title: SLE_untreated_patient2_rep1

description: Gene expression before treatment

value: Monocytes


title: Reference_DASL_P30 rep1

status: Public on Mar 11 2014

type: RNA

city: La Jolla

first: Maggie

last: Chow

state: CA

address: 8110 La Jolla Shores Dr. Ste 201

department: Neuroscience

country: USA

institute: NIH-UC San Diego Autism Center of Excellence

description: Reference RNA

hyb_protocol: Illumina hybridization protocol

scan_protocol: Illumina scanning protocol

data_processing: Data not normalized

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Stratagene Universal Reference pooled RNA

label_protocol: DASL- and IVT-based protocols

extract_protocol: Ambion MELT kit for frozen brain samples and Roche High Pure FFPE RNA Micro Kit for formalin fixed samples

tag: tissue

tag: assay

value: DASL

tag: heat treatment

value: Heating at 95C for 30 min


title: Reference_DASL_B10 rep1

description: Reference RNA

source_name: Ambion FirstChoice Human Brain Reference RNA

value: brain

value: Heating at 95C for 10 min


title: Reference_DASL_B30 rep1

description: Reference RNA


title: Reference_DASL_B0 rep1

description: Reference RNA

value: Heating at 95C for 0 min


title: Reference_DASL_B10 rep2

description: Reference RNA


title: Reference_DASL_B0 rep2

description: Reference RNA


title: Control_EHL, C4

city: Helsinki

first: Mark

middle: Andrew

last: Screen

address: Biomedicum1, Haartmaninkatu 8

department: Dpt. of Medical Genetics

country: Finland

institute: Folkhälsan Institute of Genetics, University of Helsinki

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2.0 Arrays.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000.

data_processing: Expression values were determined using Affymetrix Microarray Suite 5.0. GeneSpring GX version 11.0 was used to analyze the data using MAS5.0 normalization with all probes with absent flags removed from the data. The data was baseline transformed to the median of all samples. The condition average signal for each probe was filtered by significance using an unpaired t-test with unequal variance (Welch correction, P<0.05) using multiple testing correction (Benjamini-Hochberg), followed by a two-fold change cut-off.

label: biotin

source_name: Extensor digitorum longus, healthy control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA using one-cycle amplification (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: disease state

value: healthy

value: extensor digitorum longus

tag: age at biopsy

tag: Sex

value: male

tag: individual identifier


title: TMD_TP, T6

source_name: Tibialis posterior, TMD

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA using two-cycle amplification (Expression Analysis Technical Manual, 2001, Affymetrix).

value: tibial muscular dystrophy (TMD)

value: tibialis posterior


title: TMD_EHL, T4

source_name: Extensor digitorum longus, TMD


title: Control_TA, C3

source_name: Tibialis anterior, healthy control

value: tibialis anterior


title: Control_EHL, C2


title: TMD_SOL, T5

source_name: Soleus, TMD

value: soleus


title: TMD_GL, T2

source_name: Gastrocnemius medialis, TMD

value: gastrocnemius medialis


title: TMD_TA, T3

source_name: Tibialis anterior, TMD


title: TMD_TA, T7


title: Control_SOL, C5

source_name: Soleus, healthy control


title: TMD_EHL, T1


title: Control_TP, C1

source_name: Tibialis posterior, healthy control


title: HD1287 ( 4019614134_E)

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description:
HD1287
4019614134_E

hyb_protocol: Hybridization to HumanHT-12 v3 Expression BeadChip as per Illumina protocol

scan_protocol: Illumina BeadStation 500 SentrixScanVersion 2.3.0.13

data_processing: Following background subtraction, the raw signal intensities extracted with Illumina Genome Studio v2010.1 Gene Expression 1.6.0 software were scaled to the mean intensity of the dataset.

source_name: Whole Blood

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions

value: Healthy

value: P3 TRANSPLANTATION-BUMC (26) 11Jun08 Liver Transplant for Modules


title: HD1285 ( 4019614133_A)

description:
HD1285
4019614133_A


title: BAY-IMM-032 ( 4019614132_A)

description:
BAY-IMM-032
4019614132_A

value: Transplant ACR


title: HD1284 ( 4019614132_D)

description:
HD1284
4019614132_D


title: BAY-IMM-051 ( 4019614134_B)

description:
BAY-IMM-051
4019614134_B


title: 780 ( 4020480004_E)

description:
780
4020480004_E


title: BAY-IMM-029\n ( 4019614129_E)

description:
BAY-IMM-029\n
4019614129_E


title: BAY-IMM-053 ( 4019614132_E)

description:
BAY-IMM-053
4019614132_E


title: HD1286 ( 4019614133_D)

description:
HD1286
4019614133_D


title: HD1214 ( 4020480004_A)

description:
HD1214
4020480004_A


title: Healthy Reference Pool ( 4019614134_A)

description:
Healthy Reference Pool
4019614134_A

value: Reference Pool


title: HD1223 ( 4019614129_D)

description:
HD1223
4019614129_D


title: BAY-IMM-013\n ( 4019614129_A)

description:
BAY-IMM-013\n
4019614129_A


title: HD1208 ( 4020480004_C)

description:
HD1208
4020480004_C


title: 765 ( 4020480004_D)

description:
765
4020480004_D


title: BAY-IMM-028\n ( 4019614129_C)

description:
BAY-IMM-028\n
4019614129_C


title: HD1235 ( 4019614088_D)

description:
HD1235
4019614088_D


title: BAY-IMM-020\n ( 4019614088_F)

description:
BAY-IMM-020\n
4019614088_F

value: Transplant ACR\n


title: HD1231 ( 4019614129_F)

description:
HD1231
4019614129_F


title: 10057/1 ( 1965120016_F)

description:
10057/1
1965120016_F

value: Control BCG+

value: P22 TUBERCULOSIS-UK (15) 11Jun08 TB for Modules


title: HD1239 ( 4019614088_A)

description:
HD1239
4019614088_A


title: HD1211 ( 4019614084_F)

description:
HD1211
4019614084_F


title: BAY-IMM-018\n ( 4019614088_B)

description:
BAY-IMM-018\n
4019614088_B


title: BAY-IMM-009 ( 4019614084_C)

description:
BAY-IMM-009
4019614084_C


title: BAY-IMM-019 ( 4019614088_C)

description:
BAY-IMM-019
4019614088_C


title: Healthy Reference Pool ( 4019614084_D)

description:
Healthy Reference Pool
4019614084_D


title: 10029/1 ( 1965120016_B)

description:
10029/1
1965120016_B

value: Control BCG-


title: HD1288 ( 4019614084_E)

description:
HD1288
4019614084_E


title: 10035/1 ( 1957955088_F)

description:
10035/1
1957955088_F

value: PTB


title: 10027/1 ( 1957955088_A)

description:
10027/1
1957955088_A


title: 10040/1 ( 1957955087_A)

description:
10040/1
1957955087_A


title: 10053/1 ( 1957955087_E)

description:
10053/1
1957955087_E


title: 10052/1 ( 1957955086_E)

description:
10052/1
1957955086_E


title: 10003/1 ( 1957955069_A)

description:
10003/1
1957955069_A


title: XLA 344 ( 4150401014_C)

description:
XLA 344
4150401014_C

value: Patient


title: XLA 347 ( 4150401014_E)

description:
XLA 347
4150401014_E


title: XLA 229 ( 4150401014_A)

description:
XLA 229
4150401014_A


title: 10045/1 ( 1957955086_B)

description:
10045/1
1957955086_B


title: 10026/1 ( 1957955068_C)

description:
10026/1
1957955068_C


title: 10013/1 ( 1957955067_B)

description:
10013/1
1957955067_B


title: 10039/1 ( 1957955068_E)

description:
10039/1
1957955068_E


title: 10044/1 ( 1957955068_A)

description:
10044/1
1957955068_A


title: 10056/1 ( 1957955069_E)

description:
10056/1
1957955069_E


title: XLA 96 ( 4150401013_F)

description:
XLA 96
4150401013_F


title: 10034/1 ( 1957955067_D)

description:
10034/1
1957955067_D


title: HD-9 ( 4150401014_F)

description:
HD-9
4150401014_F


title: HD-8 ( 4150401014_D)

description:
HD-8
4150401014_D


title: XLA 346 ( 4150401013_E)

description:
XLA 346
4150401013_E


title: HD-7 ( 4150401013_C)

description:
HD-7
4150401013_C


title: XLA 93 ( 4150401013_D)

description:
XLA 93
4150401013_D


title: HD-5 ( 4150401012_E)

description:
HD-5
4150401012_E


title: HD-6 ( 4150401013_B)

description:
HD-6
4150401013_B


title: XLA 345 ( 4150401012_C)

description:
XLA 345
4150401012_C


title: TH-Bp-M029 ( 4038364006_E)

description:
TH-Bp-M029
4038364006_E

value: melioidosis

value: P25 BURKHOLDERIA-THAILAND (28) 19May08 Test set R9 vs R6


title: XLA 11 ( 4150401011_A)

description:
XLA 11
4150401011_A


title: XLA 207T ( 4150401012_B)

description:
XLA 207T
4150401012_B


title: TH-Bp-M030 ( 4038364006_F)

description:
TH-Bp-M030
4038364006_F


title: HD-4 ( 4150401012_A)

description:
HD-4
4150401012_A


title: TH-Bp-I025 ( 4038364004_F)

description:
TH-Bp-I025
4038364004_F

value: Other infection


title: HD-3 ( 4150401011_E)

description:
HD-3
4150401011_E


title: HD-2 ( 4150401011_D)

description:
HD-2
4150401011_D


title: HD-1 ( 4150401011_C)

description:
HD-1
4150401011_C


title: TH-Bp-H004 ( 4038364006_B)

description:
TH-Bp-H004
4038364006_B


title: TH-Bp-I026 ( 4038364006_A)

description:
TH-Bp-I026
4038364006_A


title: TH-Bp-H002 ( 4038364002_F)

description:
TH-Bp-H002
4038364002_F


title: TH-Bp-M022 ( 4038364001_C)

description:
TH-Bp-M022
4038364001_C


title: TH-Bp-I022 ( 4038364002_C)

description:
TH-Bp-I022
4038364002_C


title: TH-Bp-M028 ( 4038364006_D)

description:
TH-Bp-M028
4038364006_D


title: TH-Bp-R009 ( 4038364001_B)

description:
TH-Bp-R009
4038364001_B

value: Recovery melioidosis


title: XLA 207D ( 4150401011_B)

description:
XLA 207D
4150401011_B


title: TH-Bp-R010 ( 4038364002_E)

description:
TH-Bp-R010
4038364002_E


title: TH-Bp-H001 ( 4038250011_A)

description:
TH-Bp-H001
4038250011_A


title: TH-Bp-I020 ( 4038364001_E)

description:
TH-Bp-I020
4038364001_E


title: TH-Bp-DM008 ( 4038364004_A)

description:
TH-Bp-DM008
4038364004_A

value: Healthy with DM


title: TH-Bp-M024 ( 4038364002_A)

description:
TH-Bp-M024
4038364002_A


title: TH-Bp-R008 ( 4038250011_F)

description:
TH-Bp-R008
4038250011_F


title: TH-Bp-M026 ( 4038364004_C)

description:
TH-Bp-M026
4038364004_C


title: TH-Bp-I021 ( 4038364001_F)

description:
TH-Bp-I021
4038364001_F


title: TH-Bp-M023 ( 4038364001_D)

description:
TH-Bp-M023
4038364001_D


title: TH-Bp-M025 ( 4038364002_B)

description:
TH-Bp-M025
4038364002_B


title: TH-Bp-I023 ( 4038364002_D)

description:
TH-Bp-I023
4038364002_D


title: TH-Bp-DM007 ( 4038250010_F)

description:
TH-Bp-DM007
4038250010_F


title: TH-Bp-M021 ( 4038250011_C)

description:
TH-Bp-M021
4038250011_C


title: TH-Bp-M017 ( 4038250010_B)

description:
TH-Bp-M017
4038250010_B


title: TH-Bp-I015 ( 1955247043_F)

description:
TH-Bp-I015
1955247043_F

value: other infection

value: P25 BURKHOLDERIA-THAILAND (33) 19May08 P25_33_10Oct07_Bp Batch1_Tr


title: TH-Bp-I017 ( 4038250010_D)

description:
TH-Bp-I017
4038250010_D


title: TH-Bp-R007 ( 4038250010_E)

description:
TH-Bp-R007
4038250010_E


title: TH-Bp-M014 ( 1955247043_C)

description:
TH-Bp-M014
1955247043_C


title: TH-Bp-M016 ( 4038250010_A)

description:
TH-Bp-M016
4038250010_A


title: TH-Bp-I012 ( 1955247036_C)

description:
TH-Bp-I012
1955247036_C


title: TH-Bp-M015 ( 1955247043_D)

description:
TH-Bp-M015
1955247043_D


title: TH-Bp-I011 ( 1955247034_E)

description:
TH-Bp-I011
1955247034_E


title: TH-Bp-H/DM006 ( 1955247043_A)

description:
TH-Bp-H/DM006
1955247043_A

value: Diabetes


title: TH-Bp-M009 ( 1955247033_F)

description:
TH-Bp-M009
1955247033_F


title: TH-Bp-R004 ( 1955247034_F)

description:
TH-Bp-R004
1955247034_F

value: Recovery


title: TH-Bp-H/DM005 ( 1955247036_E)

description:
TH-Bp-H/DM005
1955247036_E


title: TH-Bp-I010 ( 1955247034_D)

description:
TH-Bp-I010
1955247034_D


title: TH-Bp-I016 ( 4038250010_C)

description:
TH-Bp-I016
4038250010_C


title: TH-Bp-I009 ( 1955247033_E)

description:
TH-Bp-I009
1955247033_E


title: TH-Bp-R006 ( 1955247043_B)

description:
TH-Bp-R006
1955247043_B


title: TH-Bp-R003 ( 1955247033_A)

description:
TH-Bp-R003
1955247033_A


title: TH-Bp-H/DM004 ( 1955247033_B)

description:
TH-Bp-H/DM004
1955247033_B


title: TH-Bp-I014 ( 1955247043_E)

