title: Lesion control (D), in the lesion (M), 60 days post-op, biol rep1


title: pancreatic cancer patient 97

status: Public on Jan 01 2012

type: RNA

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

hyb_protocol: According to manufacturer's instructions (febit biomed).

scan_protocol: Images were detected inside the geniom rt analyzer version 3. Wizard software on standard Microsoft Windows Workstation PC.

data_processing: Summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1. All analyses were carried out using R.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Pancreas RNA from pancreatic cancer patient

label_protocol: MPEA, microfluidic primer extension assay, biotin labeling.

growth_protocol: Stored at -20 degrees Celsius.

extract_protocol: Standard extraction of miRNAs from tissue samples using the miRNeasy kit (Qiagen, Hilden).

tag: tissue

value: pancreas

tag: disease state

value: pancreatic cancer


title: pancreatic cancer patient 96


title: pancreatic cancer patient 95


title: Lesion control (D), in the lesion (M), 30 days post-op, biol rep2

city: Beijing

first: Li

last: Xiaoguang

address: No.37 of Xueyuan Road, Haidian District

department: School of Biological Science and Medical Engineering

country: China

institute: Beihang University

description: Gene expression data from adult rat of  lesion control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were analyzed with Expression Console Software using RMA algorithm.

organism: Rattus norvegicus

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 30 days after operation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: The experimental rats were kept at a temperature of 24-26ºC, and humidity of 35-45% with twelve h light-dark cycles. Food and water were provided ad libitum. Supplemental oral feedings were given as necessary.

extract_protocol: The samples for microarray analysis were homogenized in 1 ml Trizol (Invitrogen, Carlsbad, CA), and RNA extracted using RNEasy miniprep columns (Qiagen, Valencia, CA) according to the manufacturer’s instructions. An average of 40-60 ug RNA was obtained from 80-120 mg of tissue pooled from four animals for microarray analysis which was performed using an Affymetrix GeneChipÒ Rat Genome 230 2.0 chip for each time point. All assays were performed at least in triplicate biological independent pooled samples.

treatment_protocol: Wistar rats weighing 250-300 g each were anaesthetized , followed by transection at the T7-8 level removing a spinal cord segment 5.0 mm in length. The blade was repeatedly scraped along the ventral surface of the spinal canal, and any residual fibers at the lesion site were removed by aspiration. The animals were divided into 3 groups. One group (NT-3-chitosan tube) received a chitosan tube of 5 mm in length, with a 2.2 mm outer diameter and 2.0   mm in inner diameter, seeded with the NT-3-chitosan carriers, implanted into the lesioned area. A second group (tube alone) had implanted only an empty chitosan tube. A third group (lesion control) received no treatment after the operation.

value: 5mm long segments in the T7-T8 lesioned area of the spinal cord

tag: treatment

value: spinal cord injury and no control treatment

tag: time

value: 30 days after operation

tag: strain

value: Wistar rat

tag: gender

value: female

tag: age

value: adult rat, i.e. 2 months after birth


title: Lesion control (D), in the lesion (M), 30 days post-op, biol rep3


title: Lesion control (D), in the lesion (M), 30 days post-op, biol rep1


title: pancreatic cancer patient 94


title: Lesion control (D), in the lesion (M), 90 days post-op, biol rep1

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 90 days after operation

value: 90 days after operation


title: Patient 2_Om_Day 0

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

country: United Kingdom

institute: Biomathematics & Statistics Scotland

hyb_protocol: The labeled and fragmented cRNA (10mg) was used for the hybridization to the Affymetrix (Santa Clara, CA) gene chips HS 1a520180 for 16 hr at 45C. An automated process of washing and staining in the Affymetrix Fluidics Station 400 was performed.

scan_protocol: Affymetrix arrays were scanned using the Affymetrix 3000G scanner. Absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v1 software.

data_processing: CEL files were transferred to MadMax website (https://madmax.bioinformatics.nl), and data analysis was performed using the statistical programming language R and the R libraries offered by the Bioconductor project. The data were first explored for quality control purposes and were normalized the GCRMA method within Bioconductor.

source_name: Patient 2_Om_Day 0

label_protocol: 2 μg of high quality total RNA, verified using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies), was used with the Affymetrix Eukaryotic One-Cylce Target Labeling and Control reagents (#900493) following the manufacturers instructions to generate Biotin-labeled antisense cRNA.

extract_protocol: Total RNA was extracted from the adipose tissue tissue using an RNeasy Lipid tissue mini kit followed by incubation with RNase free DNase (Qiagen, Crawley, West Sussex) for DNA-free RNA following the manufacturer's instructions.

value: Female

value: omental adipose tissue

tag: time post vbg

value: Day 0


title: Patient 3_Sub C_4 months

source_name: Patient 3_Sub C_4 months

value: sub cutaneous adipose tissue

value: 4 months


title: Patient 3_Sub C_Day 0

source_name: Patient 3_Sub C_Day 0


title: Lesion control (D), in the lesion (M), 20 days post-op, biol rep3

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 20 days after operation

value: 20 days after operation


title: Patient 2_Sub C_4 months

source_name: Patient 2_Sub C_4 months


title: Patient 3_Sub C_12 months

source_name: Patient 3_Sub C_12 months

value: 12 months


title: Patient 2_Sub C_12 months

source_name: Patient 2_Sub C_12 months


title: Lesion control (D), in the lesion (M), 20 days post-op, biol rep2


title: pancreatic cancer patient 93


title: Patient 2_Sub C_Day 0

source_name: Patient 2_Sub C_Day 0


title: Good responder UPN753_GR

type: genomic

city: Nijmegen

first: Roland

middle: P.

last: Kuiper

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: Formalin-fixed paraffin-embedded primary tumour tissue vs. normal colon tissue

hyb_protocol: Samples were hybridized for 48 hours at 42°C using a MAUI hybridization system (Biomicro Systems, Salt Lake City, USA)

scan_protocol: Scanning was performed using an Axon Genepix 4200AL microarray scanner.

data_processing: The NimbleScan 2.4 software package (NimbleGen Systems Inc., Madison, USA) was used to calculate log2 ratio’s after performing spatial correction, normalization and a 25kb average smoothing window on the data. Further data interpretation and CNA calling was done with Nexus Copy Number 5.0 software (Biodiscovery, El Segundo, USA) using the Rank Segmentation Algorithm.

molecule: genomic DNA

source_name: Tumor (FFPE)

label_protocol: 500 ng of amplified DNA from test and reference samples were labelled with Cy3 and Cy5, respectively, using random-primed  labelling (Bioprime genomic DNA labelling kit, Invitrogen, Breda, the Netherlands)

extract_protocol: Genomic DNA was extracted from manually microdissected 50 µm sections of FFPE tissue and amplified using  ENZO Bioscore amplification kit

tag: response

value: Good responder

value: primary colorectal cancer tumor

value: cetuximab in combination with capecitabine, oxaliplatin, and bevacizuma

source_name: Normal colon (FFPE)

tag: sample type

value: reference

value: normal colon


title: Bad responder UPN715_BR

value: Bad responder


title: pancreatic cancer patient 92

value: pancreas

value: pancreatic cancer


title: Patient 1_Om_Day 0

source_name: Patient 1_Om_Day 0


title: Bad responder UPN717_BR


title: pancreatic cancer patient 90


title: Lesion control (D), in the lesion (M), 10 days post-op, biol rep3

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 10 days after operation

value: 5mm long segments in the T7-T8 lesioned area of the spinal cord

value: spinal cord injury and no control treatment

value: 10 days after operation

value: Wistar rat

value: female

value: adult rat, i.e. 2 months after birth


title: pancreatic cancer patient 91


title: Lesion control (D), in the lesion (M), 10 days post-op, biol rep2


title: Good responder UPN677_GR


title: Patient 1_Sub C_12 months

source_name: Patient 1_Sub C_12 months

value: Female

value: sub cutaneous adipose tissue


title: pancreatic cancer patient 89


title: Lesion control (D), in the lesion (M), 10 days post-op, biol rep1


title: Lesion control (D), in the lesion (M), 20 days post-op, biol rep1

value: 20 days after operation


title: pancreatic cancer patient 88


title: Bad responder UPN676_BR


title: Lesion control (D), in the lesion (M), 3 days post-op, biol rep3

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 3 days after operation

value: 3 days after operation


title: Good responder UPN625_GR

value: Good responder

value: primary colorectal cancer tumor


title: pancreatic cancer patient 87

source_name: Pancreas RNA from pancreatic cancer patient


title: Patient 1_Sub C_Day 0

source_name: Patient 1_Sub C_Day 0

value: Day 0


title: Bad responder UPN601_BR

value: cetuximab in combination with capecitabine, oxaliplatin, and bevacizuma

value: reference

value: normal colon


title: Good responder UPN554_GR


title: genomic DNA from PBL DNA replicate of WBC6 [WBC11]

city: Los Angeles

first: Mihaela

last: Campan

address: 1441 Eastlake Ave

country: USA

institute: University of Southern California

description: PBL

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 setting

data_processing: BeadStudio software v.3.0 with the methylation module 3.2.5

label: Cy5 and Cy3

source_name: PBL

label_protocol: Standard Illumina Protocol

extract_protocol:
DNA was extracted from the tissue samples using standard phenol/chloroform-based  procedures. The PBL DNA was extracted using the  Qiagen QIAamp DNA Blood kit following the manufacturer's instructions.
DNA was bisulfite converted using the Zymo Research EZ96 DNA methylation kit following the manufacturer's instructions.

