title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC09

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 60
Sentrix_ID 4
Sentrix_Position L
BS conversion C1 Grn 651
BS conversion C2 Grn 771
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC09


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC02

status: Public on Mar 30 2013

type: genomic

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

country: United Kingdom

institute: University College London

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 50
Sentrix_ID 4
Sentrix_Position J
BS conversion C1 Grn 584
BS conversion C2 Grn 531
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner settings

data_processing: BeadStudio software v3.2

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA from cervical smear cells LBC02

label_protocol: Standard Illumina Protocol for Infinium 27k Chip

extract_protocol: DNA was extracted from liquid based cytology samples of women using the Qiagen DNeasy Blood and Tissue kit (Qiagen Ltd, UK)

tag: sample type

tag: cytology

value: HPV+ve/Cyto-ve


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC17

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 43
Sentrix_ID 4
Sentrix_Position C
BS conversion C1 Grn 606
BS conversion C2 Grn 565
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC17


title: Sham-GA-1Day-2

type: RNA

city: Bronx

first: christopher

middle: p

last: cardozo

state: NY

address: 130 West Kingsbridge Road

department: CMSCI

country: USA

institute: Bronx VA Medical Center

description: Sample name: 1461

hyb_protocol: according the the manufacturers recommended procedures

data_processing: Preprocessing was performed using the RMA function of the Oligo package for Bioconductor.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: soleus

extract_protocol: Pieces of muscle weighing approximately 20 g were homogenized in Trizol reagent.  Total RNA was then extracted following the manufacturers recommended procedures and further purified on RNAeasy columns (Qiagen) then quantified by absorbance at 260 nm.  RNA integrity numbers were greater than 8.0 for all samples.

tag: strain

value: Wistar

tag: gender

value: Female

tag: spine surgery

tag: electrical stimulation (es)

value: No

tag: gastrocnemius ablation (ga)

value: Sham

tag: time after es/ga (days)

tag: tissue

value: soleus


title: Sham-GA-7Days-1

description: Sample name: 1452

scan_protocol: according the the manufacturers recommended procedures


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC19

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 39
Sentrix_ID 4
Sentrix_Position E
BS conversion C1 Grn 654
BS conversion C2 Grn 887
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC19


title: GA-7Days-1

description: Sample name: 1447

label_protocol: according the the manufacturers recommended procedures

value: Yes


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC26

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 41
Sentrix_ID 4
Sentrix_Position B
BS conversion C1 Grn 703
BS conversion C2 Grn 559
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC26

value: HPV+ve/Cyto+ve


title: Sham-GA-3Days-3

description: Sample name: 1437


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC34

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 38
Sentrix_ID 3
Sentrix_Position L
BS conversion C1 Grn 979
BS conversion C2 Grn 1005
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC34


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC32

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 52
Sentrix_ID 4
Sentrix_Position A
BS conversion C1 Grn 753
BS conversion C2 Grn 768
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC32


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC27

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 36
Sentrix_ID 4
Sentrix_Position D
BS conversion C1 Grn 586
BS conversion C2 Grn 671
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC27


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC28

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 20
Sentrix_ID 3
Sentrix_Position K
BS conversion C1 Grn 944
BS conversion C2 Grn 819
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC28


title: Sham-GA-3Days-2

description: Sample name: 1436


title: SPF 3

city: Toronto

first: Flavia

last: Lakschevitz

state: ON

address: 150 College st room 221

department: Faculty of Dentistry

country: Canada

institute: University of Toronto

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Raw data was pre-processed using lumi R package.  Background correction was done in Genomestudio. The quantile normalization method implemented in lumi R package was used to normalize the data

organism: Mus musculus

source_name: Bone Marrow

label_protocol: Biotinylated cRNA were prepared with the Ambion Amplification kit:  - Illumina TotalPrep-96 RNA Amplification Kit cat# 4393543

extract_protocol: Following neutrophil isolation, total RNA was extracted with mirVANA kit from Ambion, followed by clean-up and DNase I treatment with Ambion kit in accordance with protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: group

value: control

value: male

tag: age

value: 6 - 8 weeks

tag: cell type

value: PMN


title: Sham-GA-3Days-1

description: Sample name: 1435


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC29

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 37
Sentrix_ID 3
Sentrix_Position I
BS conversion C1 Grn 837
BS conversion C2 Grn 1031
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC29


title: Heart_pravastatin_rep4

status: Public on Mar 31 2013

city: Shimotsuke

first: Masafumi

last: Kumazaki

state: Tochigi

address: 3311-1 Yakushiji

department: Pharmacology

country: Japan

institute: Jichi Medical University

hyb_protocol: The fragmented and labeled amplified cDNA was hybridized to a GeneChip Mouse Genome 430 2.0 Array (Affymetrix) for 18 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with Workstation (Affymetrix).

data_processing: The CEL file data were analyzed with Microarray Suite version 5.0 (MAS 5.0) to generate CHP files (represented in Sample tables below). Subsequent data processing involved normalizing to the median expression value of all samples with GeneSpring GX version 11.0 software (Agilent Technologies).

source_name: Mouse heart treated with pravastatin_4

label_protocol: Amplified cDNA was prepared from 100 ng of total RNA using an Ovation RNA Amplification System V2 Kit (NuGEN Technologies) and purified using a PCR purification kit (Qiagen). According to the manufacturer’s instructions, 3.75 µg of purified cDNA was fragmented and labeled using an FL-Ovation cDNA Biotin Module V2 Kit (NuGEN Technologies).

growth_protocol: Male C57BL/6J mice (n = 20) were obtained from Charles River Laboratories Japan (Yokohama, Japan) at six weeks of age and maintained under specific pathogen-free conditions with controlled temperature and humidity and a 12-h light/12-h dark cycle. They were given standard chow (CE-2; CLEA Japan, Tokyo, Japan) and water ad libitum.

extract_protocol: Total RNA was isolated from the left ventricle of each animal using an RNeasy Fibrous Tissue Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: After two weeks of acclimation, the mice were divided into the following five groups: (1) control, (2) 4.5 mg/kg/day pitavastatin calcium (Livalo tablet, Kowa, Nagoya, Japan), (3) 21.0 mg/kg/day pravastatin sodium (Mevalotin tablet, Daiichi-Sankyo, Tokyo, Japan), (4) 10.9 mg/kg/day rosuvastatin calcium (Crestor tablet, Shionogi, Osaka, Japan), and (5) 11.4 mg/kg/day atorvastatin calcium hydrate (Lipitor tablet, Astellas, Tokyo, Japan). Each statin tablet was powdered and given as a food admixture; the doses were calculated on the basis of daily food consumption (0.15 g/gBW). After four weeks, heart samples were obtained from each mouse under diethyl ether anesthesia.

value: left ventricle of heart

tag: agent

value: pravastatin (Mevalotin)


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC24

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 53
Sentrix_ID 3
Sentrix_Position G
BS conversion C1 Grn 956
BS conversion C2 Grn 792
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC24


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC39

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 33
Sentrix_ID 3
Sentrix_Position D
BS conversion C1 Grn 959
BS conversion C2 Grn 780
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC39


title: GA-3Days-2

description: Sample name: 1428


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC16

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 34
Sentrix_ID 3
Sentrix_Position J
BS conversion C1 Grn 562
BS conversion C2 Grn 835
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC16


title: SPF 1

description: replicate 1


title: SPF 2

description: replicate 2


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC10

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 33
Sentrix_ID 3
Sentrix_Position H
BS conversion C1 Grn 1144
BS conversion C2 Grn 1028
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC10


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC11

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 63
Sentrix_ID 3
Sentrix_Position E
BS conversion C1 Grn 807
BS conversion C2 Grn 754
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC11


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC13

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 34
Sentrix_ID 3
Sentrix_Position C
BS conversion C1 Grn 331
BS conversion C2 Grn 589
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC13


title: GA-3Days-3

description: Sample name: 1429


title: GA-3Days-1

description: Sample name: 1427


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC22

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 31
Sentrix_ID 3
Sentrix_Position F
BS conversion C1 Grn 983
BS conversion C2 Grn 1113
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC22


title: GA-1Day-3

description: Sample name: 1426

source_name: soleus


title: GA-1Day-2

description: Sample name: 1425


title: germ-free 3

description: replicate 3

value: germ free


title: germ-free 2

description: replicate 2


title: germ-free 1

description: replicate 1


title: GA-1Day-1

description: Sample name: 1423


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC12

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 25
Sentrix_ID 2
Sentrix_Position K
BS conversion C1 Grn 913
BS conversion C2 Grn 1039
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC12


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC35

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 60
Sentrix_ID 2
Sentrix_Position J
BS conversion C1 Grn 682
BS conversion C2 Grn 686
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC35


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC01

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 33
Sentrix_ID 3
Sentrix_Position A
BS conversion C1 Grn 931
BS conversion C2 Grn 679
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC01


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC43

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 21
Sentrix_ID 3
Sentrix_Position B
BS conversion C1 Grn 963
BS conversion C2 Grn 729
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC43