description:
TH-Bp-I014
1955247043_E


title: TH-Bp-M010 ( 1955247034_B)

description:
TH-Bp-M010
1955247034_B


title: TH-Bp-M007 ( 1955247031_F)

description:
TH-Bp-M007
1955247031_F


title: TH-Bp-I007 ( 1955247031_D)

description:
TH-Bp-I007
1955247031_D


title: TH-Bp-M008 ( 1955247033_D)

description:
TH-Bp-M008
1955247033_D


title: TH-Bp-I006 ( 1955247031_C)

description:
TH-Bp-I006
1955247031_C


title: TH-Bp-I013 ( 1955247036_D)

description:
TH-Bp-I013
1955247036_D


title: TH-Bp-R005 ( 1955247036_F)

description:
TH-Bp-R005
1955247036_F


title: TH-Bp-M006 ( 1955247031_E)

description:
TH-Bp-M006
1955247031_E


title: TH-Bp-M012 ( 1955247036_A)

description:
TH-Bp-M012
1955247036_A


title: TH-Bp-I008 ( 1955247033_C)

description:
TH-Bp-I008
1955247033_C


title: TH-Bp-I004 ( 1955247029_F)

description:
TH-Bp-I004
1955247029_F


title: TH-Bp-I001 ( 1955247028_A)

description:
TH-Bp-I001
1955247028_A


title: TH-Bp-M001 ( 1955247028_C)

description:
TH-Bp-M001
1955247028_C


title: TH-Bp-M002 ( 1955247028_D)

description:
TH-Bp-M002
1955247028_D


title: BAY-SLE-186-V1 ( 4032149093_A)

description:
BAY-SLE-186-V1
4032149093_A

value: SLE

value: P2 LUPUS - ALR (27) 16May08 P2 LUPUS - ALR (27) 16May08 Run 3


title: TH-Bp-M003 ( 1955247029_A)

description:
TH-Bp-M003
1955247029_A


title: TH-Bp-H/DM003 ( 1955247031_A)

description:
TH-Bp-H/DM003
1955247031_A


title: BAY-SLE-179-V1 ( 4032149090_A)

description:
BAY-SLE-179-V1
4032149090_A


title: BAY-H256-V1 ( 4032149086_F)

description:
BAY-H256-V1
4032149086_F

value: Healthy


title: BAY-H255-V1 ( 4032149088_F)

description:
BAY-H255-V1
4032149088_F


title: BAY-SLE-168-V1 ( 4032149087_D)

description:
BAY-SLE-168-V1
4032149087_D


title: BAY-H260-V1 ( 4032149092_E)

description:
BAY-H260-V1
4032149092_E


title: BAY-H247-V1 ( 4032149088_E)

description:
BAY-H247-V1
4032149088_E


title: BAY-SLE-169-V1 ( 4032149088_A)

description:
BAY-SLE-169-V1
4032149088_A


title: BAY-H243-V1 ( 4032149086_E)

description:
BAY-H243-V1
4032149086_E


title: TH-Bp-H/DM002 ( 1955247029_D)

description:
TH-Bp-H/DM002
1955247029_D


title: BAY-SLE-202-V1 ( 4032149092_A)

description:
BAY-SLE-202-V1
4032149092_A


title: BAY-SLE-157-V1 ( 4032149087_A)

description:
BAY-SLE-157-V1
4032149087_A


title: BAY-H225-V1 ( 4032149077_E)

description:
BAY-H225-V1
4032149077_E


title: BAY-SLE-142-V1 ( 4032149086_A)

description:
BAY-SLE-142-V1
4032149086_A


title: BAY-SLE-79-V1 ( 4032149076_A)

description:
BAY-SLE-79-V1
4032149076_A


title: BAY-SLE-91-V2 ( 4032149077_A)

description:
BAY-SLE-91-V2
4032149077_A


title: BAY-H222-V1 ( 4032149072_F)

description:
BAY-H222-V1
4032149072_F


title: BAY-H231-V1 ( 4032149077_F)

description:
BAY-H231-V1
4032149077_F


title: BAY-H237-V1 ( 4032149073_F)

description:
BAY-H237-V1
4032149073_F


title: BAY-H241-V1 ( 4032149078_E)

description:
BAY-H241-V1
4032149078_E


title: ESCC-246T

type: genomic

city: shenzhen

first: Lin

last: Li

address: Beishan Industrial Zone

country: China

institute: BGI

description: Esophageal Cancer Project

hyb_protocol: The labeled genomic DNA (31μg) was dried at 45℃ and diluted in 5.6 μl Sample Tracking Control. Then hybridized in 14.4 μl Hybridization solution (containing 2X Hybridization Buffer, Hybridization Component A, Alignment Oligo). Arrays were hybridized in Maui hybridization stations for 40-72 hr at 42 °C, and then washed in 42 °C with buffer (containing VWR Water, 10X Wash Buffer (I, II or III), 1M DTT) by using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on a NimbleGen MS 200 Microarray Scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Arrays were processed using NimbleScan 2.6 software,which transformed image signal to digital signal, following using segMNT algorithm to analyse the normalized signal ratio.
Final vaues are reported as 'log2 (EXP_NORM/REF_NORM)' in linked segMNT supplementary files.

molecule: genomic DNA

source_name: tumor DNA from esophageal

label_protocol: 1. Add 4μL β-mercaptoethanol to 2200μL Random Primer Buffer, Mix by pulse-vortexing. Use 1050 μL Random Primer Buffer (containing β-mercaptoethanol) to dilute cy3-Random Nonamers and cy5-Random Nonamers respectively. 2. Add 500ng genomic DNA to LHC(Labeling and Hybridization Control). Then add 2μLLCH-1 to test Sample, and 2μLLCH-2 to Reference Sample, amount to 40μL respectively. Add test Sample (containing LLCH-1) to cy3-Random Nonamers, and Reference Sample (containing LLCH-2) to cy5-Random Nonamers, amount to 80μL respectively. 98 °C for 10 min，4°C for 2min. 3. Prepare dNTP/Klenow Master Mix (20μL): 8μL Nuclease-free Water, 10μL 10mM dNTP Mix, 2μL Klenow Fragment (3’->5’ exo-)50U/μl. 4. Add dNTP/Klenow Master Mix (20μL) to Sample mixtures (80μL) respectively. 37 °C  for 2 hr. 5. Add 21.5μL Stop Solution to stop reaction. 6. Then purify the label reaction liquid.

extract_protocol: Use QIAamp DNA Blood Mini kit to extract genomic DNA. 1. Pipet 20 μl QIAGEN Protease (or proteinase K) into the bottom of a 1.5 ml microcentrifuge tube. 2. Add 200 μl whole blood in 200 μl PBS. Add 4 μl of an RNase A stock solution (100 mg/ml) to the sample. 3. Add 200 μl Buffer AL to the sample. Mix by pulse-vortexing for 15 s. 4. Incubate at 56°C for 10 min. DNA yield reaches a maximum after lysis for 10 min at 56°C. 5. Briefly centrifuge the 1.5 ml microcentrifuge tube to remove drops from the inside of the lid. 6. Add 200 μl ethanol (96–100%) to the sample, and mix again by pulse-vortexing for 15 s. After mixing, briefly centrifuge the 1.5 ml microcentrifuge tube to remove drops from the inside of the lid. 7. Carefully apply the mixture from step 6 to the QIAamp Mini spin column (in a 2 ml collection tube) without wetting the rim. Close the cap, and centrifuge at 6000 x g (8000 rpm) for 1 min. Place the QIAamp Mini spin column in a clean 2 ml collection tube (provided), and discard the tube containing the filtrate. 8. Carefully open the QIAamp Mini spin column and add 500 μl Buffer AW1 without wetting the rim. Close the cap and centrifuge at 6000 x g (8000 rpm) for 1 min. Place the QIAamp Mini spin column in a clean 2 ml collection tube (provided), and discard the collection tube containing the filtrate. 9. Carefully open the QIAamp Mini spin column and add 500 μl Buffer AW2 without wetting the rim. Close the cap and centrifuge at full speed (20,000 x g; 14,000 rpm) for 3 min. 10. Recommended: Place the QIAamp Mini spin column in a new 2 ml collection tube and discard the old collection tube with the filtrate. Centrifuge at full speed for 1 min. 11. Place the QIAamp Mini spin column in a clean 1.5 ml microcentrifuge tube, and discard the collection tube containing the filtrate. Carefully open the QIAamp Mini spin column and add 200 μl Buffer AE or distilled water. Incubate at room temperature (15–25°C) for 1 min, and then centrifuge at 6000 x g (8000 rpm) for 1 min.

tag: gender

value: M

tag: age

tag: survival (days)

tag: tnm

tag: tissue type

value: esophageal tumor

source_name: normal DNA from blood

value: normal blood


title: ESCC-243T

description: Esophageal Cancer Project

value: F


title: ESCC-242T

description: Esophageal Cancer Project


title: ESCC-250T

description: Esophageal Cancer Project


title: BAY-SLE-60-V1 ( 4032149074_A)

description:
BAY-SLE-60-V1
4032149074_A


title: BAY-SLE-171-V1 ( 4032149073_A)

description:
BAY-SLE-171-V1
4032149073_A


title: BAY-H242-V1 ( 4032149086_D)

description:
BAY-H242-V1
4032149086_D


title: BAY-SLE-187-V2 ( 4032149069_A)

description:
BAY-SLE-187-V2
4032149069_A


title: ESCC-240T

description: Esophageal Cancer Project


title: BAY-H217-V1 ( 4032149072_E)

description:
BAY-H217-V1
4032149072_E


title: ESCC-233T

description: Esophageal Cancer Project


title: ESCC-237T

description: Esophageal Cancer Project


title: BAY-SLE-141-V1 ( 4032149072_A)

description:
BAY-SLE-141-V1
4032149072_A


title: BAY-SLE-113-V4 ( 4078729050_D)

description:
BAY-SLE-113-V4
4078729050_D

value: P2 LUPUS - ALR (94) 10Apr08 Run4


title: BAY-SLE-113-V3 ( 4078729050_C)

description:
BAY-SLE-113-V3
4078729050_C


title: BAY-SLE-113-V2 ( 4078729050_B)

description:
BAY-SLE-113-V2
4078729050_B


title: ESCC-219T

description: Esophageal Cancer Project


title: BAY-H260-V1 ( 4078729049_D)

description:
BAY-H260-V1
4078729049_D


title: BAY-H225-V1 ( 4078729050_E)

description:
BAY-H225-V1
4078729050_E


title: BAY-SLE-182-V2 ( 4032149071_E)

description:
BAY-SLE-182-V2
4032149071_E


title: BAY-SLE-171-V5 ( 4078729049_C)

description:
BAY-SLE-171-V5
4078729049_C


title: BAY-SLE-20-V1 ( 4032149071_A)

description:
BAY-SLE-20-V1
4032149071_A


title: BAY-H184-V2 ( 4078729050_F)

description:
BAY-H184-V2
4078729050_F


title: BAY-SLE-175-V6 ( 4078729049_B)

description:
BAY-SLE-175-V6
4078729049_B


title: BAY-H188-V1 ( 4078729048_F)

description:
BAY-H188-V1
4078729048_F


title: BAY-SLE-179-V4 ( 4078729049_A)

description:
BAY-SLE-179-V4
4078729049_A


title: BAY-H249-V1 ( 4078729048_E)

description:
BAY-H249-V1
4078729048_E


title: ESCC-212T

description: Esophageal Cancer Project


title: ESCC-211T

description: Esophageal Cancer Project


title: ESCC-204T

description: Esophageal Cancer Project


title: ESCC-201T

description: Esophageal Cancer Project


title: ESCC-214T

description: Esophageal Cancer Project


title: ESCC-207T

description: Esophageal Cancer Project


title: ESCC-191T

description: Esophageal Cancer Project


title: ESCC-205T

description: Esophageal Cancer Project


title: ESCC-190T

description: Esophageal Cancer Project


title: ESCC-216T

description: Esophageal Cancer Project


title: TH-Bp-I002 ( 1955247028_B)

description:
TH-Bp-I002
1955247028_B


title: ESCC-185T

description: Esophageal Cancer Project


title: ESCC-184T

description: Esophageal Cancer Project


title: ESCC-180T

description: Esophageal Cancer Project


title: ESCC-178T

description: Esophageal Cancer Project


title: BAY-SLE-198-V4 ( 4078729048_C)

description:
BAY-SLE-198-V4
4078729048_C


title: BAY-SLE-189-V10 ( 4078729047_D)

description:
BAY-SLE-189-V10
4078729047_D


title: ESCC-175T

description: Esophageal Cancer Project


title: BAY-SLE-198-V2 ( 4078729048_A)

description:
BAY-SLE-198-V2
4078729048_A


title: BAY-SLE-198-V3 ( 4078729048_B)

description:
BAY-SLE-198-V3
4078729048_B


title: BAY-SLE-198-V5 ( 4078729048_D)

description:
BAY-SLE-198-V5
4078729048_D


title: BAY-SLE-189-V9 ( 4078729047_C)

description:
BAY-SLE-189-V9
4078729047_C


title: BAY-H214-V1 ( 4078729047_E)

description:
BAY-H214-V1
4078729047_E


title: BAY-SLE-189-V1 ( 4078729047_A)

description:
BAY-SLE-189-V1
4078729047_A


title: ESCC-183T

description: Esophageal Cancer Project


title: ESCC-171T

description: Esophageal Cancer Project


title: BAY-H159-V1 ( 4078729041_E)

description:
BAY-H159-V1
4078729041_E


title: ESCC-158T

description: Esophageal Cancer Project


title: ESCC-162T

description: Esophageal Cancer Project


title: BAY-SLE-188-V15 ( 4078729041_B)

description:
BAY-SLE-188-V15
4078729041_B


title: BAY-SLE-215-V2 ( 4078729041_D)

description:
BAY-SLE-215-V2
4078729041_D


title: BAY-SLE-215-V1 ( 4078729041_C)

description:
BAY-SLE-215-V1
4078729041_C


title: BAY-SLE-188-V13 ( 4078729041_A)

