title: 1106

source_name: aorta, BXD9/TyJ


title: 1105

status: Public on Nov 18 2012

type: RNA

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

country: USA

institute: UCLA

hyb_protocol: The HT_MG-430A Array plate consists of 96 single MG-430A arrays arranged into standard SBS 96 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer's recommendations.

scan_protocol: Scanned images were subjected to visual inspection, and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression Console (Affymetrix).

data_processing: The image data was processed using the Affymetrix GCOS algorithm utilizing quantile normalization or the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene.

label: Biotin

molecule: total RNA

organism: Mus musculus

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays.

growth_protocol: 16-week-old male mice were maintained on a 12 hr light dark cycle and were fed a chow diet.

extract_protocol: Qiazol with homogenization followed by RNeasy spin columns with optional DNase per the manufacturer's protocol.

tag: strain

tag: genotype

value: wild-type

tag: tissue

value: aorta

tag: gender

value: male

tag: age

value: 16 weeks


title: 1079

source_name: aorta, BXD33/TyJ


title: 1070

source_name: aorta, BXD5/TyJ


title: 1120

source_name: aorta, BXH19/TyJ


title: 1168

source_name: aorta, BXD38/TyJ


title: 1154

source_name: aorta, BXH10/TyJ


title: 1034

source_name: aorta, BXD42/TyJ


title: 1130

source_name: aorta, BXD36/TyJ


title: 1146

source_name: aorta, BXD6/TyJ


title: 1071

source_name: aorta, BXD29-Tlr4<lps-2J>/J


title: 1080


title: 1111

source_name: aorta, BXD27/TyJ


title: 1167


title: 1129


title: 1033


title: 1081

source_name: aorta, BXD34/TyJ


title: 1098

source_name: aorta, BXD8/TyJ


title: 1140

source_name: aorta, BXD32/TyJ


title: 997

source_name: aorta, BXD40/TyJ


title: 1147


title: 998


title: 1082


title: 1072


title: 1124

source_name: aorta, BXD28/TyJ


title: 1025

source_name: aorta, BXD39/TyJ


title: 1069


title: 1099


title: 1141


title: 1100


title: 1078

source_name: aorta, BXD24/TyJ-Cep290<rd16>/J


title: 963

source_name: aorta, BXD22/TyJ


title: 980

source_name: aorta, BXD20/TyJ


title: 993

source_name: aorta, BXD2/TyJ


title: 1122

source_name: aorta, BXD21/TyJ


title: 1148

source_name: aorta, BXD19/TyJ


title: 994


title: 1119

source_name: aorta, BXD12/TyJ


title: 1107

source_name: aorta, BXD1/TyJ


title: 1157


title: 1024

source_name: aorta, BXD13/TyJ


title: 1123


title: 981


title: 962


title: 1075

source_name: aorta, BXD15/TyJ


title: 1149


title: 1118


title: 1023


title: 1021

source_name: aorta, BXD14/TyJ


title: 1076


title: 1158


title: 990

source_name: aorta, BXD18/TyJ


title: 1086

source_name: aorta, BXA4/PgnJ


title: 1015

source_name: aorta, BXA8/PgnJ


title: 1077


title: 960

source_name: aorta, BXD11/TyJ


title: 1013

source_name: aorta, BXA7/PgnJ


title: 1085


title: 1020


title: 1014


title: 1016


title: 1083

source_name: aorta, BXA26/PgnJ


title: 1084


title: 985

source_name: aorta, BXA25/PgnJ


title: 1012

source_name: aorta, BXA2/PgnJ


title: 1088

source_name: aorta, BXA24/PgnJ


title: 984


title: 1011


title: 1087


title: 1092

source_name: aorta, BXA14/PgnJ


title: 995

source_name: aorta, BXA16/PgnJ


title: 996


title: 1114


title: 1094

source_name: aorta, BXA11/PgnJ


title: 1095


title: 1093

source_name: aorta, BXA1/PgnJ


title: 1112

source_name: aorta, BXA13/PgnJ


title: 991

source_name: aorta, BTBR T<+> tf/J

value: BTBR T<+> tf/J


title: 1091


title: 1089

source_name: aorta, BXA12/PgnJ


title: 1090


title: 1109

source_name: aorta, AXB8/PgnJ


title: 992


title: 1113


title: 1164

source_name: aorta, AXB6/PgnJ


title: 1110


title: 1022

source_name: aorta, BUB/BnJ

value: BUB/BnJ


title: 968

source_name: aorta, BALB/cJ

value: BALB/cJ


title: 1163


title: 1155

source_name: aorta, AXB5/PgnJ


title: 1156


title: 969


title: 1131

source_name: aorta, AXB24/PgnJ


title: 1132


title: 978

source_name: aorta, AXB4/PgnJ


title: 979


title: 1161

source_name: aorta, AXB23/PgnJ


title: 1162


title: 1038


title: 1135

source_name: aorta, AXB19b/PgnJ


title: 1003


title: 1150

source_name: aorta, AXB19/PgnJ


title: 1136


title: Streptococcus agalactiae strain A909 heat stress 37C v 42C rep 2a

city: Baltimore

first: Julie

middle: C

last: Dunning Hotopp

state: MD

address: 20 Penn St.; HSF-II; S203B

department: Institute for Genomic Sciences

institute: Univeristy of Maryland Baltimore

description: Cy3- and Cy5-labeled probes were synthesized from total RNA. Total of 3 hybridizations/condition. The geometric mean ratio was calculated for all good spots across all three hybridizations.

hyb_protocol: Probe pairs were resuspended in 5X SSC, 50% formamide, 0.1% SDS, 0.1 mM DTT, and 0.35 mg/mL salmon sperm DNA and hybridized to slides overnight at 42 oC. The hybridized slides were washed twice in 2X SSC, 0.1% SDS at 55 oC; twice in 0.1X SSC, 0.1% SDS at room temperature; twice in 0.1X SSC at room temperature; and once in MilliQ water at room temperature.

scan_protocol: Scanned using a GenePix4000B scanner (Molecular Devices).

data_processing: Ratios were normalized using iterative log mean centering with a 50K low intensity filter.

organism: Streptococcus agalactiae

label_protocol: Amino-allyl-dUTP Cy3 and Cy5 labeled probes were synthesized from 2 μg of total RNA using Superscript II (Invitrogen), Superscript III (Invitrogen), or Powerscript (BD Biosciences). The reactions were purified using QIAquick PCR purification kit (Qiagen) using modified phosphate buffers. Cy3- or Cy5-dyes (GE Healthcare) were chemically coupled to the incorporated amino-allyl dUTP in carbonate buffer.

growth_protocol: Streptococcus agalactiae were grown for 16 hours at 37°C in Todd-Hewitt broth at normal pH 7.7.  The bacteria were then diluted 1:100 into fresh Todd-Hewitt broth and grown at 37°C to OD650 of approximately 0.300.  Bacteria then split into two aliquots. One aliquot of bacteria then grown at 37°C for another 30 minutes prior to RNA extraction.  One aliquot of bacteria then grown at 42°C for 30 minutes prior to RNA extraction.

extract_protocol: Total RNA was isolated from Streptococcus agalactiae using the following method. Bacteria were grown in Todd-Hewitt broth to early-log phase, corresponding to OD650 approximately 0.300.  Bacteria then split into two aliquots. One aliquot of bacteria grown at 37°C for another 30 minutes prior to RNA extraction.  One aliquot of bacteria grown at 42°C for 30 minutes prior to RNA extraction.  Total RNA isolation was then performed from both samples in parallel.  Bacteria were collected by centrifugation and resuspended in RNA Protect Reagent (Qiagen).  The bacteria were again pelleted by centrifugation and resuspended in buffer containing 25% glucose, 10 mM Tris, 1 mM EDTA (pH 8.0) with lysozyme (3 mg/ml) and mutanolysin (200 mcg/ml).  The bacteria were then incubated at room temperature for 10 minutes to weaken the cell wall and facilitate bacterial lysis. Bacteria were collected by centrifugation, resuspended in RNA lysis buffer (Qiagen) and lysed by centrifugation through a QiaShredder spin column. RNA was then purified using the RNeasy kit (Qiagen). Contaminating DNA was removed by on-column DNAse digestion using RNAse-free DNAse (Qiagen). The concentration of the final RNA preparation was determined using a NanoDrop ND-1000 spectrophotometer (NanDrop Technologies) before the addition of RNase inhibitor (Invitrogen).  Aliquots of the final RNA preparation were stored at -80˚C.

treatment_protocol: Streptococcus agalactiae were grown in rich media (Todd-Hewitt broth) at normal pH 7.7, at 37°C to early log phase growth. One aliquot of bacteria were then grown at 37°C for another 30 minutes prior to RNA extraction.

tag: Streptococcus agalactiae strain A909

source_name: Streptococcus agalactiae A909 37C early log phase, exposed to 42C

treatment_protocol: Streptococcus agalactiae were grown in rich media (Todd-Hewitt broth) at normal pH 7.7, at 37°C to early log phase growth. One aliquot of bacteria were then grown at 42°C for 30 minutes prior to RNA extraction.

tag: Streptococcus agalactiae A909


title: 1160

source_name: aorta, AXB13/PgnJ


title: 1007

source_name: aorta, AXB15/PgnJ


title: 1005

source_name: aorta, AXB2/PgnJ


title: 983

source_name: aorta, AXB19a/PgnJ


title: 982


title: 1006


title: 1004


title: 1010

source_name: aorta, AXB12/PgnJ


title: 1159


title: Cow 2526

city: Jouy-en-Josas

first: Nuria

last: Mach

state: Ile de France

address: Rue de Vilvert

department: Animal Genetics and Integrative Biology (GABI)

country: France

institute: INRA

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-13.CEL

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C with constant rotational mixing at 60 rpm on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneGhip Scanner 7G and Affymetrix GeneChip Operating Software version 1.4

data_processing: All microarray analysis including preprocessing, normalization and statistical analysis was carried out using R Software (version 2.10 and Bioconductor version 2.5). Data were quality assessed before and after normalization using a number of built-in quality control methods implemented in the Bioconductor affycoretools and associated packages to identify eventual irregularities of array hybridization, RNA degradation, and data normalization. Expression levels of probe sets were summarized using the library GC content-corrected robust multichip average algorithm (GC-RMA; (Wu et al., 2004), employing the empirical Bayes approach for background correction followed by quantile normalization.

label: biotin

organism: Bos taurus

source_name: Control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Santa Clara, CA, Affymetrix).