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC48

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 35
Sentrix_ID 2
Sentrix_Position I
BS conversion C1 Grn 706
BS conversion C2 Grn 530
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC48


title: PC3-ML (Clone 1) Rep2

city: Philadelphia

first: Alessandro

last: Fatatis

state: PA

address: 245 N. 15th Street - MS488

department: Pharmacology and Physiology & Pathology and Laboratory Medicine

institute: Drexel University

description: Gene expression data from PC3-ML (clone 1) cells

hyb_protocol: Aliquots of 15μg of amplified biotinylated RNA were hybridized to HuGene-1_0-st-v1 arrays (Affymetrix).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: GeneSpring software version 11.5 was used to filter and complete the statistical analysis. CEL files were loaded to GeneSpring and probeset summarization was conducted using the RMA 16 algorithm.  For each probe, the median of the log summarized values from all the samples was calculated and subtracted from each sample.

source_name: Prostate Cancer cells

label_protocol: Biotinylated cRNA were prepared according to The Encore™ Biotin Module protocol (NuGen)

growth_protocol: All cell lines were cultured at 37°C and 5% CO2 in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone) and 0.1% gentamicin (Invitrogen).

extract_protocol: Total RNA was purified with Qiagen RNeasy Mini kit according to the manufacturer's instructions

tag: cell line

value: Single-cell progeny of PC3ML cells

tag: bone metastatic potential

value: Bone metastastic


title: PC3-ML (Clone 3) Rep2

description: Gene expression data from PC3-ML(clone 3) cells


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC46

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 26
Sentrix_ID 2
Sentrix_Position L
BS conversion C1 Grn 741
BS conversion C2 Grn 718
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC46


title: Sham-SCI-3

description: Sample name: 1318

value: Laminectomy Only


title: PC3-ML (Clone 3) Rep1


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC14

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 38
Sentrix_ID 2
Sentrix_Position G
BS conversion C1 Grn 1112
BS conversion C2 Grn 1139
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC14

value: HPV+ve/Cyto-ve


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC04

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 21
Sentrix_ID 2
Sentrix_Position H
BS conversion C1 Grn 807
BS conversion C2 Grn 810
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC04


title: Sham-SCI-1

description: Sample name: 1316

value: Wistar

value: Female


title: Sham-SCI-2

description: Sample name: 1317

value: No


title: PC3-ML (Clone 1) Rep1


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC30

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 35
Sentrix_ID 2
Sentrix_Position F
BS conversion C1 Grn 976
BS conversion C2 Grn 767
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC30


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC20

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 36
Sentrix_ID 2
Sentrix_Position C
BS conversion C1 Grn 1206
BS conversion C2 Grn 1004
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC20


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC47

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 35
Sentrix_ID 2
Sentrix_Position E
BS conversion C1 Grn 1056
BS conversion C2 Grn 967
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC47


title: DU-145 (PDGFRα) Rep2

description: Gene expression data fromDU-145 (PDGFRα) cells

value: DU-145 cells with overexpression of PDGFRα

value: non-bone metastatic


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC36

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 34
Sentrix_ID 2
Sentrix_Position D
BS conversion C1 Grn 706
BS conversion C2 Grn 900
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC36

value: HPV+ve/Cyto+ve


title: DU-145 (PDGFRα) Rep1


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC18

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 28
Sentrix_ID 2
Sentrix_Position B
BS conversion C1 Grn 951
BS conversion C2 Grn 696
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC18


title: SCI-Sham_ES-3

description: Sample name: 1314

value: SCI

value: Yes

value: soleus


title: SCI-Sham_ES-2

description: Sample name: 1312


title: SCI-ES-7Days-3

description: Sample name: 1309


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC21

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 45
Sentrix_ID 1
Sentrix_Position K
BS conversion C1 Grn 632
BS conversion C2 Grn 742
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC21


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC08

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 53
Sentrix_ID 2
Sentrix_Position A
BS conversion C1 Grn 807
BS conversion C2 Grn 824
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC08


title: DU-145 Rep2

description: Gene expression data from DU-145 cells


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC41

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 44
Sentrix_ID 1
Sentrix_Position L
BS conversion C1 Grn 1117
BS conversion C2 Grn 938
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC41


title: DU-145 Rep1

description: Gene expression data from DU-145 cells


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC23

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 44
Sentrix_ID 1
Sentrix_Position J
BS conversion C1 Grn 834
BS conversion C2 Grn 614
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC23


title: SCI-ES-7Days-2

description: Sample name: 1305

source_name: soleus


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC05

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 46
Sentrix_ID 1
Sentrix_Position I
BS conversion C1 Grn 742
BS conversion C2 Grn 797
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC05


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC38

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 36
Sentrix_ID 1
Sentrix_Position H
BS conversion C1 Grn 718
BS conversion C2 Grn 974
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC38


title: PC3-N(PDGFRα) Rep1

description: Gene expression data from PC3-N (PDGFRα) cells

value: PC3N cells with overexpression of PDGFRα


title: PC3-N(PDGFRα) Rep2


title: SCI-ES-3Days-2

description: Sample name: 1297


title: SCI-ES-7Days-1

description: Sample name: 1302


title: PC3-N Rep2

description: Gene expression data from PC3-N cells


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC40

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 36
Sentrix_ID 1
Sentrix_Position G
BS conversion C1 Grn 933
BS conversion C2 Grn 936
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC40


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC03

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 33
Sentrix_ID 1
Sentrix_Position F
BS conversion C1 Grn 809
BS conversion C2 Grn 871
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC03


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC37

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 31
Sentrix_ID 1
Sentrix_Position E
BS conversion C1 Grn 841
BS conversion C2 Grn 751
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC37


title: 2-DS_19

city: Chiba

first: Semba

last: Toshihisa

state: Chiba

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

department: Molecular Diagnosis

institute: Graduate School of Medicine, Chiba University

description: Gene expression data from pooled livers (from 3 mice) at 19 weeks

hyb_protocol: Following fragmentation, 19 ug of cRNA were hybridized for 16 hr at 45C on GeneChip®Mouse Genome 430 2.0 Array. GeneChip® Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were  analyzed under the R/Bioconductor environment (http://cran.at.r-project.org) with MBEI (PM only) of package affy.

source_name: livers from mice at 19 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol, one-cycle, from 5ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: FLS and DS mice, aged 12 weeks, were obtained from Aburabi Laboratories, Shionogi Research Laboratories (Shionogi and Co., Ltd, Shiga, Japan). The mice, kept in separate cages to prevent fighting, were housed in an air-conditioned room at 23±3 C and 50±20% relative humidity, with a 12 h light/12 h dark cycle (6:00-18:00 hours). All mice were given a standard pellet diet (CE-2; Clea Japan Inc, Tokyo, Japan), and free access to water.

extract_protocol: Total RNA was extracted from the livers of 3 FLS and 3 DS mice at 19 weeks of age using RNeasy mini kits (QIAGEN Inc., Valencia, CA, USA).

treatment_protocol: After administration of pentobarbital (Nembutal, Abbott Laboratories, Chicago, IL, USA) for euthanizing the animals, saline perfusion was performed to remove organ blood, and the livers were immediately removed, weighed, and sliced; one portion was fixed in a 15% neutral formalin buffer solution, pH 7.4, (Wako Pure Chemicals, Tokyo, Japan) and embedded in paraffin for histological analysis, and the rest were snap frozen in liquid nitrogen and stored at -80 °C for subsequent analysis. All experiments were carried out in accordance with the Animal Experimentation Guidelines of Chiba University.

value: DS

value: liver


title: SCI-ES-3Days-1

description: Sample name: 1291


title: 1-FLS_19

value: FLS


title: SCI-ES-3Days-3

description: Sample name: 1299


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC15

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 63
Sentrix_ID 1
Sentrix_Position D
BS conversion C1 Grn 633
BS conversion C2 Grn 585
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC15


title: PC3-ML Rep2

description: Gene expression data from PC3-ML cells

source_name: Prostate Cancer cells


title: PC3-ML Rep1

description: Gene expression data from PC3-ML cells


title: SCI-ES-1Day-3

description: Sample name: 1285


title: PC3-N Rep1

description: Gene expression data from PC3-N cells


title: CD133-positive tumor-initiating cells

city: Los Angeles

first: Keigo

last: Machida

state: CA

address: 2011 Zonal Ave., HMR503C

department: Molecular Microbiology and Immunology

institute: University of Southern California

description: NANOG positive (TISC) liver tumor-initiating cells.

hyb_protocol: Labeling was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

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

data_processing: The data were analyzed using Partek Genomic Suite (v.6) using the Partek default RMA normalization method.

source_name: CD133-positive liver tumor-initiating cells

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

growth_protocol:
In vitro cultured tumor-initiating cells.
Male mice, weighing 25–30 g, were purchased from Charles River Labs (Wilmington, MA). Cells were maintained as a monolayer culture in DMEM with 10% fetal bovine serum and 1% penicillin (Life Technologies, Inc., Carlsbad, CA) at 37°C in a humidified atmosphere of 5% CO2. Viability of sorted cells was assessed by trypan blue staining.