description:
BAY-SLE-188-V13
4078729041_A


title: ESCC-159T

description: Esophageal Cancer Project


title: ESCC-155T

description: Esophageal Cancer Project


title: ESCC-154T

description: Esophageal Cancer Project


title: BAY-SLE-188-V9 ( 4078729040_C)

description:
BAY-SLE-188-V9
4078729040_C


title: BAY-SLE-189-V2 ( 4078729047_B)

description:
BAY-SLE-189-V2
4078729047_B


title: BAY-SLE-188-V11 ( 4078729040_E)

description:
BAY-SLE-188-V11
4078729040_E


title: ESCC-153T

description: Esophageal Cancer Project


title: BAY-SLE-188-V12 ( 4078729040_F)

description:
BAY-SLE-188-V12
4078729040_F


title: ESCC-144T

description: Esophageal Cancer Project


title: ESCC-141T

description: Esophageal Cancer Project


title: ESCC-139T

description: Esophageal Cancer Project


title: ESCC-128T

description: Esophageal Cancer Project


title: ESCC-127T

description: Esophageal Cancer Project


title: BAY-SLE-188-V8 ( 4078729040_B)

description:
BAY-SLE-188-V8
4078729040_B


title: ESCC-116T

description: Esophageal Cancer Project


title: BAY-SLE-188-V2 ( 4078729039_B)

description:
BAY-SLE-188-V2
4078729039_B


title: BAY-SLE-188-V6 ( 4078729039_F)

description:
BAY-SLE-188-V6
4078729039_F


title: BAY-SLE-188-V5 ( 4078729039_E)

description:
BAY-SLE-188-V5
4078729039_E


title: ESCC-147T

description: Esophageal Cancer Project


title: BAY-SLE-188-V7 ( 4078729040_A)

description:
BAY-SLE-188-V7
4078729040_A


title: BAY-SLE-188-V4 ( 4078729039_D)

description:
BAY-SLE-188-V4
4078729039_D


title: BAY-SLE-188-V10 ( 4078729040_D)

description:
BAY-SLE-188-V10
4078729040_D


title: BAY-SLE-188-V3 ( 4078729039_C)

description:
BAY-SLE-188-V3
4078729039_C


title: BAY-SLE-188-V1 ( 4078729039_A)

description:
BAY-SLE-188-V1
4078729039_A


title: BAY-SLE-185-V6 ( 4078729038_E)

description:
BAY-SLE-185-V6
4078729038_E


title: BAY-H259-V1 ( 4078729038_F)

description:
BAY-H259-V1
4078729038_F


title: BAY-SLE-185-V1 ( 4078729038_A)

description:
BAY-SLE-185-V1
4078729038_A


title: BAY-SLE-185-V3 ( 4078729038_B)

description:
BAY-SLE-185-V3
4078729038_B


title: BAY-SLE-185-V5 ( 4078729038_D)

description:
BAY-SLE-185-V5
4078729038_D


title: ESCC-129T

description: Esophageal Cancer Project


title: ESCC-112T

description: Esophageal Cancer Project


title: ESCC-100T

description: Esophageal Cancer Project


title: ESCC-098T

description: Esophageal Cancer Project


title: BAY-SLE-185-V4 ( 4078729038_C)

description:
BAY-SLE-185-V4
4078729038_C


title: ESCC-070T

description: Esophageal Cancer Project


title: ESCC-083T

description: Esophageal Cancer Project


title: BAY-SLE-184-V3 ( 4078729037_E)

description:
BAY-SLE-184-V3
4078729037_E


title: BAY-SLE-184-V1 ( 4078729037_D)

description:
BAY-SLE-184-V1
4078729037_D


title: ESCC-069T

description: Esophageal Cancer Project


title: ESCC-060T

description: Esophageal Cancer Project


title: ESCC-107T

description: Esophageal Cancer Project


title: ESCC-057T

description: Esophageal Cancer Project


title: ESCC-059T

description: Esophageal Cancer Project


title: ESCC-078T

description: Esophageal Cancer Project


title: ESCC-249T

description: Esophageal Cancer Project


title: ESCC-038T

description: Esophageal Cancer Project


title: BAY-SLE-172-V6 ( 4078729037_C)

description:
BAY-SLE-172-V6
4078729037_C


title: HCT116 siMYCLo-2-2 Cancer reference kit-1

city: Columbus

first: Taewan

last: Kim

state: OH

institute: The Ohio State University

description:
HCT116 siMYCLo-2-2
nCounter Human Cancer Reference kit

hyb_protocol: Hybridization reactions were performed according to manufacturer's instructions with 5µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 64°C for a minimum of 18 h.

scan_protocol: A high-density scan (600 fields of view) was performed.

data_processing: The analysis of raw data was performed with nSlover Analysis Software provided by NanoString Technologies. The raw data was normalized with GADPH expression.

source_name: Colorectal cancer-derived HCT116 cell line

growth_protocol: Cells were grown in 37 degree humidified incubator with 5% CO2.

extract_protocol: Total RNA samples were prepared using TRIZOL (Invitrogen) in accordance with manufacturer's instruction.

treatment_protocol: Cells were transfected with siRNA (Final concentration: 50nM for HCT116 and 100nM for PC3) by using Lipofectamine RNAiMAX from Invitrogen as the instruction of manufacturer.

tag: cell line

tag: treatment

value: siRNA targeting CARLo-3


title: BAY-SLE-163-V2 ( 4078729033_B)

description:
BAY-SLE-163-V2
4078729033_B


title: HCT116 siMYCLo-2-2 Cancer reference kit-2

value: Colorectal cancer-derived HCT116 cell line


title: BAY-SLE-172-V1 ( 4078729037_A)

description:
BAY-SLE-172-V1
4078729037_A


title: BAY-SLE-163-V1 ( 4078729033_A)

description:
BAY-SLE-163-V1
4078729033_A


title: BAY-H241-V1 ( 4078729033_F)

description:
BAY-H241-V1
4078729033_F


title: BAY-SLE-123-V7 ( 4078729032_C)

description:
BAY-SLE-123-V7
4078729032_C


title: BAY-SLE-163-V5 ( 4078729033_D)

description:
BAY-SLE-163-V5
4078729033_D


title: ESCC-039T

description: Esophageal Cancer Project


title: BAY-SLE-123-V6 ( 4078729032_B)

description:
BAY-SLE-123-V6
4078729032_B


title: BAY-SLE-142-V5 ( 4078729032_F)

description:
BAY-SLE-142-V5
4078729032_F


title: BAY-SLE-142-V4 ( 4078729032_D)

description:
BAY-SLE-142-V4
4078729032_D


title: BAY-SLE-113-V1 ( 4078729050_A)

description:
BAY-SLE-113-V1
4078729050_A


title: Human blood, Control 18

city: Ancona

first: Tiziana

last: Casoli

address: Via Birarelli 8

department: Scientific Technological Area

country: Italy

institute: INRCA

description:
Sample name: C443
Selective amplification of mtDNA

hyb_protocol: The chips were hybridized for 16 h at 49°C, then washed and stained in Fluidics Station 450 according to the suggested protocol.

scan_protocol: Chips were scanned in Affymetrix GeneChip Scanner 3000 7G and data acquisition was performed using the Affymetrix Genechip Command Console (AGCC) software.

data_processing:
Data analysis was carried out with GSEQ 4.1 with “model type” set at diploid to enable the detection of heteroplasmy and “quality score threshold” set at 3 to provide the best base calling accuracy and rate. The other parameters used by the algorithm were No Signal Threshold= 2, Weak Signal Fold Threshold= 20, Large SNR Threshold= 20, Min Fraction of Calls of Samples = 0.5, Trace Threshold = 1, Sequence Profile Threshold = -0.175.
Output files utilized for this study were the SNP View and Probe Intensity Files that provide, for each np, the base calls classified as homoplasmic or heteroplasmic and values of fluorescence intensity of the four bases for both sense and antisense filaments. The quantitative estimates of allelic contribution were used to calculate REA (Ratio of Expected Allele) index which is the log ratio of the signal intensity of the reference allele at any site, as indicated in the RCRS, to the average signal intensity of the other three alleles from the sense and antisense strand.

source_name: blood, Age-matched control

label_protocol: Total DNA was amplified by means of REPLI-g mitochondrial DNA kit (Qiagen) that contains DNA polymerase, buffers, and reagents for the specific amplification of the mitochondrial genome using Multiple Displacement Amplification (MDA). After purification, DNA was quantified  spectrophotometrically  and Genechip Resequencing array kit (Affymetrix) was employed for fragmentation and labeling.

extract_protocol: Total DNA was extracted using a QIAamp DNA blood mini kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol:
Subjects were enrolled from October 2009 to September 2010 at the Geriatrics Operative Unit of INRCA in Fermo (Italy). Patients were diagnosed according to NINCDS-ADRDA criteria for probable AD by means of an extended neuropsychological and functional evaluation, neuroimaging and laboratory tests.
Controls consisted in volunteers and spouses of the patients and were submitted to the same clinic and neuropsychological assessment as the AD group. Each participant underwent blood withdrawal with sodium citrate as anticoagulant.

value: Age-matched control

value: Whole blood

tag: iadl

tag: mmse


title: BAY-SLE-163-V3 ( 4078729033_C)

description:
BAY-SLE-163-V3
4078729033_C


title: BAY-SLE-172-V5 ( 4078729037_B)

description:
BAY-SLE-172-V5
4078729037_B


title: Human blood, Control 17

description:
Sample name: C442
Selective amplification of mtDNA


title: HCT116 siMYCLo-2-2 Cancer reference kit-3


title: BAY-H255-V1 ( 4078729031_E)

description:
BAY-H255-V1
4078729031_E


title: Human blood, Control 15

description:
Sample name: C436
Selective amplification of mtDNA


title: BAY-SLE-123-V5 ( 4078729032_A)

description:
BAY-SLE-123-V5
4078729032_A


title: BAY-H233-V1 ( 4078729031_F)

description:
BAY-H233-V1
4078729031_F


title: Human blood, Control 14

description:
Sample name: C433
Selective amplification of mtDNA


title: Human blood, Control 13

description:
Sample name: C432
Selective amplification of mtDNA


title: BAY-SLE-110-V3 ( 4078729025_E)

description:
BAY-SLE-110-V3
4078729025_E


title: BAY-SLE-121-V3 ( 4078729031_C)

description:
BAY-SLE-121-V3
4078729031_C


title: BAY-SLE-121-V1 ( 4078729031_A)

description:
BAY-SLE-121-V1
4078729031_A


title: BAY-SLE-121-V4 ( 4078729031_D)

description:
BAY-SLE-121-V4
4078729031_D


title: Human blood, Control 12

description:
Sample name: C431
Selective amplification of mtDNA


title: BAY-SLE-99-V4 ( 4078729025_C)

description:
BAY-SLE-99-V4
4078729025_C


title: BAY-SLE-121-V2 ( 4078729031_B)

description:
BAY-SLE-121-V2
4078729031_B


title: BAY-SLE-99-V2 ( 4078729025_B)

description:
BAY-SLE-99-V2
4078729025_B


title: BAY-SLE-99-V1 ( 4078729025_A)

description:
BAY-SLE-99-V1
4078729025_A


title: Human blood, Control 10

description:
Sample name: C429
Selective amplification of mtDNA


title: Human blood, Control 9

description:
Sample name: C428
Selective amplification of mtDNA


title: Human blood, Control 8

description:
Sample name: C427
Selective amplification of mtDNA


title: Human blood, Control 16

description:
Sample name: C438
Selective amplification of mtDNA


title: Human blood, Control 11

description:
Sample name: C430
Selective amplification of mtDNA


title: Human blood, Control 7

description:
Sample name: C426
Selective amplification of mtDNA


title: BAY-SLE-182-V4 ( 4078729020_E)

description:
BAY-SLE-182-V4
4078729020_E


title: BAY-SLE-110-V2 ( 4078729025_D)

description:
BAY-SLE-110-V2
4078729025_D


title: Human blood, Control 6

description:
Sample name: C424
Selective amplification of mtDNA


title: BAY-SLE-95-V6 ( 4078729020_B)

description:
BAY-SLE-95-V6
4078729020_B


title: Human blood, Control 3

description:
Sample name: C421
Selective amplification of mtDNA


title: Human blood, Control 4

description:
Sample name: C422
Selective amplification of mtDNA


title: Human blood, Control 5

description:
Sample name: C423
Selective amplification of mtDNA


title: Human blood, Control 2

description:
Sample name: C418
Selective amplification of mtDNA


title: BAY-SLE-91-V7 ( 4078729015_D)

description:
BAY-SLE-91-V7
4078729015_D


title: BAY-SLE-95-V7 ( 4078729020_C)

description:
BAY-SLE-95-V7
4078729020_C


title: BAY-H231-V1 ( 4078729020_F)

description:
BAY-H231-V1
4078729020_F


title: Human blood, Control 1

description:
Sample name: C413
Selective amplification of mtDNA


title: Human blood, AD 18

description:
Sample name: A28
Selective amplification of mtDNA

source_name: blood, Alzheimer's patient

value: Alzheimer's patient


title: Human blood, AD 14

description:
Sample name: A22
Selective amplification of mtDNA


title: Human blood, AD 17

description:
Sample name: A25
Selective amplification of mtDNA


title: Human blood, AD 15

description:
Sample name: A23
Selective amplification of mtDNA


title: Human blood, AD 16

description:
Sample name: A24
Selective amplification of mtDNA


title: BAY-SLE-80-V9 ( 4078729015_A)

description:
BAY-SLE-80-V9
4078729015_A


title: Human blood, AD 13

description:
Sample name: A20
Selective amplification of mtDNA


title: BAY-H243-V1 ( 4078729015_E)

description:
BAY-H243-V1
4078729015_E


title: Human blood, AD 11

description:
Sample name: A18
Selective amplification of mtDNA


title: Human blood, AD 10

description:
Sample name: A17
Selective amplification of mtDNA


title: Human blood, AD 9

description:
Sample name: A16
Selective amplification of mtDNA


title: BAY-SLE-182-V1 ( 4078729020_D)

description:
BAY-SLE-182-V1
4078729020_D


title: BAY-SLE-80-V1 ( 4078729013_A)

description:
BAY-SLE-80-V1
4078729013_A


title: BAY-SLE-80-V10 ( 4078729015_B)