value: PBL DNA

value: normal


title: Bad responder UPN699_BR

value: Bad responder


title: pancreatic cancer patient 86

value: pancreas

value: pancreatic cancer


title: pancreatic cancer patient 85


title: Lesion control (D), in the lesion (M), 3 days post-op, biol rep1

value: 5mm long segments in the T7-T8 lesioned area of the spinal cord

value: spinal cord injury and no control treatment

value: Wistar rat

value: female


title: Lesion control (D), in the lesion (M), 3 days post-op, biol rep2

value: adult rat, i.e. 2 months after birth


title: genomic DNA from PBL DNA [WBC10]

description: PBL


title: genomic DNA from PBL DNA replicate of WBC8 [WBC12]

description: PBL


title: Lesion control (D), rostral to the lesion (R), 90 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 90 days after operation

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord

value: 90 days after operation


title: pancreatic cancer patient 84


title: Bad responder UPN511_BR

value: primary colorectal cancer tumor


title: Good responder UPN665_GR

value: Good responder


title: Bad responder UPN467_BR

value: cetuximab in combination with capecitabine, oxaliplatin, and bevacizuma


title: Lesion control (D), rostral to the lesion (R), 90 days post-op, biol rep2


title: Bad responder UPN48_BR

value: reference


title: genomic DNA from PBL DNA [WBC8]

description: PBL


title: Bad responder UPN478_BR

value: normal colon


title: Patient 1_Sub C_4 months

source_name: Patient 1_Sub C_4 months

value: Female

value: sub cutaneous adipose tissue

value: 4 months


title: pancreatic cancer patient 83

value: pancreas


title: pancreatic cancer patient 82

value: pancreatic cancer


title: Bad responder UPN479_BR

value: Bad responder


title: genomic DNA from PBL DNA [WBC9]

description: PBL

value: PBL DNA

value: normal


title: Good responder UPN487_GR


title: Lesion control (D), rostral to the lesion (R), 90 days post-op, biol rep1

value: spinal cord injury and no control treatment

value: Wistar rat

value: female


title: Lesion control (D), rostral to the lesion (R), 60 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 60 days after operation

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord

value: 60 days after operation

value: adult rat, i.e. 2 months after birth


title: pancreatic cancer patient 79


title: genomic DNA from PBL DNA [WBC7]

description: PBL


title: pancreatic cancer patient 78


title: Good responder UPN437_GR

value: Good responder

value: primary colorectal cancer tumor

value: cetuximab in combination with capecitabine, oxaliplatin, and bevacizuma


title: Bad responder UPN463_BR

value: reference

value: normal colon


title: Lesion control (D), rostral to the lesion (R), 60 days post-op, biol rep1


title: pancreatic cancer patient 81


title: Bad responder UPN322_BR


title: Lesion control (D), rostral to the lesion (R), 30 days post-op, biol rep2

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 30 days after operation

value: 30 days after operation


title: Good responder UPN373_GR


title: pancreatic cancer patient 76

value: pancreas


title: Bad responder UPN392_BR


title: Lesion control (D), rostral to the lesion (R), 60 days post-op, biol rep2


title: Good responder UPN293_GR


title: Lesion control (D), rostral to the lesion (R), 30 days post-op, biol rep1


title: genomic DNA from PBL DNA [WBC1]

description: PBL


title: pancreatic cancer patient 75

value: pancreatic cancer


title: genomic DNA from PBL DNA [WBC5]

description: PBL


title: genomic DNA from ovarian cancer tissue [14430]

description: ovarian cancer

source_name: ovarian cancer

value: ovarian cancer DNA

value: tumor

tag: tumor type

value: serous adenocarcinoma


title: Lesion control (D), rostral to the lesion (R), 20 days post-op, biol rep2

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 20 days after operation

value: spinal cord injury and no control treatment

value: 20 days after operation


title: pancreatic cancer patient 74


title: genomic DNA from ovarian cancer tissue [14429]

description: ovarian cancer

value: female


title: Bad responder UPN436_BR

value: Bad responder


title: pancreatic cancer patient 80


title: genomic DNA from PBL DNA [WBC4]

description: PBL

value: PBL DNA

value: normal


title: Good responder UPN257_GR

value: Good responder


title: pancreatic cancer patient 73


title: genomic DNA from PBL DNA [WBC6]

description: PBL


title: pancreatic cancer patient 72


title: M3.T37.3

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

hyb_protocol: 300 ng of labeled cDNA from each sample was hybridized onto Agilent custom 8 x 15 K DNA-microarray against equal amount of labeled control cDNA using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Three biological replicates of each strain were hybridized onto arrays, one of the replicates with a dye swap. The arrays were hybridized 16 hours at 65ºC.

scan_protocol: GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm

data_processing: Image analysis with GenePix Pro 6.0, bad spots were manually flagged (flag-value -100). Data preprocessing in R with limma package: local background subtraction with normexp and offset 50. Log2-intensities normalized with quantile normalization across all samples.

organism: Listeria monocytogenes EGD-e

source_name: sample taken at the mid-exponential growth stage, temperature 37°C

label_protocol: Two micrograms of total RNA of each sample were converted to cDNA and labeled with fluorescent dyes (Cy3 or Cy5, GE Healthcare, Little Chalfont, United Kingdom).

growth_protocol: Strains were grown in a brain-heart infusion medium (Oxoid, Hampshire, UK) at 3°C, 10°C and 37°C and sampled at the mid-exponential growth stage.

extract_protocol: 5 ml from each sample were mixed with 1 ml of ice-cold solution containing 1 part of phenol (Sigma-Aldrich) and 9 parts of 99.5% ethanol. After 30 minutes on ice, samples were centrifuged for 5 min at 4ºC at 5000g. Bacterial pellets were immediately processed or frozen at -70ºC for later total RNA extraction. Total RNA was isolated using the Qiagen RNeasy Midi-kit (Qiagen) with slight modofications to the original kit protocol. Bacterial cells were lysed in TE buffer (Fluka Biochemica, Buchs, Switzerland) supplemented with lysozyme (25 mg/ml) and mutanolysin (250 U/ml) (Sigma-Aldrich). Two DNase treatment steps were applied to remove DNA: an initial on-column treatment with Qiagen RNase-Free DNase set (Qiagen), as well as a second DNAse treatment after isolation of total RNA using the Ambion DNA-free kit (Ambion, Austin, TX, USA). RNA yields were determined using the Nanodrop ND-1000 spectrophotometer (Nano Drop Technologies, Wilmington, DE, USA), and quality was controlled using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The purified total RNA was aliquoted and frozen -70ºC for longterm storage.

tag: temperature

tag: genotype/variation

value: ∆sigBL


title: Lesion control (D), rostral to the lesion (R), 30 days post-op, biol rep3

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord

value: Wistar rat

value: adult rat, i.e. 2 months after birth


title: genomic DNA from ovarian cancer tissue [14428]

description: ovarian cancer


title: M3.T37.2


title: Lesion control (D), rostral to the lesion (R), 10 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 10 days after operation

value: 10 days after operation


title: Lesion control (D), rostral to the lesion (R), 10 days post-op, biol rep2


title: Good responder UPN267_GR

source_name: Tumor (FFPE)

value: primary colorectal cancer tumor

value: cetuximab in combination with capecitabine, oxaliplatin, and bevacizuma

value: reference

value: normal colon


title: genomic DNA from ovarian cancer tissue [14426]

description: ovarian cancer

value: ovarian cancer DNA

value: tumor

value: serous adenocarcinoma


title: genomic DNA from ovarian cancer tissue [14425]

description: ovarian cancer

value: female


title: M3.T37.1


title: pancreatic cancer patient 71

value: pancreas

value: pancreatic cancer


title: genomic DNA from PBL DNA [WBC3]

description: PBL

value: PBL DNA

value: normal


title: Lesion control (D), rostral to the lesion (R), 10 days post-op, biol rep1

value: spinal cord injury and no control treatment


title: M3.T10.3

source_name: sample taken at the mid-exponential growth stage, temperature 10°C

value: ∆sigBL


title: pancreatic cancer patient 70


title: pancreatic cancer patient 69


title: Good responder UPN211_GR

value: Good responder

source_name: Normal colon (FFPE)


title: Bad responder UPN169_BR

value: Bad responder


title: pancreatic cancer patient 77


title: genomic DNA from ovarian cancer tissue [14424]

description: ovarian cancer


title: pancreatic cancer patient 68


title: Good responder UPN137_GR


title: Lesion control (D), rostral to the lesion (R), 3 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 3 days after operation

