title: organism part name: 22DAP_Endosperm - rep1

value: Inbred line B73


title: pediatric acute lymphoblastic leukemia_545 [Custom TaqMan Array]

status: Public on Feb 11 2011

type: RNA

city: Rotterdam

first: Monique

last: Den Boer

address: POBox 2060

department: Pediatric Oncology

country: Netherlands

institute: Erasmus MC-Sophia Children's Hospital

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: The ∆Ct value was calculated according to the following equation: Ct value of the specific miRNA minus the Ct value of the internal reference. In case of the TaqMan MicroRNA arrays the mean Ct values for snoR-13 and snoR-14 were used as reference whereas in case of the Custom Taqman arrays snoR-1 was used.

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: pediatric acute lymphoblastic leukemia

label_protocol: not applicable

extract_protocol: RNA from the cell samples was extracted using TRIzol reagents (firma). Only RNA with an RNA Integrity Number (RIN) of  ≥ 7.5 as measured by the 2100 Bioanalyzer (Agilent, Amstelveen, the Netherlands) was used as input for the RT-qPCR reactions.

tag: subtype

value: nBM

tag: patient id

tag: prednisolone-score

value: unknown

tag: vincristine-score

tag: daunorubicin-score

tag: l-asparaginase-score


title: pediatric acute lymphoblastic leukemia_6684 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_838 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_6283 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_4139 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_4138 [Custom TaqMan Array]


title: L1085

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format.

hyb_protocol: As per manufacturer's instructions.

scan_protocol: As per manufacturer's instructions.

data_processing: Data were analyzed using the statistical language R. As Illumina identifiers are not stable and consistent between different chip versions, raw oligonucleotide sequences were converted to nuIDs. Data were transformed using the variance stabilizing transformation (vst) algorithm and subsequently normalized using robust spline normalization. Conversion to nuIDs, variance stabilizing transformation, and normalization of the data were all carried out using the Bioconductor package lumi. Quality control was performed using the Bioconductor package arrayQualityMetrics. Two supplementary/raw files are present, because each array that represents one sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

label: biotin

source_name: Osteosarcoma pre-chemotherapy biopsy

label_protocol: As per manufacturer's instructions.

extract_protocol: Osteosarcoma tissue was snap-frozen in 2-Methylbutane (Sigma-Aldrich, Zwijndrecht, the Netherlands) and stored at -70°C. Using a cryostat, 20 µm sections from each block were cut and stained with hematoxylin and eosin to ensure at least 70% tumor content and viability. RNA was isolated using TRIzol reagent (Invitrogen), followed by RNA clean-up using the QIAGEN Rneasy mini kit (Venlo, the Netherlands) with on-column DNAse treatment, according to manufacturers instructions. RNA quality and concentration were measured using an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA) and Nanodrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA), respectively.

tag: age

value: 223 months

tag: gender

value: M

tag: histological subtype

value: Chondroblastic

tag: tumor location

value: Left proximal tibia

tag: huvos grade

tag: group

value: Metastases at 21 months after diagnosis of the primary tumor

tag: status

value: Deceased at 39 months after diagnosis of the primary tumor


title: organism part name: 20DAP_Embryo - rep1

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

hyb_protocol: NimbleGen protocol for sample hybridization

scan_protocol: NimbleGen protocol for scanning one-color arrays

data_processing: RMA normalization was performed using the rma() function in the oligo package of Bioconductor (www.bioconductor.org), modified to handle possible many-to-many relationships between probes and source sequences (summarization groups). The normalization scripts are available from the PLEXdb team by request.

organism: Zea mays

source_name: embryo (organism part name: 20DAP_Embryo)

label_protocol: NimbleGen One-Color DNA Labeling Kit

extract_protocol: TRIZOL RNA extraction

tag: germplasm name

tag: organism part

value: PO:0009009 embryo

tag: development stage

value: PO:0007631 embryo development stages


title: IOR-019

value: 336 months

value: Fibroblastic

value: Femur

value: No metastases

value: Alive at 60 months after diagnosis of the primary tumor


title: organism part name: 20DAP_Endosperm - rep3

source_name: endosperm (organism part name: 20DAP_Endosperm)

value: PO:0009089 endosperm

value: PO:0007633 endosperm development stages


title: L1368

value: 177 months

value: Osteoblastic

value: Left distal femur

value: Metastases present at diagnosis

value: Alive at 95 months after diagnosis of the primary tumor


title: organism part name: 20DAP_Embryo - rep2

value: Inbred line B73


title: IOR-016

value: 696 months

value: F

value: Telangiectatic

value: Tibia

value: Unknown


title: organism part name: 20DAP_Whole Seed - rep3

description: 20DAP_Whole Seed

source_name: fruit (organism part name: 20DAP_Whole Seed)

value: PO:0007042 5 fruit formation


title: IOR-015

value: 264 months

value: M

value: Fibroblastic

value: Humerus


title: organism part name: 20DAP_Whole Seed - rep1

description: 20DAP_Whole Seed


title: organism part name: 18DAP_Pericarp - rep3

source_name: pericarp (organism part name: 18DAP_Pericarp)

value: PO:0009084 pericarp


title: pediatric acute lymphoblastic leukemia_6358 [Custom TaqMan Array]

value: T-ALL

value: unknown


title: organism part name: 20DAP_Endosperm - rep2

value: PO:0009089 endosperm

value: PO:0007633 endosperm development stages


title: organism part name: 18DAP_Pericarp - rep1


title: pediatric acute lymphoblastic leukemia_3526 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_6308 [Custom TaqMan Array]


title: organism part name: 20DAP_Endosperm - rep1


title: organism part name: 18DAP_Pericarp - rep2


title: L1369

value: 212 months

value: Osteoblastic

value: Right distal femur

value: Metastases at 17 months after diagnosis of the primary tumor

value: Deceased at 83 months after diagnosis of the primary tumor


title: L1016

value: 200 months

value: Left proximal tibia

value: Metastases at 6 months after diagnosis of the primary tumor

value: Deceased at 10 months after diagnosis of the primary tumor


title: pediatric acute lymphoblastic leukemia_3330 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_3325 [Custom TaqMan Array]


title: IOR-011

value: 204 months

value: F

value: No metastases

value: Alive at 63 months after diagnosis of the primary tumor


title: pediatric acute lymphoblastic leukemia_3311 [Custom TaqMan Array]

value: T-ALL


title: IOR-008

value: 144 months

value: Femur

value: Metastases at 44 months after diagnosis of the primary tumor

value: Deceased at 110 months after diagnosis of the primary tumor


title: pediatric acute lymphoblastic leukemia_3044 [Custom TaqMan Array]

value: unknown


title: IOR-004

value: 228 months

value: M

value: Osteoblastic

value: Metastases at 24 months after diagnosis of the primary tumor

value: Alive at 123 months after diagnosis of the primary tumor


title: pediatric acute lymphoblastic leukemia_1701 [Custom TaqMan Array]