description:
BAY-SLE-80-V10
4078729015_B


title: BAY-SLE-80-V8 ( 4078729013_F)

description:
BAY-SLE-80-V8
4078729013_F


title: BAY-SLE-80-V5 ( 4078729013_E)

description:
BAY-SLE-80-V5
4078729013_E


title: BAY-SLE-141-V5 ( 4078729033_E)

description:
BAY-SLE-141-V5
4078729033_E


title: BAY-SLE-80-V3 ( 4078729013_C)

description:
BAY-SLE-80-V3
4078729013_C


title: BAY-SLE-80-V4 ( 4078729013_D)

description:
BAY-SLE-80-V4
4078729013_D


title: Human blood, AD 8

description:
Sample name: A15
Selective amplification of mtDNA


title: Human blood, AD 6

description:
Sample name: A12
Selective amplification of mtDNA


title: BAY-SLE-83-V1 ( 4078729012_E)

description:
BAY-SLE-83-V1
4078729012_E


title: BAY-H222-V1 ( 4078729012_F)

description:
BAY-H222-V1
4078729012_F


title: BAY-SLE-80-V2 ( 4078729013_B)

description:
BAY-SLE-80-V2
4078729013_B


title: Human blood, AD 7

description:
Sample name: A14
Selective amplification of mtDNA


title: Human blood, AD 12

description:
Sample name: A19
Selective amplification of mtDNA


title: BAY-SLE-60-V7 ( 4078729012_D)

description:
BAY-SLE-60-V7
4078729012_D


title: UNC-HIV-314-G3W0 ( 4078729060_F)

description:
UNC-HIV-314-G3W0
4078729060_F

value: P23 CHAVI (82) 03Apr08 Acute 9 + Healthy Controls


title: BAY-SLE-20-V4 ( 4078729012_A)

description:
BAY-SLE-20-V4
4078729012_A


title: BAY-SLE-20-V5 ( 4078729012_B)

description:
BAY-SLE-20-V5
4078729012_B


title: Human blood, AD 3

description:
Sample name: A7
Selective amplification of mtDNA


title: BAY-SLE-60-V6 ( 4078729012_C)

description:
BAY-SLE-60-V6
4078729012_C


title: BAY-SLE-91-V1 ( 4078729015_C)

description:
BAY-SLE-91-V1
4078729015_C


title: Human blood, AD 4

description:
Sample name: A8
Selective amplification of mtDNA


title: Human blood, AD 5

description:
Sample name: A9
Selective amplification of mtDNA


title: Human blood, AD 1

description:
Sample name: A5
Selective amplification of mtDNA


title: Human blood, AD 2

description:
Sample name: A6
Selective amplification of mtDNA


title: UNC-HIV-319-G3W8 ( 4078729060_D)

description:
UNC-HIV-319-G3W8
4078729060_D


title: UNC-HIV-059-G3W0 ( 4078729060_B)

description:
UNC-HIV-059-G3W0
4078729060_B


title: UNC-HIV-069-G3W8 ( 4078729060_C)

description:
UNC-HIV-069-G3W8
4078729060_C


title: UNC-HIV-043-G3W0 ( 4078729060_A)

description:
UNC-HIV-043-G3W0
4078729060_A


title: SAJ-HIV-136-G1W0 ( 4111031228_F)

description:
SAJ-HIV-136-G1W0
4111031228_F

value: AHI Enrollment


title: SAJ-HIV-144-G1W2 ( 4111031228_D)

description:
SAJ-HIV-144-G1W2
4111031228_D

value: AHI Week 2


title: SAJ-HIV-139-G1W1 ( 4111031228_E)

description:
SAJ-HIV-139-G1W1
4111031228_E

value: AHI Week 1


title: SAJ-HIV-161-G1W4 ( 4111031228_C)

description:
SAJ-HIV-161-G1W4
4111031228_C

value: AHI Week 4


title: MAL-HIV-189-G3W0 ( 4111031221_E)

description:
MAL-HIV-189-G3W0
4111031221_E


title: MAL-HIV-192-G3W0 ( 4111031240_E)

description:
MAL-HIV-192-G3W0
4111031240_E


title: MAL-HIV-201-G3W8 ( 4111031240_F)

description:
MAL-HIV-201-G3W8
4111031240_F


title: M-treated VSMCs 2

first: S.

middle: Joseph

last: Huang

state: Ohio

department: Ob/Gyn

hyb_protocol: Amplified RNA was hybridized to HumanHT-12 v4 Expression BeadChip using Illumina's Whole-Genome Gene Expression Direct Hybridization Assay Guide. Hybridized samples were washed using same Hybridization Assay Guide and stained with Amersham Cy3-Streptavidin (GE Healthcare PA43001).

scan_protocol: BeadChips were scanned using the Illumina HiScan System.

data_processing: The data were normalised 75th percentile shift and transforming the baseline to the median of all samples with GX 12.6.1 software

source_name: Aorta

label_protocol: Total RNA samples were normalized to 500ng using Thermoscientific Nanodrop concentration readings. Samples were then amplified using Ambion's Illumina TotalPrep RNA Amplification Kit (P/N AMIL1791) following Ambion's protocol. Amplified RNA samples were measured for their concentration using the Thermoscientific Nanodrop and normalized to 750ng.

growth_protocol: VSMCs were cultured in medium 231(M231; Life Technologies) with smooth muscle growth supplement which includes 5% FBS; 2 ng/ml human basic fibroblast growth factor, 0.5 ng/ml human epidermal growth factor, 5 ng/ml heparin, 0.2 µg/ml insulin and 5 µg/ml BSA (Life Technologies) with 100U/ml penicillin, 100 ug/ml streptomycin, 0.25 ug/ml fungizone.

extract_protocol: Total RNA was isolated using Qiagen miRNeasy Mini Kit (Qiagen, Valencia, CA) and RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: VSMCs were treated with or without ETO, M or P for 24 hours.

value: vascular smooth muscle cell

value: pre-menopausal

value: Female


title: ETO-treated VSMCs 3

value: ETO


title: P-treated VSMCs 2

value: P


title: P-treated VSMCs 3


title: MAL-HIV-197-G3W8 ( 4111031221_D)

description:
MAL-HIV-197-G3W8
4111031221_D

value: Healthy


title: MAL-HIV-210-G3W8 ( 4111031240_B)

description:
MAL-HIV-210-G3W8
4111031240_B


title: ETO-treated VSMCs 1


title: M-treated VSMCs 3

value: M


title: Vehicle-treated VSMCs 2


title: MAL-HIV-190-G3W1 ( 4111031221_C)

description:
MAL-HIV-190-G3W1
4111031221_C


title: P-treated VSMCs 1


title: MAL-HIV-188-G3W0 ( 4111031221_B)

description:
MAL-HIV-188-G3W0
4111031221_B


title: Vehicle-treated VSMCs 3


title: SAJ-HIV-323-G1W24 ( 4111031228_A)

description:
SAJ-HIV-323-G1W24
4111031228_A

value: AHI Week 24


title: ETO-treated VSMCs 2


title: SAJ-HIV-154-G1W12 ( 4111031228_B)

description:
SAJ-HIV-154-G1W12
4111031228_B

value: AHI Week 12


title: BAY-SLE-95-V3 ( 4078729020_A)

description:
BAY-SLE-95-V3
4078729020_A

value: SLE

value: P2 LUPUS - ALR (94) 10Apr08 Run4


title: Vehicle-treated VSMCs 1


title: SAJ-HIV-153-G3W0 ( 4111031241_E)

description:
SAJ-HIV-153-G3W0
4111031241_E


title: MAL-HIV-198-G3W0 ( 4111031240_D)

description:
MAL-HIV-198-G3W0
4111031240_D


title: M-treated VSMCs 1


title: SAJ-HIV-164-G3W8 ( 4111031241_D)

description:
SAJ-HIV-164-G3W8
4111031241_D


title: SAJ-HIV-145-G3W0 ( 4111031241_C)

description:
SAJ-HIV-145-G3W0
4111031241_C


title: dARiPS_clone1.4_rep1

city: Bonn

first: Asifiqbal

middle: M

last: Kadari

state: NRW

address: sigmund-freud strasse 25

department: stem cell engineering group

country: Germany

institute: Institute of reconstructive neurobiology, University of Bonn

description:
Replicate 1
9275880059_I

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization from limma package in R

source_name: trans gene free AR1034ZIMA iPS clone 1.4

label_protocol: Biotinylated cRNA were prepared with the Ambion IlluminaTotalPrep96 kit for Illumina arrays.

growth_protocol: Human iPSCs and ESCs were maintained on matrigel-coated dishes in mTeSR1 (STEMCELL Technologies) or PluriSTEM (EMD Millipore) medium. Human iPS colonies were treated with alphazyme (PAA) (1ml/well in 6-well plate) for 5 to 10 minutes to obtain single cells. 100,000 to 200,000 cells were seeded in each well of a 6-well plate having mTeSR1or PluriSTEM medium with 10μM Rock inhibitor, Y27632 (Sigma-Aldrich) to prevent the cell apoptosis

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Human iPSCs were maintained on matrigel-coated dishes in mTeSR1 (STEMCELL Technologies) or PluriSTEM (EMD Millipore) medium. Human iPS colonies were treated with alphazyme (PAA) (1ml/well in 6-well plate) for 5 to 10 minutes to obtain single cells. 100,000 to 200,000 cells were seeded in each well of a 6-well plate having mTeSR1or PluriSTEM medium with 10μM Rock inhibitor, Y27632 (Sigma-Aldrich) to prevent the cell apoptosis. 24 hours later medium was changed to mTeSR1 or PluriSTEM containing 2  μM TAT–Cre. Cells were incubated with TAT-Cre recombinant protein for 5 hours.

tag: cell type

value: iPS cells


title: MAL-HIV-200-G3W0 ( 4111031240_A)

description:
MAL-HIV-200-G3W0
4111031240_A

value: P23 CHAVI (82) 03Apr08 Acute 9 + Healthy Controls


title: WT plus mucin vs minus mucin_Biological Rep 3

city: Merced

first: Clarissa

middle: Jane

last: Nobile

address: 5200 North Lake Rd

department: Molecular and Cell Biology

institute: University of California - Merced

description:
WT plus mucin vs WT minus mucin replicate 3
252016610082_Blk7

hyb_protocol: 0.4 ug Cy3-labelled cDNA and 0.4 ug Cy5-labelled cDNA were hybridized onto custom Agilent 8*15k microarrays (AMADID #020166)

scan_protocol: 4000B Axon Instrument Scanner

data_processing: Arrays were gridded with Gene Pix Pro software version 7, Lowess normalization was performed using a Goulphar script for R

organism: Candida albicans

source_name: WT plus mucin  replicate 3

label_protocol: cDNA was synthesized from 8 ug total RNA using Superscript II Reverse Transcriptase (Invitrogen, 18064-014), according to the manufacturer’s instruction, and using a mixture of 0.5 mM 3:2 aminoally-dUTP (Ambion 8437):dNTPs. cDNA was dye coupled to either Cy3 or Cy5 (GE Healthcare PA23001 or PA25001)

growth_protocol: Log phase in the presence and absence of mucin for 8 hours at 37C using RPMI 1640 (Gibco 31800-089) buffered with 165mM MOPS and supplemented with 0.2% NaHCO3 and 2% glucose with and without 0.5% mucin

extract_protocol: Total RNA extracted using Ambion RiboPure Yeast RNA Kit (AM1926)

tag: source strain background

tag: strain

value: mucin

source_name: WT minus mucin replicate 3

value: no mucin


title: dARiPS_clone1.4_rep2

description:
Replicate 2
9275880059_K


title: Fibroblast_rep1

description:
Replciate 1
9275880059_J

source_name: Human Fibroblast AR1034ZIMA

value: fibroblasts


title: dARiPS_clone1.2_rep1

description:
Replicate 1
9275880059_E

source_name: trans gene free AR1034ZIMA iPS clone 1.2


title: MAL-HIV-187-G3W1 ( 4111031215_E)

description:
MAL-HIV-187-G3W1
4111031215_E


title: dARiPS_clone1.2_rep2

description:
Replicate 2
9275880059_G


title: MAL-HIV-212-G3W8 ( 4111031241_A)

description:
MAL-HIV-212-G3W8
4111031241_A


title: Fibroblast_rep2

description:
Replicate 2
9275880059_L


title: ARiPS_clone1_rep2

description:
Replicate 2
9275880059_C

source_name: AR1034ZIMA loxP-modified iPS clone 1


title: MAL-HIV-221-G1W12 ( 4111031215_F)

description:
MAL-HIV-221-G1W12
4111031215_F


title: HESI3_rep2

description:
Replicate 2
9275880059_D

source_name: Human embryonic stem cell line I3

value: ES cells


title: SAD-HIV-111-G3W8 ( 4111031242_E)

description:
SAD-HIV-111-G3W8
4111031242_E


title: MAL-HIV-206-G1W2 ( 4111031215_C)

description:
MAL-HIV-206-G1W2
4111031215_C

value: AHI Week 2


title: MAL-HIV-209-G1W4 ( 4111031215_D)

description:
MAL-HIV-209-G1W4
4111031215_D

value: AHI Week 4


title: MAL-HIV-205-G1W1 ( 4111031215_B)

description:
MAL-HIV-205-G1W1
4111031215_B

value: AHI Week 1


title: Brain_Hypothalamus_Ultradian_WT_R15

city: Guildford

first: Emma

last: Laing

address: Stag Hill

country: United Kingdom

institute: University of Surrey

hyb_protocol: Labelled cRNA (1.65 μg) was hybridized on a Whole Mouse Genome 4 x 44K oligonucleotide microarray (G4122F, AMADID 014868; Agilent Technologies). Standard manufacturer's instructions for one-colour gene expression hybridization and washing steps were followed. The microarrays were hybridized at 65°C for 17 h in an Agilent hybridization oven with rotisserie at 10 rpm. The microarrays were washed with Agilent Wash Buffer 1, pre-warmed Wash Buffer 2 (37C) and acetonitrile according to the manufacturer’s instructions. The last washing step was performed with Agilent Stabilization and Drying Solution for 30 sec.