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

tag: phenotype

value: mesenchmal

tag: passage

value: male


title: 2B4_control_rep1

city: Beijing

first: Weihua

last: Li

address: 38 Xue Yuan Road, Beijing 100191, P. R. China

country: China

institute: Peking University Health Science Center

description: replicate 1

scan_protocol: Standard Illumina scanning protocol

data_processing: The data normalization was performed using average normalization

source_name: 2B4, control

label_protocol: Biotinylated cRNA were generated with the Illumina TotalPrep RNA Amplification Kit  ®  TotalPrep RNA Amplification Kit

growth_protocol: All cells were cultured in RPMI 1640 (GIBCO, Grand Island, NY, USA) supplemented with 10% fetal bovine serum in a humidified atmosphere containing 5% CO2 at 37 °C

extract_protocol: Total RNA was extracted using Trizol reagent.QIAGEN RNeasy mini kit was used to totally eliminate DNA contamination in the total RNA.

treatment_protocol: 2B4 and 1E8 cells were incubated with 100 μM ATP or without ATP (controls) for 6 h or 12 h.

tag: subclone

tag: treatment


title: 2B4_ATP_6h_rep1

description: replicate 1

source_name: 2B4, ATP, 6h

value: ATP for 6 hours


title: SCI-ES-1Day-1

description: Sample name: 1281

tag: strain


title: 2B4_ATP_12h_rep1

description: replicate 1

value: ATP for 12 hours


title: 1E8_ATP_12h_rep1

description: replicate 1


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC25

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 31
Sentrix_ID 1
Sentrix_Position A
BS conversion C1 Grn 852
BS conversion C2 Grn 572
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC25

tag: sample type

tag: cytology


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC07

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 24
Sentrix_ID 1
Sentrix_Position B
BS conversion C1 Grn 1049
BS conversion C2 Grn 665
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC07

value: HPV+ve/Cyto-ve


title: SCI-ES-1Day-2

description: Sample name: 1284

value: Wistar

tag: gender

value: Female

tag: spine surgery

tag: electrical stimulation (es)


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC45

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 30
Sentrix_ID 1
Sentrix_Position C
BS conversion C1 Grn 1109
BS conversion C2 Grn 641
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC45


title: CD133-negative liver cells

description: Control cells.

source_name: CD133-negative control cells

tag: tissue

value: CD133-negative control cells

value: epithelial


title: SCI-Sham_ES-1

description: Sample name: 1279

value: No

tag: gastrocnemius ablation (ga)

tag: time after es/ga (days)


title: 1E8_ATP_6h_rep1

description: replicate 1

source_name: 1E8, ATP, 6h


title: 1E8_control_rep1

description: replicate 1

source_name: 1E8, control


title: HC11_ 2% FBS, NO(EGF), dexamethasone, ovine prolactin_ 72 hours_repx3_2

status: Public on Mar 29 2013

city: Houston

first: Eylem

last: Aydogdu

state: TX

address: 3605 Cullen Blvd SERC Bldg. #545

institute: University of Houston

description: Fully differentiated HC11 cells were acquired after induction of differentiation.Differentiation was induced by the removal of EGF from the medium and lowering of FBS to 2% for 48 hours. Full differentiation was accomplished through the subsequent addition of 100nM dexamethasone and 1ug/mL ovine prolactin for 72 hours.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

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

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between SNK6 and “SNT16” samples using the probe repeats as individual samples. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: mouse mammary stem-like cell differentiation is induced with lowering the FBS( 2%) conc.,removel of EGF from medium and addition of dexamethasone, ovine prolactin, differentiated cell collected after 72 hours.

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (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 Cy3 dye staining.

growth_protocol: HC11 mammary epithelial cells were grown in RPMI 1640 supplemented with 10% FBS, L-glutamine, 5mg/mL insulin, 10ng/mL epidermal growth factor (EGF) and 50mg/mL gentamicin; all cell culture reagents were purchased from Sigma. Proliferating cells were collected under the same conditions. pre-differentiation was induced by the removal of EGF from the medium and lowering of FBS to 2% for 48 hours. Full differentiation was accomplished through the subsequent addition of 100nM dexamethasone and 1ug/mL ovine prolactin for 72 hours.

extract_protocol: Total RNA, including miRNA, was extracted using Trizol precipitation and purified using Qiagen miRNeasy kit followed by an on-column DNase1 digestion (Qiagen, Valencia, CA). Quantitative and qualitative analysis of RNA was performed on the NanoDrop 1000 spectrophotometer (Thermoscientific) and the Agilent 2100 bioanalyzer (Agilent), respectively.

tag: cell type

value: HC11 mammary epithelial cells

tag: differentiation stage

value: mouse mammary, differentiated cells, epithelial


title: HC11_ 10% FBS, 10mg/ml(EGF)_48h_repx3_2

description: HC11 mammary epithelial cells were grown in RPMI 1640 supplemented with 10% FBS, L-glutamine, 5mg/mL insulin, 10ng/mL epidermal growth factor (EGF) and 50mg/mL gentamicin. Proliferating cells were collected under the same conditions after 48h incubation.

source_name: mouse mammary stem-like cell_grown in medium 10% FBS, 10mg/ml(EGF)_proliferating cells collected after 48h

value: mouse mammary, proliferation stage, sten cell-like cells, epithelial


title: Replicate 1

city: Ames

first: Zuo-Wei

last: Wu

state: IA

address: 1113 Veterinary Medicine Bldg

institute: Iowa state university

description:
Biological replicate 1
131

hyb_protocol: The slides were blocked in 50 ml prehybridization buffer (5x SSC, 0.1% SDS, 1% BSA) for an hour. Then equal amount (3ug) Cy dye-labeled cDNA from IA3902 and NCTC11168 was mixed in 65 ul hybridization buffer (40% formamide, 5x SSC, 0.1% SDS, 0.6 ug/uL Salmon Sperm DNA) and applied to blocked slides. The hybridization was perfomed at 42oC for 16-20 hours. Hybed slides were washed in low stringency (2x SSC, 0.1% SDS), medium stringency (0.1x SSC, 0.1% SDS) and high stringency (0.1x SSC) wash buffer for 5 minutes, twice respectively.

scan_protocol: Arrays were scanned at 532-nm (Cy3) and 635-nm (Cy5) wavelengths using a ScanArray3000 scanner (PerkinElmer, Waltham, MA) at a 10µm resolution following the manufacturer's protocol

data_processing: Fluorescence intensities of each spot were extracted using the Imagene 8.0 software (Axon Instruments, Foster City, California). Because the probes of the whole array were disigned for mutiple C. jejuni strains (RM1221, 81-176, 269.97, NCTC11168, CG8421, plasmid pCJ1170) and used as pan-array,  in this study only the probes primarily targeted at NCTC11168 CDS were retained for following analysis.  (i) The backround correction was performed by substracting the local background median value from the signal median value, and the signal for two replicates / probe was averaged; (ii) the fluorescence intensity in each wavelength was log2 transformed and normalized using locally weighted linear regression (lowess) performed by Rcode; (iii) for  genes with more than one probe, only the genes with all the probes showing  the same regulation  trend were kept; (iv) T-test was performed to determine the differentially expressed genes.

organism: Campylobacter jejuni

source_name: hypervirulent clone

label_protocol: 5 µg of total RNA were primed with 2 µl of 3mg/ml random hexamer primer at 70°C for 10 min, then reversed transcribed at 42°C overnight in the presence of 400 U SuperScript III RTase (Invitrogen) and 0.6 ul 25mM laleling mix (2:3 aa-dUTP to dTTP). The purified aminoallyl-labeled cDNA was then dissolved in 4.5 ul 0.1 M sodium carbonate buffer pH 9.3 and incorporated with 4.5ul Cy3 or Cy5 dye.

growth_protocol: C. jejuni cells were incubated for 20hrs on Mueller-Hinton (MH) agar

extract_protocol: Total RNA was extracted using the RNeasy kit from Qiagen following manufacturer's instruction

tag: strain phenotype

value: causing sheep abortion

source_name: non-abortifacient strain

value: Non abortifacient


title: Replicate 3

description:
Biological replicate 3
519


title: Replicate 2

description:
Biological replicate 2
135


title: HC11_ 10% FBS, 10mg/ml(EGF)_48h_repx3_1

value: mouse mammary, proliferation stage, stem cell-like cells, epithelial


title: HC11_ 2% FBS, NO(EGF), dexamethasone, ovine prolactin_ 72 hours_repx3_1


title: GT1_2

first: daniel

last: beiting

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

description: Toxoplasma

data_processing: The data were quantile normalized without background subtraction using Illumina GenomeStudio V1.8

source_name: Toxoplasma infected (GT1)

label_protocol: Biotin labeled complementary RNA (cRNA) was made using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: HFF cells were cultured to confluency in T25 flasks in DMEM media supplemented with 10% iron-fortified calf serum, antibiotics, and L-glutamine

extract_protocol: Cells were lysed by treatement with Buffer RLT (Qiagen) and passage over QiaShredder columns (Qiagen).  Total RNA was isolated using the Qiagen Rneasy Plus kit.

treatment_protocol: RNA was immediately isolated from the cells approximately 12 prior to parasite egress and host cell lysis.