title: organism part name: 18DAP_Embryo - rep3

source_name: embryo (organism part name: 18DAP_Embryo)

value: Inbred line B73

value: PO:0009009 embryo

value: PO:0007631 embryo development stages


title: organism part name: 18DAP_Whole Seed - rep1

description: 18DAP_Whole Seed

source_name: fruit (organism part name: 18DAP_Whole Seed)

value: PO:0007042 5 fruit formation


title: organism part name: 18DAP_Endosperm - rep3

source_name: endosperm (organism part name: 18DAP_Endosperm)

value: PO:0009089 endosperm

value: PO:0007633 endosperm development stages


title: organism part name: 18DAP_Embryo - rep1


title: organism part name: 18DAP_Endosperm - rep1


title: IOR-001

value: 264 months

value: Metastases at 10 months after diagnosis of the primary tumor

value: Alive at 36 months after diagnosis of the primary tumor


title: pediatric acute lymphoblastic leukemia_748 [Custom TaqMan Array]

value: T-ALL


title: organism part name: 16DAP_Embryo - rep2

source_name: embryo (organism part name: 16DAP_Embryo)


title: organism part name: 18DAP_Whole Seed - rep3

description: 18DAP_Whole Seed


title: organism part name: 18DAP_Endosperm - rep2


title: organism part name: 16DAP_Embryo - rep3


title: 35855-05

value: 385 months

value: Possibly chondromyxoid fibroma like

value: Right humerus

value: Deceased at 18 months after diagnosis of the primary tumor


title: organism part name: 20DAP_Whole Seed - rep2

description: 20DAP_Whole Seed


title: organism part name: 16DAP_Embryo - rep1


title: organism part name: 16DAP_Endosperm - rep2

source_name: endosperm (organism part name: 16DAP_Endosperm)


title: organism part name: 16DAP_Whole Seed - rep3

description: 16DAP_Whole Seed

source_name: fruit (organism part name: 16DAP_Whole Seed)


title: organism part name: 16DAP_Endosperm - rep3


title: organism part name: 18DAP_Whole Seed - rep2

description: 18DAP_Whole Seed


title: 24939-05

value: 129 months

value: F

value: Chondroblastic

value: Left distal femur

value: Unknown

value: Metastases present at diagnosis

value: Deceased at 4 months after diagnosis of the primary tumor


title: pediatric acute lymphoblastic leukemia_697 [Custom TaqMan Array]

value: unknown


title: organism part name: 18DAP_Embryo - rep2

value: Inbred line B73

value: PO:0009009 embryo

value: PO:0007631 embryo development stages


title: organism part name: 16DAP_Endosperm - rep1

value: PO:0009089 endosperm

value: PO:0007633 endosperm development stages


title: 4474-05P

value: 468 months

value: Fibroblastic

value: Metastases at 36 months after diagnosis of the primary tumor

value: Deceased at 189 months after diagnosis of the primary tumor


title: 35215-05

value: 220 months

value: M

value: Osteoblastic

value: Right proximal tibia

value: Alive at 26 months after diagnosis of the primary tumor


title: organism part name: 16DAP_Whole Seed - rep2

description: 16DAP_Whole Seed

value: PO:0007042 5 fruit formation


title: pediatric acute lymphoblastic leukemia_4623 [Custom TaqMan Array]

value: hyperdiploid

value: sensitive


title: organism part name: 16DAP_Whole Seed - rep1

description: 16DAP_Whole Seed

value: Inbred line B73


title: pediatric acute lymphoblastic leukemia_4988 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_419 [Custom TaqMan Array]

value: T-ALL

value: unknown


title: pediatric acute lymphoblastic leukemia_3150 [Custom TaqMan Array]


title: 21150-03

value: 205 months

value: Chondroblastic

value: Left distal femur

value: Metastases at 9 months after diagnosis of the primary tumor

value: Deceased at 35 months after diagnosis of the primary tumor


title: pediatric acute lymphoblastic leukemia_2900 [Custom TaqMan Array]

value: resistant


title: organism part name: 14DAP_Endosperm - rep3

source_name: endosperm (organism part name: 14DAP_Endosperm)

value: PO:0009089 endosperm

value: PO:0007633 endosperm development stages


title: organism part name: 14DAP_Whole Seed - rep3

description: 14DAP_Whole Seed

source_name: fruit (organism part name: 14DAP_Whole Seed)


title: organism part name: 14DAP_Endosperm - rep1


title: 19264-05

value: 181 months

value: M

value: Sclerosing

value: Metastases at 25 months after diagnosis of the primary tumor

value: Alive at 25 months after diagnosis of the primary tumor


title: organism part name: 14DAP_Whole Seed - rep2

description: 14DAP_Whole Seed

value: PO:0007042 5 fruit formation


title: organism part name: 12DAP_Endosperm - rep3

source_name: endosperm (organism part name: 12DAP_Endosperm)

value: Inbred line B73


title: 26814-04

value: 183 months

value: Osteoblastic

value: Distal femur

value: Metastases present at diagnosis

value: Deceased at 27 months after diagnosis of the primary tumor


title: organism part name: 14DAP_Endosperm - rep2


title: 20014-05

value: 200 months

value: Right proximal femur

value: Deceased at 30 months after diagnosis of the primary tumor


title: 1988-92P

value: 948 months

value: Humerus

value: Unknown

value: Metastases at 12 months after diagnosis of the primary tumor

value: Deceased at 18 months after diagnosis of the primary tumor


title: 17022-03

value: 204 months

value: F

value: Left femur

value: Metastases at 9 months after diagnosis of the primary tumor

value: Deceased at 33 months after diagnosis of the primary tumor


title: 16530-03

value: 180 months

value: M

value: Chondroblastic

value: Right proximal tibia

value: Deceased at 13 months after diagnosis of the primary tumor


title: pediatric acute lymphoblastic leukemia_4041 [Custom TaqMan Array]

value: hyperdiploid

value: resistant

value: sensitive


title: organism part name: 12DAP_Endosperm - rep2

value: Inbred line B73

value: PO:0009089 endosperm

value: PO:0007633 endosperm development stages


title: pediatric acute lymphoblastic leukemia_2329 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_2066 [Custom TaqMan Array]

value: unknown


title: organism part name: 14DAP_Whole Seed - rep1

description: 14DAP_Whole Seed

value: PO:0007042 5 fruit formation


title: organism part name: 10DAP_Whole Seed - rep1

description: 10DAP_Whole seed

source_name: fruit (organism part name: 10DAP_Whole Seed)


title: organism part name: 12DAP_Whole Seed - rep1

description: 12DAP_Whole Seed

source_name: fruit (organism part name: 12DAP_Whole Seed)


