM

value: PEL cell line BCLM


title: TNT_70%-3

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

description: Gene expression after 24h exposure to 0.498 mg/L TNT

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

scan_protocol: An Agilent G2565CA Scanner (Agilent Technologies, Palo Alto, CA) was used to scan microarray images.

data_processing: Microarray image processing and data pre-processing were performed Agilent's Feature Extraction software v 9.5 following the manufacturer’s protocol and recommendations.

organism: Daphnia magna

source_name: TNT exposure, TNT treatment, 24h, replicate 3

label_protocol: cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling kit; Agilent, Palo Alto, CA).

growth_protocol: Exposures were conducted in quadruplicated 1L glass beakers containing 750 ml of exposure water and 60 D. magna (6-8 days old) for 24 hours at 24 ± 1°C using a 16:8 photoperiod.  The LAAP exposure was conducted using five replicates containing 115 D. magna each to increase statistical power.  At the conclusion of each exposure, D. magna in each replicate and exposure were counted, weighed and flash-frozen then stored at -80oC until needed

extract_protocol: Total RNA was isolated using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and quantity was determined using a Nanodrop® ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). Total RNA was stored at -80oC until analyzed.

treatment_protocol: Acetone was used as solvent carrier. Exposures were done with moderately hard-reconstituted water. An equivalent volume of clean acetone (≤ 1 mL/L) was spiked into control medium to ensure acetone did not confound results.

value: whole organism

tag: mc

value: 0.498 mg/L TNT


title: aMSC_1_Rep3

city: Pullman

first: Timothy

middle: J.

last: Doyle

state: WA

address: 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description: Gene expression data from aggregated MSC-1 cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip RGU34A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip® scanner 3000.

data_processing:
The data were analyzed with Gene Chip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 125.
Algorithm: ExpressionStat 5.0

source_name: Aggregated MSC-1 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 10-20-day old mouse primary Sertoli cells and MSC-1 cell line were allowed to aggregate at 37 degrees Celsius for 48 hrs in media containing Ham's F10 media with supplements, and 10% FBS

extract_protocol: RNA was extracted using Invitrogen Trizol RNA extraction kit using the manufactorers protocol

value: Sertoli cell line (MSC-1)


title: Burkitt's-like Lymphoma cell line DG75 [AffyNsp250]

source_name: Burkitt's-like Lymphoma cell line DG75

value: B-cell

value: Burkitt's-like Lymphoma cell line DG75


title: aMSC_1_Rep2


title: Lrg47_HSC_2

source_name: Hematopoietic stem cells (HSCs) isolated from Lrg-47-/- mutant mice


title: TNT_70%-4

source_name: TNT exposure, TNT treatment, 24h, replicate 4


title: aMSC_1_Rep1


title: Lrg47_HSC_1


title: WT_HSC_1


title: TNT_CON-3

description: Gene expression after 24h exposure to control water

source_name: TNT exposure, control treatment, 24h, replicate 3

value: control


title: Lrg47_HSC_3


title: apSC_Rep3

description: Gene expression data from aggregated primary Sertoli cell

source_name: Aggregated Primary Sertoli cells

tag: strain

value: Primary Sertoli cell


title: WT_HSC_2


title: apSC_Rep2


title: TNT_70%-1

source_name: TNT exposure, TNT treatment, 24h, replicate 1


title: apSC_Rep1


title: TNT_CON-2

source_name: TNT exposure, control treatment, 24h, replicate 2

tag: sample type


title: TNB_70%-4

description: Gene expression after 24h exposure to 0.386 mg/L TNB

source_name: TNB exposure, TNB treatment, 24h, replicate 4

value: 0.386 mg/L TNB


title: cardiomyocyte, rep2

source_name: single cell

value: cardiomyocyte, single cell

value: No transfection


title: TNT_CON-4

source_name: TNT exposure, control treatment, 24h, replicate 4


title: TNT_CON-1

source_name: TNT exposure, control treatment, 24h, replicate 1


title: TNB_70%-3

source_name: TNB exposure, TNB treatment, 24h, replicate 3


title: TNT_70%-2

source_name: TNT exposure, TNT treatment, 24h, replicate 2


title: TNB_CON-3

source_name: TNB exposure, control treatment, 24h, replicate 3


title: TNB_CON-1

source_name: TNB exposure, control treatment, 24h, replicate 1


title: TNB_CON-4

source_name: TNB exposure, control treatment, 24h, replicate 4


title: Flag_delta_flap_Rpb2

source_name: FLAG ChIP DNA from delta flap Rpb2

growth_protocol: Delta-Flap Rpb2-FLAG cells were grown as monolayers in DMEM supplemented with Tet free FBS and sodium bicarbonate (0.375%) and hygromycin (200 μg/mL).