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord

value: 3 days after operation

value: Wistar rat

value: adult rat, i.e. 2 months after birth


title: M3.T10.1


title: M3.T10.2


title: genomic DNA from ovarian cancer tissue [14423]

description: ovarian cancer


title: genomic DNA from PBL DNA [WBC2]

description: PBL


title: Lesion control (D), rostral to the lesion (R), 3 days post-op, biol rep2


title: genomic DNA from ovarian cancer tissue [14422]

description: ovarian cancer


title: pancreatic cancer patient 67


title: Lesion control (D), rostral to the lesion (R), 3 days post-op, biol rep1


title: Good responder UPN133_GR

value: primary colorectal cancer tumor

value: cetuximab in combination with capecitabine, oxaliplatin, and bevacizuma

value: reference

value: normal colon


title: pancreatic cancer patient 66


title: pancreatic cancer patient 65


title: M3.T3.3

source_name: sample taken at the mid-exponential growth stage, temperature 3°C


title: M3.T3.2


title: Lesion control (D), rostral to the lesion (R), 20 days post-op, biol rep3

value: 20 days after operation

value: female


title: genomic DNA from ovarian cancer tissue [14420]

description: ovarian cancer

value: ovarian cancer DNA

value: tumor

value: serous adenocarcinoma


title: M3.T3.1


title: Lesion control (D), rostral to the lesion (R), 1 day post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 1 day after operation

value: spinal cord injury and no control treatment

value: 1 day after operation


title: M2.T37.3

value: ∆sigL


title: Tube alone (K), caudal to the lesion (C), 90 days post-op, biol rep3

description: Gene expression data from adult rat of  tube alone treatment

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 90 days after operation

value: 5mm long segments caudal to the T7-T8 lesioned area of the spinal cord

value: spinal cord injury and tube control treatment

value: 90 days after operation


title: pancreatic cancer patient 64

source_name: Pancreas RNA from pancreatic cancer patient

value: pancreas

value: pancreatic cancer


title: genomic DNA from ovarian cancer tissue [14418]

description: ovarian cancer


title: genomic DNA from ovarian cancer tissue [14419]

description: ovarian cancer


title: genomic DNA from ovarian cancer tissue [14421]

description: ovarian cancer


title: Bad responder UPN215_BR

value: Bad responder

value: primary colorectal cancer tumor


title: Good responder UPN226_GR

value: Good responder

value: cetuximab in combination with capecitabine, oxaliplatin, and bevacizuma

value: reference


title: pancreatic cancer patient 63


title: Lesion control (D), rostral to the lesion (R), 1 day post-op, biol rep1

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord

value: Wistar rat

value: female

value: adult rat, i.e. 2 months after birth


title: pancreatic cancer patient 62


title: M2.T37.2


title: M2.T37.1


title: pancreatic cancer patient 61


title: Tube alone (K), caudal to the lesion (C), 90 days post-op, biol rep2


title: Lesion control (D), rostral to the lesion (R), 1 day post-op, biol rep2

value: spinal cord injury and no control treatment


title: M2.T10.3


title: genomic DNA from ovarian cancer tissue [14417]

description: ovarian cancer

value: ovarian cancer DNA

value: tumor

value: serous adenocarcinoma


title: genomic DNA from ovarian cancer tissue [14415]

description: ovarian cancer


title: Bad responder UPN263_BR

value: normal colon


title: genomic DNA from ovarian cancer tissue [14416]

description: ovarian cancer


title: M2.T10.1

value: ∆sigL


title: Tube alone (K), caudal to the lesion (C), 60 days post-op, biol rep3

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 60 days after operation

value: 5mm long segments caudal to the T7-T8 lesioned area of the spinal cord

value: spinal cord injury and tube control treatment

value: 60 days after operation


title: M2.T10.2


title: genomic DNA from ovarian cancer tissue [14414]

description: ovarian cancer


title: Tube alone (K), caudal to the lesion (C), 90 days post-op, biol rep1

value: 90 days after operation


title: Tube alone (K), caudal to the lesion (C), 60 days post-op, biol rep1


title: pancreatic cancer patient 58

value: pancreas

value: pancreatic cancer


title: Good responder UPN116_GR

value: Good responder

value: primary colorectal cancer tumor

value: cetuximab in combination with capecitabine, oxaliplatin, and bevacizuma

value: reference


title: Good responder UPN246_GR


title: Tube alone (K), caudal to the lesion (C), 60 days post-op, biol rep2

value: Wistar rat

value: female

value: adult rat, i.e. 2 months after birth


title: pancreatic cancer patient 60


title: pancreatic cancer patient 57


title: pancreatic cancer patient 59


title: pancreatic cancer patient 56


title: Tube alone (K), caudal to the lesion (C), 30 days post-op, biol rep3

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 30 days after operation

value: 30 days after operation


title: pancreatic cancer patient 55


title: Tube alone (K), caudal to the lesion (C), 30 days post-op, biol rep2


title: genomic DNA from ovarian cancer tissue [14409]

description: ovarian cancer

value: ovarian cancer DNA

value: tumor

value: serous adenocarcinoma


title: genomic DNA from ovarian cancer tissue [14412]

description: ovarian cancer


title: M2.T3.2

value: ∆sigL


title: M2.T3.3


title: pancreatic cancer patient 54


title: M2.T3.1


title: M1.T37.3

value: ∆sigB


title: Tube alone (K), caudal to the lesion (C), 30 days post-op, biol rep1

value: 5mm long segments caudal to the T7-T8 lesioned area of the spinal cord

value: spinal cord injury and tube control treatment


title: Tube alone (K), caudal to the lesion (C), 20 days post-op, biol rep2

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 20 days after operation

value: 20 days after operation


title: genomic DNA from ovarian cancer tissue [14411]

description: ovarian cancer


title: M1.T37.2


title: genomic DNA from ovarian cancer tissue [14404]

description: ovarian cancer


title: Tube alone (K), caudal to the lesion (C), 20 days post-op, biol rep3


title: genomic DNA from ovarian cancer tissue [14408]

description: ovarian cancer


title: Tube alone (K), caudal to the lesion (C), 10 days post-op, biol rep2

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 10 days after operation

value: 10 days after operation


title: M1.T37.1


title: genomic DNA from ovarian cancer tissue [14410]

description: ovarian cancer


title: genomic DNA from ovarian cancer tissue [14406]

description: ovarian cancer


title: pancreatic cancer patient 53

value: pancreas

value: pancreatic cancer


title: genomic DNA from ovarian cancer tissue [14405]

description: ovarian cancer


title: Tube alone (K), caudal to the lesion (C), 20 days post-op, biol rep1


title: Tube alone (K), caudal to the lesion (C), 10 days post-op, biol rep3


title: pancreatic cancer patient 52


title: pancreatic cancer patient 51


title: pancreatic cancer patient 50


title: genomic DNA from ovarian cancer tissue [14403]

description: ovarian cancer


title: M1.T10.1


title: M1.T10.2


title: Tube alone (K), caudal to the lesion (C), 10 days post-op, biol rep1


title: genomic DNA from ovarian cancer tissue [14402]

description: ovarian cancer


title: pancreatic cancer patient 48


title: M1.T3.2


title: M1.T10.3


title: M1.T3.3


title: Tube alone (K), caudal to the lesion (C), 3 days post-op, biol rep3

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 3 days after operation

value: 3 days after operation


title: pancreatic cancer patient 47


title: pancreatic cancer patient 46


title: genomic DNA from ovarian cancer tissue [12867]

description: ovarian cancer

source_name: ovarian cancer

value: endometrioid adenocarcinoma


title: Tube alone (K), caudal to the lesion (C), 3 days post-op, biol rep2

value: Wistar rat


title: genomic DNA from ovarian cancer tissue [12866]

description: ovarian cancer

value: female

value: mucinous adenocarcinoma


title: pancreatic cancer patient 45


title: M1.T3.1


title: pancreatic cancer patient 49


title: Tube alone (K), caudal to the lesion (C), 1 day post-op, biol rep2

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 1 day after operation

value: 1 day after operation

value: adult rat, i.e. 2 months after birth


title: genomic DNA from ovarian cancer tissue [14401]

description: ovarian cancer

value: ovarian cancer DNA

value: tumor


title: Tube alone (K), caudal to the lesion (C), 1 day post-op, biol rep3


title: WT.T37.2

source_name: sample taken at the mid-exponential growth stage, temperature 37°C

value: wild-type


title: Lesion control (D), rostral to the lesion (R), 20 days post-op, biol rep1

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 20 days after operation

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord

value: spinal cord injury and no control treatment


title: WT.T37.3


title: genomic DNA from ovarian cancer tissue [12865]

description: ovarian cancer

value: clear cell carcinoma


title: Tube alone (K), caudal to the lesion (C), 3 days post-op, biol rep1

value: 5mm long segments caudal to the T7-T8 lesioned area of the spinal cord

value: spinal cord injury and tube control treatment


title: genomic DNA from ovarian cancer tissue [12864]

description: ovarian cancer

value: mixed clear cell and endometroid adenocarcinoma


title: genomic DNA from ovarian cancer tissue [12863]

description: ovarian cancer


title: pancreatic cancer patient 44

value: pancreas

value: pancreatic cancer


title: pancreatic cancer patient 43


title: WT.T10.3


title: WT.T37.1


title: genomic DNA from ovarian cancer tissue [12862]

description: ovarian cancer

value: endometrioid adenocarcinoma


title: pancreatic cancer patient 39


title: pancreatic cancer patient 41


title: pancreatic cancer patient 42


title: pancreatic cancer patient 40


title: Tube alone (K), in the lesion (M), 3 days post-op, biol rep2

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 3 days after operation

value: 5mm long segments in the T7-T8 lesioned area of the spinal cord

value: 3 days after operation

value: Wistar rat


title: Tube alone (K), caudal to the lesion (C), 1 day post-op, biol rep1

value: 1 day after operation

value: female


title: WT.T3.1


title: Tube alone (K), in the lesion (M), 3 days post-op, biol rep1

value: adult rat, i.e. 2 months after birth


title: WT.T10.2

source_name: sample taken at the mid-exponential growth stage, temperature 10°C


title: WT.T10.1


title: WT.T3.3


title: genomic DNA from ovarian cancer tissue [12855]

description: ovarian cancer

value: ovarian cancer DNA

value: tumor


title: genomic DNA from ovarian cancer tissue [12767]

description: ovarian cancer


title: Tube alone (K), rostral to the lesion (R), 90 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 90 days after operation