tag: cell line

value: HFF line BJ-5ta

value: fibroblast

tag: infection

value: Toxoplasma (GT1)


title: Pru_3

description: Toxoplasma

source_name: Toxoplasma infected (Prugniaud)

value: Toxoplasma (Prugniaud)


title: VEG_3

description: Toxoplasma

source_name: Toxoplasma infected (VEG)

value: Toxoplasma (VEG)


title: GT1_1

description: Toxoplasma


title: VEG_1

description: Toxoplasma


title: Pru_2

description: Toxoplasma


title: VEG_2

description: Toxoplasma


title: NcLiv_2

description: Neospora

source_name: Neospora infected (NcLiv)

value: Neospora (NcLiv)


title: Pru_1

description: Toxoplasma


title: NcLiv_1

description: Neospora


title: uninf_2

description: uninfected

source_name: uninfected

value: uninfected


title: person2297_1sttrimester_euthymic_tempus

city: Munich

first: Divya

last: Mehta

country: Germany

institute: MPI

description: Sample name: 206

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Microarray expression analysis was performed in R, using beadarray (providing routines to handle Illumina BeadStudio data) , limma (for statistical routines) and vsn (for normalization) packages. Raw microarray scan files were exported using the Illumina Beadstudio program and loaded into R for downstream analysis. The data were transformed and normalized using the variance stabilizing normalization method. Of the probes present on the Human HT-12v4, a total of 15456 probes passing the filter criteria of Illumina probe detection p-value of < 0.01 in at least 10% of the samples were used for subsequent analysis.

source_name: whole blood

label_protocol: biotin

extract_protocol: RNA was isolated from peripheral blood collected in Tempus RNA tubes (Applied Biosystems, Darmstadt, Germany) at all three investigated time points for each woman in the discovery sample as well as during the third trimester only for the replication sample. RNA was isolated using the Versagene kit (Gentra Systems, Minneapolis, U.S.A.), quantified using the Nanophotometer and quality checks were performed on the Agilent Bioanalyzer.

value: peripheral blood

tag: individual

value: person 2297

tag: time

value: 1st trimester

tag: condition

value: euthymic


title: person2291_postpartum_euthymic_tempus

description: Sample name: 205

tag: treatment

value: person 2291

value: postpartum


title: person2297_3rdtrimester_euthymic_tempus

description: Sample name: 207

value: 3rd trimester


title: person2298_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 209

value: person 2298

value: always depressed


title: uninf_1

description: uninfected


title: person2298_postpartum_alwaysdepressed_tempus

description: Sample name: 210


title: uninf_3

description: uninfected


title: NB_E_645

city: Heidelberg

first: Thomas

last: Wolf

address: Im Neuenheimer Feld 580

institute: DKFZ

hyb_protocol: Hybridization was performed following the manufacturer's protocol. In brief, 1650 ng of Cy3-labeled cRNA was hybridized on 4x44K custom microarrays using Agilent's High-RPM Gene Expression Hyb Kit. Hybridization was performed for 17 hours at 65°C in a rotating hyb oven at 10 rpm according the company's recommendations.

scan_protocol: After washing and scanning, resulting TIFF-images were processed using Agilent's Feature Extraction software Version 9.5.1.

data_processing: Data normalization using the quantile algorithm, Reference: G. K. Smyth. Limma: linear models for microarray data. In: R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.) Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York, 2005. pp. 397-420.

source_name: tumor sample

label_protocol: Labeling was performed according to Agilent's recommentdations. In brief, 1µg total of tumor RNA was linearily amplified and labeled with Cy3 using Agilent's one-color Quick Amp Labeling Kit following the instructions of the protocol.

extract_protocol: 30-60mg of snap-frozen neuroblastoma specimen was cryo-sliced and were homogenized in TRIzol reagent (Invitrogen, Karlsruhe, Germany) using the FastPrep FP120 cell disruptor (Qbiogene, Inc, Carlsbad, CA, USA).Total RNA was isolated following the TRIzol protocol (Invitrogen) and RNA integrity was assessed using the 2100 Bioanalyzer (Agilent, Waldbronn, Germany). Only samples with an RNA Integrity Number >7.5 were taken for further analysis.

treatment_protocol: All neuroblastoma samples of this set were obtained prior to any cytotoxic treatment and were snap-frozen immediately after surgery. Prior to RNA extraction tumor cell content was checked by a pathologist and only samples with >60% tumor content were processed further.

value: Neuroblastoma

tag: Sex

value: F

tag: mycn (1

value: not amplified; Amp:amplified; n.a.:not available):1

tag: Stage

tag: age (1

value: <18 months; 2:>18 months):1


title: NB_E_646

value: <18 months; 2:>18 months):2


title: person2291_1sttrimester_euthymic_tempus

description: Sample name: 203


title: NB_E_647

value: M

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: NB_E_644


title: NB_E_648


title: NB_E_649


title: person2291_3rdtrimester_euthymic_tempus

description: Sample name: 204


title: person2297_postpartum_euthymic_tempus

description: Sample name: 208


title: person2242_postpartum_alwaysdepressed_tempus

description: Sample name: 202

value: person 2242


title: NB_E_643


title: person2242_1sttrimester_alwaysdepressed_tempus

description: Sample name: 200

value: peripheral blood


title: NB_E_642


title: person2242_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 201


title: person2155_postpartum_euthymic_tempus

description: Sample name: 197

value: person 2155


title: person2155_preconception_euthymic_tempus

description: Sample name: 194

value: preconception


title: person2031_1sttrimester_PPD_tempus

description: Sample name: 193

value: person 2031

value: 1st trimester

value: PPD


title: person2221_3rdtrimester_euthymic_tempus

description: Sample name: 198

value: person 2221

value: 3rd trimester

value: euthymic


title: person2155_1sttrimester_euthymic_tempus

description: Sample name: 195


title: person2221_postpartum_euthymic_tempus

description: Sample name: 199

value: postpartum


title: person2031_3rdtrimester_PPD_tempus

description: Sample name: 190


title: person2125_postpartum_alwaysdepressed_tempus

description: Sample name: 189

value: person 2125

value: always depressed


title: NB_E_641

value: Neuroblastoma

value: F


title: NB_E_640

value: not amplified; Amp:amplified; n.a.:not available):1

value: <18 months; 2:>18 months):1


title: NB_E_639


title: NB_E_638

value: M


title: person2155_3rdtrimester_euthymic_tempus

description: Sample name: 196

value: peripheral blood


title: person2031_preconception_PPD_tempus

description: Sample name: 192


title: person2125_2ndtrimester_alwaysdepressed_tempus

description: Sample name: 187

value: 2nd trimester


title: NB_E_635

value: not amplified; Amp:amplified; n.a.:not available):Amp

value: <18 months; 2:>18 months):2


title: NB_E_632


title: person2125_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 188


title: person2031_postpartum_PPD_tempus

description: Sample name: 191

value: person 2031


title: person2122_postpartum_alwaysdepressed_tempus

description: Sample name: 186

value: person 2122


title: NB_E_633


title: NB_E_630


title: NB_E_631


title: NB_E_634


title: NB_E_629


title: NB_E_637


title: person2122_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 185


title: NB_E_627


title: NB_E_636


title: person2122_1sttrimester_alwaysdepressed_tempus

description: Sample name: 184

value: 1st trimester


title: NB_E_628


title: person2061_1sttrimester_control_tempus

description: Sample name: 181

value: person 2061

value: control


title: person2061_3rdtrimester_control_tempus

description: Sample name: 182

value: 3rd trimester


title: person1833_1sttrimester_euthymic_tempus

description: Sample name: 179

value: person 1833

value: euthymic


title: person1833_3rdtrimester_euthymic_tempus

description: Sample name: 180


title: person1872_1sttrimester_euthymic_tempus

description: Sample name: 176

value: person 1872


title: NB_E_623

value: Neuroblastoma


title: NB_E_626

value: F


title: person2061_postpartum_control_tempus

description: Sample name: 183

value: postpartum


title: NB_E_622

value: M

value: not amplified; Amp:amplified; n.a.:not available):1

value: <18 months; 2:>18 months):1


title: person1872_3rdtrimester_euthymic_tempus

description: Sample name: 177

value: peripheral blood


title: NB_E_624

value: <18 months; 2:>18 months):2


title: person1872_postpartum_euthymic_tempus

description: Sample name: 178


title: NB_E_625


title: NB_E_621


title: NB_E_619


title: NB_E_618


title: person1923_postpartum_alwaysdepressed_tempus

description: Sample name: 173

value: person 1923

value: always depressed


title: person1840_1sttrimester_alwaysdepressed_tempus

description: Sample name: 172

value: person 1840

value: 1st trimester


title: NB_E_620


title: person1840_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 174


title: NB_E_617


title: person1840_preconception_alwaysdepressed_tempus

description: Sample name: 171

value: preconception


title: NB_E_615


title: person1840_postpartum_alwaysdepressed_tempus

description: Sample name: 175


title: NB_E_613


title: person1814_1sttrimester_euthymic_tempus

description: Sample name: 170

value: person 1814


title: NB_E_614

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: NB_E_616


title: NB_E_612


title: person1729_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 166

value: person 1729

value: 3rd trimester


title: NB_E_610

value: Neuroblastoma


title: person1704_3rdtrimester_PPD_tempus

description: Sample name: 161

value: person 1704

value: PPD


title: person1923_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 165


title: person1814_3rdtrimester_euthymic_tempus

description: Sample name: 168

value: euthymic


title: NB_E_611

value: not amplified; Amp:amplified; n.a.:not available):1


title: NB_E_607

value: M


title: NB_E_608

value: F

value: <18 months; 2:>18 months):1


title: person1704_1sttrimester_PPD_tempus

description: Sample name: 160

value: peripheral blood


title: NB_E_609


title: NB_E_606


title: NB_E_604

value: <18 months; 2:>18 months):2


title: NB_E_603

value: not amplified; Amp:amplified; n.a.:not available):n.a.