title: 14971-03

value: Sclerosing

value: Left distal femur

value: Metastases present at diagnosis

value: Alive at 45 months after diagnosis of the primary tumor


title: organism part name: 12DAP_Whole Seed - rep3

description: 12DAP_Whole Seed


title: organism part name: 8DAP_Whole Seed - rep2

description: 8DAP_Whole Seed

source_name: fruit (organism part name: 8DAP_Whole Seed)


title: organism part name: 10DAP_Whole Seed - rep2

description: 10DAP_Whole seed


title: pediatric acute lymphoblastic leukemia_1708 [Custom TaqMan Array]

source_name: pediatric acute lymphoblastic leukemia


title: organism part name: 12DAP_Endosperm - rep1


title: pediatric acute lymphoblastic leukemia_1566 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_1251 [Custom TaqMan Array]


title: organism part name: 10DAP_Whole Seed - rep3

description: 10DAP_Whole seed


title: pediatric acute lymphoblastic leukemia_1207 [Custom TaqMan Array]


title: organism part name: 12DAP_Whole Seed - rep2

description: 12DAP_Whole Seed


title: 09799-04

source_name: Osteosarcoma pre-chemotherapy biopsy

value: 144 months

value: Tibia

value: Metastases at 30 months after diagnosis of the primary tumor

value: Alive at 37 months after diagnosis of the primary tumor


title: pediatric acute lymphoblastic leukemia_884 [Custom TaqMan Array]


title: organism part name: 8DAP_Whole Seed - rep1

description: 8DAP_Whole Seed


title: 09541-05

value: 81 months

value: F

value: Osteoblastic

value: Humerus

value: Metastases at 5 months after diagnosis of the primary tumor

value: Deceased at 11 months after diagnosis of the primary tumor


title: organism part name: 6DAP_Whole Seed - rep1

description: 6DAP_Whole seed::Whole seed::6DAP::Tissues were harvested from middle one third of the ear for seeds samples at 6DAP and all later stages.

source_name: fruit (organism part name: 6DAP_Whole Seed)

value: Inbred line B73


title: organism part name: 6DAP_Whole Seed - rep3


title: pediatric acute lymphoblastic leukemia_199 [Custom TaqMan Array]

value: hyperdiploid

value: unknown


title: organism part name: 6DAP_Whole Seed - rep2

value: PO:0007042 5 fruit formation


title: organism part name: 8DAP_Whole Seed - rep3

description: 8DAP_Whole Seed


title: 00917-04

value: 170 months

value: M

value: Left distal femur

value: Alive at 46 months after diagnosis of the primary tumor


title: 07677-05

value: 133 months

value: Fibroblastic

value: Metastases at 10 months after diagnosis of the primary tumor

value: Alive at 28 months after diagnosis of the primary tumor


title: 00043-05

value: 174 months

value: Giant cell rich

value: Metastases present at diagnosis

value: Deceased after 27 months.


title: 00745-04

value: 162 months

value: Osteoblastic

value: Left proximal humerus

value: Metastases at 16 months after diagnosis of the primary tumor

value: Deceased at 21 months after diagnosis of the primary tumor


title: organism part name: 4DAP_Whole Seed - rep1

description: 4DAP_Whole Seed::Whole Seed::4DAP::Seeds were shaved off the cob with a razor blade and included some cob and silk tissue.

source_name: fruit (organism part name: 4DAP_Whole Seed)

value: Inbred line B73

value: PO:0007042 5 fruit formation


title: organism part name: 4DAP_Whole Seed - rep3


title: pediatric acute lymphoblastic leukemia_V9266 [Custom TaqMan Array]

value: resistant

value: sensitive


title: pediatric acute lymphoblastic leukemia_6485 [TaqMan MicroRNA Array]

data_processing: The ∆Ct value was calculated according to the following equation: Ct value of the specific miRNA minus the Ct value of the internal reference. In case of the TaqMan MicroRNA Array MicroRNA arrays the mean Ct values for snoR-13 and snoR-14 were used as reference whereas in case of the Custom TaqMan MicroRNA Array arrays snoR-1 was used.

value: thymocytes

value: unknown


title: pediatric acute lymphoblastic leukemia_6210 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_6512 [TaqMan MicroRNA Array]


title: organism part name: R2_Innermost Husk - rep1

description: R2_Innermost Husk::Innermost Husk::R2::Approximately 10 cm from the middle of innermost husk with light green color was harvested.

source_name: inflorescence bract of ear (organism part name: R2_Innermost Husk)

value: PO:0006337 inflorescence bract of ear


title: organism part name: 2DAP_Whole Seed - rep1

description: 2DAP_Whole Seed::Whole Seed::2Days After Pollination (DAP)::Seeds were shaved off the cob with a razor blade and included some cob and silk tissue.

source_name: fruit (organism part name: 2DAP_Whole Seed)


title: organism part name: R2_Innermost Husk - rep2


title: organism part name: R2_Outer Husk - rep2

description: R2_Outer Husk::Outer Husk::R2::Approximately 10 cm from the middle of the second husk from outside (to avoid pollen contamination) was sampled.

source_name: inflorescence bract of ear (organism part name: R2_Outer Husk)


title: organism part name: 2DAP_Whole Seed - rep3


title: pediatric acute lymphoblastic leukemia_V9759 [Custom TaqMan Array]


title: organism part name: 2DAP_Whole Seed - rep2


title: organism part name: R2_Outer Husk - rep3


title: organism part name: R2_Innermost Husk - rep3


title: pediatric acute lymphoblastic leukemia_8710 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_4181 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_4182 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_8537 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_4179 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_2044 [TaqMan MicroRNA Array]

value: nBM


title: pediatric acute lymphoblastic leukemia_3239 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_3564 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_3381 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_3181 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_2557 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_1601 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_1671 [Custom TaqMan Array]


title: organism part name: R2_Thirteenth Leaf - rep3

description: R2_Thirteenth Leaf::Thirteenth Leaf::Reproductive 2 (R2), 10-14 days after silk emergence::Approximately 10 cm section of the base of thirteenth leaf (excluding sheath) was harvested.

source_name: adult leaf (organism part name: R2_Thirteenth Leaf)

value: PO:0006340 adult leaf

value: PO:0007042 5 fruit formation,PO:0001053 3 leaf fully expanded


title: organism part name: R2_Outer Husk - rep1


title: pediatric acute lymphoblastic leukemia_1649 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_2909 [Custom TaqMan Array]

value: BCR-ABL


title: organism part name: R2_Thirteenth Leaf - rep1


title: organism part name: R1_Innermost Husk - rep3

description: R1_Innermost Husk::Innermost Husk::R1::Approximately 10 cm from the middle of innermost husk with light yellow color was harvested.

source_name: inflorescence bract of ear (organism part name: R1_Innermost Husk)

value: PO:0007016 4 flowering


title: organism part name: R1_Anthers - rep2

description: R1_Anthers::Anthers::R1::Unopened spikelets were collected from the secondary branches of a tassel in which some of the spikelets were in the middle of primary branch were open.