scan_protocol: The processed microarrays were scanned using an Agilent Microarray Scanner with a resolution of 5 μm, exploiting the extended dynamic range feature. The two images derived from each slide scanned at 10% and 100% PMT were imported into Agilent Feature Extraction software (Version 10.7.1.1) for image analysis.

data_processing: Expression levels were analyzed using the standard protocol of GeneSpring version 12 (Agilent). Filtering applied per the default detection thresholds of GeneSpring.

organism: Mus musculus

source_name: Ultradian_WT 15

label_protocol: Two hundred ng of total RNA was used to synthesize cRNA lablled with Cy3

growth_protocol: Mouse total brains were collected after in the 17th ultradian cycle, and immediately placed in a RNA stabalizing solution and frozen to -80 degrees Celcius

extract_protocol: RNA extraction from hypothalamus with the RNeasy kit (Qiagen)

treatment_protocol: Tissue blocks of the hypothalamus were dissected and RNA was extracted

tag: tissue

tag: sleep protocol

value: Ultradian light-dark cycle

tag: genotype/variation

value: Wildtype


title: SAD-HIV-243-G3W8 ( 4111031242_C)

description:
SAD-HIV-243-G3W8
4111031242_C

value: Healthy


title: ARiPS_clone1_rep1

description:
Replicate 1
9275880059_A


title: Brain_Hypothalamus_Ultradian_WT_R14

source_name: Ultradian_WT 14


title: Brain_Hypothalamus_Ultradian_WT_R13

source_name: Ultradian_WT 13


title: HESI3_rep1

description:
Replicate 1
9275880059_B


title: MAL-HIV-203-G1W0 ( 4111031215_A)

description:
MAL-HIV-203-G1W0
4111031215_A

source_name: Whole Blood

value: AHI Enrollment


title: SAD-HIV-097-G3W0 ( 4111031242_F)

description:
SAD-HIV-097-G3W0
4111031242_F


title: SAD-HIV-227-G3W0 ( 4111031242_D)

description:
SAD-HIV-227-G3W0
4111031242_D


title: WT plus mucin vs minus mucin_Biological Rep 2

description:
WT plus mucin vs WT minus mucin replicate 2
252016610071_BlkH

source_name: WT plus mucin replicate 2

source_name: WT minus mucin replicate 2


title: SAD-HIV-228-G3W0 ( 4111031242_B)

description:
SAD-HIV-228-G3W0
4111031242_B


title: WT plus mucin vs minus mucin_Biological Rep 1

description:
WT plus mucin vs WT minus mucin replicate 1
252016610071_BlkG

source_name: WT plus mucin replicate 1

source_name: WT minus mucin replicate 1


title: SAD-HIV-229-G3W0 ( 4111031242_A)

description:
SAD-HIV-229-G3W0
4111031242_A


title: MAL-HIV-222-G1W24 ( 4111031209_F)

description:
MAL-HIV-222-G1W24
4111031209_F

value: AHI Week 24


title: UNC-HIV-314-G3W0 ( 4078729078_F)

description:
UNC-HIV-314-G3W0
4078729078_F


title: MAL-HIV-183-G1W1 ( 4111031209_B)

description:
MAL-HIV-183-G1W1
4111031209_B


title: MAL-HIV-193-G1W4 ( 4111031209_E)

description:
MAL-HIV-193-G1W4
4111031209_E


title: Brain_Hypothalamus_Ultradian_WT_R12

source_name: Ultradian_WT 12


title: MAL-HIV-184-G3W0 ( 4111031214_C)

description:
MAL-HIV-184-G3W0
4111031214_C


title: MAL-HIV-186-G1W0 ( 4111031209_A)

description:
MAL-HIV-186-G1W0
4111031209_A


title: MAL-HIV-185-G1W2 ( 4111031209_D)

description:
MAL-HIV-185-G1W2
4111031209_D


title: Brain_Hypothalamus_Ultradian_WT_R11

source_name: Ultradian_WT 11


title: Brain_Hypothalamus_Ultradian_WT_R9

source_name: Ultradian_WT 9


title: UNC-HIV-045-G3W8 ( 4078729074_A)

description:
UNC-HIV-045-G3W8
4078729074_A


title: UNC-HIV-177-G3W0 ( 4078729078_A)

description:
UNC-HIV-177-G3W0
4078729078_A


title: Brain_Hypothalamus_Ultradian_Coach_R7

source_name: Ultradian_Coach 7

value: Coach


title: UNC-HIV-076-G3W0 ( 4078729076_F)

description:
UNC-HIV-076-G3W0
4078729076_F


title: SAD-HIV-231-G3W0 ( 4111031243_A)

description:
SAD-HIV-231-G3W0
4111031243_A


title: UNC-HIV-091-G3W8 ( 4078729077_D)

description:
UNC-HIV-091-G3W8
4078729077_D


title: Brain_Hypothalamus_Ultradian_WT_R8

source_name: Ultradian_WT 8


title: Brain_Hypothalamus_Ultradian_WT_R10

source_name: Ultradian_WT 10


title: UNC-HIV-055-G1W12 ( 4078729073_D)

description:
UNC-HIV-055-G1W12
4078729073_D

value: AHI Week 12


title: Brain_Hypothalamus_Ultradian_Coach_R6

source_name: Ultradian_Coach 6


title: UNC-HIV-068-G1W24 ( 4078729073_E)

description:
UNC-HIV-068-G1W24
4078729073_E


title: Brain_Hypothalamus_Ultradian_Coach_R8

source_name: Ultradian_Coach 8


title: Iliac artery necropsy_no treatment control_rep3

city: Vermillion

first: Kathleen

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

description: Approval for all animal procedures was obtained from the Institutional Animal Care and Use Committee.

hyb_protocol: 10 micrograms of biotinylated cRNA were mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C.

scan_protocol: The slides were scanned in an Axon GenePix 4000B scanner.

data_processing: global median normalization, CodeLink Expression Analysis 4.1.0.4163

organism: Macaca fascicularis

source_name: Iliac artery necropsy_high fat diet_no treatment

label_protocol: Biotinylated cRNA was prepared using the MessageAmp II-Biotin Enhanced Kit from Ambion from 0.275 micrograms total RNA starting material.

extract_protocol: The iliac artery samples were obtained at necropsy.  The artery samples were placed in RNAlater (Ambion) in the surgical suite.  For processing, RNAlater was blotted off and the artery sample was minced with scalpels, and homogenized in TRI reagent (MRC) with a Polytron (Brinkmann).  The samples were centrifuged in the presence of bromochloropropane and sodium acetate.  The RNA-containing upper layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity of total RNA was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

value: Cynomolgus monkey

value: greater than 11 years

value: female

tag: high fat diet

value: 6.5 years

tag: ovariectomized

value: ~4 years

value: iliac artery necropsy

tag: atherosclerotic plaque size pretreatment

tag: atherosclerotic plaque size postreatment

tag: animal id


title: Iliac artery necropsy_no treatment control_rep4

tag: age

tag: gender


title: UNC-HIV-030-G1W2 ( 4078729073_B)

description:
UNC-HIV-030-G1W2
4078729073_B

value: P23 CHAVI (82) 03Apr08 Acute 9 + Healthy Controls


title: Brain_Hypothalamus_Ultradian_Coach_R5

source_name: Ultradian_Coach 5


title: 5C0090T

description: Esophageal Cancer Project

hyb_protocol: The Cy3-labeled test DNA and Cy5-labeled reference DNA were mixed and combined with 2× Hybridization buffer, 10× blocking agent (Agilent), and Human Cot-1 DNA. The hybridization mixture was dispensed to a microarray chip and assembled with an Agilent SureHyb chamber. The assembled slide chamber was placed in the rotator rack in a hybridization oven set to 65°C for 40 hours with suitable rotation.

scan_protocol: Arrays were scanned on a were scanned on an Agilent Microarray Scanner G2565C with 2-μm resolution.

data_processing:
Data were extracted from scanned images using the Feature Extraction software, version 11 (Agilent). The text files were then imported for analysis into Genomic Workbench, lite edition 6.5 (Agilent).
Final vaues are reported as 'log2 (EXP_NORM/REF_NORM)' in linked supplementary files.

source_name: tumor DNA from esophageal

label_protocol: Equal amounts of the test DNA (1 μg or 0.5 μg) and reference DNA (1 μg or 0.5 μg), were digested with AluI and RsaI. The digested test DNA and reference DNA were labeled with cyanine (Cy)5-deoxyuridine triphosphate (dUTP) or Cy3-dUTP, respectively, using the SureTag Complete DNA Labeling Kit (Agilent).

extract_protocol: DNA samples were isolated using a QIAamp DNA Mini Kit according to the manufacturer’s instructions (Qiagen, Germantown, MD).

value: F

tag: survival (days)

tag: tnm

tag: tissue type

value: esophageal tumor

source_name: normal DNA from blood

value: normal blood


title: UNC-HIV-029-G1W0 ( 4078729073_A)

description:
UNC-HIV-029-G1W0
4078729073_A

source_name: Whole Blood


title: 5C0089T

description: Esophageal Cancer Project

value: M


title: UNC-HIV-031-G1W4 ( 4078729073_C)

description:
UNC-HIV-031-G1W4
4078729073_C

value: AHI Week 4


title: Brain_Hypothalamus_Ultradian_Coach_R4

source_name: Ultradian_Coach 4

value: Ultradian light-dark cycle


title: UNC-HIV-020-G1W0 ( 4078729072_F)

description:
UNC-HIV-020-G1W0
4078729072_F

value: AHI Enrollment


title: Iliac artery necropsy_no treatment control_rep2

tag: treatment


title: 5C0088T

description: Esophageal Cancer Project


title: Iliac artery necropsy_no treatment control_rep1


title: Iliac artery necropsy_Equol treatment_rep4

source_name: Iliac artery necropsy_high fat diet_Equol treatment

value: Equol

tag: duration

value: 8 months


title: 5C0087T

description: Esophageal Cancer Project


title: 5C0078T

description: Esophageal Cancer Project


title: Iliac artery necropsy_Equol treatment_rep3


title: Brain_Hypothalamus_Ultradian_Coach_R3

source_name: Ultradian_Coach 3

value: Coach


title: 5C0093T

description: Esophageal Cancer Project


title: UNC-HIV-044-G1W12 ( 4078729072_B)

description:
UNC-HIV-044-G1W12
4078729072_B

value: AHI Week 12


title: UNC-HIV-028-G3W0 ( 4078729070_F)

description:
UNC-HIV-028-G3W0
4078729070_F

value: Healthy


title: Brain_Hypothalamus_Ultradian_Coach_R2

source_name: Ultradian_Coach 2


title: UNC-HIV-027-G1W4 ( 4078729072_C)

description:
UNC-HIV-027-G1W4
4078729072_C


title: Brain_Hypothalamus_Ultradian_Coach_R1

source_name: Ultradian_Coach 1


title: UNC-HIV-065-G1W24 ( 4078729072_A)

description:
UNC-HIV-065-G1W24
4078729072_A

value: AHI Week 24


title: UNC-HIV-012-G1W0 ( 4078729057_E)

description:
UNC-HIV-012-G1W0
4078729057_E


title: 5C0077T

description: Esophageal Cancer Project


title: UNC-HIV-025-G1W1 ( 4078729072_E)

description:
UNC-HIV-025-G1W1
4078729072_E

value: AHI Week 1


title: Iliac artery necropsy_Equol treatment_rep1

value: Cynomolgus monkey

value: greater than 11 years

value: female

value: 6.5 years

value: ~4 years


title: UNC-HIV-026-G1W2 ( 4078729072_D)

description:
UNC-HIV-026-G1W2
4078729072_D

value: AHI Week 2

value: P23 CHAVI (82) 03Apr08 Acute 9 + Healthy Controls


title: MAL-HIV-215-G3W8 ( 4111031241_B)

description:
MAL-HIV-215-G3W8
4111031241_B


title: Brain_Hypothalamus_Ultradian_WT_R7

source_name: Ultradian_WT 7

value: Wildtype


title: 5C0072T

description: Esophageal Cancer Project

value: M

value: esophageal tumor

value: normal blood


title: 5C0074T

description: Esophageal Cancer Project


title: UNC-HIV-021-G1W1 ( 4078729057_C)

description:
UNC-HIV-021-G1W1
4078729057_C


title: Brain_Hypothalamus_Ultradian_WT_R6

source_name: Ultradian_WT 6

value: Ultradian light-dark cycle


title: UNC-HIV-038-G3W8 ( 4078729056_F)

description:
UNC-HIV-038-G3W8
4078729056_F


title: UNC-HIV-062-G1W24 ( 4078729056_E)

description:
UNC-HIV-062-G1W24
4078729056_E


title: Brain_Hypothalamus_Ultradian_WT_R5

source_name: Ultradian_WT 5


title: Iliac artery necropsy_Equol treatment_rep2

value: iliac artery necropsy

value: Equol

value: 8 months


title: UNC-HIV-037-G1W12 ( 4078729056_D)

description:
UNC-HIV-037-G1W12
4078729056_D

value: AHI Week 12


title: UNC-HIV-039-GW12 ( 4078729057_B)

description:
UNC-HIV-039-GW12
4078729057_B


title: 5C0071T

description: Esophageal Cancer Project


title: UNC-HIV-010-G1W4 ( 4078729056_C)

description:
UNC-HIV-010-G1W4
4078729056_C

value: AHI Week 4


title: 5C0070T

description: Esophageal Cancer Project


title: UNC-HIV-063-G1W24 ( 4078729057_A)

description:
UNC-HIV-063-G1W24
4078729057_A

value: AHI Week 24


title: UNC-HIV-009-G1W2 ( 4078729056_B)

description:
UNC-HIV-009-G1W2
4078729056_B


title: 5C0069T

description: Esophageal Cancer Project


title: UNC-HIV-058-G1W24 ( 4078729054_E)

description:
UNC-HIV-058-G1W24
4078729054_E


title: Brain_Hypothalamus_Ultradian_WT_R3

source_name: Ultradian_WT 3


title: Brain_Hypothalamus_Ultradian_WT_R4

source_name: Ultradian_WT 4


title: 5C0065T

description: Esophageal Cancer Project


title: UNC-HIV-011-G3W0 ( 4078729054_D)