treatment_protocol: Delta-Flap Rpb2-FLAG cells were treated with doxycycline (2 μg/mL).

tag: cell line

value: FLAG

source_name: Input ChIP DNA from delta flap Rpb2

value: none, input DNA


title: TNB_CON-2

source_name: TNB exposure, control treatment, 24h, replicate 2


title: TNB_70%-1

source_name: TNB exposure, TNB treatment, 24h, replicate 1


title: TNB_70%-2

source_name: TNB exposure, TNB treatment, 24h, replicate 2


title: RDX_70%-2

description: Gene expression after 24h exposure to 29.8 mg/L RDX

source_name: RDX exposure, RDX treatment, 24h, replicate 2

value: 29.8 mg/L RDX


title: RDX_70%-4

source_name: RDX exposure, RDX treatment, 24h, replicate 4


title: RDX_CON-3

source_name: RDX exposure, control treatment, 24h, replicate 3


title: Normal Control Tonsil2 [AffyNsp250]

source_name: tonsil tissue from healthy donor

value: tonsil tissue from healthy donor


title: RDX_CON-4

source_name: RDX exposure, control treatment, 24h, replicate 4


title: Flag_Rpb2

source_name: FLAG ChIP DNA from wt Rpb2

source_name: Input ChIP DNA from wt Rpb2


title: RDX_CON-1

source_name: RDX exposure, control treatment, 24h, replicate 1


title: RDX_70%-3

source_name: RDX exposure, RDX treatment, 24h, replicate 3


title: RDX_CON-2

source_name: RDX exposure, control treatment, 24h, replicate 2


title: DNB_70%-4

description: Gene expression after 24h exposure to 9.51 mg/L DNB

source_name: DNB exposure, DNB treatment, 24h, replicate 4

value: 9.51 mg/L DNB


title: DNB_70%-3

source_name: DNB exposure, DNB treatment, 24h, replicate 3


title: E18.5 GR ablation rep5

first: Scott

middle: Andrew

last: Ochsner

department: Molecular and Cellular Biology

description: Mice lack GR specifically in mesenchymal cells generated using a mouse line that expresses the Cre from a BAC containing the locus of the collagen type (I)-alpha-2 gene (Col1-Cre)

hyb_protocol: Standard Affymetrix bihybridization protocol according to manufacturer's instruction.

scan_protocol: Standard Affymetrix scanning protocol according to manufacturer's instruction.

data_processing: Analysis of array data was performed using the R/Bioconductor and MeV 4.0. Data were normalized, and expression values were computed using the GCRMA method.

source_name: lung

label_protocol: Standard Affymetrix biotin labeling protocol using 1-2 micrograms of total RNA according to manufacturer's instruction.

growth_protocol: Staged matings were set up to harvest embryonic organs at desired stages of fetal development. In the case of a vaginal plug in the morning, noon of the same day was designated E0.5. At the embryonic day of interest, mothers were killed by CO2 and the pups were collected by Caesarean section. Complete uteri were removed and transferred to ice-cold PBS, and embryonic lungs were dissected out.

extract_protocol: Left lung lobes were immersed in RNALater solution (Sigma-Aldrich Chemie GmbH, Munich, Germany), snap frozen in liquid nitrogen, and stored at .80 C. Total RNA was prepared with the RNeasy Mini Kit (QIAGEN, Hilden, Germany) and its quality was assessed on RNA LabChips (Agilent Technologies, Santa Clara, CA).

tag: age

tag: genotype

value: lung

tag: genetic background


title: DNB_70%-1

source_name: DNB exposure, DNB treatment, 24h, replicate 1


title: DNB_70%-2

source_name: DNB exposure, DNB treatment, 24h, replicate 2


title: E18.5 GR ablation rep2


title: DNB_CON-4

source_name: DNB exposure, control treatment, 24h, replicate 4


title: E16.5 GR ablation rep5


title: E18.5 GR ablation rep3


title: E18.5 GR ablation rep1


title: E16.5 GR ablation rep2


title: DNB_CON-3

source_name: DNB exposure, control treatment, 24h, replicate 3


title: E16.5 GR ablation rep3