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord

value: 90 days after operation


title: Tube alone (K), in the lesion (M), 3 days post-op, biol rep3


title: genomic DNA from ovarian cancer tissue [12854]

description: ovarian cancer


title: genomic DNA from ovarian cancer tissue [12853]

description: ovarian cancer


title: genomic DNA from ovarian cancer tissue [12766]

description: ovarian cancer

value: mucinous adenocarcinoma


title: genomic DNA from ovarian cancer tissue [12852]

description: ovarian cancer


title: pancreatic cancer patient 38


title: Tube alone (K), rostral to the lesion (R), 90 days post-op, biol rep2


title: pancreatic cancer patient 36


title: pancreatic cancer patient 37


title: genomic DNA from ovarian cancer tissue [12764]

description: ovarian cancer

value: serous adenocarcinoma


title: WT.T3.2

value: wild-type


title: Tube alone (K), rostral to the lesion (R), 60 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 60 days after operation

value: spinal cord injury and tube control treatment

value: 60 days after operation


title: Tube alone (K), rostral to the lesion (R), 60 days post-op, biol rep2


title: pancreatic cancer patient 35

value: pancreas

value: pancreatic cancer


title: pancreatic cancer patient 34


title: Tube alone (K), rostral to the lesion (R), 90 days post-op, biol rep1


title: pancreatic cancer patient 31


title: pancreatic cancer patient 30


title: pancreatic cancer patient 32


title: Tube alone (K), rostral to the lesion (R), 60 days post-op, biol rep1


title: pancreatic cancer patient 29


title: M18_cell_37℃_rep2

city: Shanghai

first: daqiang

last: wu

address: 800 Dongchuan Road

department: School of life science and biotechnology

institute: Shanghaijiaotong University

description: gene expression at 37℃

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US)Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes with Gene Expression Wash Buffer Kit( Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions。

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent technologies, Santa Clara, CA, US) using default parameters.

organism: Pseudomonas aeruginosa

source_name: Cells, 37℃,replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the  Low RNA Input Linear Amplification  kit (Agilent technologies, Santa Clara, CA, US) according to the manufacturer's instructions,and purified by RNeasy mini kit ( QIAGEN, GmBH, Germany).

growth_protocol: Cells were grown to OD600=5.0-6.0 (late exponential phase) in LB medium at 28℃ and 37℃, respectively.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen,Carlsbad, CA, USA).

tag: growth phase

value: late exponential phase


title: pancreatic cancer patient 28


title: pancreatic cancer patient 27


title: genomic DNA from ovarian cancer tissue [12762]

description: ovarian cancer


title: Tube alone (K), rostral to the lesion (R), 30 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 30 days after operation

value: 30 days after operation


title: pancreatic cancer patient 33


title: M18_cell_37℃_rep1

description: gene expression at 37℃

source_name: Cells, 37℃,replicate 1


title: pancreatic cancer patient 26

source_name: Pancreas RNA from pancreatic cancer patient


title: M18_cell_37℃_rep3

description: gene expression at 37℃

source_name: Cells, 37℃,replicate 3


title: pancreatic cancer patient 25


title: M18_cell_28℃_rep3

description: gene expression at 28℃

source_name: Cells, 28℃,replicate 3


title: M18_cell_28℃_rep1

description: gene expression at 28℃

source_name: Cells, 28℃,replicate 1


title: M18_cell_28℃_rep2

description: gene expression at 28℃

source_name: Cells, 28℃,replicate 2


title: pancreatic cancer patient 24


title: Tube alone (K), rostral to the lesion (R), 20 days post-op, biol rep2

value: 20 days after operation

value: Wistar rat


title: Tube alone (K), rostral to the lesion (R), 20 days post-op, biol rep1

value: female


title: Tube alone (K), rostral to the lesion (R), 10 days post-op, biol rep2

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 10 days after operation

value: 10 days after operation

value: adult rat, i.e. 2 months after birth


title: Tube alone (K), rostral to the lesion (R), 30 days post-op, biol rep1


title: Tube alone (K), rostral to the lesion (R), 3 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 3 days after operation

value: 3 days after operation


title: pancreatic cancer patient 21


title: pancreatic cancer patient 22


title: pancreatic cancer patient 23


title: pancreatic cancer patient 19


title: pancreatic cancer patient 18


title: pancreatic cancer patient 17


title: Tube alone (K), rostral to the lesion (R), 3 days post-op, biol rep1

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord


title: pancreatic cancer patient 16


title: Tube alone (K), rostral to the lesion (R), 3 days post-op, biol rep2


title: Tube alone (K), rostral to the lesion (R), 20 days post-op, biol rep3


title: Tube alone (K), rostral to the lesion (R), 30 days post-op, biol rep2


title: pancreatic cancer patient 15


title: Tube alone (K), rostral to the lesion (R), 10 days post-op, biol rep1


title: Tube alone (K), rostral to the lesion (R), 1 day post-op, biol rep1

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 1 day after operation

value: 1 day after operation


title: Tube alone (K), rostral to the lesion (R), 1 day post-op, biol rep3


title: NT-3-chitosan tube (S), caudal to the lesion (C), 90 days post-op, biol rep3

description: Gene expression data from adult rat of  NT-3-chitosan tube treatment

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 90 days after operation

value: 5mm long segments caudal to the T7-T8 lesioned area of the spinal cord

value: spinal cord injury and NT-3-chitosan tube treatment

value: 90 days after operation


title: NT-3-chitosan tube (S), caudal to the lesion (C), 90 days post-op, biol rep2


title: pancreatic cancer patient 20


title: NT-3-chitosan tube (S), caudal to the lesion (C), 60 days post-op, biol rep3

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 60 days after operation


title: pancreatic cancer patient 14


title: NT-3-chitosan tube (S), caudal to the lesion (C), 60 days post-op, biol rep1


title: Tube alone (K), rostral to the lesion (R), 1 day post-op, biol rep2

value: spinal cord injury and tube control treatment


title: NT-3-chitosan tube (S), caudal to the lesion (C), 60 days post-op, biol rep2

value: 60 days after operation


title: NT-3-chitosan tube (S), caudal to the lesion (C), 90 days post-op, biol rep1


title: NT-3-chitosan tube (S), caudal to the lesion (C), 30 days post-op, biol rep3

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 30 days after operation


title: pancreatic cancer patient 12

value: pancreas


title: pancreatic cancer patient 13

value: pancreatic cancer


title: pancreatic cancer patient 11


title: pancreatic cancer patient 8


title: pancreatic cancer patient 9


title: pancreatic cancer patient 6


title: pancreatic cancer patient 7


title: NT-3-chitosan tube (S), caudal to the lesion (C), 30 days post-op, biol rep2


title: NT-3-chitosan tube (S), caudal to the lesion (C), 20 days post-op, biol rep2

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 20 days after operation


title: NT-3-chitosan tube (S), caudal to the lesion (C), 30 days post-op, biol rep1


title: pancreatic cancer patient 4


title: pancreatic cancer patient 10


title: pancreatic cancer patient 5


title: NT-3-chitosan tube (S), caudal to the lesion (C), 20 days post-op, biol rep1


title: pancreatic cancer patient 2


title: pancreatic cancer patient 3


title: ECs from EC/NSPC co-culture, incubated with PD 173074  2

type: other

city: Albuquerque

first: Tamara

last: Roitbak

state: NM

address: 2212 Lomas NE

department: Neurosurgery

institute: UNM

description: miRNA expression data from  EC/NSPC co-culture treated with FGF/VEGF receptor inhibitor

hyb_protocol: Following labeling, 21.5 ul of biotin-labeled RNA was hybridized for 16 hr at 48C on Affymetrix miRNA 2.0 Arrays. The miRNA 2.0 Arrays were washed and stained in the Affymetrix Fluidics Station 450 using fludics script FS450_0003.

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

data_processing: Data files were analyzed with Affymetrix miRNAQCtool using RMA background correction and quantile normalization (Default settings)

molecule: other

organism: Mus musculus

source_name: Mouse primary brain endothelial cells (Celprogen) grown in  co-culture with neural stem/progenitor cells isolated from E14 mouse embryonic brain

label_protocol: FlashTag RNA Labeling with Genisphere RNA Labeling Kit

growth_protocol: ECs were grown in transwell co-culture with NSPCs,in growth factor-free NSPC medium with addition of 5% FBS, at 37C, in CO2 incubator

extract_protocol: After 24 hours in transwell co-culture, the ECs and NSPCs were separated and miRNA s were isolated using mirVana miRNA (AB/Ambion) isolation kit

treatment_protocol: co-cultures were treated with : PD 173074 (1mM in DMSO), SB431542 (10μM in DMSO), or 2μl/mL DMSO (control), for 24 hours.

tag: cell type

value: primary brain endothelial cells (Celprogen, San Diego, CA, catalog # 11053-07)

value: ECs isolated from the mouse forebrain microvessels and NSPCs from telencephalon of E-14 mouse embryo


title: ECs from EC/NSPC co-culture incubated with SB431542  2

description: miRNA expression data from from EC/NSPC co-culture treated withTGF-β  receptor inhibitor


title: ECs from EC/NSPC co-culture incubated with DMSO (control)  1

description: miRNA expression data from  EC/NSPC co-culture treated with DMSO (control)


title: ECs from EC/NSPC co-culture incubated with SB431542  1

value: EC/NSPC co-culture treated withTGF-β  receptor inhibitor


title: ECs from EC/NSPC co-culture incubated with DMSO (control)  2

value: EC/NSPC co-culture treated with DMSO (control)


title: NT-3-chitosan tube (S), caudal to the lesion (C), 10 days post-op, biol rep1

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 10 days after operation

value: Wistar rat

value: female


title: pancreatic cancer patient 1


title: NT-3-chitosan tube (S), caudal to the lesion (C), 20 days post-op, biol rep3

value: 20 days after operation

value: adult rat, i.e. 2 months after birth


title: pancreatitis patient 27

source_name: Pancreas RNA from pancreatitis patient

value: pancreatitis


title: ECs from EC/NSPC co-culture, incubated with PD 173074  1

value: EC/NSPC co-culture treated with FGF/VEGF receptor inhibitor


title: pancreatitis patient 26


title: NT-3-chitosan tube (S), caudal to the lesion (C), 3 days post-op, biol rep2