description:
UNC-HIV-011-G3W0
4078729054_D

value: Healthy


title: UNC-HIV-036-G1W12 ( 4078729054_C)

description:
UNC-HIV-036-G1W12
4078729054_C


title: Brain_Hypothalamus_Ultradian_WT_R2

source_name: Ultradian_WT 2


title: UNC-HIV-007-G1W4 ( 4078729054_B)

description:
UNC-HIV-007-G1W4
4078729054_B


title: 5C0062T

description: Esophageal Cancer Project


title: UNC-HIV-008-G1W0 ( 4078729056_A)

description:
UNC-HIV-008-G1W0
4078729056_A

value: AHI Enrollment


title: Brain_Hypothalamus_Ultradian_Boxhill_R6

source_name: Ultradian_Boxhill 6

value: Boxhill


title: Brain_Hypothalamus_Ultradian_WT_R1

source_name: Ultradian_WT 1


title: Brain_Hypothalamus_Ultradian_Boxhill_R7

source_name: Ultradian_Boxhill 7


title: Brain_Hypothalamus_Ultradian_Boxhill_R5

source_name: Ultradian_Boxhill 5


title: UNC-HIV-035-G1W24 ( 4078729053_F)

description:
UNC-HIV-035-G1W24
4078729053_F


title: UNC-HIV-003-G1W2 ( 4078729053_C)

description:
UNC-HIV-003-G1W2
4078729053_C


title: UNC-HIV-004-G1W4 ( 4078729053_D)

description:
UNC-HIV-004-G1W4
4078729053_D


title: UNC-HIV-005-G1W12 ( 4078729053_E)

description:
UNC-HIV-005-G1W12
4078729053_E


title: 5C0067T

description: Esophageal Cancer Project

source_name: tumor DNA from esophageal

value: F

source_name: normal DNA from blood


title: UNC-HIV-006-G1W0 ( 4078729054_A)

description:
UNC-HIV-006-G1W0
4078729054_A

source_name: Whole Blood


title: UNC-HIV-002-G1W1 ( 4078729053_B)

description:
UNC-HIV-002-G1W1
4078729053_B

value: AHI Week 1


title: 5C0059T

description: Esophageal Cancer Project


title: 5C0061T

description: Esophageal Cancer Project


title: UNC-HIV-001-G1W0 ( 4078729053_A)

description:
UNC-HIV-001-G1W0
4078729053_A

value: P23 CHAVI (82) 03Apr08 Acute 9 + Healthy Controls


title: BAY-H256-V1 ( 4043631009_F)

description:
BAY-H256-V1
4043631009_F

value: P12 SOJIA-CHILDRENS (86) 01Apr08 ANAJIS 040108


title: Brain_Hypothalamus_Ultradian_Boxhill_R4

source_name: Ultradian_Boxhill 4


title: 5C0043T

description: Esophageal Cancer Project

value: M


title: BAY-H240-V1 ( 4043631008_D)

description:
BAY-H240-V1
4043631008_D


title: 5C0044T

description: Esophageal Cancer Project

value: esophageal tumor


title: Brain_Hypothalamus_Ultradian_Boxhill_R3

source_name: Ultradian_Boxhill 3


title: BAY-H244-V1 ( 4043631007_B)

description:
BAY-H244-V1
4043631007_B


title: FR-SYS23-M6 ( 4038364021_F)

description:
FR-SYS23-M6
4038364021_F

value: SOJIA


title: FR-SYS23-J1 ( 4038364021_D)

description:
FR-SYS23-J1
4038364021_D


title: Brain_Hypothalamus_Ultradian_Boxhill_R1

source_name: Ultradian_Boxhill 1

value: Ultradian light-dark cycle


title: FR-SYS17-J1 ( 4038364019_A)

description:
FR-SYS17-J1
4038364019_A


title: BAY-H228-V1 ( 4038364021_B)

description:
BAY-H228-V1
4038364021_B


title: 5C0040T

description: Esophageal Cancer Project

value: normal blood


title: FR-SYS17-M6 ( 4038364019_C)

description:
FR-SYS17-M6
4038364019_C


title: BAY-H225-V1 ( 4038364019_D)

description:
BAY-H225-V1
4038364019_D


title: Brain_Hypothalamus_WT_R6

growth_protocol: Mouse total brains were collected after 12 hours of sleep deprivation, and immediately placed in a RNA stabalising solution and frozen to -80 degrees Celcius

extract_protocol: RNA extraction from hypothalamus and cortex tissue with the RNeasy kit (Qiagen)

treatment_protocol: Tissue blocks of the hypothalamus and frontal cortex were dissected and RNA was extracted

value: Sleep displacement

value: Wildtype


title: FR-SYS17-M1 ( 4038364019_B)

description:
FR-SYS17-M1
4038364019_B


title: Brain_Hypothalamus_WT_R8


title: 5C0057T

description: Esophageal Cancer Project


title: FR-SYS23-M1 ( 4038364021_E)

description:
FR-SYS23-M1
4038364021_E


title: FR-SYS22-M6 ( 4038364012_D)

description:
FR-SYS22-M6
4038364012_D


title: Brain_Hypothalamus_WT_R7


title: 5C0038T

description: Esophageal Cancer Project


title: 5C0036T

description: Esophageal Cancer Project


title: Brain_Hypothalamus_WT_R5


title: 5C0034T

description: Esophageal Cancer Project


title: 5C0033T

description: Esophageal Cancer Project


title: 5C0045T

description: Esophageal Cancer Project


title: 5C0030T

description: Esophageal Cancer Project


title: BAY-H257-V1 ( 4038364026_E)

description:
BAY-H257-V1
4038364026_E


title: Brain_Hypothalamus_WT_R3


title: BAY-H216-V1 ( 4038364012_A)

description:
BAY-H216-V1
4038364012_A


title: FR-SYS22-J1 ( 4038364012_B)

description:
FR-SYS22-J1
4038364012_B


title: FR-SYS22-M1 ( 4038364012_C)

description:
FR-SYS22-M1
4038364012_C


title: Brain_Hypothalamus_Ultradian_Boxhill_R2

source_name: Ultradian_Boxhill 2


title: BAY-H200-V1 ( 1955116022_D)

description:
BAY-H200-V1
1955116022_D


title: BAY-H184-V2 ( 1930630101_E)

description:
BAY-H184-V2
1930630101_E


title: FR-SYS02-M6 ( 1955116022_C)

description:
FR-SYS02-M6
1955116022_C


title: BAY-H219-V1 ( 4038364016_F)

description:
BAY-H219-V1
4038364016_F


title: FR-SYS13-M6 ( 1930630101_D)

description:
FR-SYS13-M6
1930630101_D


title: FR-SYS13-M1 ( 1930630101_C)

description:
FR-SYS13-M1
1930630101_C


title: BAY-H199-V1 ( 1965120048_D)

description:
BAY-H199-V1
1965120048_D


title: 5C0027T

description: Esophageal Cancer Project


title: FR-SYS10-M6 ( 1965120038_D)

description:
FR-SYS10-M6
1965120038_D


title: FR-SYS02-M1 ( 1955116022_B)

description:
FR-SYS02-M1
1955116022_B


title: Brain_Hypothalamus_WT_R2


title: Brain_Hypothalamus_Coach_R8

value: Coach


title: Brain_Hypothalamus_WT_R4


title: 5C0025T

description: Esophageal Cancer Project


title: Brain_Hypothalamus_Coach_R7


title: 5C0020T

description: Esophageal Cancer Project


title: Brain_Hypothalamus_WT_R1


title: FR-SYS13-J1 ( 1930630101_A)

description:
FR-SYS13-J1
1930630101_A


title: FR-SYS10-J1 ( 1965120038_C)

description:
FR-SYS10-J1
1965120038_C


title: 5C0015T

description: Esophageal Cancer Project


title: FR-SYS10-M1 ( 1965120038_B)

description:
FR-SYS10-M1
1965120038_B


title: FR-SYS02-J1 ( 1955116022_A)

description:
FR-SYS02-J1
1955116022_A


title: Brain_Hypothalamus_Coach_R5


title: 5C0026T

description: Esophageal Cancer Project


title: FR-SYS03-J1 ( 1930630057_A)

description:
FR-SYS03-J1
1930630057_A


title: BAY-H037-V1 ( 1965120038_A)

description:
BAY-H037-V1
1965120038_A


title: BAY-H201-V1 ( 1930630057_D)

description:
BAY-H201-V1
1930630057_D


title: FR-SYS03-M1 ( 1930630057_C)

description:
FR-SYS03-M1
1930630057_C


title: 5C0012T

description: Esophageal Cancer Project


title: 5C0011T

description: Esophageal Cancer Project


title: 5C0013T

description: Esophageal Cancer Project


title: FR-SYS24-M3 ( 1930630041_E)

description:
FR-SYS24-M3
1930630041_E


title: FR-SYS03-M6 ( 1930630057_E)

description:
FR-SYS03-M6
1930630057_E


title: Brain_Hypothalamus_Coach_R2


title: FR-SYS24-M1 ( 1930630041_C)

description:
FR-SYS24-M1
1930630041_C


title: Brain_Hypothalamus_Boxhill_R8


title: 5B0587T

description: Esophageal Cancer Project


title: FR-SYS06-M1 ( 1930630040_E)

description:
FR-SYS06-M1
1930630040_E


title: FR-SYS05-J1 ( 1930630036_D)

description:
FR-SYS05-J1
1930630036_D


title: Brain_Hypothalamus_Coach_R1


title: FR-SYS24-J1 ( 1930630041_A)

description:
FR-SYS24-J1
1930630041_A


title: Brain_Hypothalamus_Coach_R3


title: Brain_Hypothalamus_Coach_R6


title: FR-SYS06-J1 ( 1930630040_C)

description:
FR-SYS06-J1
1930630040_C


title: Brain_Hypothalamus_Coach_R4


title: FR-SYS06-M4 ( 1930630040_B)

description:
FR-SYS06-M4
1930630040_B


title: 5B0586T

description: Esophageal Cancer Project


title: FR-SYS05-M6 ( 1930630036_A)

description:
FR-SYS05-M6
1930630036_A


title: 5B0579T

description: Esophageal Cancer Project


title: 5B0584T

description: Esophageal Cancer Project


title: FR-SYS05-M1 ( 1930630036_B)

description:
FR-SYS05-M1
1930630036_B


title: H192 ( 1930630040_A)

description:
H192
1930630040_A


title: 5B0577T

description: Esophageal Cancer Project


title: 5B0575T

description: Esophageal Cancer Project


title: FR-SYS04-M6 ( 1930630014_E)

description:
FR-SYS04-M6
1930630014_E


title: Brain_Hypothalamus_Boxhill_R6


title: 5B0306T

description: Esophageal Cancer Project


title: BAY-H202-V1 ( 1930630014_B)

description:
BAY-H202-V1
1930630014_B


title: FR-SYS04-J1 ( 1930630014_C)

description:
FR-SYS04-J1
1930630014_C


title: Brain_Hypothalamus_Boxhill_R7


title: FR-SYS08-M6 ( 1930630131_F)

description:
FR-SYS08-M6
1930630131_F


title: BAY-H164-V1 ( 1930630131_C)

description:
BAY-H164-V1
1930630131_C


title: FR-SYS08-M1 ( 1930630131_D)

description:
FR-SYS08-M1
1930630131_D


title: Brain_Hypothalamus_Boxhill_R5


title: 5B0302T

description: Esophageal Cancer Project


title: Brain_Hypothalamus_Boxhill_R3


title: Brain_Frontal_Cortex_WT_R8


title: FR-SYS08-J1 ( 1930630131_B)

description:
FR-SYS08-J1
1930630131_B


title: Caco-2 cells_1.6 µM CYN_24 hr_rep 6

city: Fougères

first: Antoine

last: Huguet

address: 10B rue Claude Bourgelat

country: France

institute: Anses

description: Gene expression after 24hr in 1.6 µM CYN exposed Caco-2 cells

hyb_protocol: For the experiments we used 4 X 44K Whole Human Genome 70-mer oligo-chips (G4112F; Agilent Technologies). Hybridisation of Cyanine-3-labeled cRNA samples was performed onto each microarray for 17 hrs at 65°C with an HSPro4800 hybridisation automatic station (Tecan) and using the Gene Expression Wash Pack kit (Agilent Technologies) and the “Stabilization and Drying Solution” kit (Agilent Technologies) according to the manufacturers’ protocols.

scan_protocol: The absorbance was measured at 532 nm with an Innoscan 900AL scanner (Innopsys, Carbonne, France).

data_processing: Raw data, corresponding to the median pixel intensity for each probe, were extracted with Mapix software, version 5.0. The quality of the extracted raw data was checked for signal homogeneity using the Pearson correlation. A Lowess normalisation was performed on the raw data with R software using the Linear Model for Microarray Data Bioconductor package. A background signal was calculated from the mean of the one hundred lowest values of each sample. Following this, the normalised data were filtered on threshold intensity (3 times the background signal): for each probe, values were selected if the median value for at least one experimental condition was higher than the threshold intensity. This dataset, including the 28 616 post-filtering probes, was labelled “filtered data”.

source_name: Caco-2 cells, 1.6 µM CYN, 24 hour, biological replicate 6

label_protocol: For probe preparation, 200 ng of total RNA were reverse transcribed into double strand cDNA and then amplified and labelled into cRNA with cyanine-3 CTP using the “Low Input QuickAmp Labeling” kit according to the manufacturer’s protocol (Agilent Technologies, Massy, France). Cyanine-3-labeled cRNA was purified using the “RNeasy Mini” kit according to the manufacturer’s instructions (Qiagen, Courtaboeuf, France), cyanine incorporation was monitored with a NanoPhotometer (Implen, Munich, Germany), and cyanine-3-labeled cRNA was fragmented for 30 min at 60°C.

growth_protocol: Caco-2 cells were seeded at 6 x 104 cells/cm2 in 24-well plates and grown in MEM supplemented with 10% fœtal calf serum for 23-25 days. The medium was changed three times a week.