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

treatment_protocol: The experiment was carried out in a complete randomized blocked designed structure comprising 14 Holstein-Friesian cows (6 second parity, 2 third parity and 6 older cows), selected from a 550-cow herd. Cows were paired in 7 blocks on the basis of similarity in parity (second parity, third parity and older cows), expected date of calving, and milk performance in the previous lactation (in order of priority). Cows within each block were randomly allocated to one of two treatment groups, “Omega” or “Control”.

tag: breed

value: Holstein-Friesian

tag: block

tag: expected date of calving

tag: parity

tag: milk performance in the previous lactation for the first 100 days

tag: fat production in the previous lactation for the first 100 days

tag: protein production in the previous lactation for the first 100 days

value: Mammary gland

tag: agent

value: Control


title: 1008


title: 1009


title: 1151


title: 1102

source_name: aorta, AXB10/PgnJ


title: Streptococcus agalactiae strain A909 heat stress 37C v 42C rep 2b

source_name: Streptococcus agalactiae A909 37C early log phase


title: Cow 3340

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-10.CEL

source_name: Omega

value: Omega


title: Cow 3275

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-14.CEL


title: 1101


title: Cow 4429

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-12.CEL


title: Cow 3457

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-11.CEL


title: 953

source_name: aorta, AXB1/PgnJ


title: 925

source_name: aorta, A/J

value: A/J


title: Cow 4423

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-09.CEL


title: Cow 9734

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-07.CEL


title: Cow 3951

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-03.CEL


title: Cow 4431

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-06.CEL


title: 945

source_name: aorta, 129X1/SvJ


title: Cow 3251

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-02.CEL


title: 948

source_name: aorta, AKR/J

value: AKR/J


title: Cow 4476

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-04.CEL


title: 926


title: Cow 3583

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-08.CEL


title: 946


title: Cow 3522

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-05.CEL


title: Cow 2392

description:
Gene expression data from mammary gland tissue
CEL file (original name): 101134-01.CEL


title: BD2-Y

status: Public on Nov 17 2012

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip cDNA Synthesis  Kit (Affymetrix )

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

organism: Homo sapiens

label_protocol: GeneChip 2-cycle target labeling kit cDNA Synthesis  Kit (Affymetrix )

extract_protocol: Cells lysed in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA)

tag: cell type

value: monocytes

tag: treated with

value: BD2 (5 micrograms/ml, Peprotech)

tag: replicates

value: Y


title: BD3-U

value: BD3  (20 micrograms/ml, Peprotech)

value: U


title: HKLM-Y

value: HKLM (10^8 cells/ml InvivoGen)


title: BD3-aster

value: aster


title: BD2-U


title: BD2-aster


title: PNG-aster

value: PGN (5 micrograms/ml, InvivoGen)


title: BD3-Y


title: HKLM-U


title: HKLM-aster


title: PNG-Y


title: Control-aster


title: Control-Y


title: PC3_HIC1_sample

city: Shanghai

first: Jianhua

last: Wang

address: No.280 Chongqing Road

department: School of Medicine

country: China

institute: Shanghai Jiaotong University

description: Gene expression in PC3 cell line, H1C1 over-expressed

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: PC3 cell line, HIC1 gene

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: The LNCaP metastatic subline C4-2B, and PC3 were obtained from the American Type Culture Collection (ATCC, Rockville, MD) and cultured in RPMI Medium 1640 supplemented with 10% fetal bovine serum (FBS) (Invitrogen Corp, Carlsbad, CA). The human prostate epithelial cell line (PrEC) (PriCells Co., LTD, Wuhan, China) was cultured in keratinocyte medium supplemented with 5 ng/ml human recombinant epithelial growth factor and 50 µg/ml bovine pituitary extract (Invitrogen Corp, Carlsbad, CA).

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: For restoring expression of HIC1 in PC3 and C4-2B cell lines, human full length HIC1 cDNA was inserted into lentivirus vector pHR-SIN-CSIGW under the control of SFFV promoter for stable expression. The fragment of HIC1 was inserted between SpeI and NdeI restriction sites according to the protocol. The construction was verified by sequencing. Supernatants were collected 36–48h after transfection, filtered through a 0.4 µm filter, and used directly to infect tumor cells. Two rounds of infection 8 h apart were usually sufficient to infect >90% of cells. Transduced cells with high GFP levels were then isolated by fluorescence-activated cell sorting (FACS).

value: prostate

tag: cell line

value: LNCaP

tag: cell subline


title: C4-2B_HIC1_sample

description: Gene expression in C4-2B cell line, H1C1 over-expressed

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: C4-2B cell line, HIC1 gene