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 3 days after operation

value: 5mm long segments caudal to the T7-T8 lesioned area of the spinal cord

value: 3 days after operation


title: NT-3-chitosan tube (S), caudal to the lesion (C), 10 days post-op, biol rep3

value: spinal cord injury and NT-3-chitosan tube treatment

value: 10 days after operation


title: NT-3-chitosan tube (S), caudal to the lesion (C), 10 days post-op, biol rep2


title: NT-3-chitosan tube (S), caudal to the lesion (C), 1 day post-op, biol rep2

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 1 day after operation

value: 1 day after operation


title: NT-3-chitosan tube (S), caudal to the lesion (C), 3 days post-op, biol rep3


title: NT-3-chitosan tube (S), in the lesion (M), 90 days post-op, biol rep3

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 90 days after operation

value: 5mm long segments in the T7-T8 lesioned area of the spinal cord

value: 90 days after operation


title: ASC 72hr rep1

city: Palo Alto

first: Thomas

middle: A

last: Rando

address: 3801 miranda ave.

department: Department of Neurology and Neurological Sciences

institute: Stanford University School of Medicine

description: Total RNAs were isolated using Trizol (Invitrogen). Reverse transcription and amplification was performed as described by the manufacturer (Applied Biosystems). Diluted cDNAs were loaded onto the Taqman Array Rodent MicroRNA A or B Cards v2.0 and real-time PCR was performed using ABI 7900HT Fast Real-Time PCR System using recommended cycling condition (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles).

hyb_protocol: Not applicable

scan_protocol: Not applicable

data_processing: Raw CT value was extracted using ABI Taqman SDS v2.3 software. miRNA gene expressions were normalized to U6 snRNA: delta CT = Ct_miRNA - Ct_U6snRNA. Relative quantitation of miRNA gene expressions was performed using delta delta CT method (see Supplementary files on Series record).

label: FAM

source_name: Muscle stem cells

label_protocol: Not applicable

tag: protocol

value: activated stem cells (ASC)

value: male

value: 8 weeks


title: NT-3-chitosan tube (S), caudal to the lesion (C), 1 day post-op, biol rep3


title: NT-3-chitosan tube (S), in the lesion (M), 90 days post-op, biol rep2


title: NT-3-chitosan tube (S), caudal to the lesion (C), 3 days post-op, biol rep1


title: ASC 60hr rep1

extract_protocol: Total RNAs were isolated using Trizol (Invitrogen).


title: ASC 60hr rep2


title: ASC 60hr rep3


title: pancreatitis patient 22

value: pancreas


title: pancreatitis patient 21


title: NT-3-chitosan tube (S), caudal to the lesion (C), 1 day post-op, biol rep1

value: Wistar rat


title: pancreatitis patient 20


title: ASC 72hr rep2


title: pancreatitis patient 24


title: NT-3-chitosan tube (S), in the lesion (M), 90 days post-op, biol rep1

value: female


title: ASC 36hr rep3


title: pancreatitis patient 19


title: ASC 36hr rep2


title: pancreatitis patient 18


title: NT-3-chitosan tube (S), in the lesion (M), 60 days post-op, biol rep3

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 60 days after operation

value: 60 days after operation


title: NT-3-chitosan tube (S), in the lesion (M), 60 days post-op, biol rep1

value: adult rat, i.e. 2 months after birth


title: pancreatitis patient 23

value: pancreatitis


title: ASC 36hr rep1


title: NT-3-chitosan tube (S), in the lesion (M), 30 days post-op, biol rep3

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 30 days after operation

value: 30 days after operation


title: pancreatitis patient 17


title: QSC 0hr rep3

value: quiescent  stem cells (QSC)


title: NT-3-chitosan tube (S), in the lesion (M), 60 days post-op, biol rep2


title: NT-3-chitosan tube (S), in the lesion (M), 30 days post-op, biol rep2


title: pancreatitis patient 16


title: pancreatitis patient 14


title: pancreatitis patient 15


title: QSC 0hr rep1


title: QSC 0hr rep2


title: ASC 72hr rep3


title: pancreatitis patient 13


title: NT-3-chitosan tube (S), in the lesion (M), 20 days post-op, biol rep5

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 20 days after operation

value: 20 days after operation


title: pancreatitis patient 12


title: pancreatitis patient 11


title: pancreatitis patient 10


title: NT-3-chitosan tube (S), in the lesion (M), 10 days post-op, biol rep2

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 10 days after operation

value: spinal cord injury and NT-3-chitosan tube treatment


title: NT-3-chitosan tube (S), in the lesion (M), 30 days post-op, biol rep1


title: pancreatitis patient 9


title: NT-3-chitosan tube (S), in the lesion (M), 20 days post-op, biol rep3


title: pancreatitis patient 8


title: NT-3-chitosan tube (S), in the lesion (M), 10 days post-op, biol rep3

value: 10 days after operation


title: NT-3-chitosan tube (S), in the lesion (M), 10 days post-op, biol rep1


title: NT-3-chitosan tube (S), in the lesion (M), 20 days post-op, biol rep2


title: pancreatitis patient 7


title: NT-3-chitosan tube (S), in the lesion (M), 3 days post-op, biol rep3

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 3 days after operation

value: 3 days after operation


title: pancreatitis patient 5


title: pancreatitis patient 6


title: NT-3-chitosan tube (S), in the lesion (M), 3 days post-op, biol rep1

value: 5mm long segments in the T7-T8 lesioned area of the spinal cord


title: NT-3-chitosan tube (S), in the lesion (M), 3 days post-op, biol rep2


title: NT-3-chitosan tube (S), rostral to the lesion (R), 90 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 90 days after operation

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord

value: 90 days after operation


title: NT-3-chitosan tube (S), rostral to the lesion (R), 90 days post-op, biol rep2


title: NT-3-chitosan tube (S), rostral to the lesion (R), 90 days post-op, biol rep1


title: 12.5 hpf embryo T1 morpholino injected rep2

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray  processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent  Technologies). Briefly, 1.65 μg Cy3-labeled fragmented cRNA in hybridization buffer was  hybridized overnight (17 hours, 65 °C) to Agilent Whole Zebrafish Genome Oligo Microarrays  4x44K using Agilent’s recommended hybridization chamber and oven.Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1  for 1 min at room temperature followed by a second wash with preheated Agilent Gene  Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with  acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s  Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) was used to read out and process the  microarray image files

organism: Danio rerio

source_name: 12.5hpf embryo

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Adult AB strain fish were maintained bred under standard conditions at 28°C. Collected embryos were staged according to Kimmel ref is Kimmel et al 1995; Dev. Dyn. 203: 253-310.

extract_protocol: Control and “T1” morpholino-injected embryos were snap frozen at 12.5hpf for RNA extraction. Two biological repeats were then sent to Miltenyo Biotec for gene expression profiling using a one-colour Agilent Whole Zebrafish Genome Microarray.

treatment_protocol: Embryos at the 1 cell stage were injected with the following morpholinos obtained from Gene Tools: defbl1 “T1”: 5’-GGGCTTCATGTTGGATTCTTCAGAT-3’; defbl1 “T2”:5’-TTCTTCAGATGATGGCAGTCCTGGG-3’; defbl1 “S1”: 5’-  15  AGCAAACATACGAAACTTACAGTGC-3’. Approximately 1nl DNA was injected into embryos at a concentration of 62.5μM (“T1”), 250μM (“T2”) and 500μM (“S1”). Control embryos were injected with Gene Tools standard control morpholino.

tag: developmental stage

value: defbl1 morpholinos

value: embryo


title: pancreatitis patient 4

tag: tissue

value: pancreas


title: NT-3-chitosan tube (S), rostral to the lesion (R), 60 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 60 days after operation

value: Wistar rat


title: 12.5 hpf embryo Control rep2

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files

value: Gene Tools standard control morpholino


title: 12.5 hpf embryo T1 morpholino injected rep1


title: 12.5 hpf embryo Control rep1


title: NT-3-chitosan tube (S), rostral to the lesion (R), 60 days post-op, biol rep2

value: 60 days after operation

value: female


title: healthy individual 22

source_name: Pancreas RNA from healthy individual

tag: disease state

value: healthy


title: pancreatitis patient 3

value: pancreatitis


title: pancreatitis patient 2


title: healthy individual 20


title: NT-3-chitosan tube (S), rostral to the lesion (R), 30 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 30 days after operation

tag: treatment

value: 30 days after operation

value: adult rat, i.e. 2 months after birth


title: pancreatitis patient 1


title: NT-3-chitosan tube (S), rostral to the lesion (R), 60 days post-op, biol rep1

value: spinal cord injury and NT-3-chitosan tube treatment

tag: time


title: healthy individual 19


title: NT-3-chitosan tube (S), rostral to the lesion (R), 30 days post-op, biol rep1

tag: strain


title: zf_ovary_bpae-2_D

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

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

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 μm resolution

data_processing: Microarray image processing and data pre-processing were performed Agilent's Feature Extraction software v 9.5 following the manufacturer’s protocol and recommendations.  Fastlo normalization was implemented in R 2.10.1

source_name: ovary from fish exposed to bpa for 96 h

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

growth_protocol: Sexually mature adult fathead minnows (5-6 month old) and zebrafish (ab wild-type strain; 6-7 month old) were obtained from an on-site aquatic culture facility at the US EPA Mid-Continent Ecology Division, Duluth, MN, USA. Both species were held under a 16:8 light:dark photoperiod and fed brine shrimp to satiation twice daily. However, fathead minnows were fed frozen adult brine shrimp (San Francisco Bay Brand, Newark, CA, USA) while zebrafish were fed newly hatched (< 24 h old) brine shrimp nauplii (BioMarine Brand artemia cysts; Hawthorne, CA, USA). Fish survival, water temperature (mean ± SD; 25.0±0.3; both species), and dissolved oxygen (mean ± SD; zebrafish 6.7±0.3 mg/L; fathead 7.0±0.2) were monitored daily over the duration of the exposure and did not vary significantly between treatment groups or species.