title: person1729_preconception_alwaysdepressed_tempus

description: Sample name: 163

value: always depressed


title: person1353_postpartum_control_tempus

description: Sample name: 159

value: person 1353

value: postpartum

value: control


title: person1729_1sttrimester_alwaysdepressed_tempus

description: Sample name: 164

value: person 1729

value: 1st trimester


title: person1353_preconception_control_tempus

description: Sample name: 157

value: preconception


title: person1704_postpartum_PPD_tempus

description: Sample name: 162

value: person 1704


title: NB_E_602

value: Neuroblastoma

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: NB_E_605

value: not amplified; Amp:amplified; n.a.:not available):1


title: NB_E_599


title: NB_E_600

value: M


title: NB_E_601

value: F


title: NB_E_597

value: <18 months; 2:>18 months):1


title: NB_E_598


title: person1923_1sttrimester_alwaysdepressed_tempus

description: Sample name: 156

value: peripheral blood

value: person 1923


title: person1212_3rdtrimester_euthymic_tempus

description: Sample name: 154

value: person 1212

value: 3rd trimester

value: euthymic


title: person1212_postpartum_euthymic_tempus

description: Sample name: 155

value: postpartum


title: person1353_3rdtrimester_control_tempus

description: Sample name: 158

value: person 1353

value: control


title: person1212_1sttrimester_euthymic_tempus

description: Sample name: 153

value: 1st trimester


title: person2042_postpartum_PPD_tempus

description: Sample name: 150

value: person 2042

value: PPD


title: NB_E_595

value: Neuroblastoma


title: person1132_postpartum_euthymic_tempus

description: Sample name: 152

value: person 1132


title: NB_E_596

value: not amplified; Amp:amplified; n.a.:not available):1


title: person1515_postpartum_PPD_tempus

description: Sample name: 149

value: person 1515


title: person3438_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 144

value: person 3438

value: always depressed


title: person3438_1sttrimester_alwaysdepressed_tempus

description: Sample name: 143

value: peripheral blood


title: person2042_3rdtrimester_PPD_tempus

description: Sample name: 146


title: person3438_postpartum_alwaysdepressed_tempus

description: Sample name: 145


title: NB_E_590

value: M

value: <18 months; 2:>18 months):1


title: person1132_3rdtrimester_euthymic_tempus

description: Sample name: 151

value: 3rd trimester


title: person1515_1sttrimester_PPD_tempus

description: Sample name: 147


title: NB_E_593

value: F


title: NB_E_589

value: not amplified; Amp:amplified; n.a.:not available):Amp

value: <18 months; 2:>18 months):2


title: person3208_postpartum_control_tempus

description: Sample name: 142

value: person 3208

value: postpartum

value: control


title: NB_E_592


title: NB_E_587


title: person3208_3rdtrimester_control_tempus

description: Sample name: 141


title: NB_E_586


title: person1515_3rdtrimester_PPD_tempus

description: Sample name: 148

value: PPD


title: person3381_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 139

value: person 3381


title: person3287_postpartum_control_tempus

description: Sample name: 137

value: person 3287


title: NB_E_588

value: Neuroblastoma

value: not amplified; Amp:amplified; n.a.:not available):1


title: person3381_1sttrimester_alwaysdepressed_tempus

description: Sample name: 138

value: 1st trimester


title: person3262_postpartum_euthymic_tempus

description: Sample name: 135

value: person 3262

value: euthymic


title: NB_E_594


title: NB_E_582


title: NB_E_591


title: NB_E_583


title: person3381_postpartum_alwaysdepressed_tempus

description: Sample name: 140

value: peripheral blood

value: always depressed


title: person3287_3rdtrimester_control_tempus

description: Sample name: 136

value: 3rd trimester


title: NB_E_584

value: M

value: <18 months; 2:>18 months):1


title: NB_E_585

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: NB_E_581

value: F

value: <18 months; 2:>18 months):2


title: NB_E_579


title: person3262_3rdtrimester_euthymic_tempus

description: Sample name: 134


title: NB_E_577


title: NB_E_580


title: person3262_1sttrimester_euthymic_tempus

description: Sample name: 133


title: NB_E_578


title: NB_E_576


title: NB_E_575


title: person3242_postpartum_alwaysdepressed_tempus

description: Sample name: 132

value: person 3242

value: postpartum


title: person3240_2ndtrimester_control_tempus

description: Sample name: 126

value: person 3240

value: 2nd trimester

value: control


title: person3242_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 130


title: NB_E_574

value: Neuroblastoma

value: not amplified; Amp:amplified; n.a.:not available):1


title: person2042_1sttrimester_PPD_tempus

description: Sample name: 131

value: person 2042

value: 1st trimester

value: PPD


title: person3240_3rdtrimester_control_tempus

description: Sample name: 127

value: peripheral blood


title: person3160_postpartum_euthymic_tempus

description: Sample name: 123

value: person 3160

value: euthymic


title: person3240_postpartum_control_tempus

description: Sample name: 128


title: person2037_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 122

value: person 2037

value: 3rd trimester

value: always depressed


title: person3242_1sttrimester_alwaysdepressed_tempus

description: Sample name: 129


title: NB_E_568

value: M

value: <18 months; 2:>18 months):1


title: NB_E_565


title: NB_E_573

value: F

value: <18 months; 2:>18 months):2


title: NB_E_566


title: person2042_preconception_PPD_tempus

description: Sample name: 125

value: preconception


title: person3160_3rdtrimester_euthymic_tempus

description: Sample name: 124


title: NB_E_563


title: NB_E_564


title: NB_E_571


title: NB_E_572


title: NB_E_567


title: NB_E_570


title: person3100_3rdtrimester_PPD_tempus

description: Sample name: 120

value: person 3100


title: NB_E_562

value: Neuroblastoma


title: person3100_1sttrimester_PPD_tempus

description: Sample name: 119


title: NB_E_569

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: NB_E_561


title: person1729_postpartum_alwaysdepressed_tempus

description: Sample name: 167

value: person 1729

value: postpartum


title: person3100_postpartum_PPD_tempus

description: Sample name: 121

value: PPD


title: person2904_postpartum_euthymic_tempus

description: Sample name: 117

value: peripheral blood

value: person 2904


title: person1990_1sttrimester_PPD_tempus

description: Sample name: 118

value: person 1990

value: 1st trimester


title: person2904_3rdtrimester_euthymic_tempus

description: Sample name: 116

value: 3rd trimester

value: euthymic


title: person3059_1sttrimester_euthymic_tempus

description: Sample name: 113

value: person 3059


title: NB_E_559

value: M

value: not amplified; Amp:amplified; n.a.:not available):1


title: NB_E_560

value: <18 months; 2:>18 months):2


title: person3059_postpartum_euthymic_tempus

description: Sample name: 110


title: person2037_postpartum_alwaysdepressed_tempus

description: Sample name: 112

value: person 2037

value: always depressed


title: person2904_1sttrimester_euthymic_tempus

description: Sample name: 115


title: person3059_3rdtrimester_euthymic_tempus

description: Sample name: 114


title: person3044_1sttrimester_euthymic_tempus

description: Sample name: 108

value: person 3044


title: person3059_preconception_euthymic_tempus

description: Sample name: 111

value: preconception


title: NB_E_554

value: Neuroblastoma


title: NB_E_555


title: NB_E_553


title: NB_E_551

value: F

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: NB_E_552


title: person3044_preconception_euthymic_tempus

description: Sample name: 107

value: peripheral blood


title: NB_E_550


title: person2887_3rdtrimester_PPD_tempus

description: Sample name: 104

value: person 2887

value: PPD


title: NB_E_556


title: NB_E_557


title: NB_E_549

value: <18 months; 2:>18 months):1


title: NB_E_558


title: NB_E_548


title: NB_E_547


title: person2887_postpartum_PPD_tempus

description: Sample name: 105

value: postpartum


title: person3044_3rdtrimester_euthymic_tempus

description: Sample name: 109

value: 3rd trimester

value: euthymic


title: person2887_1sttrimester_PPD_tempus

description: Sample name: 103

value: 1st trimester


title: person3044_postpartum_euthymic_tempus

description: Sample name: 106


title: person3010_postpartum_alwaysdepressed_tempus

description: Sample name: 101

value: person 3010


title: person3010_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 100


title: person2037_1sttrimester_alwaysdepressed_tempus

description: Sample name: 99


title: person2887_preconception_PPD_tempus

description: Sample name: 102


title: NB_E_544

value: M

value: not amplified; Amp:amplified; n.a.:not available):1


title: NB_E_546

value: <18 months; 2:>18 months):2


title: person3010_2ndtrimester_alwaysdepressed_tempus

description: Sample name: 98

value: 2nd trimester

value: always depressed


title: NB_E_543

value: Neuroblastoma


title: NB_E_545


title: NB_E_541

value: F


title: NB_E_542

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: person2975_preconception_euthymic_tempus