tag: tissue


title: PNG-U


title: Control-U


title: 6hr SD X3349_15423_72

city: Sao Paulo

first: Renata

last: Pellegrino

address: Rua NApoleao de Barros 925

country: Brazil

institute: UNIFESP

description:
6hr SD
Lung

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA, Bioconductor, R

source_name: 6hr SD

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol plus Rneasy QIAGEN

tag: time

value: 6 hr

tag: treatment

value: sleep deprivation SD

value: lung

tag: genetic background


title: 6hr SS X3349_15431_80

description:
6hr SS
Lung

source_name: 6hr SS

value: spontaneous sleep SS


title: 6hr SD X3349_15425_74

description:
6hr SD
Lung


title: C4-2B_GFP_sample

description: Gene expression in C4-2B cell line, control

source_name: C4-2B cell line, control


title: 6hr SD X3349_15424_73

description:
6hr SD
Lung


title: 3hr SS X3349_15428_77

description:
3hr SS
Lung

source_name: 3hr SS

value: 3 hr


title: PC3_GFP_sample

description: Gene expression in PC3 cell line, control

source_name: PC3 cell line, control


title: 6hr SS X3349_15430_79

description:
6hr SS
Lung


title: 3hr SS X3349_15429_78

description:
3hr SS
Lung


title: 3hr SS X3349_15427_76

description:
3hr SS
Lung


title: 3hr SS X3349_15426_75

description:
3hr SS
Lung


title: 6hr SS X3349_15417_66

description:
6hr SS
Lung


title: 3hr SD X3349_15421_70

description:
3hr SD
Lung

source_name: 3hr SD


title: 6hr SS X3349_15416_65

description:
6hr SS
Lung


title: 3hr SD X3349_15420_69

description:
3hr SD
Lung


title: 3hr SS X3349_15410_59

description:
3hr SS
Lung


title: 0 hr CTL X3349_15406_55

description:
0 hr CTL
Lung

source_name: 0 hr CTL

value: 0 hr

value: control CTL


title: 3hr SS X3349_15411_60

description:
3hr SS
Lung


title: 6hr SD X3349_15422_71

description:
6hr SD
Lung


title: 3hr SS X3349_15408_57

description:
3hr SS
Lung


title: 6hr SS X3349_15414_63

description:
6hr SS
Lung


title: 3hr SS X3349_15412_61

description:
3hr SS
Lung


title: 3hr SD X3349_15419_68

description:
3hr SD
Lung


title: 6hr SS X3349_15413_62

description:
6hr SS
Lung


title: 3hr SS X3349_15409_58

description:
3hr SS
Lung


title: 0 hr CTL X3349_15407_56

description:
0 hr CTL
Lung


title: 6hr SS X3349_15415_64

description:
6hr SS
Lung


title: 3hr SD X3349_15418_67

description:
3hr SD
Lung


title: 0 hr CTL X3349_15404_53

description:
0 hr CTL
Lung


title: 952

tag: strain

tag: genotype

value: wild-type

value: aorta

tag: gender

value: male

tag: age

value: 16 weeks


title: 6hr SD X3349_15401_50

description:
6hr SD
Lung


title: 0 hr CTL X3349_15403_52

description:
0 hr CTL
Lung


title: 6hr SD X3349_15399_48

description:
6hr SD
Lung


title: 3hr SD X3349_15392_41

description:
3hr SD
Lung


title: 6hr SD X3349_15400_49

description:
6hr SD
Lung


title: 6hr SD X3349_15398_47

description:
6hr SD
Lung


title: 0 hr CTL X3349_15390_39

description:
0 hr CTL
Lung


title: 947

value: AKR/J


title: 0 hr CTL X3349_15405_54

description:
0 hr CTL
Lung


title: 3hr SD X3349_15394_43

description:
3hr SD
Lung


title: 6hr SD X3349_15402_51

description:
6hr SD
Lung


title: 0 hr CTL X3349_15389_38

description:
0 hr CTL
Lung


title: 3hr SD X3349_15397_46

description:
3hr SD
Lung


title: 9hr SS X3349_15381_30

description:
9hr SS
Lung

source_name: 9hr SS

value: 9 hr


title: 12hr SS X3349_15385_34

description:
12hr SS
Lung

source_name: 12hr SS

value: 12 hr


title: 12hr SS X3349_15386_35

description:
12hr SS
Lung


title: 3hr SD X3349_15395_44

description:
3hr SD
Lung


title: 9hr SD X3349_15374_23

description:
9hr SD
Lung

source_name: 9hr SD


title: 12hr SS X3349_15370_19

description:
12hr SS
Lung


title: 9hr SS X3349_15382_31

description:
9hr SS
Lung


title: 12hr SD X3349_15375_24

description:
12hr SD
Lung

source_name: 12hr SD


title: 12hr SS X3349_15383_32

description:
12hr SS
Lung


title: 0 hr CTL X3349_15391_40

description:
0 hr CTL
Lung


title: 0 hr CTL X3349_15387_36

description:
0 hr CTL
Lung


title: 12hr SS X3349_15368_17

description:
12hr SS
Lung


title: 12hr SD X3349_15377_26

description:
12hr SD
Lung


title: 12hr SS X3349_15367_16

description:
12hr SS
Lung


title: 3hr SD X3349_15396_45

description:
3hr SD
Lung


title: 9hr SS X3349_15380_29

description:
9hr SS
Lung


title: 9hr SS X3349_15379_28

description:
9hr SS
Lung


title: 9hr SD X3349_15371_20

description:
9hr SD
Lung


title: 12hr SD X3349_15378_27

description:
12hr SD
Lung


title: 12hr SS X3349_15366_15

description:
12hr SS
Lung


title: 9hr SS X3349_15364_13

description:
9hr SS
Lung


title: 9hr SD X3349_15372_21

description:
9hr SD
Lung


title: 12hr SD X3349_15376_25

description:
12hr SD
Lung


title: 9hr SS X3349_15365_14

description:
9hr SS
Lung


title: 12hr SS X3349_15369_18

description:
12hr SS
Lung


title: 9hr SS X3349_15362_11

description:
9hr SS
Lung


title: 9hr SD X3349_15373_22

description:
9hr SD
Lung


title: 9hr SS X3349_15361_10

description:
9hr SS
Lung


title: 9hr SS X3349_15363_12

description:
9hr SS
Lung


title: 12hr SD X3349_15359_8

description:
12hr SD
Lung


title: 12hr SD X3349_15358_7

description:
12hr SD
Lung


title: 9hr SD X3349_15356_5

description:
9hr SD
Lung


title: 9hr SD X3349_15354_3

description:
9hr SD
Lung


title: 9hr SD X3349_15352_1

description:
9hr SD
Lung


title: 9hr SD X3349_15355_4

description:
9hr SD
Lung


title: 6hr SS X3350_15508_157

description:
6hr SS
Heart

value: heart


title: 3hr SS X3350_15507_156

description:
3hr SS
Heart


title: 6hr SS X3350_15509_158

description:
6hr SS
Heart


title: 12hr SD X3349_15360_81

description:
12hr SD
Lung


title: 6hr SD X3350_15500_149

description:
6hr SD
Heart


title: 12hr SD X3349_15357_6

description:
12hr SD
Lung


title: 9hr SD X3349_15353_2

description:
9hr SD
Lung


title: 6hr SS X3350_15510_159

description:
6hr SS
Heart


title: 6hr SD X3350_15503_152

description:
6hr SD
Heart


title: 3hr SS X3350_15504_153

description:
3hr SS
Heart


title: 6hr SD X3350_15501_150

description:
6hr SD
Heart


title: 3hr SD X3350_15497_146

description:
3hr SD
Heart


title: 6hr SS X3350_15511_160

description:
6hr SS
Heart


title: 3hr SS X3350_15506_155

description:
3hr SS
Heart


title: 3hr SD X3350_15498_147

description:
3hr SD
Heart


title: 3hr SD X3350_15496_145

description:
3hr SD
Heart


title: 3hr SD X3350_15499_148

description:
3hr SD
Heart


title: 3hr SS X3350_15505_154

description:
3hr SS
Heart


title: 6hr SS X3350_15492_141

description:
6hr SS
Heart


title: 6hr SS X3350_15493_142

description:
6hr SS
Heart


title: 6hr SD X3350_15502_151

description:
6hr SD
Heart


title: 6hr SS X3350_15495_144

description:
6hr SS
Heart


title: 12hr SS X3349_15384_33

description:
12hr SS
Lung


title: Erythroid progenitor cells at StageE2, no EPO, biological rep3

city: Bangalore

first: Aishwarya

last: Narayanan

address: 5th Floor, KBP, Bellary Road

country: India

institute: Strand Life Sciences

description: Gene expression data from E2 stage bone marrow erythroid progenitor cells without exposure to EPO

hyb_protocol: Following fragmentation, 10 ug's of cRNA's were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430.2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data was analyzed with GC-RMA using default analysis settings and quantile as normalization method in GeneSpring(version 11.5). After normalization, the data was baseline transformed to the median of all samples.

source_name: Murine bone marrow erythroid proerythroblast cells without exposure to EPO

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

growth_protocol: For cell preparations, marrow was isolated from femurs and tibia of 8-12 week wild-type C57Bl/6 female mice. Preparations were exposed to NH4Cl, recovered through FBS/IMDM, and cultured in SP34ex medium. At day 3, stage E1 cells were isolated by Lin+ depletion, and Kit+ CD71+ selection. At day 3.5 (and in parallel cultures) stage E2 cells were isolated by Lin+ depletion, Kit+ depletion, and CD71+ selection.

treatment_protocol: Cells from bone marrow erythroid progenitor cell E1 and E2 stages were cultured for 5.5hr (106 cells/mL) in the absence of hematopoietic cytokines, and were challenged with EPO (+/- 4U/mL, 90 minutes)

value: wild-type C57Bl/6

value: female

value: bone marrow

tag: Stage


title: Erythroid progenitor cells at StageE2, plus EPO, biological rep3

description: Gene expression data from E2 stage bone marrow erythroid progenitor cells, exposed to EPO

source_name: Murine bone marrow erythroid proerythroblast cells, exposed to EPO

value: EPO


title: Erythroid progenitor cells at StageE2, no EPO, biological rep2


title: 3hr SS X3350_15489_138

description:
3hr SS
Heart


title: Erythroid progenitor cells at StageE2, plus EPO, biological rep2


title: 6hr SS X3350_15494_143

description:
6hr SS
Heart

value: 6 hr


title: 3hr SS X3350_15487_136

description:
3hr SS
Heart

value: spontaneous sleep SS


title: 6hr SS X3350_15491_140

description:
6hr SS
Heart


title: 3hr SS X3350_15486_135

description:
3hr SS
Heart

value: 3 hr


title: 0 hr CTL X3350_15484_133

description:
0 hr CTL
Heart

value: 0 hr


title: 3hr SS X3350_15488_137

description:
3hr SS
Heart


title: Erythroid progenitor cells at StageE2, plus EPO, biological rep1


title: 0 hr CTL X3350_15483_132

description:
0 hr CTL
Heart

value: control CTL


title: 0 hr CTL X3350_15485_134

description:
0 hr CTL
Heart


title: liver cancer associated mesenchymal stem cells vs. liver normal mesenchymal stem cells  LC8/LN8

city: beijing

first: yan

last: xin long

address: 27 Taiping Road

institute: Beijing Institute of Transfusion Medicine

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: 8 represents LC8-MSCs

label_protocol: 10 µg of 8 (LC8-MSCs) derived RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label; and the N8 (LN8-MSCs) was labeled by Cy5.

growth_protocol: Liver cancer associated MSCs and liver normal MSCs were cultured in α-MEM containing 10% selected fetal bovine serum (FBS) and 1 ng/ml basic fibroblast growth factor (bFGF, R&D Systems, Minneapolis, MN),

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: When LC-MSCs and LN-MSCs were reached 70% confluence, these MSCs was washed with PBS and cultured in serum free α-MEM for 36 hour,

value: liver cancer associated mesenchymal stem cells MSCs

tag: disease state

value: liver cancer

source_name: N8 represents LN8-MSCs

value: liver nomal mesenchymal stem cells


title: Erythroid progenitor cells at StageE1, plus EPO, biological rep4

description: Gene expression data from E1 stage bone marrow erythroid progenitor cells, exposed to EPO

source_name: Murine bone marrow erythroid CFUe- like progenitor cells, exposed to EPO


title: 0 hr CTL X3350_15482_131

description:
0 hr CTL
Heart


title: 3hr SS X3350_15490_139

description:
3hr SS
Heart


title: Erythroid progenitor cells at StageE1, plus EPO, biological rep3


title: Erythroid progenitor cells at StageE1, plus EPO, biological rep1


title: 6hr SD X3350_15480_129

description:
6hr SD
Heart

value: sleep deprivation SD


title: 0 hr CTL X3350_15481_130

description:
0 hr CTL
Heart


title: Erythroid progenitor cells at StageE1, no EPO, biological rep4

description: Gene expression data from E1 stage bone marrow erythroid progenitor cells without exposure to EPO

source_name: Murine bone marrow erythroid CFUe- like progenitor cells without exposure to EPO


title: Erythroid progenitor cells at StageE1, plus EPO, biological rep2


title: 6hr SD X3350_15478_127

description:
6hr SD
Heart

source_name: 6hr SD


title: Erythroid progenitor cells at StageE1, no EPO, biological rep2


title: Erythroid progenitor cells at StageE1, no EPO, biological rep3


title: Erythroid progenitor cells at StageE1, no EPO, biological rep1


title: 6hr SD X3350_15479_128

description:
6hr SD
Heart


title: 0 hr CTL X3350_15471_120

description:
0 hr CTL
Heart


title: 3hr SD X3350_15472_121

description:
3hr SD
Heart


title: 0 hr CTL X3350_15469_118

description:
0 hr CTL
Heart


title: 6hr SD X3350_15476_125

description:
6hr SD
Heart


title: 3hr SD X3350_15475_124

description:
3hr SD
Heart


title: 0 hr CTL X3350_15468_117

description:
0 hr CTL
Heart


title: 12hr SS X3350_15466_115

description:
12hr SS
Heart


title: 0 hr CTL X3350_15470_119

description:
0 hr CTL
Heart


title: 3hr SD X3350_15473_122

description:
3hr SD
Heart


title: 3hr SD X3350_15474_123

description:
3hr SD
Heart


title: time: MARCH - rep2

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

institute: Iowa State University

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 1E-L, UD:0000010 2E-L
age: >10 years
growth media: field soil
time=MARCH rep 2 (May still include original submitter created erros/discrepancies)

hyb_protocol: CNB Grapegen Affymetrix hybridization

scan_protocol: CNB Grapegen Affymetrix scanning

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

organism: Vitis vinifera

source_name: axillary inflorescence bud (time: MARCH)

label_protocol: CNB Grapegen Affymetrix labeling

growth_protocol: Growth Description:  No irrigation

extract_protocol: total RNA isolation followed by RNeasy purification

value: March

value: axillary inflorescence bud

tag: cultivar

value: Tempranillo


title: 6hr SD X3350_15477_126

description:
6hr SD
Heart

value: heart


title: time: APRIL - rep3

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 2E-L, UD:0000011 3E-L
age: >10 years
growth media: field soil
time=APRIL rep 1 (May still include original submitter created erros/discrepancies)

source_name: axillary inflorescence bud (time: APRIL)

value: April


title: time: MARCH - rep3

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 1E-L, UD:0000010 2E-L
age: >10 years
growth media: field soil
time=MARCH rep 3 (May still include original submitter created erros/discrepancies)


title: time: APRIL - rep2

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 2E-L, UD:0000011 3E-L
age: >10 years
growth media: field soil
time=APRIL rep 1. (May still include original submitter created erros/discrepancies)


title: time: MARCH - rep1

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 1E-L, UD:0000010 2E-L
age: >10 years
growth media: field soil
time=MARCH rep 1 (May still include original submitter created erros/discrepancies)


title: 12hr SS X3350_15465_114

description:
12hr SS
Heart

value: 12 hr


title: time: APRIL - rep1


title: time: JANUARY - rep3

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 1E-L
age: >10 years
growth media: field soil
time=JANUARY rep 3 (May still include original submitter created erros/discrepancies)

source_name: axillary inflorescence bud (time: JANUARY)

value: January


title: 12hr SS X3350_15464_113

description:
12hr SS
Heart


title: 0 hr CTL X3350_15467_116

description:
0 hr CTL
Heart


title: time: JANUARY - rep2

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 1E-L
age: >10 years
growth media: field soil
time=JANUARY rep 2 (May still include original submitter created erros/discrepancies)


title: time: NOVEMBER - rep3

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 43E-L, UD:0000043 47E-L
age: >10 years
growth media: field soil
time=NOVEMBER rep 3 (May still include original submitter created erros/discrepancies)

source_name: axillary inflorescence bud (time: NOVEMBER)

value: November


title: 9hr SS X3350_15462_111

description:
9hr SS
Heart

value: 9 hr


title: time: JANUARY - rep1

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 1E-L
age: >10 years
growth media: field soil
time=JANUARY rep 1 (May still include original submitter created erros/discrepancies)


title: time: NOVEMBER - rep1

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 43E-L, UD:0000043 47E-L
age: >10 years
growth media: field soil
time=NOVEMBER rep 1 (May still include original submitter created erros/discrepancies)


title: 9hr SS X3350_15460_109

description:
9hr SS
Heart

value: spontaneous sleep SS


title: time: SEPTEMBER - rep3

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 38E-L, UD:0000040 39E-L
age: >10 years
growth media: field soil
time=SEPTEMBER rep 3 (May still include original submitter created erros/discrepancies)

source_name: axillary inflorescence bud (time: SEPTEMBER)

value: September


title: 9hr SS X3350_15461_110

description:
9hr SS
Heart


title: 9hr SS X3350_15459_108

description:
9hr SS
Heart


title: 12hr SD X3350_15458_107

description:
12hr SD
Heart


title: 12hr SD X3350_15457_106

description:
12hr SD
Heart


title: JS-K 24 H, Biological Replicate 2

city: Bethesda

first: Robert

last: Cheng

address: 10 Center Drive

department: CCR

institute: NCI

description: Gene expression data from U937 cells exposed to JS-K for 24 h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe set summarization files were generated in Expression Console and normalizaed in BRB-ArrayTools iwth GC-RMA algorithm

source_name: JS-K 24 H, Biological Replicate 2

label_protocol: 200 ng of RNA was reverse transcribed with random hexamer primer, amplified and terminal labeled with biotin using Affymetrix Whole Transcript Sense Target Labeling kit according to manufacturer’s protocol.