extract_protocol: Total RNA was isolated from ovary tissue of both fathead minnow and zebrafish using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and RNA was quantified spectrophotometrically (Nanodrop). Total RNA samples were stored at -80oC until used for microarray analyses.

treatment_protocol: Fish were exposed to 0, 0.01, 0.1, 1.0, 10, or 100 µg BPA/L delivered in a continuous flow (45 ml/min) of sand filtered, UV treated, Lake Superior Water, without the use of carrier solvents. Following approximately 36 h of chemical (or control water) delivery to condition the tanks (20 L aquaria filled with 10 L of exposure water) and exposure apparatus, exposures were initiated by loading fish into the conditioned tanks. The design employed six replicate tanks per treatment. Three of the replicates were loaded with three male and three female zebrafish per tank, while the remaining three replicates were loaded with three male and three female fathead minnows. Addition of fish to the exposure tanks was staggered by replicate such that all sampling could be completed within 60 min of the desired 96 h exposure duration. Zebrafish were loaded and sampled one day prior to loading and sampling the fathead minnows so that three of the four exposure days for each species directly overlapped. After 96 h of exposure, fish were anesthetized in a buffered solution of tricaine methanesulfonate (MS-222; Finquel; Argent, Redmond, WA, USA) and weighed. Blood was collected from the caudal vasculature using microhematocrit tubes, centrifuged to separate the plasma, and plasma was stored at -80oC until analyzed. Liver, gonad, and brain tissues (including pituitary gland) were snap frozen in liquid nitrogen and stored at -80oC until extracted.

tag: ct-id

tag: agent

value: BPA

tag: dose

value: 0.01 µg BPA/L

value: ovary

tag: rep(tank)

value: ZF 3

tag: take down date

tag: gender

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: plasma vtg (mg/ml)

tag: array rep

value: D

tag: slide

tag: array


title: NT-3-chitosan tube (S), rostral to the lesion (R), 20 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 20 days after operation

tag: tissue

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord

value: 20 days after operation

tag: age


title: zf_ovary_bpae-2_B

value: ZF 2

value: B


title: healthy individual 17

value: pancreas

tag: disease state


title: healthy individual 18


title: zf_ovary_bpae-1_E

value: 0.1 µg BPA/L

value: E


title: NT-3-chitosan tube (S), rostral to the lesion (R), 20 days post-op, biol rep1

tag: treatment

tag: time

value: Wistar rat

value: female


title: zf_ovary_bpae-2_A

tag: ct-id

value: A


title: zf_ovary_bpae-2_E

tag: agent


title: healthy individual 21

value: healthy


title: zf_ovary_bpae-2_C

value: BPA

tag: dose

value: C


title: zf_ovary_bpae-1_D

value: ovary

tag: rep(tank)


title: healthy individual 16


title: zf_ovary_bpae-1_B

tag: take down date


title: zf_ovary_bpae-1_A

value: ZF 1

tag: gender


title: NT-3-chitosan tube (S), rostral to the lesion (R), 20 days post-op, biol rep2

value: spinal cord injury and NT-3-chitosan tube treatment

tag: strain

value: adult rat, i.e. 2 months after birth


title: NT-3-chitosan tube (S), rostral to the lesion (R), 10 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 10 days after operation

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord

value: 10 days after operation


title: NT-3-chitosan tube (S), rostral to the lesion (R), 30 days post-op, biol rep2

value: 30 days after operation


title: zf_ovary_con_F

source_name: ovary from fish exposed to control water for 96 h

value: control

value: ZF 3

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)


title: NT-3-chitosan tube (S), rostral to the lesion (R), 10 days post-op, biol rep2


title: NT-3-chitosan tube (S), rostral to the lesion (R), 10 days post-op, biol rep1


title: zf_ovary_bpae-1_C

value: 0.1 µg BPA/L

tag: plasma vtg (mg/ml)

tag: array rep


title: healthy individual 15

value: pancreas


title: zf_ovary_con_E

value: E

tag: slide

tag: array


title: NT-3-chitosan tube (S), rostral to the lesion (R), 3 days post-op, biol rep3

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 3 days after operation

tag: tissue

value: 3 days after operation

value: Wistar rat

value: female

tag: age


title: healthy individual 14

tag: disease state

value: healthy


title: healthy individual 12


title: healthy individual 13


title: zf_ovary_con_D

value: ovary

value: ZF 2

value: D


title: healthy individual 11


title: healthy individual 10


title: pancreatitis patient 25

source_name: Pancreas RNA from pancreatitis patient

value: pancreatitis


title: NT-3-chitosan tube (S), rostral to the lesion (R), 1 day post-op, biol rep2

source_name: 5 mm long segments rostral to the lesioned area were sampled under RNAase-free conditions 1 day after operation

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord

tag: treatment

value: spinal cord injury and NT-3-chitosan tube treatment

tag: time

value: 1 day after operation

value: adult rat, i.e. 2 months after birth


title: healthy individual 9


title: zf_ovary_con_C

tag: ct-id

tag: agent

value: control

value: ZF 1

value: C


title: SKNAS_G_3

city: Detroit

first: Magen

middle: Marie

last: Johnson

state: MI

address: 540 E Canfield

department: Pharmacology

institute: Wayne State University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina BeadStudio

source_name: SKNAS 36 fold nurr1 overexpression biological replicate 3

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: organ

value: Brain

tag: disease

value: Neuroblastoma

tag: derived from metastatic site

value: Bone Marrow

tag: growth properties

value: Adherent

tag: morphology

value: Epithelial

tag: cell type

value: Neuroblast

value: 6 yrs

value: Female

tag: ethnicity

value: Caucasian


title: NT-3-chitosan tube (S), rostral to the lesion (R), 3 days post-op, biol rep1

value: 3 days after operation

tag: strain

value: Wistar rat

tag: gender

value: female


title: NT-3-chitosan tube (S), rostral to the lesion (R), 1 day post-op, biol rep3

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord

value: spinal cord injury and NT-3-chitosan tube treatment

value: 1 day after operation


title: SKNAS_G_1

source_name: SKNAS 36 fold nurr1 overexpression biological replicate 1


title: zf_ovary_bpa100_F

value: BPA

tag: dose

value: 100 µg BPA/L

value: ovary

tag: rep(tank)

value: ZF 2

tag: take down date

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: plasma vtg (mg/ml)

tag: array rep

tag: slide

tag: array


title: healthy individual 8

tag: tissue

value: pancreas

tag: disease state

value: healthy


title: zf_ovary_con_B

tag: ct-id

tag: agent

value: control

value: ZF 1

value: B


title: zf_ovary_bpa100_D

value: D


title: NT-3-chitosan tube (S), rostral to the lesion (R), 3 days post-op, biol rep2

tag: treatment

tag: time

value: 3 days after operation

tag: age

value: adult rat, i.e. 2 months after birth


title: SKNAS_G_2

source_name: SKNAS 36 fold nurr1 overexpression biological replicate 2

tag: organ

value: Brain

tag: disease

value: Neuroblastoma

tag: derived from metastatic site

value: Bone Marrow

tag: growth properties

value: Adherent

tag: morphology

value: Epithelial

tag: cell type

value: Neuroblast

value: 6 yrs

tag: gender

value: Female

tag: ethnicity

value: Caucasian


title: NT-3-chitosan tube (S), rostral to the lesion (R), 1 day post-op, biol rep1

value: 5mm long segments rostral to the T7-T8 lesioned area of the spinal cord

value: spinal cord injury and NT-3-chitosan tube treatment

value: 1 day after operation

tag: strain

value: Wistar rat

value: female


title: zf_ovary_con_A

value: control

value: ovary

tag: rep(tank)

value: ZF 3

tag: take down date

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: plasma vtg (mg/ml)

tag: array rep

value: A

tag: slide

tag: array


title: zf_ovary_bpa100_E

tag: ct-id

tag: agent

value: BPA

tag: dose

value: 100 µg BPA/L

tag: tissue

value: ZF 1

value: E


title: lung_silica_2

first: Raymond

middle: J

last: Langley

state: New Mexico

address: 2425 Ridgecrest Dr

department: immunology

institute: LRRI

hyb_protocol: Biotin-labeled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix), and 20 mg of the labeled cRNA was fragmented. The cRNA and fragmented cRNA quality was assessed by the Agilent 2100 Bioanalyzer (Agilent; Foster City, CA) and the RNA 6000 Nano LabChip kit (Agilent). The labeled fragmented cRNA was hybridized to Affymetrix GeneChip Rat 230 2.0 arrays for 16 h at 45oC following the Affymetrix protocol specific to this array type. Washing and staining were performed on the Affymetrix fluidics (450) station according to the antibody amplification protocol (Fluidics script: EukGE-WS2v5).

scan_protocol: The Gene Chips were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The analysis was performed with GeneSpring software package (Agilent Technologies, Santa Clara, CA).  All samples were subject to per-chip normalization. Data were filtered twice, a fold change filter (2 fold up or down), and the Statistical Analysis of Microarray software (http://www-stat.stanford.edu/~tibs/SAM/), to find all genes with a < 10% false positive q-score.

molecule: polyA RNA

source_name: lung, chronically exposed to silica

label_protocol: Biotinylated cRNA was synthesized by in vitro transcription using the GeneChip IVT Labeling kit (Affymetrix).

extract_protocol: Lung tissues were homogenized in the presence of TRI reagent (MRC Molecular Research Center, Cincinnati, OH). Total RNA was isolated using the 1-bromo-3-chloropropane (BCP) phase separation reagent (MRC Molecular Research Center). RNA was precipitated by 2-propanol and washed with 75% ethanol.