description: Sample name: 96

value: peripheral blood

value: person 2975

value: preconception


title: person2975_1sttrimester_euthymic_tempus

description: Sample name: 97


title: person2975_postpartum_euthymic_tempus

description: Sample name: 95


title: person2975_3rdtrimester_euthymic_tempus

description: Sample name: 94


title: NB_E_539


title: NB_E_540


title: NB_E_537

value: <18 months; 2:>18 months):1


title: NB_E_538


title: person2955_preconception_PPD_tempus

description: Sample name: 92

value: person 2955

value: PPD


title: person2955_1sttrimester_PPD_tempus

description: Sample name: 93


title: NB_E_536


title: NB_E_533


title: NB_E_535


title: NB_E_534


title: person1952_postpartum_euthymic_tempus

description: Sample name: 90

value: person 1952

value: postpartum

value: euthymic


title: person2955_3rdtrimester_PPD_tempus

description: Sample name: 89

value: 3rd trimester


title: person2955_postpartum_PPD_tempus

description: Sample name: 91


title: person2942_preconception_euthymic_tempus

description: Sample name: 87

value: person 2942


title: person2942_1sttrimester_euthymic_tempus

description: Sample name: 88

value: 1st trimester


title: NB_E_530

value: not amplified; Amp:amplified; n.a.:not available):1


title: person2907_preconception_euthymic_tempus

description: Sample name: 81

value: person 2907


title: person2907_postpartum_euthymic_tempus

description: Sample name: 82


title: person2942_3rdtrimester_euthymic_tempus

description: Sample name: 85


title: person2849_postpartum_alwaysdepressed_tempus

description: Sample name: 80

value: person 2849

value: always depressed


title: person2907_3rdtrimester_euthymic_tempus

description: Sample name: 84


title: person1814_postpartum_euthymic_tempus

description: Sample name: 169

value: person 1814


title: person1952_3rdtrimester_euthymic_tempus

description: Sample name: 83

value: peripheral blood


title: person2942_postpartum_euthymic_tempus

description: Sample name: 86


title: NB_E_532

value: Neuroblastoma


title: NB_E_523

value: <18 months; 2:>18 months):2


title: NB_E_524


title: NB_E_529


title: NB_E_531


title: person2849_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 79


title: NB_E_526


title: NB_E_525

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: NB_E_521

value: M


title: person2849_1sttrimester_alwaysdepressed_tempus

description: Sample name: 78


title: person2901_postpartum_PPD_tempus

description: Sample name: 77

value: person 2901

value: PPD


title: person2901_3rdtrimester_PPD_tempus

description: Sample name: 76


title: NB_E_528

value: <18 months; 2:>18 months):1


title: NB_E_520


title: NB_E_522


title: NB_E_518


title: NB_E_519

value: F


title: person2901_1sttrimester_PPD_tempus

description: Sample name: 75


title: NB_E_517


title: person2901_preconception_PPD_tempus

description: Sample name: 74

value: preconception


title: NB_E_516


title: person2693_postpartum_euthymic_tempus

description: Sample name: 73

value: person 2693

value: postpartum

value: euthymic


title: person2777_postpartum_PPD_tempus

description: Sample name: 68

value: person 2777


title: person2777_1sttrimester_PPD_tempus

description: Sample name: 66

value: 1st trimester


title: person2777_3rdtrimester_PPD_tempus

description: Sample name: 67

value: 3rd trimester


title: NB_E_515


title: NB_E_513

value: not amplified; Amp:amplified; n.a.:not available):1


title: NB_E_512


title: person2693_3rdtrimester_euthymic_tempus

description: Sample name: 72

value: peripheral blood


title: person2693_preconception_euthymic_tempus

description: Sample name: 70


title: person1952_1sttrimester_euthymic_tempus

description: Sample name: 69

value: person 1952


title: NB_E_514

value: Neuroblastoma

value: <18 months; 2:>18 months):2


title: person2776_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 62

value: person 2776

value: always depressed


title: person2693_1sttrimester_euthymic_tempus

description: Sample name: 71


title: person2776_1sttrimester_alwaysdepressed_tempus

description: Sample name: 65


title: person2776_postpartum_alwaysdepressed_tempus

description: Sample name: 63


title: NB_E_506

value: M


title: NB_E_504

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: NB_E_502


title: person2775_1sttrimester_euthymic_tempus

description: Sample name: 61

value: person 2775


title: NB_E_510

value: F


title: NB_E_511


title: NB_E_507


title: NB_E_508

value: <18 months; 2:>18 months):1


title: NB_E_509


title: NB_E_505


title: NB_E_527


title: person2775_3rdtrimester_euthymic_tempus

description: Sample name: 59


title: NB_E_503


title: person2774_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 57

value: person 2774


title: NB_E_499


title: person2774_postpartum_alwaysdepressed_tempus

description: Sample name: 58

value: postpartum


title: person2763_postpartum_PPD_tempus

description: Sample name: 56

value: person 2763

value: PPD


title: person1990_postpartum_PPD_tempus

description: Sample name: 53

value: person 1990


title: person2775_postpartum_euthymic_tempus

description: Sample name: 60

value: euthymic


title: NB_E_500


title: NB_E_501

value: not amplified; Amp:amplified; n.a.:not available):1


title: person2776_preconception_alwaysdepressed_tempus

description: Sample name: 64

value: peripheral blood

value: preconception


title: NB_E_498

value: Neuroblastoma

value: <18 months; 2:>18 months):2


title: person2763_3rdtrimesterNA_tempus

description: Sample name: 55

value: 3rd trimester


title: NB_E_496

value: M


title: person2018_preconception_alwaysdepressed_tempus

description: Sample name: 51

value: person 2018

value: always depressed


title: person2763_1sttrimesterNA_tempus

description: Sample name: 54

value: 1st trimester


title: person2018_postpartum_alwaysdepressed_tempus

description: Sample name: 50


title: NB_E_495

value: <18 months; 2:>18 months):1


title: NB_E_494


title: person2018_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 49


title: person2699_1sttrimester_PPD_tempus

description: Sample name: 48

value: person 2699


title: NB_E_492

value: F


title: NB_E_493


title: NB_E_490


title: person2699_postpartum_PPD_tempus

description: Sample name: 47

value: postpartum


title: NB_E_491


title: person2018_1sttrimester_alwaysdepressed_tempus

description: Sample name: 52


title: NB_E_488

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: NB_E_489


title: person2699_preconception_PPD_tempus

description: Sample name: 45

value: PPD


title: person2694_postpartum_PPD_tempus

description: Sample name: 44

value: person 2694


title: person2699_3rdtrimester_PPD_tempus

description: Sample name: 46


title: person2651_postpartum_euthymic_tempus

description: Sample name: 41

value: person 2651

value: euthymic


title: person2694_1sttrimester_PPD_tempus

description: Sample name: 42

value: peripheral blood


title: NB_E_487

value: Neuroblastoma

value: not amplified; Amp:amplified; n.a.:not available):1


title: person2694_3rdtrimester_PPD_tempus

description: Sample name: 43

value: 3rd trimester


title: NB_E_484

value: M


title: NB_E_486


title: person2651_3rdtrimester_euthymic_tempus

description: Sample name: 40


title: person2645_postpartum_euthymic_tempus

description: Sample name: 38

value: person 2645


title: NB_E_482


title: person2645_3rdtrimester_euthymic_tempus

description: Sample name: 37


title: NB_E_481

value: <18 months; 2:>18 months):2


title: NB_E_478


title: NB_E_479


title: NB_E_485


title: NB_E_480


title: person2595_preconception_euthymic_tempus

description: Sample name: 33

value: person 2595

value: preconception


title: NB_E_483

value: <18 months; 2:>18 months):1


title: person2595_1sttrimester_euthymic_tempus

description: Sample name: 34

value: 1st trimester


title: person2595_3rdtrimester_euthymic_tempus

description: Sample name: 35


title: NB_E_477


title: person2511_postpartum_euthymic_tempus

description: Sample name: 32

value: person 2511

value: postpartum


title: NB_E_476

value: not amplified; Amp:amplified; n.a.:not available):n.a.