growth_protocol: U937 cells were cultured with RPMI 1640 with 10% FBS and grow at 37C 5% CO2 incubator

extract_protocol: Total RNA was isolated with Trizol. RNA quality was checked on Agilent Bioanalyzer. All samples used for microarray analysis have high quality score (RIN >9).

value: leukemia cell


title: time: SEPTEMBER - rep2

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 38E-L, UD:0000040 39E-L
age: >10 years
growth media: field soil
time=SEPTEMBER rep 2 (May still include original submitter created erros/discrepancies)


title: 9hr SD X3350_15455_104

description:
9hr SD
Heart


title: time: SEPTEMBER - rep1

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 38E-L, UD:0000040 39E-L
age: >10 years
growth media: field soil
time=SEPTEMBER rep 1 (May still include original submitter created erros/discrepancies)


title: time: NOVEMBER - rep2

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 43E-L, UD:0000043 47E-L
age: >10 years
growth media: field soil
time=NOVEMBER rep 2 (May still include original submitter created erros/discrepancies)


title: 9hr SD X3350_15453_102

description:
9hr SD
Heart


title: time: JULY - rep3

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 29E-L, UD:0000031 31E-L
age: >10 years
growth media: field soil
time=JULY rep 3 (May still include original submitter created erros/discrepancies)

source_name: axillary inflorescence bud (time: JULY)

value: July


title: 9hr SD X3350_15452_101

description:
9hr SD
Heart


title: 9hr SD X3350_15454_103

description:
9hr SD
Heart


title: JS-K 24 H, Biological Replicate 1

source_name: JS-K 24 H, Biological Replicate 1


title: 12hr SS X3350_15449_98

description:
12hr SS
Heart

source_name: 12hr SS


title: 12hr SD X3350_15456_105

description:
12hr SD
Heart

source_name: 12hr SD


title: 12hr SS X3350_15451_100

description:
12hr SS
Heart


title: 12hr SS X3350_15450_99

description:
12hr SS
Heart


title: JS-K 24 H, Biological Replicate 3

source_name: JS-K 24 H, Biological Replicate 3


title: time: JULY - rep2

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 29E-L, UD:0000031 31E-L
age: >10 years
growth media: field soil
time=JULY rep 2 (May still include original submitter created erros/discrepancies)


title: JS-K 4 H, Biological Replicate 3

description: Gene expression data from U937 cells exposed to JS-K for 4 h

source_name: JS-K 4 H, Biological Replicate 3


title: JS-K 4 H, Biological Replicate 2

source_name: JS-K 4 H, Biological Replicate 2


title: time: JULY - rep1

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 29E-L, UD:0000031 31E-L
age: >10 years
growth media: field soil
time=JULY rep 1 (May still include original submitter created erros/discrepancies)


title: 12hr SS X3350_15447_96

description:
12hr SS
Heart


title: time: JUNE - rep3

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 20E-L, UD:0000025 21E-L
age: >10 years
growth media: field soil
time=JUNE rep 3 (May still include original submitter created erros/discrepancies)

source_name: axillary inflorescence bud (time: JUNE)

value: June


title: JS-K 4 H, Biological Replicate 1

source_name: JS-K 4 H, Biological Replicate 1


title: time: MAY - rep3

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 15E-L
age: >10 years
growth media: field soil
time=MAY rep 3 (May still include original submitter created erros/discrepancies)

source_name: axillary inflorescence bud (time: MAY)

value: May


title: Erythroid progenitor cells at StageE2, no EPO, biological rep1

description: Gene expression data from E2 stage bone marrow erythroid progenitor cells without exposure to EPO

source_name: Murine bone marrow erythroid proerythroblast cells without exposure to EPO

value: wild-type C57Bl/6

value: female

value: bone marrow


title: JS-K 90 min, Biological Replicate 1

description: Gene expression data from U937 cells exposed to JS-K for 90 min

source_name: JS-K 90 min, Biological Replicate 1


title: time: JUNE - rep2

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 20E-L, UD:0000025 21E-L
age: >10 years
growth media: field soil
time=JUNE rep 2 (May still include original submitter created erros/discrepancies)

value: axillary inflorescence bud


title: time: MAY - rep2

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 15E-L
age: >10 years
growth media: field soil
time=MAY rep 2 (May still include original submitter created erros/discrepancies)

value: Tempranillo


title: time: JUNE - rep1

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 20E-L, UD:0000025 21E-L
age: >10 years
growth media: field soil
time=JUNE rep 1 (May still include original submitter created erros/discrepancies)


title: JS-K 90 min, Biological Replicate 3

source_name: JS-K 90 min, Biological Replicate 3


title: 12hr SD X3350_15437_86

description:
12hr SD
Heart

value: sleep deprivation SD

value: heart


title: 9hr SS X3350_15444_93

description:
9hr SS
Heart

source_name: 9hr SS


title: 12hr SD X3350_15440_89

description:
12hr SD
Heart

value: 12 hr


title: Vehicle Control, Biological Replicate 3

description: Gene expression data from U937 cells exposed to DMSO

source_name: Vehicle Control, Biological Replicate 3


title: 9hr SS X3350_15445_94

description:
9hr SS
Heart


title: 12hr SD X3350_15438_87

description:
12hr SD
Heart


title: 12hr SS X3350_15448_97

description:
12hr SS
Heart


title: 9hr SD X3350_15434_83

description:
9hr SD
Heart

source_name: 9hr SD


title: 9hr SS X3350_15446_95

description:
9hr SS
Heart


title: Vehicle Control, Biological Replicate 2

source_name: Vehicle Control, Biological Replicate 2


title: 12hr SD X3350_15441_90

description:
12hr SD
Heart


title: JS-K 90 min, Biological Replicate 2

source_name: JS-K 90 min, Biological Replicate 2


title: 9hr SS X3350_15442_91

description:
9hr SS
Heart


title: 9hr SD X3350_15435_84

description:
9hr SD
Heart


title: time: MAY - rep1

description:
germplasm name: Tempranillo cv.
organism part: axillary inflorescence bud ('PO:0004711')
development stage: 15E-L
age: >10 years
growth media: field soil
time=MAY rep 1 (May still include original submitter created erros/discrepancies)


title: 9hr SS X3350_15443_92

description:
9hr SS
Heart


title: 9hr SD X3350_15436_85

description:
9hr SD
Heart


title: 12hr SD X3350_15439_88

description:
12hr SD
Heart


title: 9hr SD X3350_15433_82

description:
9hr SD
Heart


title: Vehicle Control, Biological Replicate 1

source_name: Vehicle Control, Biological Replicate 1


title: 12hr SS X3350_15463_112

description:
12hr SS
Heart

source_name: 12hr SS


title: 5# sheep 3 dpi

status: Public on Nov 16 2012

city: Hangzhou

first: Aifang

last: Du

state: Zhejiang

address: Yuhangtang Road 866

department: College of Animal Sciences, Zhejiang University

institute: Institute of Preventive Veterinary Medicine

description: Gene expression at 3 days post infection in 5# Haemonchus contortus infected-sheep T lymphocytes

hyb_protocol: Labeled cRNA were hybridized to Agilent Whole Sheep Genome Oligo Microarrays according to the protocols provided by the manufacturer. After hybridization, microarrays were washed  with GE Wash Buffer 1 (Agilent) and GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Microarrays were scanned by Agilent scanistor, scan resolution 5μm, PMT 100%.

data_processing: Feature Extraction software was used to read the raw data. The raw data files were processed using the Agi4x44PreProcess package based on linear models for microarray data (limma) package developed within the Bioconductor project in the R statistical programming environment. Background correction and normalization, probes filtering and replicated probes merger were included in data preprocessing to generate microarray results for gene expression profiling.

organism: Ovis aries

source_name: 5# H. contortus infected-sheep T lymphocytes, 3 dpi

label_protocol: Cy3 (GE healthcare) was labeled with synthesized cRNA using Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, , and purified using Rneasy Mini kit (Qiagen).

extract_protocol: The total RNA from the lymphocyte samples was obtained using TRIzol reagent (Invitrogen) following the manufacturer’s instructions and further purified using an RNeasy Mini kit (Qiagen). The quantity and quality of acquired RNA was measured using an Infinigen SSP-3300 ultramicrospectrophotometer and an Agilent 2100 Bioanalyzer.

treatment_protocol: Peripheral blood samples from Haemonchus contortus infected sheep were collected in sodium citrate coated tubes at 0, 3-5, 25-30 and 60 days post-challenge (34) and were equally mixed with Hanks. Miscible liquids were slowly added above the isometric lymphocyte separation medium (Huadong Medicine). T Lymphocytes were then separated by centrifugation at 2000 g for 25 min, washed twice in Hanks and re-suspended in TRIzol reagent (Invitrogen).

tag: individual

value: 5# sheep

tag: infectious agent

value: Haemonchus contortus

value: T lymphocytes


title: 5# sheep 30 dpi

description: Gene expression at 30 days post infection in 5# Haemonchus contortus infected-sheep T lymphocytes

source_name: 5# H. contortus infected-sheep T lymphocytes, 30 dpi


title: HepG2 exposed to DMSO for 24h, biological rep 1

city: Maastricht

first: Stan

last: Gaj

state: Limburg

address: Universiteitssingel 50

department: Department of Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: 12.5µg of cRNA were hybridized for 16 hr on 45°C on GeneChip Human Genome U133 Plus 2.0 Array, using Affymetrix® GeneChip® Fluidics Station 450 and the GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Arrays were scanned using genechip scanner 3000 7G

data_processing: The Affymetrix CEL files were imported in R 2.12.2 under BioConductor v2.7 (Gentleman et al., 2004). Probe sets were reannotated using the BrainArray custom CDF v13.0 annotations for both EnsEMBL genes and transcripts, generating two separate datasets. These custom CDFs were based on EnsEMBL v58. Next, both datasets were separately log transformed, RMA normalised and further evaluated through an extensive quality control pipeline consisting of box plots, fitPLM, NUSE, RLE, clustering/heat maps, PCA and correlation plots. There were no technically deviating arrays. The limma package (Smyth, 2005) was applied for computing a linear model using time and dose as main components. The resulting p-values were FWER-corrected using the False Discovery Rate (FDR) approach. Genes were considered to be differentially expressed (DE) when their (i) absolute fold change ≥ 1.5; (ii) q-value (FDR) < than 0.05; (iii) average expression in at least one of the two experimental groups > 6 (log2-scale).