source_name: anther (sensu Zea) (organism part name: R1_Anthers)

value: PO:0006473 anther (sensu Zea)

value: PO:0007012 3 infloresence visible (sensu Poaceae)


title: organism part name: R2_Thirteenth Leaf - rep2


title: organism part name: R1_Innermost Husk - rep2


title: organism part name: R1_Innermost Husk - rep1


title: pediatric acute lymphoblastic leukemia_2050 [Custom TaqMan Array]


title: organism part name: R1_Pre-pollination Cob - rep2

description: R1_Pre-pollination Cob::Pre-pollination Cob::R1, silks emerge from the husk::Sample were collected on the day of silk emergence. Husks, silks, and ear stem from the topmost earshoot were removed. Middle one third part of the ear was harvested.

source_name: central spike of ear (organism part name: R1_Pre-pollination Cob)

value: PO:0006505 central spike of ear

value: PO:0007016 flowering


title: organism part name: R1_Anthers - rep1


title: organism part name: R1_Silks - rep3

description: R1_Silks::Silk::R1::Silk was collected only from the non-pollinated ears approximately on the day of silk emergence. Day of the silk emergence was estimated from neighboring non-sampled plants.

source_name: style (sensu Zea) (organism part name: R1_Silks)

value: PO:0006488 style (sensu Zea)


title: pediatric acute lymphoblastic leukemia_838 [TaqMan MicroRNA Array]


title: organism part name: R1_Anthers - rep3

value: Inbred line B73


title: pediatric acute lymphoblastic leukemia_545 [TaqMan MicroRNA Array]


title: organism part name: R1_Pre-pollination Cob - rep1


title: organism part name: R1_Pre-pollination Cob - rep3


title: organism part name: R1_Silks - rep2


title: organism part name: R1_Silks - rep1


title: pediatric acute lymphoblastic leukemia_1253 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_9923 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_6684 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_3513 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_6283 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_4139 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_2003 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_1718 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_1614 [Custom TaqMan Array]


title: organism part name: V18_Meiotic Tassel - rep1

description: V18_Meiotic Tassel::Meiotic Tassel::V18::Tassel representing a stage of active meiosis of pollen mother cell was visually selected.

source_name: tassel (organism part name: V18_Meiotic Tassel)

value: PO:0020126 tassel

value: PO:0007082 LP.20 twenty or more leaves whorls visible


title: organism part name: V13_Immature Tassel - rep1

description: V13_Immature Tassel::Immature Tassel::Vegetative 13 (V13)::Approximately 2.0 cm tassel excluding the tassel stalk was harvested.

source_name: tassel (organism part name: V13_Immature Tassel)

value: PO:0007104 LP.15 15 leaves visible


title: organism part name: 4DAP_Whole Seed - rep2

value: PO:0007042 5 fruit formation


title: organism part name: VT_Thirteenth Leaf - rep3

description: VT_Thirteenth Leaf::Thirteenth Leaf::Vegetative Tasseling (VT), last branch of the tassel fully emerged::Approximately 10 cm section of the base of thirteenth leaf (excluding sheath) was harvested.

source_name: adult leaf (organism part name: VT_Thirteenth Leaf)

value: PO:0007082 LP.20 twenty or more leaves whorls visible,PO:0001052 2 leaf expansion stage


title: organism part name: V13_Immature Tassel - rep2


title: organism part name: V13_Immature Tassel - rep3


title: organism part name: V18_Meiotic Tassel - rep2


title: organism part name: V18_Immature Cob - rep2

description: V18_Immature Cob::Immature Cob::Vegetative 18 (V18), 18 extended leaves::Topmost ear shoot (approximately 2.0 cm long) was harvested. The ear stem was not included.

source_name: central spike of ear (organism part name: V18_Immature Cob)

value: PO:0007082 LP.20 twenty of more leaves whorls visible


title: pediatric acute lymphoblastic leukemia_6358 [TaqMan MicroRNA Array]

value: T-ALL

value: unknown


title: pediatric acute lymphoblastic leukemia_1204 [Custom TaqMan Array]

value: sensitive

value: resistant


title: pediatric acute lymphoblastic leukemia_6308 [TaqMan MicroRNA Array]


title: organism part name: VT_Thirteenth Leaf - rep2

value: PO:0006340 adult leaf


title: organism part name: V18_Meiotic Tassel - rep3


title: organism part name: V9_Immature Leaves - rep3

description: V9_Immature Leaves::Immature Leaves::V9::For collection of this and following three leaf samples at V9 stage, a approximately 10 cm section of the stalk was cut starting approximately 3 cm below the leaf-sheath junction of the eighth leaf and going upwards. From this section, all the leaves were separated. For this samples, immature yellow leaves (17th leaf and above), which likely also included undifferentiated sheaths, were collected.

source_name: vascular leaf (organism part name: V9_Immature Leaves)

value: PO:0009025 vascular leaf

value: PO:0007116 LP.11 11 leaves visible,PO:0001052 2 leaf expansion stage


title: pediatric acute lymphoblastic leukemia_789 [Custom TaqMan Array]

source_name: pediatric acute lymphoblastic leukemia

value: BCR-ABL


title: organism part name: V18_Immature Cob - rep3

value: PO:0006505 central spike of ear


title: organism part name: VT_Thirteenth Leaf - rep1


title: pediatric acute lymphoblastic leukemia_374 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_4138 [TaqMan MicroRNA Array]


title: organism part name: V18_Immature Cob - rep1


title: organism part name: V9_Immature Leaves - rep1


title: pediatric acute lymphoblastic leukemia_3526 [TaqMan MicroRNA Array]


title: organism part name: V9_Immature Leaves - rep2


title: pediatric acute lymphoblastic leukemia_3330 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_6341 [Custom TaqMan Array]


title: organism part name: V9_Thirteenth Leaf - rep3

description: V9_Thirteenth Leaf::Thirteenth Leaf::V9::From the leaves separated for harvesting V9_immature Leaves, thirteenth leaf with yet-undifferentiated sheath was collected.

source_name: adult leaf (organism part name: V9_Thirteenth Leaf)


title: pediatric acute lymphoblastic leukemia_3822 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_3325 [TaqMan MicroRNA Array]


title: organism part name: V9_Thirteenth Leaf - rep2


title: organism part name: V9_Eleventh Leaf - rep3

description: V9_Eleventh Leaf::Eleventh Leaf::V9::From the leaves separated for harvesting V9_immature Leaves, eleventh leaf with slight green pigmentation at the base and undifferentiated sheath was collected.