title: person2651_1sttrimester_euthymic_tempus

description: Sample name: 39


title: person2595_postpartum_euthymic_tempus

description: Sample name: 36


title: person2511_1sttrimester_euthymic_tempus

description: Sample name: 30


title: person2511_3rdtrimester_euthymic_tempus

description: Sample name: 31


title: NB_E_473

value: F


title: NB_E_470


title: NB_E_474


title: NB_E_472


title: NB_E_471


title: NB_E_475

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: person2496_preconception_PPD_tempus

description: Sample name: 25

value: person 2496

value: PPD


title: person2496_1sttrimester_PPD_tempus

description: Sample name: 26

value: peripheral blood


title: person2500_postpartum_alwaysdepressed_tempus

description: Sample name: 29

value: person 2500

value: always depressed


title: NB_E_467

value: Neuroblastoma

value: M

value: not amplified; Amp:amplified; n.a.:not available):1


title: person2495_postpartum_PPD_tempus

description: Sample name: 22

value: person 2495


title: person2496_postpartum_PPD_tempus

description: Sample name: 24


title: NB_E_469


title: NB_E_463


title: NB_E_465


title: NB_E_462


title: NB_E_468


title: NB_E_464


title: person2500_1sttrimester_alwaysdepressed_tempus

description: Sample name: 27


title: person2476_postpartum_PPD_tempus

description: Sample name: 18

value: person 2476


title: person2467_postpartum_euthymic_tempus

description: Sample name: 16

value: person 2467

value: euthymic


title: person2467_3rdtrimester_euthymic_tempus

description: Sample name: 15

value: 3rd trimester


title: NB_E_466

value: <18 months; 2:>18 months):1


title: person2495_3rdtrimester_PPD_tempus

description: Sample name: 21


title: person2496_3rdtrimester_PPD_tempus

description: Sample name: 23


title: person2476_1sttrimester_PPD_tempus

description: Sample name: 19

value: 1st trimester


title: person2467_1sttrimester_euthymic_tempus

description: Sample name: 14


title: person2456_postpartum_alwaysdepressed_tempus

description: Sample name: 13

value: person 2456

value: postpartum


title: NB_E_460


title: NB_E_461


title: person2476_3rdtrimester_PPD_tempus

description: Sample name: 17


title: person2495_1sttrimester_PPD_tempus

description: Sample name: 20


title: person2500_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 28


title: NB_E_458


title: NB_E_454

value: F


title: person2456_3rdtrimester_alwaysdepressed_tempus

description: Sample name: 12


title: NB_E_457

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: NB_E_456

value: <18 months; 2:>18 months):2


title: NB_E_455


title: NB_E_459


title: person2444_postpartum_euthymic_tempus

description: Sample name: 10

value: peripheral blood

value: person 2444


title: person2456_1sttrimester_alwaysdepressed_tempus

description: Sample name: 11

value: always depressed


title: person2444_3rdtrimester_euthymic_tempus

description: Sample name: 9


title: person1851_postpartum_euthymic_tempus

description: Sample name: 3

value: person 1851


title: person1851_3rdtrimester_euthymic_tempus

description: Sample name: 2


title: person2443_1sttrimester_euthymic_tempus

description: Sample name: 5

value: person 2443


title: person2443_3rdtrimester_euthymic_tempus

description: Sample name: 6


title: person2443_postpartum_euthymic_tempus

description: Sample name: 7


title: NB_E_448

value: Neuroblastoma

value: M

value: not amplified; Amp:amplified; n.a.:not available):1


title: NB_E_445


title: person2444_preconception_euthymic_tempus

description: Sample name: 8

value: preconception

value: euthymic


title: person1990_3rdtrimester_PPD_tempus

description: Sample name: 1

value: person 1990

value: 3rd trimester

value: PPD


title: NB_E_450

value: <18 months; 2:>18 months):1


title: NB_E_451

value: F


title: NB_E_447


title: NB_E_497


title: NB_E_453


title: NB_E_452


title: person1851_1sttrimester_euthymic_tempus

description: Sample name: 4

value: 1st trimester


title: NB_E_444


title: NB_E_449

value: <18 months; 2:>18 months):2


title: NB_E_443


title: NB_E_446


title: NB_E_440


title: NB_E_439


title: NB_E_441


title: T98G-190, rep1

city: Boston

first: christine

middle: elaine

last: briggs

state: MA

address: 736 Cambridge Street

department: Center for Cancer Systems Biology

institute: christine briggs

description:
5753685166_J
Replicate 1 of 2.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were log2 transformed in R. For the fold-change analysis (performed in R with limma-Bioconductor), quantile normalization was performed on each 'source' independently because these 2 experiments involve different cell types and were run on different arrays and analyzed independently.

source_name: T98G (human glioblastoma), miR190

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: Cells were grown in tissue culture as previously described (Naumov et al. JNCI 2006).

extract_protocol: Cells were harvested and RNA was extracted as previously described (Almog et al. Cancer Research 2009). Briefly, total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer's protocol. RNA integrity and concentration were determined using RNA 6000 Nano Lab on Chip kits and Agilent 2100 Bioanalyzer (Agilent, CA).

treatment_protocol: No treatments were done. Instead, cells were infected with a viral vector carrying either GFP (control) or miR190.

value: glioblastoma

tag: overexpressing


title: NB_E_438

tag: tissue


title: NB_E_442


title: T98G-190, rep2

description:
5753685166_K
Replicate 2 of 2.


title: KHOS-GFP, rep2

description:
5975000016_D
Replicate 2 of 2.

source_name: KHOS (human osteosarcoma), GFP control

value: KHOS

value: osteosarcoma

value: GFP


title: T98G-GFP, rep2

description:
5753685166_I
Replicate 2 of 2.

source_name: T98G (human glioblastoma), GFP control


title: T98G-GFP, rep1

description:
5753685166_H
Replicate 1 of 2.


title: NB_E_437

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: NB_E_436

value: Neuroblastoma


title: KHOS-190, rep2

description:
5975000016_B
Replicate 2 of 2.

source_name: KHOS (human osteosarcoma), miR190


title: NB_E_435

value: M


title: NB_E_430

value: not amplified; Amp:amplified; n.a.:not available):1


title: NB_E_434


title: NB_E_432


title: NB_E_429


title: NB_E_426


title: NB_E_427


title: NB_E_420


title: KHOS-GFP, rep1

description:
5975000016_C
Replicate 1 of 2.


title: NB_E_433


title: KHOS-190, rep1

description:
5975000016_A
Replicate 1 of 2.


title: NB_E_423


title: NB_E_428


title: NB_E_419


title: NB_E_416


title: NB_E_425


title: NB_E_431


title: NB_E_422


title: NB_E_424


title: NB_E_421


title: NB_E_418


title: NB_E_414


title: NB_E_411


title: NB_E_417


title: NB_E_415


title: NB_E_412


title: NB_E_409


title: NB_E_410


title: NB_E_413


title: NB_E_408


title: NB_E_407


title: NB_E_406


title: NB_E_405


title: NB_E_398


title: NB_E_395


title: NB_E_402


title: NB_E_401


title: HepG2 RAW Dec 16, 2011 rep2

city: Sapporo

first: Hiroe

last: Hara-Yamamura

state: Hokkaido

address: Kita 13-jo, Nishi 8-chome

department: Graduate School of Engineering

institute: Hokkaido University

hyb_protocol: Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.

scan_protocol: After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).

data_processing: For microarray analysis, probe-level data in CEL files were normalized by MAS5 using AGCC and transferred to the Subio Platform ver. 1.15 (Subio, Inc., Tokyo, Japan).

source_name: human hepatoma cell line, HepG2

label_protocol: Target preparation were carried out as described in the manufacturer’s instruction.

growth_protocol: Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.

extract_protocol: Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: Prior to exposure, 36 mL filtered water was combined with 4 mL of ×10 concentrated MEM, and supplemented with 1% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Finally, pH was adjusted to 7.2-7.5 by adding 7.5% sodium hydrogen carbonate solution. Cells were seeded onto culture vessels in 105 cell/mL and incubated overnight to grow 40-50% confluent. The normal culture medium was replaced by the prepared water samples and incubated for 48 h.

tag: cell bank no

value: male

tag: age of sampling

value: 15 years

tag: tissue derived

value: liver

tag: case history

value: hepatocyte carcinoma

tag: life span

value: infinite

tag: classification

value: transformed

tag: treatments

value: exposed to raw wastewater

tag: sample preparation

value: pre-filtered and mixed with concentrated culture medium

tag: sampling date


title: HepG2 RAW Dec 16, 2011 rep1

tag: cell line


title: NB_E_404

value: F

value: <18 months; 2:>18 months):1


title: NB_E_389

value: <18 months; 2:>18 months):2


title: HepG2 control Dec 16, 2011 rep1

value: exposed to MQ water


title: NB_E_388


title: NB_E_397


title: NB_E_400


title: NB_E_391


title: NB_E_403


title: HepG2 S-MBR B Dec 16, 2011 rep2

value: exposed to effluent from submerged membrane bioreactor (S-MBR) with higher sludge conc, 8,000 mg/L


title: NB_E_392


title: NB_E_394

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: NB_E_386

value: Neuroblastoma


title: NB_E_396

value: M


title: NB_E_385


title: NB_E_393

value: not amplified; Amp:amplified; n.a.:not available):1


title: HepG2 control Dec 16, 2011 rep2

value: male


title: NB_E_399


title: NB_E_390


title: NB_E_387


title: HepG2 S-MBR B Dec 16, 2011 rep1

value: 15 years


title: HepG2 S-MBR A Dec 16, 2011 rep1

value: liver

value: exposed to effluent from submerged membrane bioreactor (S-MBR) with lower sludge conc, 1,000 mg/L


title: NB_E_383


title: HepG2 AS Oct 16, 2011 rep2

value: hepatocyte carcinoma

value: infinite

value: exposed to effluent from activated sludge process (AS)


title: HepG2 S-MBR A Dec 16, 2011 rep2

value: transformed

value: pre-filtered and mixed with concentrated culture medium


title: NB_E_382

value: F

value: <18 months; 2:>18 months):1


title: NB_E_379

value: <18 months; 2:>18 months):2


title: HepG2 AS-MBR Oct 16, 2011 rep2

value: exposed to effluent from air-sparged side-stream membrane bioreactor (AS-MBR)


title: NB_E_380


title: NB_E_384


title: HepG2 AS-MBR Oct 16, 2011 rep1


title: NB_E_376


title: HepG2 AS Oct 16, 2011 rep1


title: NB_E_378


title: NB_E_381


title: HepG2 control Oct 16, 2011 rep1

value: exposed to MQ water


title: NB_E_374

value: Neuroblastoma


title: NB_E_375

value: M


title: NB_E_372

value: not amplified; Amp:amplified; n.a.:not available):Amp


title: NB_E_373

value: not amplified; Amp:amplified; n.a.:not available):1


title: NB_E_377


title: Normal#4 (RNA)

first: Takahiro

last: Kogawa

address: 1515 Holcomb Blvd

department: Breast Medical

institute: MD Anderson

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes according to the manufacturer's instructions. On completion of the fragmentation reaction, 100 µl of fragmentation mixture were hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100%, XDR Lo 10%).