source_name: hepatocellular carcinoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit

growth_protocol: HepG2 cells were maintained as a monolayer culture in 95% humidity, atmosphere with 5% of CO2 and 37 ºC. HepG2 cells were passaged at pre-confluent densities with the use of a trypsin-EDTA solution. Cells were cultured and passaged in a Minimal Essential Medium (MEM) with 10% of Foetal Bovine serum, 1% penicillin/streptomycin, 1% sodium-pyruvate and 1% non-essential amino acids.

extract_protocol: Trizol extraction was performed using the miRNAeasy kit from qiagen accoding to the manufacturer’s protocol

treatment_protocol: When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing either compound or solvent (0.5% DMSO, 0.5% EtOH or PBS)

tag: compound

value: DMSO


title: 3# sheep 30 dpi

description: Gene expression at 30 days post infection in 3# Haemonchus contortus infected-sheep T lymphocytes

source_name: 3# H. contortus infected-sheep T lymphocytes, 30 dpi

value: 3# sheep


title: HepG2 exposed to BaP for 12h, biological rep 2

value: BaP


title: 9hr SD X3350_15432_81

description:
9hr SD
Heart

value: 9 hr


title: 3# sheep 3 dpi

description: Gene expression at 3 days post infection in 3# Haemonchus contortus infected-sheep T lymphocytes

source_name: 3# H. contortus infected-sheep T lymphocytes, 3 dpi


title: 2# sheep 0 dpi

description: Gene expression at 0 days post infection in 2# Haemonchus contortus infected-sheep T lymphocytes

source_name: 2# H. contortus infected-sheep T lymphocytes, 0 dpi

value: 2# sheep


title: 3# sheep 60 dpi

description: Gene expression at 60 days post infection in 3# Haemonchus contortus infected-sheep T lymphocytes

source_name: 3# H. contortus infected-sheep T lymphocytes, 60 dpi


title: HepG2 exposed to BaP for 12h, biological rep 1


title: HepG2 exposed to BaP for 24h, biological rep 1


title: 5# sheep 60 dpi

description: Gene expression at 60 days post infection in 5# Haemonchus contortus infected-sheep T lymphocytes

source_name: 5# H. contortus infected-sheep T lymphocytes, 60 dpi


title: 2# sheep 60 dpi

description: Gene expression at 60 days post infection in 2# Haemonchus contortus infected-sheep T lymphocytes

source_name: 2# H. contortus infected-sheep T lymphocytes, 60 dpi


title: 3# sheep 0 dpi

description: Gene expression at 0 days post infection in 3# Haemonchus contortus infected-sheep T lymphocytes

source_name: 3# H. contortus infected-sheep T lymphocytes, 0 dpi


title: 5# sheep 0 dpi

description: Gene expression at 0 days post infection in 5# Haemonchus contortus infected-sheep T lymphocytes

source_name: 5# H. contortus infected-sheep T lymphocytes, 0 dpi


title: POMCDicerKO 3 mouse

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

description: Gene expression data from the arcuate hypothalamic subdissection in 2-week old POMCDicerKO mouse

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing: Raw data was background adjusted, normalized and summarized by Robust Multi-array Analysis (RMA) using the Affy package from Bioconductor on R language.

source_name: Hypothalamic microdissections

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

growth_protocol: Mice were maintained on a 12h-light/12h-dark cycle with free access to water and standard chow (2014; Teklad).

extract_protocol: Total RNA was extracted using the RNeasy micro spin columns  (Qiagen, Venlo, The Netherlands).

treatment_protocol: Total RNA was extracted from hypothalamic microdissections of 2-week old control and POMCDicerKO mice

value: Hypothalamic microdissections

value: mixed C57Bl/6J, FVB/N and 129

value: POMCDicerKO


title: 5# sheep 0 dpi rep

description: Gene expression at 0 days post infection in 5# Haemonchus contortus infected-sheep T lymphocytes, replicate

source_name: 5# H. contortus infected-sheep T lymphocytes, 0 dpi, rep

value: female


title: POMCDicerKO 1 mouse


title: HepG2 exposed to BaP for 24h, biological rep 2


title: HepG2 exposed to DMSO for 12h, biological rep 2


title: HepG2 exposed to DMSO for 24h, biological rep 2


title: Control 2 mouse

description: Gene expression data from the arcuate hypothalamic subdissection in 2-week old control mouse

value: Ctrl


title: POMCDicerKO 2 mouse


title: 2# sheep 3 dpi

description: Gene expression at 3 days post infection in 2# Haemonchus contortus infected-sheep T lymphocytes

source_name: 2# H. contortus infected-sheep T lymphocytes, 3 dpi


title: 2# sheep 30 dpi

description: Gene expression at 30 days post infection in 2# Haemonchus contortus infected-sheep T lymphocytes

source_name: 2# H. contortus infected-sheep T lymphocytes, 30 dpi


title: HepG2 exposed to DMSO for 12h, biological rep 1


title: Control 3 mouse


first: Luciano

last: Castiello

state: Maryland

department: DTM

institute: NIH/CC

description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 3 hybridized on slide # 5747 position 4

hyb_protocol: Samples were hybridized according to the Two-color Microarray-based Gene Expression Analysis (quick Amp Labeling) protocol from Agilent Version 5.7

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software was used with dafault settings for processed signals

source_name: mature Dendritic Cells of Donor

label_protocol: Test RNA and Universal Reference RNA () were amplified and labeled according to the Two-color Microarray-based Gene Expression Analysis (quick Amp Labeling) protocol from Agilent Version 5.7

growth_protocol: Monocytes were cultured with GMCSF (1000 IU/ml) and IL4 (1000 IU/ml) for 3 days to obtain immature dendritic cells. To induce maturation LPS (30 ng/ml) and IFNg (1000 IU/ml) were added to the culture and cell were harvested 24 h later

extract_protocol: Total RNA extracted using miRNeasy kit from Qiagen

tag: cell type

value: mature Dendritic Cells

tag: donor

tag: apheresis

tag: manufacture

tag: slide #

tag: position # on slide

source_name: Universal Human Reference RNA

tag: sample type

value: reference

tag: vendor

value: Stratagene Catalog #740000


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 3 hybridized on slide # 5747 position 2


title: Monocytes of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5745 position 3

source_name: Monocytes of Donor

value: Monocytes


description: mature Dendritic Cells of Donor # 882 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5746 position 4


title: Monocytes of Donor # 85 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5744 position 1


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 5 hybridized on slide # 5745 position 1

source_name: mature Dendritic Cells of Donor1


title: Monocytes of Donor # 340 from monocytes deriving from apheresis # 2 manufacture 1 hybridized on slide # 5744 position 4


title: LU_48hr_infect_rep2

city: ya'an

first: zhicai

last: ZUO

state: sichuan

address: xinkang road

department: College of Veterinary Medicine

institute: Sichuan Agricultural University

description:
Gene expression after 48hr in APP-infected swine lung
M-P-5

hyb_protocol: Labeling and hybridization of the cRNA was performed with Agilent Whole Porcine Genome Oligo (4X44K) Microarrays (one-color platform) at the National Engineering Center for Biochip at Shanghai, according to the manufacturer’s protocols.

scan_protocol: The slides were scanned and analyzed using the histogram method with default settings in an Agilent G2565AA and Agilent G2565BA Microarray Scanner System with SureScan Technology.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Sus scrofa

source_name: lung, 48hr, APP-infected swine

label_protocol: cDNA was synthesized from 2 μg of total-RNA using the direct cDNA Labeling System. Aminoallyl-cRNA was synthesized from cDNA using the Superscript Indirect cDNA Labeling System. The cRNA was purified and DNase treated using RNeasy QIAGEN RNeasy® Mini Kit. RNA integrity was confirmed with a bioanalyzer (model 2100; Agilent Technologies, Palo Alto, CA) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from tissues by using Trizol reagent (Invitrogen). RNA was purified and DNase treated using the RNeasy QIAGEN RNeasy® Mini Kit.

treatment_protocol: In the TG, lung and hilar node were collected 48 hours post-inoculation Actinobacillus pleuropneumoniae (APP) from three swines after abattage and used for total RNA extraction. Another three swines from the CG were sacrificed at the same time and their lung and hilar node collected.

value: male

value: 2.5 months

tag: infection agent

value: 1 mL containing 3.8×10^7 cfu/mL pleuropneumoniae serotype I

tag: sample collection time

value: 48 hours post-inoculation

tag: tissue

value: lung


title: ko CD4 equivalent dendritic cell

city: Rehovot

first: Alexander

last: Mildner

address: 234 Herzl street

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Gene expression data from in vitro Flt3-L derived dendritic cells

scan_protocol: According to Affymetrix standard protocols, using Affymetrix GeneChip 3000 7G plus scanner

data_processing: RMA was carried out using Partek Genomic Suite 6.5 (Inc. St. Charles, MO; www.partek.com)

source_name: In vitro Flt3-L derived dendritic cells

growth_protocol: For the generation of in vitro BM-derived DCs, 5 x 10e6 BM cells were cultured for 8 days in full RPMI (Gibco) media containing 10% FCS (Biochrom), 1% Pen/Strep, 1% MEM-EAGLE non-essential amino acids, 1% L-glutamine solution, 1% sodium pyruvate solution (all from Biological Industries) and supplemented with 200ng/ml Flt3-L (Peprotech).

extract_protocol: In vitro derived CD4+ equivalent dendritic cells were idenitificated as B220- CD11c+ CD172+ CD24low CD11b+ and CD8α+ equivalent DCs as B220- CD11c+ CD172- CD24+ CD11blow and sorted with a FACS-Aria. RNA was isolated with the miRNeasy Kit from Qiagen.

treatment_protocol: Every 3rd day, the cells received 1/3 volume fresh media with 200ng/ml Flt3-L.