extract_protocol: Following cell treatments, total RNA was isolated using the NucleoSpin® RNA II kit according to the manufacturer’s instructions with a final elution volume of 10 µL of RNase free water (Macherey-Nagel, Hoerd, France). RNA was quantified with the BioSpec-Nano (Shimadzu, Marne la Vallée, France), and RNA integrity was assessed with the “Experion RNA StdSens analysis” kit using the Experion automated electrophoresis system (Bio-Rad, Marnes-la-Coquette, France). Only RNA with an RNA quality indicator ≥ 9 was used for further experiments (Experion software 3.0; Bio-Rad).

treatment_protocol: Differentiated Caco-2 cells were exposed for 24 hrs to 1.6 µM of cylindrospermopsin in medium at 37°C in an atmosphere containing 5% CO2. A vehicle control (sterile water) was also included for each experiment. Six independent experiments were performed.

tag: cell line

value: differentiated Caco-2 cells


title: FR-SYS04-M1 ( 1930630014_A)

description:
FR-SYS04-M1
1930630014_A


title: 5B0304T

description: Esophageal Cancer Project


title: Caco-2 cells_1.6 µM CYN_24 hr_rep 5

source_name: Caco-2 cells, 1.6 µM CYN, 24 hour, biological replicate 5


title: FR-SYS11-M6 ( 1955116001_D)

description:
FR-SYS11-M6
1955116001_D


title: Brain_Hypothalamus_Boxhill_R2


title: Caco-2 cells_1.6 µM CYN_24 hr_rep 4

source_name: Caco-2 cells, 1.6 µM CYN, 24 hour, biological replicate 4


title: 5B0301T

description: Esophageal Cancer Project


title: Brain_Hypothalamus_Boxhill_R4


title: 5B0292T

description: Esophageal Cancer Project


title: 5B0296T

description: Esophageal Cancer Project


title: Caco-2 cells_1.6 µM CYN_24 hr_rep 2

source_name: Caco-2 cells, 1.6 µM CYN, 24 hour, biological replicate 2


title: Brain_Hypothalamus_Boxhill_R1


title: FR-SYS11-M1 ( 1955116001_C)

description:
FR-SYS11-M1
1955116001_C


title: FR-SYS11-J1 ( 1955116001_A)

description:
FR-SYS11-J1
1955116001_A


title: Brain_Frontal_Cortex_WT_R7


title: FR-SYS09-J1 ( 1955116019_E)

description:
FR-SYS09-J1
1955116019_E


title: FR-SYS09-M1 ( 1955116019_C)

description:
FR-SYS09-M1
1955116019_C


title: Brain_Frontal_Cortex_WT_R5


title: Brain_Frontal_Cortex_WT_R6


title: Caco-2 cells_1.6 µM CYN_24 hr_rep 3

source_name: Caco-2 cells, 1.6 µM CYN, 24 hour, biological replicate 3


title: 5B0282T

description: Esophageal Cancer Project


title: Caco-2 cells_0 µM CYN_24 hr_rep 5

description: Gene expression after 24hr in 0 µM CYN exposed Caco-2 cells

source_name: Caco-2 cells, 0 µM CYN, 24 hour, biological replicate 5


title: 5B0280T

description: Esophageal Cancer Project


title: Caco-2 cells_0 µM CYN_24 hr_rep 4

source_name: Caco-2 cells, 0 µM CYN, 24 hour, biological replicate 4


title: 5B0287T

description: Esophageal Cancer Project


title: FR-SYS09-M6 ( 1955116019_A)

description:
FR-SYS09-M6
1955116019_A


title: 5B0283T

description: Esophageal Cancer Project


title: 5B0278T

description: Esophageal Cancer Project


title: Brain_Frontal_Cortex_WT_R3


title: Brain_Frontal_Cortex_WT_R4


title: A549

city: Newark

first: Melissa

middle: B.

last: Rogers

state: NJ

address: 185 south orange ave.

department: Biochem. & Molec. Biology

institute: Rutgers NJMS

data_processing: normalization, quantile

source_name: A549 lung adenocarcinoma cells

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM,D5796, Sigma−Aldrich) supplemented with 5% fetal bovine serum and 2 mM glutamine in 7% CO2 at 37°C.

extract_protocol: RNA enriched for small RNAs was isolated using the mirVana™ miRNA Isolation Kit (Life Technologies).

value: transformed, malignant


title: Brain_Frontal_Cortex_WT_R2


title: Caco-2 cells_0 µM CYN_24 hr_rep 2

source_name: Caco-2 cells, 0 µM CYN, 24 hour, biological replicate 2


title: 5B0276T

description: Esophageal Cancer Project


title: CHL-PID-646 ( 1955116018_F)

description:
CHL-PID-646
1955116018_F


title: Brain_Frontal_Cortex_WT_R1


title: 5B0271T

description: Esophageal Cancer Project


title: BEAS tra2

source_name: mycoplasma transformed BEAS-2B cells, line 2


title: BEAS-2B

source_name: non-transformed BEAS-2B bronchial epithelial cells

value: immortalized


title: BEAS tra1

source_name: mycoplasma transformed BEAS-2B cells, line 1


title: Caco-2 cells_1.6 µM CYN_24 hr_rep 1

source_name: Caco-2 cells, 1.6 µM CYN, 24 hour, biological replicate 1


title: FR-SYS20-J15 ( 1955116018_C)

description:
FR-SYS20-J15
1955116018_C

source_name: Whole Blood


title: 5B0269T

description: Esophageal Cancer Project

source_name: tumor DNA from esophageal

source_name: normal DNA from blood


title: 5B0259T

description: Esophageal Cancer Project


title: Caco-2 cells_0 µM CYN_24 hr_rep 1

source_name: Caco-2 cells, 0 µM CYN, 24 hour, biological replicate 1


title: Brain_Frontal_Cortex_Coach_R8


title: Brain_Frontal_Cortex_Coach_R6


title: FR-SYS12-J1 ( 1955116018_D)

description:
FR-SYS12-J1
1955116018_D


title: FR-SYS12-M1 ( 1955116018_E)

description:
FR-SYS12-M1
1955116018_E


title: FR-SYS20-J1 ( 1955116018_B)

description:
FR-SYS20-J1
1955116018_B


title: CHL-PID-645 ( 1955116017_E)

description:
CHL-PID-645
1955116017_E


title: Brain_Frontal_Cortex_Coach_R7


title: Caco-2 cells_0 µM CYN_24 hr_rep 3

source_name: Caco-2 cells, 0 µM CYN, 24 hour, biological replicate 3


title: 5B0258T

description: Esophageal Cancer Project


title: 5B0257T

description: Esophageal Cancer Project


title: Brain_Frontal_Cortex_Coach_R5


title: 5B0255T

description: Esophageal Cancer Project


title: Brain_Frontal_Cortex_Coach_R3


title: FR-SYS25-M6 ( 1955116017_D)

description:
FR-SYS25-M6
1955116017_D


title: 5B0245T

description: Esophageal Cancer Project


title: FR-SYS25-M1 ( 1955116017_B)

description:
FR-SYS25-M1
1955116017_B


title: 5B0218T

description: Esophageal Cancer Project


title: Brain_Frontal_Cortex_Coach_R4


title: 5B0213T

description: Esophageal Cancer Project


title: 5B0215T

description: Esophageal Cancer Project


title: FR-SYS25-J1 ( 1955116017_A)

description:
FR-SYS25-J1
1955116017_A


title: FR-SYS07-M3 ( 1955116016_D)

description:
FR-SYS07-M3
1955116016_D


title: 5B0203T

description: Esophageal Cancer Project


title: Brain_Frontal_Cortex_Coach_R1


title: FR-SYS07-M1 ( 1955116016_C)

description:
FR-SYS07-M1
1955116016_C


title: Brain_Frontal_Cortex_Coach_R2


title: Brain_Frontal_Cortex_Boxhill_R7


title: BAY-H159-V1 ( 1955116012_E)

description:
BAY-H159-V1
1955116012_E

value: Healthy


title: 5B0200T

description: Esophageal Cancer Project


title: Brain_Frontal_Cortex_Boxhill_R8

value: Boxhill


title: FR-SYS16-M1 ( 1955116012_C)

description:
FR-SYS16-M1
1955116012_C


title: FR-SYS16-M2 ( 1955116012_D)

description:
FR-SYS16-M2
1955116012_D


title: Brain_Frontal_Cortex_Boxhill_R4


title: FR-SYS07-J1 ( 1955116016_A)

description:
FR-SYS07-J1
1955116016_A


title: FR-SYS19-J1 ( 1955116009_F)

description:
FR-SYS19-J1
1955116009_F


title: FR-SYS16-J1 ( 1955116012_B)

description:
FR-SYS16-J1
1955116012_B


title: 5B0194T

description: Esophageal Cancer Project


title: 5B0176T

description: Esophageal Cancer Project


title: Brain_Frontal_Cortex_Boxhill_R5


title: Brain_Frontal_Cortex_Boxhill_R3


title: CCR6+ CD4+ T cells_activated_3day_rep1

city: San Diego

first: Anton

last: Bittner

address: 3210 Merryfield Row

department: Systems Biology

institute: Janssen R&D

description: Memory CD4+ T cells purified from PBMCs through negative selection followed by positive selection with CCR6 biotin and anti-biotin magnetic beads

hyb_protocol: All samples were hybridized in parallel to different arrays on the same HT array plate using the manufacturer's protocol.  Arrays were washed and stained on an Affymetrix GeneTitan instrument.

scan_protocol: Arrays were scanned using an Affymetrix GeneTitan MC scanner.

data_processing: Array Studio was used to perform RMA normalization from CEL files

source_name: CCR6+ CD4+ T cells_activated_3day

label_protocol: Target was prepared from 50ng total RNA using NuGEN Ovation V2 kits, followed by NuGEN Encore biotin labeling module using the manufacturer's protocol.

growth_protocol: Stimulated T cells were cultured in a 24-well tissue culture plate at 5x106 cells/well in 1ml of IMDM medium containing 10% serum replacement factor, 2mM glutamine, 1mM sodium pyruvate, 10mM HEPES, 1mM MEM nonessential amino acid solution, and 100 U/ml each of penicillin G and streptomycin.

extract_protocol: RNA was extracted with a Qiagen RNeasy kit using the manufacturer's protocol.

treatment_protocol: Purified CCR6+ T cells were stimulated with anti-CD3 and anti-CD28 coated beads (Miltenyi) at 2:1 bead/cell ratio in the presence of Th17 polarizing cytokines and antibodies including 10ng/ml IL1b (R&D), 10ng/ml IL23 (R&D), 30ng/ml TGFb1 (R&D), g/ml anti-IL4 and anti-IFN (eBioscience)

tag: stimulation

value: anti-CD3 & anti-CD28 coated beads in the presence of Th17 polarizing cytokines and antibodies


title: 5B0111T

description: Esophageal Cancer Project


title: Brain_Frontal_Cortex_Boxhill_R2

tag: tissue


title: Brain_Frontal_Cortex_Boxhill_R6

tag: sleep protocol


title: Brain_Frontal_Cortex_Boxhill_R1

tag: genotype/variation


title: CCR6+ CD4+ T cells_activated_24hr_rep2

source_name: CCR6+ CD4+ T cells_activated_24hr


title: BAY-H155-V1 ( 1955116009_C)

description:
BAY-H155-V1
1955116009_C


title: CCR6+ CD4+ T cells_activated_3day_rep2


title: FR-SYS21-M6 ( 1955116009_B)

description:
FR-SYS21-M6
1955116009_B


title: Wild type floral yound floral buds, replicate 1

city: Shanghai

first: Pingli

last: Lu

address: 220 Handan Road

department: School of Life Sciences

institute: Fudan University

description: Gene expression data from Arabidopsis wild type young floral buds

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed by using robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) with the R/Bioconductor package affy. and then converted to logarithm base 2.

organism: Arabidopsis thaliana

source_name: Arabidopsis wild type young floral buds

label_protocol: Standard Affymetrix protocol using 500 ng of total RNA

growth_protocol: Seeds were directly sown into pots containing 100g soil mixture of Metro-Mix 360 soil (Sun Gro Horticulture Canada Ltd) and Turface profile greens grade (Profile Products LLC) in 3:2 ratio by volume, with a maximum water-holding capacity of 100g (defined as 100% soil moisture). Seeds were stratified in a cold room for 2 d at 4 ℃ in the dark. After stratification, the pots with seeds were transferred into a Conviron growth chamber (Conviron Inc), which was set at our normal conditions (22 ℃, 16h day/8h night photoperied, ~300 μmol m-2 s-1 photon flux, 60% humidity) until just after flowering (bolting) when some of the plants were subjected to moderate drought stress.

extract_protocol: Total RNA was isolated from unopened flower buds using RNeasy columns following instructions from the manufacturer (Qiagen, Valencia, CA, USA).

value: Unopen flower buds

tag: cultivar

tag: genotype

value: wild type

value: Arabidopsis at day 24 after seed germination


title: FR-SYS21-M1 ( 1955116009_E)

description:
FR-SYS21-M1
1955116009_E

value: P12 SOJIA-CHILDRENS (86) 01Apr08 ANAJIS 040108


title: Wild type floral yound floral buds, replicate 2


title: cdm1 mutant floral young floral buds, replicate 2

description: Gene expression data from Arabidopsis cdm1 mutant young floral buds

source_name: Arabidopsis cdm1 young floral buds

value: cdm1 mutant


title: 5B0150T

description: Esophageal Cancer Project

value: M

value: esophageal tumor


title: 5B0045T

description: Esophageal Cancer Project

value: normal blood


title: CCR6+ CD4+ T cells_activated_24hr_rep1


title: CCR6+ CD4+ T cells_activated_6hr_rep2

source_name: CCR6+ CD4+ T cells_activated_6hr


title: CCR6+ CD4+ T cells_activated_6hr_rep1


title: FR-SYS21-J1 ( 1955116009_A)

description:
FR-SYS21-J1
1955116009_A

value: SOJIA


title: cdm1 mutant floral young floral buds, replicate 1


title: FR-SYS15-M6 ( 1955116008_E)

description:
FR-SYS15-M6
1955116008_E


title: CCR6+ CD4+ T cells_activated_4hr_rep2

source_name: CCR6+ CD4+ T cells_activated_4hr


title: CCR6+ CD4+ T cells_activated_2hr_rep1

source_name: CCR6+ CD4+ T cells_activated_2hr


title: mandible_at_E11.5_M_embryo [miRNA]

city: Tokyo

first: Yuuichi

last: Soeno

address: 1-9-20 Fujimi, Chiyoda-ku

department: Pathology

country: Japan

institute: The Nippon Dental University

description: Gene expression data from 40 embryos

hyb_protocol: 100 ng of total RNA of each sample was hybridized to a 15K Agilent 60-mer oligomicroarray according to the manufacturer's instructions.