value: Lung

value: Lewis

tag: treatment

value: exposed to silica


title: zf_ovary_bpa100_C

value: ZF 2

value: C


title: SKNAS_E_2

source_name: SKNAS 2 fold nurr1 overexpression biological replicate 2

tag: organ

value: Brain

tag: disease

value: Neuroblastoma

tag: derived from metastatic site

value: Bone Marrow

tag: growth properties

value: Adherent

tag: morphology

value: Epithelial

tag: cell type

value: Neuroblast

tag: age

value: 6 yrs

value: Female

value: Caucasian


title: SKNAS_E_3

source_name: SKNAS 2 fold nurr1 overexpression biological replicate 3

tag: gender

tag: ethnicity


title: healthy individual 7

value: pancreas

tag: disease state

value: healthy


title: healthy individual 6


title: healthy individual 5


title: healthy individual 4


title: healthy individual 3


title: SKNAS_C_3

source_name: SKNAS empty vector biological replicate 3


title: lung_silica_3

tag: strain


title: zf_ovary_bpa100_A

value: BPA

value: 100 µg BPA/L

value: ovary

tag: rep(tank)

value: ZF 3

tag: take down date

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: plasma vtg (mg/ml)

tag: array rep

value: A

tag: slide

tag: array


title: SKNAS_E_1

source_name: SKNAS 2 fold nurr1 overexpression biological replicate 1

tag: organ

value: Brain

tag: disease

tag: derived from metastatic site


title: healthy individual 2

source_name: Pancreas RNA from healthy individual

tag: tissue


title: zf_ovary_bpa100_B

tag: ct-id

tag: agent

tag: dose

value: ZF 1

value: B


title: lung_control_2

source_name: lung, from control

value: Lung

value: Lewis

tag: treatment

value: control


title: SKNAS_C_2

source_name: SKNAS empty vector biological replicate 2

value: Neuroblastoma

value: Bone Marrow

tag: growth properties

value: Adherent

tag: morphology

value: Epithelial

tag: cell type

value: Neuroblast

tag: age

value: 6 yrs

tag: gender

tag: ethnicity


title: lung_control_1

tag: strain


title: lung_silica_1

value: exposed to silica


title: Subject 19

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

scan_protocol: BeadChips were scanned using Illumina BeadArray Scanner

data_processing: The data were normalized using quantile-normalization with GenomeStudio V2010.2

source_name: PBMC

label_protocol: PCR product was prepared with standard Illumina protocol for arrays

extract_protocol: Total RNA was isolated using RNeasy kits (QIAGEN, Valencia, CA) according to manufacturer instructions.

treatment_protocol: All subjects who underwent IFN-alpha treatment received either pegylated IFN-alfa-2b (Pegintron, Schering Plough, Kenilworth, NJ; 1.5µg/kg)(n=5) or pegylated IFN-alfa-2a (Pegasys, Roche-Genentech, San Francisco, CA; 180mg)(n=6) administered subcutaneously and ribavirin (800–1400 mg/day). Participation in the treatment versus control group was determined by patients and their physician based on scheduling constraints and personal preferences and was not based on standardized criteria or controlled by study protocol.

value: IFN-alpha

tag: week 12 madrs score

tag: week 12 mfi score

tag: Sex

value: f

tag: race

value: cau

tag: education

value: high school degree

tag: past md

value: no

tag: past subsabuse

tag: bl madrs

tag: bl mfi

tag: bmi


title: zf_ovary_bpa10_F

source_name: ovary from fish exposed to bpa for 96 h

tag: ct-id

tag: agent

value: BPA

tag: dose

value: 10 µg BPA/L

tag: tissue

value: ovary

tag: rep(tank)

value: ZF 3

tag: take down date

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: plasma vtg (mg/ml)

tag: array rep

tag: slide

tag: array


title: healthy individual 1

value: pancreas

tag: disease state

value: healthy


title: zf_ovary_bpa10_D

value: ZF 2

tag: gender

value: D


title: SKNAS_C_1

source_name: SKNAS empty vector biological replicate 1

tag: organ

value: Brain

tag: disease

value: Neuroblastoma

tag: derived from metastatic site

value: Bone Marrow

tag: growth properties

value: Adherent

tag: morphology

value: Epithelial

tag: cell type

value: Neuroblast

tag: age

value: Female

tag: ethnicity

value: Caucasian


title: zf_ovary_bpa10_C

tag: ct-id

tag: agent

value: BPA

tag: dose

tag: tissue

tag: rep(tank)

tag: take down date

value: C


title: zf_ovary_bpa10_E

value: 10 µg BPA/L

value: ovary

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: plasma vtg (mg/ml)

tag: array rep

value: E

tag: slide

tag: array


title: Subject 20

tag: treatment

value: IFN-alpha

tag: week 12 madrs score

tag: week 12 mfi score

tag: Sex

value: f

tag: race

value: af am

tag: education

value: some college

tag: past md

value: no

tag: past subsabuse

tag: bl madrs

tag: bl mfi

tag: bmi


title: Subject 21

tag: age

value: cau

value: high school degree

value: yes


title: Lung-Rt Caudal Lobe_Lung_LP_048,1_7w_603_CS,PS_Lung_THI07041_Rat230_2_THI 07041

city: Raleigh

first: David

last: Dorman

address: 4700 Hillsborough Street

institute: North Carolina State Universisy

description: LP_048,1_7w_603_CS,PS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA normalization using Bioconductor Package in R

source_name: Lung-Rt Caudal Lobe

label_protocol: standard Affymetrix protocol

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen RNAeasy Mini kit

treatment_protocol:
in vivo Treatment: Cigarette Smoke, Treatment Repeat: 5, Units of Treatment Repeat: days/wk, Treatment Duration: 5, Units of Duration: weeks, Treatment Time: 3, Units of Treatment Time: hr/day, Route of Exposure: nose-only inhalation, Dose or Concentration: 0.48, Units of Dose or Concentration: mg WTPM/L
Treatment_2: in vivo Treatment: Silica, in vivo Treatment: Silica, in vivo Treatment: Silica, in vivo Treatment: Silica, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Dose or Concentration: 1, Dose or Concentration: 1, Dose or Concentration: 1, Dose or Concentration: 1, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNA later

tag: strain

value: Sprague-Dawley

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: anesthetized with sodium pentobarbital and exsanguinated by transection of the abdominal aorta

value: Male

tag: units of age

value: weeks

tag: tissue

value: Lung

tag: in vivo treatment

value: Cigarette smoke

tag: treatment2_in vivo treatment

value: Silica


title: zf_ovary_bpa10_B

tag: ct-id

tag: agent

value: BPA

tag: dose

value: 10 µg BPA/L

value: ovary

tag: rep(tank)

value: ZF 1

tag: take down date

tag: gender

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: plasma vtg (mg/ml)

tag: array rep

value: B

tag: slide

tag: array


title: Lung-Rt Caudal Lobe_Lung_LP_048,1_7w_605_CS,PS_Lung_THI07041_Rat230_2_THI 07041

description: LP_048,1_7w_605_CS,PS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age


title: lung_control_3

tag: tissue

value: Lewis

tag: treatment

value: control


title: Subject 18

value: IFN-alpha

tag: week 12 madrs score

tag: week 12 mfi score

value: f

tag: race

value: af am

tag: education

value: high school degree

tag: past md

value: no

tag: past subsabuse

tag: bl madrs

tag: bl mfi

tag: bmi


title: Lung-Rt Caudal Lobe_Lung_LP_048,1_7w_604_CS,PS_Lung_THI07041_Rat230_2_THI 07041

description: LP_048,1_7w_604_CS,PS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: good

tag: sample preservation

value: RNA later

tag: strain

value: Sprague-Dawley

value: adult

value: anesthetized with sodium pentobarbital and exsanguinated by transection of the abdominal aorta

value: Male

tag: units of age

value: weeks

value: Lung

tag: in vivo treatment

tag: treatment2_in vivo treatment


title: Lung-Rt Caudal Lobe_Lung_LP_048,1_7w_602_CS,PS_Lung_THI07041_Rat230_2_THI 07041

description: LP_048,1_7w_602_CS,PS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

value: excellent

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: tissue

value: Cigarette smoke

value: Silica


title: zf_ovary_bpa10_A

tag: ct-id

tag: agent

value: BPA

tag: dose

value: 10 µg BPA/L

value: ovary

tag: rep(tank)

value: ZF 1

tag: take down date

tag: gender

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: plasma vtg (mg/ml)

tag: array rep

value: A

tag: slide

tag: array


title: Lung-Rt Caudal Lobe_Lung_LP_048,1_7w_405_CS,IS_Lung_THI07041_Rat230_2_THI 07041

description: LP_048,1_7w_405_CS,IS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

treatment_protocol:
in vivo Treatment: Cigarette Smoke, Treatment Repeat: 5, Units of Treatment Repeat: days/wk, Treatment Duration: 5, Units of Duration: weeks, Treatment Time: 3, Units of Treatment Time: hr/day, Route of Exposure: nose-only inhalation, Dose or Concentration: 0.48, Units of Dose or Concentration: mg WTPM/L
Treatment_2: in vivo Treatment: Iraqi Sand, in vivo Treatment: Iraqi Sand, in vivo Treatment: Iraqi Sand, in vivo Treatment: Iraqi Sand, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Dose or Concentration: 1, Dose or Concentration: 1, Dose or Concentration: 1, Dose or Concentration: 1, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: good

tag: sample preservation

tag: strain

tag: individual

tag: developmental state

tag: units of age

tag: in vivo treatment

tag: treatment2_in vivo treatment

value: Iraqi Sand


title: Subject 16

tag: treatment

value: IFN-alpha

tag: week 12 madrs score

tag: week 12 mfi score

tag: age

tag: Sex

value: m

tag: race

value: af am

tag: education

value: some highschool

tag: past md

value: yes

tag: past subsabuse

value: no

tag: bl madrs

tag: bl mfi

tag: bmi


title: Subject 17

value: some college


title: Subject 15

value: high school degree


title: Subject 13

value: his


title: Subject 12


title: zf_ovary_bpa1_E

tag: ct-id

tag: agent

value: BPA

tag: dose

value: 1.0 µg BPA/L

tag: tissue

tag: rep(tank)

tag: take down date

tag: gender

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: plasma vtg (mg/ml)

tag: array rep

value: E

tag: slide

tag: array


title: HCG1/BG14 - repeat 3 - mAdbID:106672

city: Bethesda

first: Huei-Fung

last: Tsai

state: MD

address: 10 Center Dr. Bldg. 10 Rm. 11N228

department: LCID

institute: NIH/NIAID

description: mAdb experiment ID: 106672

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR on an Agilent DNA Microarray Scanner G2505B.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.

organism: Nakaseomyces glabratus

source_name: WT BG14 Control - Cy3

label_protocol:
Cy3 Labeling Protocol
Other: Ten micrograms of total RNA were used for each labeling. The RNA was reversed transcribed to cDNA to incorporate the fluorescent Cy3-dUTP (GE Health Care).