value: CD4 equivalent dendritic cell

tag: markers

value: CD11c+ CD172+ CD24low CD11b+

tag: genotype

tag: genetic background


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 2 manufacture 1 hybridized on slide # 5745 position 4


description: mature Dendritic Cells of Donor # 717 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5733 position 2


description: immature Dendritic Cells of Donor # 717 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5732 position 1

value: immature Dendritic Cells


title: LU_48hr_infect_rep1

description:
Gene expression after 48hr in APP-infected swine lung
M-P-4

tag: gender

tag: age


title: Monocytes of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5747 position 3


description: mature Dendritic Cells of Donor # 249 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5745 position 2


title: wt CD4 equivalent dendritic cell


title: Monocytes of Donor # 340 from monocytes deriving from apheresis # 3 manufacture 2 hybridized on slide # 5731 position 3


title: Control 1 mouse

value: Hypothalamic microdissections

tag: strain


title: ko CD8 equivalent dendritic cell

tag: cell type

value: CD8 equivalent dendritic cell

value: CD11c+ CD172- CD24+ CD11blow


title: Monocytes of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 2 hybridized on slide # 5732 position 3

tag: donor


title: LU_48hr_un-infect_rep2

description:
Gene expression after 48hr in APP-un-infected swine lung
M-P-2

source_name: lung, 48hr, APP-un-infected swine


title: Monocytes of Donor # 340 from monocytes deriving from apheresis # 3 manufacture 1 hybridized on slide # 5746 position 2

tag: apheresis


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 4 manufacture 4 hybridized on slide # 5731 position 1

tag: manufacture


description: immature Dendritic Cells of Donor # 852 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5743 position 3

source_name: immature Dendritic Cells of Donor

tag: slide #


title: LU_48hr_un-infect_rep3

description:
Gene expression after 48hr in APP-un-infected swine lung
M-P-3


description: mature Dendritic Cells of Donor # 852 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5730 position 4

tag: position # on slide


description: mature Dendritic Cells of Donor # 172 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5744 position 3

tag: sample type


title: wt CD8 equivalent dendritic cell


title: Huh7_DSF_rep1

city: Chiba

first: Tetsuhiro

last: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Gastroenterology and Nephrology

country: Japan

institute: Graduate School of Medicine, Chiba University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturer's instructions. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20120130) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Huh7 EpCAM+ cells, DSF-treated, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One Color Spike Mix Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the RNeasy Mini kit (Qiagen, Valencia, CA, USA) following the manufacturer's recommendations.

treatment_protocol: Huh1 cells and Huh7 cells were treated with disulfiram (0.1μM) or 5-FU (1μM) for 48 hours. Fluorescence-activated cell sorting was used to isolate EpCAM+ HCC cells.

tag: cell line

tag: treatment

value: DSF


title: LU_48hr_un-infect_rep1

description:
Gene expression after 48hr in APP-un-infected swine lung
M-P-1


title: HN_48hr_infect_rep3

description:
Gene expression after 48hr in APP-infected swine hilar node
M-L-6

source_name: hilar node, 48hr, APP-infected swine

tag: infection agent

tag: sample collection time

value: hilar lymph node


title: LU_48hr_infect_rep3

description:
Gene expression after 48hr in APP-infected swine lung
M-P-6

tag: tissue


title: Huh7_DSF_rep2

source_name: Huh7 EpCAM+ cells, DSF-treated, replicate 2


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 2 hybridized on slide # 5729 position 4

value: mature Dendritic Cells

tag: vendor


title: Huh1_DSF_rep3

source_name: Huh1 EpCAM+ cells, DSF-treated, replicate 3


title: Monocytes of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 4 hybridized on slide # 5730 position 1

value: reference


title: Huh7_5-FU_rep3

source_name: Huh7 EpCAM+ cells, 5-FU-treated, replicate 3


title: Huh7_5-FU_rep2

source_name: Huh7 EpCAM+ cells, 5-FU-treated, replicate 2


title: HN_48hr_un-infect_rep3

description:
Gene expression after 48hr in APP-un-infected swine hilar node
M-L-3

source_name: hilar node, 48hr, APP-un-infected swine


title: Huh7_control_rep2

source_name: Huh7 EpCAM+ cells, control, replicate 2

value: control


title: HN_48hr_infect_rep1

description:
Gene expression after 48hr in APP-infected swine hilar node
M-L-4


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 2 hybridized on slide # 5729 position 1

value: Stratagene Catalog #740000


title: HN_48hr_infect_rep2

description:
Gene expression after 48hr in APP-infected swine hilar node
M-L-5

value: male


description: mature Dendritic Cells of Donor # 85 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5730 position 3


title: Huh7_DSF_rep3

source_name: Huh7 EpCAM+ cells, DSF-treated, replicate 3


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 2 hybridized on slide # 5729 position 2

source_name: mature Dendritic Cells of Donor


title: Huh1_DSF_rep1

source_name: Huh1 EpCAM+ cells, DSF-treated, replicate 1


title: Huh1_DSF_rep2

source_name: Huh1 EpCAM+ cells, DSF-treated, replicate 2


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 2 hybridized on slide # 5729 position 3

source_name: Universal Human Reference RNA


title: Huh7_control_rep1

source_name: Huh7 EpCAM+ cells, control, replicate 1


title: Huh7_5-FU_rep1

source_name: Huh7 EpCAM+ cells, 5-FU-treated, replicate 1


title: Huh7_control_rep3

source_name: Huh7 EpCAM+ cells, control, replicate 3


title: Huh1_5-FU_rep3

source_name: Huh1 EpCAM+ cells, 5-FU-treated, replicate 3


description: immature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 5 manufacture 1 hybridized on slide # 5710 position 4

source_name: immature Dendritic Cells of Donor


title: HN_48hr_un-infect_rep2

description:
Gene expression after 48hr in APP-un-infected swine hilar node
M-L-2

value: 2.5 months


title: Huh1_5-FU_rep1

source_name: Huh1 EpCAM+ cells, 5-FU-treated, replicate 1


title: Monocytes of Donor # 882 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5710 position 1

source_name: Monocytes of Donor

value: Monocytes


title: HN_48hr_un-infect_rep1

description:
Gene expression after 48hr in APP-un-infected swine hilar node
M-L-1


title: Huh1_control_rep2

source_name: Huh1 EpCAM+ cells, control, replicate 2


title: Huh1_control_rep1

source_name: Huh1 EpCAM+ cells, control, replicate 1


title: Huh1_control_rep3

source_name: Huh1 EpCAM+ cells, control, replicate 3


title: Huh1_5-FU_rep2

source_name: Huh1 EpCAM+ cells, 5-FU-treated, replicate 2


title: Monocytes of Donor # 717 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5709 position 4


description: immature Dendritic Cells of Donor # 892 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5709 position 1


title: Monocytes of Donor # 910 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5707 position 4


title: Monocytes of Donor # 172 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5710 position 2


title: Monocytes of Donor # 249 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5707 position 3


description: mature Dendritic Cells of Donor # 892 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5708 position 4


title: SC4 neg shRNA, biological rep4

first: Marianne

middle: Kwang-Hee

last: Kim

address: 10 Center Dr. 4B55

department: Women's Malignancies Branch

institute: NIH/NCI

description: Gene expression data from IKKe SC4 shRNA

hyb_protocol: Hybridized to Affymetrix H133 Plus 2.0 gene chips,  following manufacturer protocol

scan_protocol: Scanned by Affymetrix GeneChip scanner 3000,  following manufacturer protocol

data_processing: CEL files were imported into GeneSpring software 11.5 (Agilent), probe levels were normalized by the GC-RMA algorithm.

source_name: ovarian cancer cells

label_protocol: RNA (1ug) was reverse transcribed with T7-oligo (dT) primers and labeled with biotin using the Affymetrix One Cycle Target Labeling Kit, following manufacturer protocol

growth_protocol: RPMI plus 10% fetal bovine serum (Hyclone, Pittsburg, PA) and standard antibiotics.

extract_protocol: Total RNAs were extracted using Trizol (Invitrogen, Carlsbad, CA) according to manufacturer protocol.

treatment_protocol: Viral supernatants were prepared by transient transfection into a CeB packaging cell line. Two rounds of viral supernatants were applied to Ovcar5 in 6-well plates over the course of 48h, and then cells were incubated with growth medium for 24h, followed by selection with 2ug/ml puromycin for 7 days.

value: adherent cells


title: Monocytes of Donor # 852 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5708 position 3


title: SC4 neg shRNA, biological rep5


title: IKKe B6 shRNA, biological rep6

description: Gene expression data from IKKe B6 shRNA

value: IKKe knockdown


title: SC4 neg shRNA, biological rep6


title: IKKe B6 shRNA, biological rep5

description: Gene expression data from IKKe B6 shRNA


description: mature Dendritic Cells of Donor # 910 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5707 position 1

source_name: mature Dendritic Cells


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 3 hybridized on slide # 5732 position 4

source_name: mature Dendritic Cells of Donor


title: Monocytes of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 5 hybridized on slide # 5707 position 2


title: SC4 neg shRNA, biological rep1


description: immature Dendritic Cells of Donor # 249 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 5709 position 2


title: SC4 neg shRNA, biological rep2


title: SC4 neg shRNA, biological rep3


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 3 hybridized on slide # 5706 position 4


title: Monocytes of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 3 hybridized on slide # 5706 position 3


title: IKKe B6 shRNA, biological rep4

description: Gene expression data from IKKe B6 shRNA


title: Cadmium_uptake_lea_V21_Soil 1_greenhouse_r3

city: Neuchatel

first: Sam

last: Ansari

state: Neuchatel

address: Quai Jeanrenaud 5

department: Research & Development

institute: Philip Morris Products SA

description:
DNA9046-021A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.

hyb_protocol: Frozen samples (-80°C) packed in dry ice were sent to DNAVision (Charleroi, Belgium). Total RNA isolation using a Trizol® method (Invitrogen 155596-018), microarray hybridization and quality check by Agilent 2100 Bioanalyzer were executed at DNAVision. Affymetrix hybridizations were performed using Affymetrix kits with catalog numbers 900652 and 900454; probe labeling was checked as suggested by the manufacturer.

scan_protocol: Standard Affymetrix scanning procedure.

data_processing:
An in-house QC pipeline was developed to assess the quality of the gene-expression data. In addition to the standard quality metrics suggested by Affymetrix, an in-house QC metrics including probe-level models, Normalized Unscaled Standard Error (NUSE) and Relative Log Expression (RLE) plots, and the analysis of DABG results were used. The QC pipeline involves a combination of Affymetrix Power Tools (APT) and Bioconductor packages, for which the Tobacco Exon Array (TobArray520623F) cdf environment was created.
As the exon array design had no mismatch probes, summarization was performed using the Robust Multiarray Average (RMA) method. A total of 272,472 probesets expression values were generated, and DABG P-values were computed to assess the significance of the signal obtained for each probeset. This involved the background probes that are spread over the chip. Those random probes have a varying GC content. Once the expression values were available, differential gene analysis was performed using moderated t-statistics in linear model LIMMA. In addition, gene sets were defined by first annotating probesets by homology to Arabidopsis thaliana genes and using Arabidopsis thaliana gene sets, and mean-rank gene-set enrichment analysis was performed.