source_name: adult leaf (organism part name: V9_Eleventh Leaf)

value: PO:0007116 LP.11 11 leaves visible,PO:0001024 rapid elongation of leaf sheath


title: organism part name: V9_Thirteenth Leaf - rep1

value: Inbred line B73


title: pediatric acute lymphoblastic leukemia_3311 [TaqMan MicroRNA Array]


title: organism part name: V9_Eighth Leaf - rep3

description: V9_Eighth Leaf::Eighth Leaf::V9::From the leaves separated for harvesting V9_immature Leaves, eighth leaf with fully differentiated sheath and dark green pigmentation was collected.

source_name: vascular leaf (organism part name: V9_Eighth Leaf)


title: organism part name: V9_Eleventh Leaf - rep1


title: pediatric acute lymphoblastic leukemia_3636 [Custom TaqMan Array]


title: Muscle Tro3

city: La Jolla

first: Gene

last: Hsiao

state: CA

address: 9500 Gilman Dr

institute: UCSD

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Data analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as the normalization method

organism: Rattus norvegicus

source_name: fatty (fa/fa), skeletal muscle (gastrocnemius), Troglitazone

label_protocol: Biotin-labeled cRNA probes were in vitro transcribed using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences).

extract_protocol: Tissue RNA was isolated using Qiagen RNeasy kits (Qiagen, Inc., Valencia, CA).  Biotinylated-cRNA made from pooled RNA preparations (RNA from two rats per preparation) was used to probe Affymetrix Rat Expression 230A GeneChips (Affymetrix) as per the Invitrogen protocol (Invitrogen, Inc., Carlsbad, CA), three arrays per group.

tag: tissue

value: skeletal muscle (gastrocnemius)

value: male

tag: strain

value: Zucker

tag: genotype/variation

value: fatty (fa/fa)

tag: pparγ ligand

value: Troglitazone


title: pediatric acute lymphoblastic leukemia_3044 [TaqMan MicroRNA Array]

tag: subtype

tag: patient id

tag: prednisolone-score

tag: vincristine-score


title: organism part name: V9_Eleventh Leaf - rep2


title: pediatric acute lymphoblastic leukemia_2710 [Custom TaqMan Array]

tag: daunorubicin-score

tag: l-asparaginase-score


title: organism part name: V9_Eighth Leaf - rep2


title: organism part name: V9_Eighth Leaf - rep1


title: pediatric acute lymphoblastic leukemia_3624 [Custom TaqMan Array]


title: Muscle Tro1

tag: gender


title: pediatric acute lymphoblastic leukemia_1701 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_2639 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_748 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_697 [TaqMan MicroRNA Array]


title: organism part name: V9_Fourth Internode - rep2

description: V9_Fourth Internode::Fourth Internode::Vegetative 9 (V9), nine extended leaves::Leaves were removed and the fourth elongated internode was collected.

source_name: shoot internode (organism part name: V9_Fourth Internode)

value: PO:0005005 shoot internode

value: PO:0007116 LP.11 11 leaves visible


title: organism part name: V9_Fourth Internode - rep3


title: pediatric acute lymphoblastic leukemia_2294 [Custom TaqMan Array]


title: Muscle Rosi3

source_name: fatty (fa/fa), skeletal muscle (gastrocnemius), Rosiglitazone

value: Rosiglitazone


title: pediatric acute lymphoblastic leukemia_2011 [Custom TaqMan Array]

value: sensitive


title: pediatric acute lymphoblastic leukemia_2209 [Custom TaqMan Array]

value: resistant


title: pediatric acute lymphoblastic leukemia_1307 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_419 [TaqMan MicroRNA Array]

value: T-ALL

value: unknown


title: pediatric acute lymphoblastic leukemia_4041 [TaqMan MicroRNA Array]

value: hyperdiploid


title: pediatric acute lymphoblastic leukemia_4623 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_4988 [TaqMan MicroRNA Array]


title: Muscle Rosi1


title: organism part name: V9_Fourth Internode - rep1


title: Muscle Rosi2


title: pediatric acute lymphoblastic leukemia_3150 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_1164 [Custom TaqMan Array]


title: Muscle Pio3

source_name: fatty (fa/fa), skeletal muscle (gastrocnemius), Pioglitazone

value: Pioglitazone


title: Muscle Pio2


title: organism part name: V7_Base of stage-2 Leaf - rep3

description: V7_Base of stage-2 Leaf::Base of stage-2 Leaf::V7::Approximately 5.0 cm pale/light yellow basal part including undifferentiated sheath of the stage-2 leaf was harvested.

source_name: vascular leaf (organism part name: V7_Base of stage-2 Leaf)

value: PO:0009025 vascular leaf

value: PO:0007101 LP.09 nine leaves visible,PO:0001052 2 leaf expansion stage


title: Muscle Tro2


title: Muscle Pio1


title: pediatric acute lymphoblastic leukemia_2900 [TaqMan MicroRNA Array]


title: Muscle LC3

source_name: lean (fa/+), skeletal muscle (gastrocnemius)

value: lean (fa/+)

value: normal chow


title: organism part name: V7_Base of stage-2 Leaf - rep2

value: Inbred line B73


title: pediatric acute lymphoblastic leukemia_1152 [Custom TaqMan Array]


title: organism part name: V7_Tip of stage-2 Leaf - rep3

description: V7_Tip of stage-2 Leaf::Tip of stage-2 Leaf::V7::Approximately 5.0 cm tip of the stage-2 leaf with visible chloroplast differentiation was harvested.

source_name: vascular leaf (organism part name: V7_Tip of stage-2 Leaf)


title: organism part name: V7_Tip of stage-2 Leaf - rep1


title: organism part name: V7_Base of stage-2 Leaf - rep1


title: organism part name: V7_Tip of stage-2 Leaf - rep2


title: organism part name: V7_First Internode - rep3

description: V7_First Internode::First Internode::Vegetative 7 (V7), seven extended leaves::Stalk was longitudinally cut in half and the first elongated internode was dissected out from both halves.

source_name: shoot internode (organism part name: V7_First Internode)

value: PO:0007101 LP.09 nine leaves visible


title: pediatric acute lymphoblastic leukemia_2006 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_4284 [Custom TaqMan Array]

value: B-other


title: pediatric acute lymphoblastic leukemia_4977 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_4234 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_2329 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_3633 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_2066 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_1566 [TaqMan MicroRNA Array]


title: Muscle LC2

value: skeletal muscle (gastrocnemius)

value: male

value: Zucker


title: Muscle FC3

source_name: fatty (fa/fa), skeletal muscle (gastrocnemius)

value: fatty (fa/fa)


title: pediatric acute lymphoblastic leukemia_1251 [TaqMan MicroRNA Array]


title: Muscle FC1


title: Muscle LC1


title: Muscle AG3

source_name: fatty (fa/fa), skeletal muscle (gastrocnemius), AG035029


title: organism part name: V7_First Internode - rep2

value: PO:0005005 shoot internode


title: organism part name: V5_Base of stage-2 Leaf - rep3

description: V5_Base of stage-2 Leaf::Base of stage-2 Leaf::V5::Approximately 5.0 cm pale/light yellow basal part including undifferentiated sheath of the stage-2 leaf was harvested.