data_processing: Extract tif images using the Feature Extraction software FE9.5 by GE1-v5_95 protocols.  Normalization was performed using global-normalization methods. Two technical replicates were integrated with mean.

source_name: normal breast , specimen

label_protocol: RNA samples were labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RNeasy micro kit (Qiagen; Valencia, CA, USA), and quality was characterized with BioAnalyzer (Agilent Technologies; Waldbronn, Germany).

treatment_protocol: For tumor samples, 5–20 frozen sections of biopsy (16 μm thick) were manually microdissected. Under the guidance of a pathologist, normal tissue was removed leaving tumor cells comprising greater than 90% of the specimen. For normal breast samples, 40–60 frozen sections of surgical specimen (16 μm thick) were subjected for microdissection manually.

tag: sample type

value: Normal

tag: er


title: NB_E_371

tag: Sex

tag: mycn (1


title: Normal#5 (RNA)

description: Two technical replicates were integrated with mean.


title: Normal#3 (RNA)


title: Normal#2 (RNA)


title: NB_E_370

tag: Stage

tag: age (1


title: NB_E_369

tag: tissue


title: NB_E_368


title: lytically induced rKSHV.219-infected inducible SLK

city: Emeryville

first: Henry

middle: H

last: Chang

address: 4560 Horton Street

department: Infectious Diseases Group

institute: Novartis Institutes for BioMedical Research

description:
lytic iSLK.219
All samples in Experiment 3 were processed in parallel, visualized on the same microarray on the same day, and the resulting microarray data was analyzed as one collective data set.

hyb_protocol: Samples were hybridized to the custom tiling microarrays according the manufacturer’s protocol (Agilent). Hybridized microarrays were washed according to the manufacturer’s protocol (Agilent).

scan_protocol: Microarrays were scanned on the GenePix 4000B scanner (Axon instruments) and all feature intensities collected using the GenePix Pro 6.0 software.

data_processing: TIFF images of scanned slides were analyzed using Feature Extraction Software version 9.5.3 (Agilent) using a custom grid file (017577_D_F_20070822). LOWESS normalized, background subtracted data were obtained from log2 of processed Red signal/processed Green signal. Agilent software was used. Data of identical probes were averaged. Data were subjected to a further linear normalization step by the average of the features detecting the spike-in transcripts. Only features that did not have any feature non-uniformity or population outlier flags contributed to the averages used for determining the normalization factor. Removed any data that failed any of the following spot quality filters: 1. gIsFound = 1 AND rIsFound = 1; 2. no PopnOL or NonUnifOL detected; 3. g OR r IsWellAboveBackground. Data of every probe was centered to the average of the corresponding control samples. Data for host genes were removed and probes against viral sequences were ordered by position in genome.

organism:
Homo sapiens
Human herpesvirus 8 strain rKSHV.219

source_name: lytically induced iSLK.219

label_protocol: The Quick Amp Labeling Kit (Agilent) was used according to the manufacturer’s protocol to generate Cy5/Cy3 labeled cRNA from 450 ng of total RNA, which contains mix of spike-in transcripts A + B (Agilent). An equal amount of the spike-in transcript mix were added to both Cy5 and Cy3 labeled samples. The spike-in transcripts were detected by E1A probes on the array and used for linear normalization subsequent to the LOWESS normalization performed by the Agilent feature extraction software.

growth_protocol: All iSLK cell lines were cultured in DMEM media supplemented with 10% FBS (Gibco) and cells stably infected with rKSHV.219 were maintained in 10 mg/mL puromycin (Invivogen).

extract_protocol: All samples were harvested in RLT buffer and RNA was isolated using the RNeasy Mini Kit according to the manufacturer’s protocol (Qiagen).

tag: infection

value: Human herpesvirus 8 strain rKSHV.219 (infection:stable)

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: Common reference: mix of several different cell types (BJAB, BCBL, iSLK, iSLK.219), both latent and lytic.

tag: common reference composition

value: cell type:mix of several different cell types (BJAB, BCBL, iSLK, iSLK.219); virus:HHV8 Type M (in BCBL) or HHV8 Type P (in iSLK.219); infection status:uninfected (BJAB and iSLK) or stably infected (latent & lytic BCBL and iSLK.219)


title: latently rKSHV.219-infected inducible SLK

description:
latent iSLK.219
All samples in Experiment 3 were processed in parallel, visualized on the same microarray on the same day, and the resulting microarray data was analyzed as one collective data set.

source_name: latently infected iSLK.219


title: Normal#1 (RNA)


title: NB_E_367


title: IBC#20 (RNA)

source_name: IBC, core-biopsy

value: IBC


title: HepG2 control Oct 16, 2011 rep2

tag: cell bank no

value: male

tag: age of sampling

value: 15 years

tag: tissue derived

value: liver

value: hepatocyte carcinoma

value: infinite


title: mock infected inducible SLK (uninfected)

description:
mock iSLK
All samples in Experiment 3 were processed in parallel, visualized on the same microarray on the same day, and the resulting microarray data was analyzed as one collective data set.

source_name: mock infected iSLK

value: mock


title: NB_E_366

value: <18 months; 2:>18 months):2


title: AD vs normal [Texas Tech_251485036822_S01_GE2-v5_91_0806_1_4]

city: Lubbock

first: Uzma

last: Qaisar

institute: Texas Tech University

description: Biological replicate

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

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

source_name: Brain microvessel

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

extract_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

tag: disease

value: Alzheimer disease


title: AD vs normal [Texas Tech_251485036822_S01_GE2-v5_91_0806_1_3]

description: Biological replicate


title: AD vs normal [Texas Tech_251485036821_S01_GE2-v5_91_0806_1_4]

description: Biological replicate


title: AD vs normal [Texas Tech_251485036823_S01_GE2-v5_91_0806_1_1]

description: Biological replicate


title: AD vs normal [Texas Tech_251485036822_S01_GE2-v5_91_0806_1_1]

description: Biological replicate


title: IBC#17 (RNA)


title: AD vs normal [Texas Tech_251485036821_S01_GE2-v5_91_0806_1_3]

description: Biological replicate


title: IBC#18 (RNA)


title: IBC#19 (RNA)


title: AD vs normal [Texas Tech_251485036822_S01_GE2-v5_91_0806_1_2]

description: Biological replicate


title: NB_E_365

value: <18 months; 2:>18 months):1


title: AD vs normal [Texas Tech_251485036821_S01_GE2-v5_91_0806_1_1]

description: Biological replicate


title: IBC#16 (RNA)


title: AD vs normal [Texas Tech_251485036820_S01_GE2-v5_91_0806_1_2]

description: Biological replicate


title: AD vs normal [Texas Tech_251485036823_S01_GE2-v5_91_0806_1_2]

description: Biological replicate


title: AD vs normal [Texas Tech_251485034901_S01_GE2-v5_91_0806_1_4]

description: Biological replicate


title: NB_E_364

value: Neuroblastoma


title: AD vs normal [Texas Tech_251485036821_S01_GE2-v5_91_0806_1_2]

description: Biological replicate


title: AD vs normal [Texas Tech_251485036824_S01_GE2-v5_91_0806_1_4]

description: Biological replicate


title: AD vs normal [Texas Tech_251485036820_S01_GE2-v5_91_0806_1_1]

description: Biological replicate


title: IBC#14 (RNA)


title: IBC#13 (RNA)


title: IBC#12 (RNA)


title: IBC#15 (RNA)


title: NB_E_363

value: M


title: NB_E_361

value: F


title: IBC#11 (RNA)


title: AD vs normal [Texas Tech_251485036824_S01_GE2-v5_91_0806_1_2]

description: Biological replicate


title: NB_E_362

value: not amplified; Amp:amplified; n.a.:not available):1


title: NB_E_360


title: AD vs normal [Texas Tech_251485034901_S01_GE2-v5_91_0806_1_2]

description: Biological replicate

value: Normal


title: AD vs normal [Texas Tech_251485034901_S01_GE2-v5_91_0806_1_3]

description: Biological replicate


title: AD vs normal [Texas Tech_251485036824_S01_GE2-v5_91_0806_1_3]

description: Biological replicate


title: AD vs normal [Texas Tech_251485034901_S01_GE2-v5_91_0806_1_1]

description: Biological replicate


title: NB_E_359


title: AD vs normal [Texas Tech_251485036824_S01_GE2-v5_91_0806_1_1]

description: Biological replicate


title: IBC#10 (RNA)