organism: Nicotiana tabacum

source_name: Leaves, V21, soil 1

label_protocol: Standard Affymetrix labeling procedure using biotin.

growth_protocol: Tobacco seeds of V5 and V21 varieties were germinated in floating trays and grown for three weeks before being transferred to 5 liter pots. Two soils were prepared, one a peaty soil (minus Cd soil, referred to as Soil 1) and the other a soil mixture containing half of the same peaty soil and half of an agricultural soil containing more bioavailable Cd (plus Cd soil, referred to as Soil 2). To ensure that there were no toxic Cd effects and to allow the monitoring of differential Cd accumulation in both tobacco varieties, the soils did not exceed 0.12 mg/kg total Cd. In each soil, six plants were planted and placed on a table according to a randomized pot design. Plants were watered daily on an automatic drip with a full fertilizer (93.03 mg N l-1, 49.94 mg P2O5 l-1, 172.27 mg K2O l-1, 13.67 mg Mg l-1, 62.03 mg Ca l-1, 27.62 mg S l-1 and microelements: 0.472 mg Fe l-1, 0.309 mg Mn l-1, 0.147 mg Zn l-1, 0.122 mg B l-1, 0.027 mg Cu l-1, 0.027 mg Mo l-1). The illumination cycle was 14/10 day/night with 24°C during the day and 20°C during the night. After nine weeks of growth and just before flowering, a pool of leaf disks at leaf stalk positions 5, 6 and, 7 and one lateral root were collected simultaneously from each plant. Full leaves 5, 6, and 7 were then collected and dried at 65°C in an oven for three days.

extract_protocol: Approximately 100 ug of plant tissue was placed in a 1.5 ml Eppendorf tube (1/3 in volume), and snap frozen in liquid nitrogen. RNA extraction was performed by the Trizol® method. 400 ul of Trizol® reagent (Invitrogen) was added to the frozen plant tissue and the sample was ground to homogeneity before an additional 600 ul of Trizol® was added. Samples were vortexed for 15 s, then incubated at for 5 min room temperature. 200 ul of chloroform was added and the tubes were gently mixed before centrifugation (12,000 x g) at 4°C for 15 min. The aqueous phase was transferred to an Eppendorf tube containing 500 ul of isopropyl alcohol. After 15 min incubation on ice, RNA was pelleted by centrifugation at 4°C for 10 min. The RNA pellet was finally washed with 1 ml of 70% ethanol, and centrifuged for five minutes a 7,500 x g. After air-drying, RNA was resuspended in 50 ul of nucleotide-free H2O. RNA concentration was analyzed by measuring optical density (OD) at 260 nm. RNA quality control was determined by OD260/OD280 and using Agilent 2100 Bioanalyzer before cDNA preparation.

tag: variety

tag: developmental stage

value: end of flowering

value: leaves

tag: stimulus

value: soil 1


title: Cadmium_uptake_roo_V21_Soil 1_greenhouse_r2

description:
DNA9046-020A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.

source_name: Roots/lateral, V21, soil 1

value: roots/lateral


title: IKKe B2 shRNA, biological rep6

description: Gene expression data from IKKe B2 shRNA


title: Cadmium_uptake_roo_V21_Soil 1_greenhouse_r1

description:
DNA9046-018A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.


title: IKKe B6 shRNA, biological rep1

description: Gene expression data from IKKe B6 shRNA


title: Cadmium_uptake_lea_V21_Soil 1_greenhouse_r2

description:
DNA9046-019D
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.


title: Cadmium_uptake_lea_V5_Soil 1_greenhouse_r1

description:
DNA9046-004A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.

source_name: Leaves, V5, soil 1


title: IKKe B6 shRNA, biological rep2

description: Gene expression data from IKKe B6 shRNA


title: IKKe B6 shRNA, biological rep3

description: Gene expression data from IKKe B6 shRNA


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 4 hybridized on slide # 5706 position 1

source_name: Universal Human Reference RNA


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 2 hybridized on slide # 5706 position 2


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 5 manufacture 1 hybridized on slide # 624 position 3


title: Cadmium_uptake_lea_V21_Soil 1_greenhouse_r1

description:
DNA9046-017A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 3 manufacture 1 hybridized on slide # 624 position 4


title: Cadmium_uptake_lea_V5_Soil 1_greenhouse_r2

description:
DNA9046-006A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.


title: IKKe B2 shRNA, biological rep4

description: Gene expression data from IKKe B2 shRNA


title: IKKe B2 shRNA, biological rep5

description: Gene expression data from IKKe B2 shRNA


title: Cadmium_uptake_roo_V5_Soil 1_greenhouse_r3

description:
DNA9046-003B
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.

source_name: Roots/lateral, V5, soil 1


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 624 position 2


title: Cadmium_uptake_lea_V21_Soil 2_greenhouse_r1

description:
DNA8273-007A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.

source_name: Leaves, V21, soil 2

value: soil 2


title: Cadmium_uptake_roo_V21_Soil 2_greenhouse_r1

description:
DNA8273-008A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.

source_name: Roots/lateral, V21, soil 2


title: Cadmium_uptake_roo_V5_Soil 1_greenhouse_r2

description:
DNA9046-001A2
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.


title: Monocytes of Donor # 892 from monocytes deriving from apheresis # 1 manufacture 1 hybridized on slide # 623 position 3


description: mature Dendritic Cells of Donor # 340 from monocytes deriving from apheresis # 1 manufacture 3 hybridized on slide # 623 position 1


title: Cadmium_uptake_roo_V21_Soil 2_greenhouse_r3

description:
DNA8273-012A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.


title: Cadmium_uptake_lea_V21_Soil 2_greenhouse_r2

description:
DNA8273-009A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.


title: IKKe B2 shRNA, biological rep2

description: Gene expression data from IKKe B2 shRNA


title: Cadmium_uptake_lea_V5_Soil 2_greenhouse_r3

description:
DNA8273-005A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.

source_name: Leaves, V5, soil 2


title: IKKe B2 shRNA, biological rep3

description: Gene expression data from IKKe B2 shRNA


title: Cadmium_uptake_roo_V21_Soil 2_greenhouse_r2

description:
DNA8273-010B
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.


title: Monocytes of Donor # 340 from monocytes deriving from apheresis # 5 manufacture 1 hybridized on slide # 623 position 2


title: IKKe B2 shRNA, biological rep1

description: Gene expression data from IKKe B2 shRNA


title: Cadmium_uptake_roo_V5_Soil 2_greenhouse_r3

description:
DNA8273-006B
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.

source_name: Roots/lateral, V5, soil 2


title: Cadmium_uptake_roo_V5_Soil 2_greenhouse_r1

description:
DNA8273-002A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.


title: Cadmium_uptake_lea_V5_Soil 2_greenhouse_r2

description:
DNA8273-003A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.


title: Diabetic visceral adipose female 11

status: Public on Nov 15 2012

city: Delhi

first: Abhay

last: Sharma

state: Delhi

address: Delhi University campus, Mall Road

department: Functional Genomics Unit

institute: CSIR-Institute of Genomics and Integrative Biology (IGIB)

description: Diabetic_Biological replicate _3_technical_replicate_2

hyb_protocol: Standard Illumina hybridization protocol was followed.

scan_protocol: Standard Illumina scanning protocol was followed.

data_processing: Non-normalized data was obtained by subtracting background from raw intensities in GenomeStudio data analysis software (Illumina). The data were normalized using average normalization. The non-diabetic group was selected as the reference, Illumina custom method was used as the error model, and Benjamini and Hochberg False Discovery Rate was used as the method for multiple testing correction.

source_name: Visceral adipose

label_protocol: Biotinylated cRNAs were prepared using Illumina TotalPrep kit (Ambion).

extract_protocol: Biopsy samples were stored in RNAlater (Ambion) in minus 80 degree C before RNA was extracted. Total cellular RNA was extracted using mirVana isolation kit (Ambion). The quantity and the quality of RNA samples were determined using Nanodrop-1000 (Thermo Fischer Scientific, Wilmington, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), in that order.

tag: gender

value: Female

tag: age

value: Viseral  Adipose

tag: disease state

value: diabetic


title: Cadmium_uptake_lea_V21_Soil 2_greenhouse_r3

description:
DNA8273-011A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.


title: Cadmium_uptake_roo_V5_Soil 2_greenhouse_r2

description:
DNA8273-004A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.


title: Diabetic visceral adipose female 12

description: Diabetic_Biological replicate _3_technical_replicate_3


title: Diabetic visceral adipose female 7

description: Diabetic_Biological replicate _1_technical_replicate_2


title: Cadmium_uptake_lea_V5_Soil 2_greenhouse_r1

description:
DNA8273-001A
Experiment type: induced stress
Experiment type 2: stress/tissue
Provider: DNAVision
QC Passed.


title: Diabetic visceral adipose female 6

description: Diabetic_Biological replicate _3_technical_replicate_1


title: Diabetic visceral adipose female 8

description: Diabetic_Biological replicate _1_technical_replicate_3


title: Diabetic visceral adipose female 10

description: Diabetic_Biological replicate _2_technical_replicate_3


title: Diabetic visceral adipose female 5

description: Diabetic_Biological replicate 3


title: EBP50 binding motifs (2 of 2 G4489A)

type: genomic

city: Taipei

first: Yih-Jyh

last: Shann

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

country: Taiwan

institute: Nation Yang-Ming University

description: Agilent-014707 Human Promoter ChIP-on-Chip Set 244K, Microarray 2 of 2 G4489A (Probe name version)

hyb_protocol: Hybridization of labeled mock and EBP50 IP DNA was performed  according to the manufacturer's instructions.

scan_protocol: Fluorescent images were obtained using Agilent Technologies Scanner G2505C US84303579.

data_processing: Agilent Feature Extraction Software (v 10.1.1.1) was used for background subtraction and LOWESS normalization. Data analysis was performed using GenomicWorkbench v5.0(Agilent Technology).

molecule: genomic DNA

source_name: Mock IP(control antibody)

label_protocol: Chromatin sample from mock IP was labeled with Cy3, sample from EBP50 IP was labeled with Cy5.

growth_protocol: The colon carcinoma cell lines SW480 were cultured in DMEM supplemented with 10% fetal calf serum at 37°C in a humidified incubator containing 5% CO2.  and the kidney epithelial cell line HEK293T were cultured in DMEM supplemented with 10%  fetal calf serum at 37°C in a humidified incubator containing 5% CO2.

extract_protocol: SW480 cells were crosslinked with formaldehyde, sonicated, and subjected to immunoprecipitation.