source_name: juvenile leaf (organism part name: V5_Base of stage-2 Leaf)

value: PO:0006339 juvenile leaf

value: PO:0007063 LP.07 seven leaves visible,PO:0001052 2 leaf expansion stage


title: organism part name: V5_Base of stage-2 Leaf - rep2


title: pediatric acute lymphoblastic leukemia_3254 [Custom TaqMan Array]

value: sensitive

value: resistant


title: pediatric acute lymphoblastic leukemia_1708 [TaqMan MicroRNA Array]

value: hyperdiploid


title: pediatric acute lymphoblastic leukemia_1207 [TaqMan MicroRNA Array]

value: unknown


title: pediatric acute lymphoblastic leukemia_3543 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_884 [TaqMan MicroRNA Array]


title: organism part name: V5_Base of stage-2 Leaf - rep1


title: organism part name: V5_Tip of stage-2 Leaf - rep3

description: V5_Tip of stage-2 Leaf::Tip of stage-2 Leaf::V5::Approximately 5.0 cm tip of the stage-2 leaf with visible chloroplast differentiation was harvested.

source_name: vascular leaf (organism part name: V5_Tip of stage-2 Leaf)

value: PO:0009025 vascular leaf


title: pediatric acute lymphoblastic leukemia_2575 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_199 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_2524 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_3144 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_V9759 [TaqMan MicroRNA Array]


title: Liver Tro3

source_name: fatty (fa/fa), liver, Troglitazone

value: liver

value: Troglitazone


title: organism part name: V5_Tip of stage-2 Leaf - rep2

value: Inbred line B73


title: Muscle AG2


title: pediatric acute lymphoblastic leukemia_2289 [Custom TaqMan Array]

source_name: pediatric acute lymphoblastic leukemia


title: pediatric acute lymphoblastic leukemia_8537 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_V9266 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_8710 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_774 [Custom TaqMan Array]


title: Liver Tro1


title: pediatric acute lymphoblastic leukemia_2176 [Custom TaqMan Array]


title: organism part name: V5_First Internode - rep3

description: V5_First Internode::First Internode::V5::Stalk was longitudinally cut in half, leaves were removed, and the first elongated internode from both halves was dissected out. These samples were collected from same plants used for collection of V5_Shoot Tip.

source_name: shoot internode (organism part name: V5_First Internode)

value: PO:0007063 LP.07 seven leaves visible


title: Muscle AG1


title: pediatric acute lymphoblastic leukemia_3381 [TaqMan MicroRNA Array]


title: Liver Tro2


title: pediatric acute lymphoblastic leukemia_738 [Custom TaqMan Array]

value: B-other


title: Liver Rosi2

source_name: fatty (fa/fa), liver, Rosiglitazone

value: Rosiglitazone


title: organism part name: V5_Tip of stage-2 Leaf - rep1


title: organism part name: V5_First Internode - rep2


title: organism part name: V5_Shoot Tip - rep3

description: V5_Shoot Tip::Shoot Tip::Vegetative 5 (V5), five fully extended leaves::Stalk was longitudinally dissected in half, leaves were removed, and the shoot tip from both halves was dissected out. Immature leaves and sheaths were included.

source_name: stem,PO:0025034 leaf,PO:0020104 leaf sheath,PO:0020148 shoot apical meristem (organism part name: V5_Shoot Tip)

value: PO:0009047 stem,PO:0025034 leaf,PO:0020104 leaf sheath,PO:0020148 shoot apical meristem


title: pediatric acute lymphoblastic leukemia_1671 [TaqMan MicroRNA Array]


title: Liver Rosi3

value: male

value: Zucker


title: Muscle FC2

value: skeletal muscle (gastrocnemius)

value: fatty (fa/fa)

value: normal chow


title: Liver Rosi1


title: Liver Pio2

source_name: fatty (fa/fa), liver, Pioglitazone

value: Pioglitazone


title: pediatric acute lymphoblastic leukemia_1649 [TaqMan MicroRNA Array]

value: resistant

value: sensitive


title: pediatric acute lymphoblastic leukemia_3239 [TaqMan MicroRNA Array]


title: organism part name: V7_First Internode - rep1

value: PO:0005005 shoot internode

value: PO:0007101 LP.09 nine leaves visible


title: Liver Pio3

value: liver


title: organism part name: V5_Shoot Tip - rep2


title: organism part name: V5_First Internode - rep1


title: pediatric acute lymphoblastic leukemia_626 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_3181 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_1966 [Custom TaqMan Array]

value: MLL


title: pediatric acute lymphoblastic leukemia_1227 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_886 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_1702 [Custom TaqMan Array]


title: organism part name: V3_Topmost Leaf - rep3

description: V3_Topmost Leaf::Topmost Leaf::V3::Whole stage-2 leaf was harvested. Stage-2 of leaf development is characterized by rapid leaf blade growth and differentiation and very little sheath growth (Sylvester, A.W. et al. 1990, Development 110:985-1000). Leaves at this stages had green tip and yellow base which included the undifferentiated sheath.

source_name: juvenile leaf (organism part name: V3_Topmost Leaf)

value: Inbred line B73

value: PO:0006339 juvenile leaf

value: PO:0007065 LP.05 5 leaves visible,PO:0001052 2 leaf expansion stage


title: organism part name: V3_Topmost Leaf - rep2


title: pediatric acute lymphoblastic leukemia_2909 [TaqMan MicroRNA Array]

value: BCR-ABL


title: Liver LC3

source_name: lean (fa/+), liver

value: lean (fa/+)


title: organism part name: V3_Topmost Leaf - rep1


title: pediatric acute lymphoblastic leukemia_1191 [Custom TaqMan Array]

value: unknown


title: pediatric acute lymphoblastic leukemia_2050 [TaqMan MicroRNA Array]


title: organism part name: V3_First Leaf and Sheath - rep2

description: V3_First Leaf and Sheath::First Leaf and Sheath::V3::Whole leaf and sheath was sampled.