scan_protocol: All hybridized microarray slides were scanned by an Agilent scanner (G2505B) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor (R) 2.13. Please note that '0.1' is the default value of non-detected probes on Feature Extraction software (Agilent; http://www.genomics.agilent.com/files/Manual/G4460-90025_FE_User.pdf, p236.)

source_name: Medial region Mandibular arch_E11.5 embryos

label_protocol: RNA sample was labeled with Cyanine-3 (Cy3) dye using miRNA Complete Labeling and Hyb kit.

growth_protocol: Timed-pregnant ICR mice were kept under a 12-h light-dark cycle and were given standard laboratory fodder and water ad libitum.

extract_protocol: Total RNA was extracted from the sample using RNeasy Micro Kit (QIAGEN) according to the manufacturer's instruction.

treatment_protocol: Dams were sacrificed by cervical dislocation and the uteri dissected out were placed in Hanks’ balanced salt solution (HBSS) at 4C. Embryos were rinsed with fresh HBSS to remove amniotic fluid and blood. Mandibular arches were collected from the embryos.

tag: strain

value: ICR

tag: developmental stage

value: Medial region Mandibular arch


title: mandible_at_E10.5_M_embryo [miRNA]

description: Gene expression data from 40 embryos

source_name: Medial region Mandibular arch_E10.5 embryos


title: CCR6+ CD4+ T cells_activated_4hr_rep1


title: BAY-H198-V1 ( 1955116008_D)

description:
BAY-H198-V1
1955116008_D


title: LKO_102412

city: Baltimore

first: Ou

last: Ma

state: MD

address: 1650 Orleans St. RM270

department: Oncology

institute: Postdoctoral Fellow

description: Replicate 2

hyb_protocol: 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed.

scan_protocol: Dried arrays were stored in a dark box until scanned with iScan System.

data_processing: Data were extracted with Gene Expression Module in GenomeStudio Software.

source_name: Mouse Bone Marrow

label_protocol: 500 ng total RNA from each sample was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) as described in the instruction manual.

growth_protocol: Lineage negative bone marrow cells were cultured in IMDM plus 10% FBS and containing 50 ng/mL murine stem cell factor (SCF), 100 ng/mL murine FLT3 ligand (FL), and 10 ng/mL murine thrombopoietin (TPO, Peprotech) for 24 hrs.

extract_protocol: Total RNA was prepared using the NucleoSpin RNA II kit with on-column DNase digestion. RNA quality was confirmed via Nanodrop-1000 spectrometric analysis and via a Bioanalyzer.

treatment_protocol: Cells were transduced with vector or Cebpa shRNA, puromycin selected, and cultured in IMDM plus 10% FBS and containing 10 ng/mL IL3, 10 ng/mL IL6, and 50ng/ml SCF for 2 days.

value: Cebpa knockdown

tag: cell type

value: lineage-negative marrow progenitors


title: Normal_rep.1_020

status: Public on Mar 10 2014

city: Oslo

first: Maria

middle: Moksnes

last: Bjaanæs

address: Ullernchausseen 70

department: Department of genetics

country: Norway

institute: Oslo Universitetssykehus

description: MicroRNA expression in normal lung tissue.

hyb_protocol: 17 ul of labeled miRNA sample using the Agilent's Hyb kit. It was then incubated at 100°C for 5 minutes before transferring to ice water. The samples were hybridized to Agilent-031181 miRNA microarray v.16, 8 x 60 K for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with GE Wash Buffer 1 and 2 (Agilent).

scan_protocol: Slides were scanned after washing using Agilent Microarray Scanner.

data_processing:
The raw data were preprocessed with Agilent's Feature Extraction Software with default parameters (Agilent feature extraction version 10.7.3.1).
Normalization was performed by using the GeneSpring GX Analysis Software v.12.1 (Agilent Technology) by the 90th percentile method. Data were preprocessed by log2 transformation and the values were baseline shifted to the median of all samples.

source_name: Normal

label_protocol: The ligation of Cy3 was done using the Agilent's miRNA Complete Labeling kit using sample input of 300 ng of total RNA. This was done according to the Agilent's MicroRNA protocol.

extract_protocol: The RNA was isolated with standard TRIZOL methods.

treatment_protocol: The tumor tissue and the normal lung tissue were harvested from the surgery and snap frozen in liquid nitrogen and stored at -80°C until RNA isolation.

value: normal lung

tag: Sex

value: male

tag: age

tag: smoking

value: former

tag: Stage

tag: egfr mutation

tag: kras mutation


title: Tumor_rep.1_154

description: MicroRNA expression in lung adenocarcinoma tissue.

source_name: Tumor

value: lung adenocarcinoma

value: female

value: smoker

value: IIa


title: Tumor_rep.1_153

value: IIIa


title: FR-SYS15-J1 ( 1955116008_B)

description:
FR-SYS15-J1
1955116008_B

data_processing: Following background subtraction, the raw signal intensities extracted with Illumina Genome Studio v2010.1 Gene Expression 1.6.0 software were scaled to the mean intensity of the dataset.

source_name: Whole Blood

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions

value: P12 SOJIA-CHILDRENS (86) 01Apr08 ANAJIS 040108


title: FR-SYS15-M1 ( 1955116008_C)

description:
FR-SYS15-M1
1955116008_C


title: CCR6+ CD4+ T cells_activated_2hr_rep2

value: anti-CD3 & anti-CD28 coated beads in the presence of Th17 polarizing cytokines and antibodies


title: B9_102412

description: Replicate 2

tag: treatment

value: control


title: Normal_rep.1_019


title: Tumor_rep.1_152

value: never

value: Ib


title: CCR6+ CD4+ T cells_resting_0hr_rep2

source_name: CCR6+ CD4+ T cells_resting_0hr


title: Tumor_rep.1_150

value: IIb


title: Normal_rep.1_018


title: Tumor_rep.1_151


title: Normal_rep.1_016


title: Normal_rep.1_017


title: Tumor_rep.1_149


title: B9_092612

description: Replicate 1


title: LKO_092612

description: Replicate 1


title: FR-SYS14-M1 ( 1955116007_E)

description:
FR-SYS14-M1
1955116007_E

value: SOJIA


title: Tumor_rep.1_148

value: Ia


title: FR-SYS14-M6 ( 1955116007_A)

description:
FR-SYS14-M6
1955116007_A


title: Normal_rep.1_014


title: Normal_rep.1_015


title: Tumor_rep.1_147


title: Normal_rep.1_013


title: FR-SYS14-J1 ( 1955116007_B)

description:
FR-SYS14-J1
1955116007_B


title: Normal_rep.1_012


title: Tumor_rep.1_142


title: Tumor_rep.1_143


title: Normal_rep.1_011


title: Tumor_rep.1_144


title: Tumor_rep.1_141


title: Tumor_rep.1_140


title: Tumor_rep.1_139


title: Tumor_rep.1_138


title: CCR6+ CD4+ T cells_resting_0hr_rep1


title: Tumor_rep.1_133


title: Tumor_rep.1_135


title: Tumor_rep.1_136


title: Tumor_rep.1_132


title: Tumor_rep.1_137


title: Tumor_rep.1_145


title: Tumor_rep.1_146


title: Normal_rep.1_009


title: Tumor_rep.1_130


title: Tumor_rep.1_134


title: Normal_rep.1_010


title: Tumor_rep.1_129


title: Tumor_rep.1_127


title: Tumor_rep.1_131


title: Tumor_rep.1_126


title: Tumor_rep.1_128


title: Tumor_rep.1_120


title: Tumor_rep.1_122


title: Tumor_rep.1_123


title: Tumor_rep.1_125


title: Tumor_rep.1_121


title: Tumor_rep.1_118


title: Tumor_rep.1_115


title: Tumor_rep.1_116


title: Tumor_rep.1_117


title: Tumor_rep.1_114


title: Tumor_rep.1_113


title: Tumor_rep.1_124


title: Tumor_rep.1_112


title: Tumor_rep.1_105


title: Tumor_rep.1_107


title: Tumor_rep.1_104


title: Tumor_rep.1_103


title: Tumor_rep.1_110


title: Tumor_rep.1_108


title: Tumor_rep.1_111


title: Tumor_rep.1_106


title: Tumor_rep.1_100


title: Tumor_rep.1_099


title: Tumor_rep.1_102


title: Tumor_rep.1_101


title: Tumor_rep.1_098


title: Tumor_rep.1_097


title: Tumor_rep.1_109


title: Normal_rep.1_008


title: Tumor_rep.1_094


title: Tumor_rep.1_093


title: Tumor_rep.1_096


title: Tumor_rep.1_095


title: Tumor_rep.1_092


title: Tumor_rep.1_091


title: Tumor_rep.1_090


title: Tumor_rep.1_089


title: Tumor_rep.1_087


title: Tumor_rep.1_088

value: IV


title: Tumor_rep.1_085


title: Tumor_rep.1_080


title: Tumor_rep.1_083


title: Tumor_rep.1_081


title: Tumor_rep.1_084


title: Tumor_rep.1_079


title: Tumor_rep.1_082


title: Tumor_rep.1_076


title: Tumor_rep.1_077


title: Tumor_rep.1_078


title: Tumor_rep.1_074


title: Tumor_rep.1_086


title: Normal_rep.1_007

value: normal lung


title: Tumor_rep.1_075

value: male


title: Tumor_rep.1_073


title: Tumor_rep.1_072


title: Tumor_rep.1_071

value: former


title: Normal_rep.1_006


title: Tumor_rep.1_070

value: lung adenocarcinoma


title: Tumor_rep.1_062


title: Tumor_rep.1_067

value: female


title: Tumor_rep.1_068

value: smoker


title: Tumor_rep.1_069


title: Tumor_rep.1_061


title: Tumor_rep.1_063


title: Tumor_rep.1_064


title: Tumor_rep.1_066

value: IIa


title: Tumor_rep.1_060


title: Tumor_rep.1_059


title: Tumor_rep.1_058


title: Normal_rep.1_005


title: Tumor_rep.1_065


title: Tumor_rep.1_056


title: Tumor_rep.1_057

value: IIIa


title: Tumor_rep.1_051


title: Tumor_rep.1_050


title: Tumor_rep.1_052


title: Normal_rep.1_004


title: Tumor_rep.1_054


title: Tumor_rep.1_053


title: Tumor_rep.1_055


title: Tumor_rep.1_049


title: Tumor_rep.1_048


title: Tumor_rep.1_047


title: Tumor_rep.1_046


title: Tumor_rep.1_044


title: Tumor_rep.1_043


title: Tumor_rep.1_042


title: Tumor_rep.1_037


title: Tumor_rep.1_034


title: Tumor_rep.1_039


title: Tumor_rep.1_040


title: Tumor_rep.1_045


title: Tumor_rep.1_038


title: Tumor_rep.1_035


title: Normal_rep.1_003


title: Normal_rep.1_002


title: Tumor_rep.1_032


title: Tumor_rep.1_033


title: Tumor_rep.1_030


title: Tumor_rep.1_029


title: Tumor_rep.1_028


title: Tumor_rep.1_031


title: Tumor_rep.1_023


title: Tumor_rep.1_025


title: Tumor_rep.1_022


title: Tumor_rep.1_024


title: Tumor_rep.1_041


title: Tumor_rep.1_021


title: Tumor_rep.1_026


title: Tumor_rep.1_036


title: Tumor_rep.1_020


title: Tumor_rep.1_019


title: Tumor_rep.1_016


title: Tumor_rep.1_017


title: Tumor_rep.1_018


title: Tumor_rep.1_027


title: Tumor_rep.1_012


title: Tumor_rep.1_013


title: Tumor_rep.1_015


title: Tumor_rep.1_014


title: Normal_rep.1_001


title: Tumor_rep.1_009


title: Tumor_rep.1_010


title: Tumor_rep.1_011


title: Tumor_rep.1_004


title: Tumor_rep.1_008


title: Tumor_rep.1_005


title: Tumor_rep.1_007


title: Tumor_rep.1_006


title: Tumor_rep.1_119


title: Tumor_rep.1_001


title: Tumor_rep.1_003


title: Tumor_rep.1_002


title: Ten-week-old chicken liver (ALV-J non-infected / infected) after infected ten weeks, rep1

city: guang-zhou

first: HongMei

state: Guang -dong

address: wu shan

institute: South China Agricultural University

description: DA1 vs. A1

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression). The ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated. Differentially detected signals were those with less than 0.01 p-values.

organism: Gallus gallus

source_name: ALV-J leukemia tumor

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore), and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags (Cy3/Cy5) were used for the two RNA samples in dual-sample experiments.

growth_protocol: One-day-old specific pathogen-free (SPF) White Leghorn female chicks were randomly allocated into two groups (25 chickens per group), housed in biosecurity isolators under quarantine conditions and negative pressure, and provided with water and commercial feed ad libitum.

extract_protocol: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada), following the manufacturer's recommended protocol.

treatment_protocol: One group of one-day-old chickens were inoculated with 0.2 ml ALV-J (NX0101) containing 106.7TCID50 / 0.2ml by the abdominal cavity, while the other group were inoculated with PBS reared as the negative control.

tag: breed

value: white Leghorn

value: 10 weeks

tag: gender

value: liver

tag: disease state

value: clinical nonage tumor

tag: infection

value: subtype J of avian leukosis virus (ALV-J)

tag: infection duration

tag: identifier

source_name: Nomal liver

value: normal


title: Ten-week-old chicken liver (ALV-J non-infected / infected) after infected ten weeks, rep2

description: DA2 vs. A2

tag: tissue


title: Ten-week-old chicken liver (ALV-J non-infected / infected) after infected ten weeks, rep3

description: DA3 vs. A3