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was isolated from log-phase culture of C. glabrata grown in YPD using Trizole (Invitrogen) and RNeasy MiniElute cleanup kit (Qiagen).

tag: strain

tag: developmental stage

value: log-phase culture

tag: genotype/variation

value: Wild Type

source_name: mt HCG1 - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: Ten micrograms of total RNA were used for each labeling. The RNA was reversed transcribed to cDNA to incorporate the fluorescent Cy5-dUTP (GE Health Care).

value: ure2 mutant


title: Lung-Rt Caudal Lobe_Lung_LP_048,1_7w_406_CS,IS_Lung_THI07041_Rat230_2_THI 07041

description: LP_048,1_7w_406_CS,IS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNA later

value: Sprague-Dawley

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: anesthetized with sodium pentobarbital and exsanguinated by transection of the abdominal aorta

tag: Sex

value: Male

tag: age

tag: units of age

value: weeks

value: Lung

tag: in vivo treatment

value: Cigarette smoke

tag: treatment2_in vivo treatment


title: zf_ovary_bpa1_D

tag: ct-id

tag: agent

tag: dose

tag: tissue

value: ovary

tag: rep(tank)

value: ZF 1

tag: take down date

tag: gender

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: plasma vtg (mg/ml)

tag: array rep

value: D

tag: slide

tag: array


title: HCG7/BG14 - repeat 3 - mAdbID:106668

description: mAdb experiment ID: 106668

tag: strain

tag: developmental stage

value: log-phase culture

tag: genotype/variation

source_name: mt HCG7 - Cy5


title: Subject 14

tag: treatment

value: IFN-alpha

tag: week 12 madrs score

tag: week 12 mfi score

tag: age

tag: Sex

value: m

tag: race

value: af am

tag: education

value: some college

tag: past md

value: no

tag: past subsabuse

value: yes

tag: bl madrs

tag: bl mfi

tag: bmi


title: zf_ovary_bpa1_C

tag: ct-id

tag: agent

value: BPA

tag: dose

value: 1.0 µg BPA/L

tag: tissue

tag: rep(tank)

value: ZF 3

tag: take down date

tag: gender

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: plasma vtg (mg/ml)

tag: array rep

value: C

tag: slide


title: Lung-Rt Caudal Lobe_Lung_LP_048,1_7w_404_CS,IS_Lung_THI07041_Rat230_2_THI 07041

description: LP_048,1_7w_404_CS,IS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: good

tag: sample preservation

value: RNA later

tag: strain

value: Sprague-Dawley

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: anesthetized with sodium pentobarbital and exsanguinated by transection of the abdominal aorta

tag: Sex

value: Male

tag: age

tag: units of age

value: weeks

value: Lung

tag: in vivo treatment

tag: treatment2_in vivo treatment

value: Iraqi Sand


title: Subject 11

tag: treatment

value: IFN-alpha

tag: week 12 madrs score

tag: week 12 mfi score

value: m

tag: race

value: cau

tag: education

value: post graduate

tag: past md

tag: past subsabuse

tag: bl madrs

tag: bl mfi

tag: bmi


title: BG14/HCG1 - repeat 4- rev. label - mAdbID:106673

description: mAdb experiment ID: 106673

source_name: WT BG14 Control - Cy5

tag: strain

tag: developmental stage

value: log-phase culture

tag: genotype/variation

value: Wild Type

source_name: mt HCG1 - Cy3

value: ure2 mutant


title: HCG1/BG14 - repeat 2 - mAdbID:106671

description: mAdb experiment ID: 106671


title: Lung-Rt Caudal Lobe_Lung_LP_048,0_7w_204_CS,AC_Lung_THI07041_Rat230_2_THI 07041

description: LP_048,0_7w_204_CS,AC_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

treatment_protocol:
in vivo Treatment: Cigarette smoke, Treatment Repeat: 5, Units of Treatment Repeat: days/wk, Treatment Duration: 5, Units of Duration: weeks, Treatment Time: 3, Units of Treatment Time: hr/day, Route of Exposure: nose-only inhalation, Dose or Concentration: 0.48, Units of Dose or Concentration: mg WTPM/L
Treatment_2: in vivo Treatment: Air Control, in vivo Treatment: Air Control, in vivo Treatment: Air Control, in vivo Treatment: Air Control, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Dose or Concentration: 0, Dose or Concentration: 0, Dose or Concentration: 0, Dose or Concentration: 0, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: bioanalyzer results

value: excellent

tag: sample preservation

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: tissue

value: Cigarette smoke

value: Air control


title: anti-miR-21-Siha vs Siha

city: guangzhou

first: yao

last: tingting

address: yanjiangxi road 107

institute: sun yat-sen memorial hospital,sun yat-sen university

description: compare gene expression profiles of control cells

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated.

source_name: Siha cells trasfected with anti-miR-21

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Cells were cultured in RPMI 1640 (Life Technologies) supplemented with 10% fetal bovine serum (Invitrogen) at 37°C with 5% CO2.

extract_protocol: Stably transfected cells and control cells were harvest, and total RNA was extracted with Trizol Reagent (Invitrogen) and ethanol precipitation.

treatment_protocol: Anti-miR-21 (Ambion) was transiently transfected into Caski and Siha cells with the siPORT NeoFx transfection reagent (Ambion). For mock transfection conditions, anti-miR miRNA was substituted with random oligonucleotides at equal concentration. All experiments were done in triplicate. At 48 h post-transfection, adherent cells were harvested.

tag: cell type

value: cervical carcinoma

tag: cell line

value: Siha cells

source_name: Siha cells control


title: BG14/HCG7 - repeat 4- rev. label - mAdbID:106669

description: mAdb experiment ID: 106669

tag: strain

tag: developmental stage

source_name: mt HCG7 - Cy3


title: Lung-Rt Caudal Lobe_Lung_LP_048,1_7w_402_CS,IS_Lung_THI07041_Rat230_2_THI 07041

description: LP_048,1_7w_402_CS,IS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: array type

tag: rna integrity number

value: RNA later

value: Sprague-Dawley

value: adult

value: anesthetized with sodium pentobarbital and exsanguinated by transection of the abdominal aorta

value: Male

tag: units of age

tag: in vivo treatment

tag: treatment2_in vivo treatment


title: Lung-Rt Caudal Lobe_Lung_LP_048,0_7w_205_CS,AC_Lung_THI07041_Rat230_2_THI 07041

description: LP_048,0_7w_205_CS,AC_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: bioanalyzer results

value: good

value: weeks

value: Lung


title: HCG1/BG14 - repeat 1 - mAdbID:106670

description: mAdb experiment ID: 106670

value: log-phase culture

tag: genotype/variation


title: zf_ovary_bpa1_A

tag: ct-id

tag: agent

value: BPA

tag: dose

value: 1.0 µg BPA/L

value: ovary

tag: rep(tank)

value: ZF 2

tag: take down date

tag: gender

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: plasma vtg (mg/ml)

tag: array rep

value: A

tag: slide

tag: array


title: zf_ovary_bpa1_B

tag: tissue

value: ZF 3

value: B


title: Subject 10

tag: treatment

value: Control

tag: week 12 madrs score

tag: week 12 mfi score

tag: age

tag: Sex

value: f

tag: race

value: cau

tag: education

value: college degree

tag: past md

value: no

tag: past subsabuse

tag: bl madrs

tag: bl mfi

tag: bmi


title: Lung-Rt Caudal Lobe_Lung_LP_048,0_7w_203_CS,AC_Lung_THI07041_Rat230_2_THI 07041

description: LP_048,0_7w_203_CS,AC_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNA later

tag: strain

value: Sprague-Dawley

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: anesthetized with sodium pentobarbital and exsanguinated by transection of the abdominal aorta

value: Male

tag: units of age

tag: in vivo treatment

value: Cigarette smoke

tag: treatment2_in vivo treatment

value: Air control


title: HCG7/BG14 - repeat 2 - mAdbID:106667

description: mAdb experiment ID: 106667

tag: developmental stage

value: log-phase culture

tag: genotype/variation

value: Wild Type

value: ure2 mutant


title: Subject 9

tag: treatment

value: Control

tag: week 12 madrs score

tag: week 12 mfi score

tag: age

tag: Sex

tag: race

value: af am

tag: education

value: post graduate

tag: past md

tag: past subsabuse

value: yes

tag: bl madrs

tag: bl mfi

tag: bmi