source_name: juvenile leaf,PO:0020104 leaf sheath (organism part name: V3_First Leaf and Sheath)

value: PO:0006339 juvenile leaf,PO:0020104 leaf sheath

value: PO:0007065 LP.05 5 leaves visible,PO:0001053 3 leaf fully expanded


title: pediatric acute lymphoblastic leukemia_3513 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_9923 [TaqMan MicroRNA Array]


title: organism part name: V3_First Leaf and Sheath - rep3


title: Liver LC2

value: male

value: Zucker


title: Liver FC3

source_name: fatty (fa/fa), liver

value: fatty (fa/fa)

value: normal chow


title: pediatric acute lymphoblastic leukemia_1718 [TaqMan MicroRNA Array]

value: sensitive

value: resistant


title: pediatric acute lymphoblastic leukemia_929 [Custom TaqMan Array]


title: organism part name: V3_First Leaf and Sheath - rep1


title: organism part name: V5_Shoot Tip - rep1

value: PO:0009047 stem,PO:0025034 leaf,PO:0020104 leaf sheath,PO:0020148 shoot apical meristem

value: PO:0007063 LP.07 seven leaves visible


title: pediatric acute lymphoblastic leukemia_873 [Custom TaqMan Array]

value: MLL


title: Liver FC2

value: liver


title: Liver LC1


title: pediatric acute lymphoblastic leukemia_888 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_1614 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_169 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_1204 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_2003 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_656 [Custom TaqMan Array]


title: organism part name: V3_Stem and SAM - rep3

description: V3_Stem and SAM::Stem and SAM::Vegetative 3 (V3), three fully extended leaves.::SAM and stem tissue above nodal roots was included. Likely included some leaf tissue that could not be separated with naked eye.

source_name: stem,PO:0020148 shoot apical meristem (organism part name: V3_Stem and SAM)

value: Inbred line B73

value: PO:0009047 stem,PO:0020148 shoot apical meristem

value: PO:0007065 LP.05 5 leaves visible


title: Liver Pio1

value: Pioglitazone


title: pediatric acute lymphoblastic leukemia_788 [Custom TaqMan Array]


title: pediatric acute lymphoblastic leukemia_789 [TaqMan MicroRNA Array]

value: BCR-ABL


title: Liver AG2

source_name: fatty (fa/fa), liver, AG035029


title: Liver AG3


title: pediatric acute lymphoblastic leukemia_374 [TaqMan MicroRNA Array]


title: organism part name: V3_Stem and SAM - rep2


title: organism part name: V3_Stem and SAM - rep1


title: Fat Tro3

source_name: fatty (fa/fa), adipose tissue (epididymal), Troglitazone

value: adipose tissue (epididymal)

value: Troglitazone


title: wt vs mutant_rep3

city: Wuerzburg

first: Stephanie

last: Schielke

address: Josef-Schneider-Str. 2 / E1

department: Institute for Hygiene and Microbiology

country: Germany

institute: University of Wuerzburg

description: Wild type samples in comparison to mutant samples lacking the transcriptional regulator FarR, both in mid-exponential growth phase in rich medium

hyb_protocol: The probes were hybridized to the microarray slides using the Hybridization Station HS 4800 Pro (Tecan) and incubated at 65°C for 16 h.

scan_protocol: The slides were scanned using the Axon GenePix Pro 4200A (Molecular Devices) and analyzed using the GenePix Pro software.

data_processing:
Computational analysis of differential expression was carried out in R using the Limma package from the Bioconductor framework. Array quality was assessed using arrayQualityMetrics and visual inspection. Spots were flagged and eliminated from analysis in obvious cases of high background or stray fluorescent signals. The data was normalized using variance stabilization after which differential expression was determined as usual by linear model fitting and statistical tests for differential expression.
P-values were multiple-testing corrected using fdr adjustment according to Benjamini and Hochberg. The resulting corrected P-values were considered significant if below 0.05.

organism: Neisseria meningitidis

source_name: Mid-exponential growth phase sample

label_protocol: The RNA was transcribed to differentially labeled cDNA using Cy3-dCTP and Cy5-dCTP (GE Healthcare) and the reverse transcriptase Superscript II followed by RNase treatment (Roche) and purification with illustra AutoSeq G50 columns (GE Healthcare).

growth_protocol: Strains MC58 and MC58 ∆farR were inoculated into PPM+ and grown for 60 minutes at 37°C and 200 rpm. The OD600 was adjusted to 0.1 for each strain and the cultures were incubated to mid log phase.

extract_protocol: Total RNA isolation was conducted using the TRIzol method (Invitrogen) with subsequent DNA digestion using the DNA-free kit (Ambion)

tag: strain/genotype variation

value: MC58 ∆farR


title: Fat Tro2

value: male

value: Zucker


title: mut vs wt_rep3


title: mut vs wt_rep2


title: pediatric acute lymphoblastic leukemia_3822 [TaqMan MicroRNA Array]


title: Liver FC1

value: fatty (fa/fa)

value: normal chow


title: organism part name: V4_Stem and SAM - rep2

description: V4_Stem and SAM::Stem and SAM::Vegetative 4 (V4), four fully extended leaves::SAM and stem tissue above nodal roots was harvested. Likely included some leaf tissue that could not be separated with naked eye.

source_name: stem,PO:0020148 shoot apical meristem (organism part name: V4_Stem and SAM)

value: PO:0007123 LP.06 six leaves visible


title: organism part name: V4_Stem and SAM - rep1


title: organism part name: V4_Stem and SAM - rep3


title: organism part name: V1_Stem and SAM - rep3

description: V1_Stem and SAM::Stem and Shoot Apical Meristem (SAM)::V1::The SAM was dissected out with naked eye and included the stem tissues above the nodal roots. Likely included some leaf tissue that could not be separated with naked eye.

source_name: stem,PO:0020148 shoot apical meristem (organism part name: V1_Stem and SAM)

value: PO:0007106 LP.03 3 leaves visible


title: organism part name: V1_Stem and SAM - rep1


title: organism part name: V1_Stem and SAM - rep2


title: pediatric acute lymphoblastic leukemia_3624 [TaqMan MicroRNA Array]

value: sensitive

value: resistant


title: Fat Rosi3

source_name: fatty (fa/fa), adipose tissue (epididymal), Rosiglitazone

value: Rosiglitazone


title: Fat Tro1


title: pediatric acute lymphoblastic leukemia_6341 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_3636 [TaqMan MicroRNA Array]


title: organism part name: V1_Pooled Leaves - rep2

description: V1_Pooled Leaves::Pooled Leaves::V1::All the leaves including two outer green leaves and the inside immature leaves were pooled.

source_name: juvenile leaf (organism part name: V1_Pooled Leaves)

value: Inbred line B73

value: PO:0006339 juvenile leaf

value: PO:0007106 LP.03 3 leaves visible,PO:0001052 2 leaf expansion stage


title: pediatric acute lymphoblastic leukemia_2639 [TaqMan MicroRNA Array]

source_name: pediatric acute lymphoblastic leukemia


title: Liver AG1

value: liver


title: Fat Rosi2


title: pediatric acute lymphoblastic leukemia_2294 [TaqMan MicroRNA Array]


title: wt vs mutant_rep2


title: wt vs mutant_rep1


title: Fat Rosi1


title: Fat Pio1

source_name: fatty (fa/fa), adipose tissue (epididymal), Pioglitazone

value: Pioglitazone


title: Fat Pio2

value: adipose tissue (epididymal)


title: mut vs wt_rep1


title: organism part name: V1_Pooled Leaves - rep3


title: Fat LC3

source_name: lean (fa/+) adipose tissue (epididymal)

value: lean (fa/+)


title: organism part name: V1_Pooled Leaves - rep1


title: fat Rep2

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: fat

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 28 arrays in the series:  AverXr = average(Xri).
Note: the hybridizations for fat Rep2 and bone Rep2 failed the first time, and Cy5 averages above do not include these two samples after we re-do these samples for processing purposes. The differences on whether to use entire 30 arrays or only the 28 array averages are small.
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

organism: Mus musculus

source_name: fat

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: Each tissue was homogenized with Polytron homogenizer model PT-1200 C (kinematica) in presence of TRIzol reagent (Invitrogen). Total RNA were extracted using TRIzol reagent according to the manufacturer's instructions and dissolved in DEPC treated water.