value: input DNA

tag: antibody

source_name: EBP50 IP

value: custom made rabbit antibody against EBP50 C-terminal peptide(N'-MARERAHQKRSSKRC-C')


title: Diabetic visceral adipose female 4

description: Diabetic_Biological replicate _2_technical_replicate_1


title: Diabetic visceral adipose female 3

description: Diabetic_Biological replicate 2


title: Non-diabetic visceral adipose female 10

description: Non-diabetic_Biological replicate _2_technical_replicate_3

value: non-diabetic


title: Non-diabetic visceral adipose female 8

description: Non-diabetic_Biological replicate _1_technical_replicate_3


title: Diabetic visceral adipose female 2

description: Diabetic_Biological replicate _1_technical_replicate_1


title: Non-diabetic visceral adipose female 6

description: Non-diabetic_Biological replicate _3_technical_replicate_1


title: Non-diabetic visceral adipose female 11

description: Non-diabetic_Biological replicate _3_technical_replicate_2


title: Non-diabetic visceral adipose female 12

description: Non-diabetic_Biological replicate _3_technical_replicate_3


title: EBP50 binding motifs (1 of 2 G4489A)

description: Agilent-014706 Human Promoter ChIP-on-Chip Set 244K, Microarray 1 of 2 G4489A (Probe name version)


title: Non-diabetic visceral adipose female 9

description: Non-diabetic_Biological replicate _2_technical_replicate_2


title: Diabetic visceral adipose female 1

description: Diabetic_Biological replicate 1


title: Diabetic visceral adipose female 9

description: Diabetic_Biological replicate _2_technical_replicate_2


title: Non-diabetic visceral adipose female 5

description: Non-diabetic_Biological replicate 3


title: Non-diabetic visceral adipose female 7

description: Non-diabetic_Biological replicate _1_technical_replicate_2


title: Diabetic female adipose 8

source_name: Subcutaneous adipose

value: Subcutaneous adipose


title: Non-diabetic visceral adipose female 1

description: Non-diabetic_Biological replicate 1


title: Non-diabetic visceral adipose female 2

description: Non-diabetic_Biological replicate _1_technical_replicate_1


title: Diabetic female adipose 6


title: Diabetic female adipose 4


title: Diabetic female adipose 7

description: Diabetic_Biological replicate _1_technical_replicate_2


title: Diabetic female adipose 3

description: Diabetic_Biological replicate 2


title: Diabetic female adipose 10


title: Diabetic female adipose 11

description: Diabetic_Biological replicate _3_technical_replicate_2


title: Diabetic female adipose 2


title: Non-diabetic visceral adipose female 3

description: Non-diabetic_Biological replicate 2


title: Non-diabetic visceral adipose female 4

description: Non-diabetic_Biological replicate _2_technical_replicate_1


title: Diabetic female adipose 5

description: Diabetic_Biological replicate 3


title: Diabetic female adipose 9


title: Diabetic female adipose 12

description: Diabetic_Biological replicate _3_technical_replicate_3


title: Non-diabetic female adipose 7


title: Non-diabetic female adipose 5

description: Non-diabetic_Biological replicate 3


title: Diabetic female adipose 1

description: Diabetic_Biological replicate 1


title: Non-diabetic female adipose 2


title: Non-diabetic female adipose 12


title: Non-diabetic female adipose 3

description: Non-diabetic_Biological replicate 2


title: Non-diabetic female adipose 10


title: Non-diabetic female adipose 6


title: Diabetic 12

source_name: Skeletal muscle

value: Male

value: Skeletal muscle


title: Non-diabetic female adipose 4


title: Diabetic 11


title: Diabetic 9


title: Diabetic 7


title: Diabetic 6

description: Diabetic_Biological replicate _3_technical_replicate_1


title: Diabetic 8

description: Diabetic_Biological replicate _1_technical_replicate_3


title: Diabetic 2

description: Diabetic_Biological replicate 2


title: Diabetic 10

description: Diabetic_Biological replicate _2_technical_replicate_3


title: Diabetic 4


title: Diabetic 5

description: Diabetic_Biological replicate _2_technical_replicate_1


title: Diabetic 3

description: Diabetic_Biological replicate 3


title: Diabetic 1

description: Diabetic_Biological replicate 1


title: Non-diabetic female adipose 11


title: Non-diabetic female adipose 9


title: Non-diabetic 10

description: Non-diabetic_Biological replicate _2_technical_replicate_3


title: Non-diabetic 11


title: Non-diabetic 9


title: Non-diabetic 7


title: PANC-1-3D spheroid-2

city: Tainan City

first: Wei-Yu

address: 2F., No. 367, Shengli Road

institute: National Health Research Institutes

description: PANC-1,3D culture for 6day,duplicate data,02

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133A 2.0 Plus GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.

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

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

source_name: PANC-1-3D spheroid

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).

growth_protocol: HPDE cells were maintained in Keratinocyte-SFM (Sigma-Aldrich); PANC-1 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and antibiotics

extract_protocol: Total RNA samples were extracted from cells or organoids using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).

treatment_protocol: no treatment

tag: cell type

value: pancreatic cancer cells

tag: culture type

value: 3D spheroid


title: Non-diabetic 3

description: Non-diabetic_Biological replicate 3


title: Non-diabetic 1

description: Non-diabetic_Biological replicate 1


title: Non-diabetic female adipose 1

description: Non-diabetic_Biological replicate 1


title: Non-diabetic 12


title: Non-diabetic 5


title: PANC-1-2D monolayer-2

description: PANC-1,2D,duplicate data,02

source_name: PANC-1-2D monolayer

value: 2D monolayer


title: HPDE-3D tubules-1

description: HPDE,3D culture for 6day,duplicate data,01

source_name: HPDE-3D tubules

value: HPDE

value: immortalized pancreatic epithelial cells

value: 3D tubules


title: HPDE-3D tubules-2

description: HPDE,3D culture for 6day,duplicate data,02


title: PANC-1-3D cluster-1

description: PANC-1,3D culture for 2day,duplicate data,01

source_name: PANC-1-3D cluster

value: 3D cluster


title: PANC-1-3D cluster-2

description: PANC-1,3D culture for 2day,duplicate data,02


title: HPDE-3D cluster-2

description: HPDE,3D culture for 2day,duplicate data,02

source_name: HPDE-3D cluster


title: PANC-1-3D spheroid-1

description: PANC-1,3D culture for 6day,duplicate data,01


title: Non-diabetic 8

description: Non-diabetic_Biological replicate _1_technical_replicate_3


title: HPDE-3D cluster-1

description: HPDE,3D culture for 2day,duplicate data,01


title: Non-diabetic 4

description: Non-diabetic_Biological replicate _1_technical_replicate_1


title: Non-diabetic 2

description: Non-diabetic_Biological replicate 2


title: water column DNA [140 m]

type: mixed

city: Boston

first: Silvia

last: Newell

state: Massachusetts

address: 675 Commonwealth Ave.

institute: Boston University

description: DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays

hyb_protocol: Samples were hybridized to duplicate arrays by overnight incubation at 65°C and washed.

scan_protocol: The arrays were scanned with a laser scanner (Molecular Devices 4300) Images were analyzed with Gene Pix Pro 6.0 software (Molecular Devices)

data_processing: Quality control was employed to remove noise by eliminating features in which the Cy3 signal was not at least twice the value of the control probes, and the Cy3/Cy5 was not at least 1% of the total amoA signal from all 31 probes.

molecule: other

organism: synthetic construct

source_name: Universal Internal Standard 20-mer

label_protocol: Hybridization targets were prepared from gel-extracted and cleaned AOA amoA qPCR products (Qiagen). Briefly, the cleaned products were labeled with amino-allyl-dUTP (Ambion) during linear amplification using random octamers and a Klenow polymerase (Applied Biosystems). The reaction contained 3.9 mM d(AGC)TP, 0.4 mM dTTP, and 4.8 mM dUaa and was amplified for 3 h at 37°C. The Klenow product was purified and conjugated with Cy3. The Cy3-labelled target (200 ng) was combined with 2x hybridization buffer (1x final concentration; Agilent) and 0.25 pmol of a Cy5-labelled complementary 20-mer standard oligonucleotide and incubated at 95°C for 5 min before being cooled to room temperature.

extract_protocol: DNA was extracted from the filters using the PureGene DNA kit (Gentra, Minneapolis, MN), following a slight modification of the manufacturer’s protocol: lysis buffer (0.9 ml) was added to the filter and incubated with gentle rotation at 55°C for 1 hr, and then at 65°C for 1 hr.  The solution was removed and the incubation repeated with fresh solution.

value: Universal Internal Standard 20-mer

organism: uncultured ammonia-oxidizing archaeon

source_name: Total DNA from water colum at 140 m

value: environmental sample


title: Non-diabetic female adipose 8

value: Female


title: water column DNA [1000 m]

source_name: Total DNA from water colum at 1000 m


title: water column DNA [80 m]

source_name: Total DNA from water colum at 80 m


title: water column DNA [20 m]

source_name: Total DNA from water colum at 20 m


title: water column DNA [40 m]

source_name: Total DNA from water colum at 40 m


title: water column DNA [120 m]

source_name: Total DNA from water colum at 120 m


title: PANC-1-2D monolayer-1

last: Wang

description: PANC-1,2D,duplicate data,01


title: water column DNA [100 m]

source_name: Total DNA from water colum at 100 m


title: Non-diabetic 6

description: Non-diabetic_Biological replicate _3_technical_replicate_1


title: water column DNA [2000 m]

source_name: Total DNA from water colum at 2000 m


title: Transdetermined hematopoietic stem cells-2

city: San Diego

first: Ignacio

last: Sancho-Martinez

state: California

address: 110 North Torrey Pines Road

department: Gene Expression Laborartory-B

institute: Salk Institute for Biological Studies

description: lamina propria of olfactory mucosa from Huamn

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip Hybridization Control Kit)

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS software according to manufacturer's protocol.

data_processing: Probe set summarization and normalization was performed using quantile normalization by affy package in R-Bioconductor.

label_protocol: Affymetrix GeneChip IVT Labeling Kit, according to manufacturer's protocol.

extract_protocol: total RNA were extracted using Rneasy (Qiagen) according to manufacturer's protocol.

value: Primary somatic cell culture


title: Olfactory Mesenchymal Stem Cells-2

source_name: Olfactory Mesenchymal Stem Cells-2


title: 9_15_2010_Ypt1(2)

city: Durham

first: Nikoleta

middle: G

last: Tsvetanova

state: NC

address: 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89672.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Saccharomyces cerevisiae

source_name: Reference RNA

label_protocol: not provided

extract_protocol: not provided

tag: channel 1

value: Reference RNA

source_name: IP RNA

tag: channel 2

value: IP RNA

tag: geneticmodification

value: tagged

tag: media

value: absent


title: Transdetermined hematopoietic stem cells-1


title: 9_15_2010_Ypt1(1)

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89671.gif


title: UPR_Mock_2

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-01/91961.gif

source_name: Reference

value: Reference

source_name: IP

value: IP

value: untagged

value: present


title: Olfactory Mesenchymal Stem Cells-1

source_name: Olfactory Mesenchymal Stem Cells-1


title: Mock normalmedium(2)

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88199.gif


title: Mock normalmedium(1)

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88198.gif