treatment_protocol: The each tissue was collected after the mouse was euthanized. Collected tissue was washed with PBS and pieces of them were kept frozen at -80C until RNA extraction.

tag: cell type

value: adult tissue cells

tag: age

value: 28 weeks

value: adult

tag: individual identifier

source_name: Universal Mouse Reference 129ES Cell

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

value: Universale Mouse Reference


title: bone Rep2

description: bone

source_name: bone

value: male


title: ES[B6R(5)] GSK 48 hours

description: 48hr GSK

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 4 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: 48hr GSK

extract_protocol: Standard ES RNA extraction with 1/2 mL Trizol. The samples were dissolved in the well with TRIzol reagent 1/2 mL.  They were then transferred to eppendorf tubes and stored at -20C until extraction proceeded.The samples were transferred to Phase Lock Gel Heavy tubes (eppendorf) and 0.2 volumes of chloroform (Sigma-Aldrich) was added to each sample.  They were mixed by hand and allowed to stand for 2-5 min at room temperature.  The samples were then separated by centrifugation for 5 minutes at 15,300 rpm on an eppendorf centrifuge at 4C.The aqeous phase was transferred to another eppendorf, and 0.8 volumes of ice-cold isopropanol was added.  They were allowed to incubate for a minimum of 10 minutes at room temperature.  If longer, they were placed at 4C.  The sample was centrifuged again at the same conditions for 15 minutes.After centrifugation, the liquid was dumped out of the tubes and the pellet was washed with 1 mL of ice-cold 70% ethanol.  The tube was spun for 5 minutes, then the ethanol was dumped out.  Excess was removed with a pipette and the pellet was allowed to air dry until no liquid remained, but no longer.  ddH2O was then added in the appropriate volume, the sample was allowed to dissolve for 5 minutes at 55C and then transferred to -20C for storage.

treatment_protocol: At 24 hours post-plating, the medium was removed, the cells were rinsed once with PBS, and the medium was replaced with regular medium containing the specified inhibitor dissolved in DMSO.  The final concentration of DMSO was 0.2% v/v in all samples, including the control.  Cells were harvested at the specified time point, either 24 or 48 hours after DMSO was added.    The cells were lysed with Trizol and placed at -20C until extraction.

value: Embryonic Stem Cells

source_name: Universal Mouse Reference Cell Line Pool

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts


title: Fat LC2

value: Zucker

value: normal chow


title: pediatric acute lymphoblastic leukemia_2710 [TaqMan MicroRNA Array]

value: resistant

value: sensitive


title: pediatric acute lymphoblastic leukemia_2209 [TaqMan MicroRNA Array]


title: Fat Pio3

value: fatty (fa/fa)


title: pediatric acute lymphoblastic leukemia_2011 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_1307 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_2006 [TaqMan MicroRNA Array]


title: pediatric acute lymphoblastic leukemia_1164 [TaqMan MicroRNA Array]


title: ES[B6R(5)] MEK 48 hours

description: 48hr MEK

source_name: 48hr MEK


title: Fat LC1


title: organism part name: VE_Primary Root - rep2

description: VE_Primary Root::Primary Root::Vegetative Emergence (VE), coleoptile barely emerges from the soil surface::This tissue was collected from greenhouse-grown plants.

source_name: primary root (organism part name: VE_Primary Root)

tag: germplasm name

value: Inbred line B73

tag: organism part

value: PO:0020127 primary root

value: PO:0007045 coleoptile emergence


title: pediatric acute lymphoblastic leukemia_1152 [TaqMan MicroRNA Array]

value: unknown


title: organism part name: VE_Primary Root - rep1

tag: development stage


title: Fat FC3

source_name: fatty (fa/fa) adipose tissue (epididymal)

tag: tissue

value: adipose tissue (epididymal)

tag: strain


title: organism part name: VE_Primary Root - rep3


title: ES[B6R(5)] Control 48 hours

description: 48hr ctrl

source_name: 48hr ctrl

value: ES[B6R(5)] Control 48 hours; ES[B6R(5)] Control 48 hours; 251508710414A1


title: organism part name: VE_Whole Seedling - rep1

description: VE_Whole Seedling::Whole Seedling::VE::All plant parts above the nodal roots were collected.

source_name: shoot system (organism part name: VE_Whole Seedling)

value: PO:0009006 shoot system

value: PO:0007112 1 main shoot growth


title: pediatric acute lymphoblastic leukemia_774 [TaqMan MicroRNA Array]


title: Fat FC2

tag: genotype/variation

tag: pparγ ligand


title: organism part name: VE_Whole Seedling - rep2


title: pediatric acute lymphoblastic leukemia_4977 [TaqMan MicroRNA Array]

tag: subtype

value: B-other

tag: patient id


title: ES[B6R(5)] FGFR 48 hours

description: 48hr FGFR

source_name: 48hr FGFR

value: Universale Mouse Reference


title: organism part name: VE_Whole Seedling - rep3


title: pediatric acute lymphoblastic leukemia_4284 [TaqMan MicroRNA Array]

tag: prednisolone-score

tag: vincristine-score


title: bone Rep1

description: bone

value: adult tissue cells

value: male

value: 28 weeks

value: adult


title: Fat AG3

source_name: fatty (fa/fa), adipose tissue (epididymal), AG035029

value: Zucker


title: Fat FC1

value: normal chow


title: large_intestine Rep2

value: large_intestine Rep2; large_intestine Rep2; 251508710706A3


title: organism part name: V1_GH_Primary Root - rep3

description: V1_GH_Primary Root::Primary Root (GH)::Vegetative 1 (V1), first leaf is fully extended at this stage::This tissue was collected from greenhouse-grown plants.

source_name: primary root (organism part name: V1_GH_Primary Root)

value: Inbred line B73

value: PO:0007106 LP.03 3 leaves visible


title: Fat AG2

value: fatty (fa/fa)


title: large_intestine Rep1

value: large_intestine Rep1; large_intestine Rep1; 251508710703A4


title: pediatric acute lymphoblastic leukemia_4234 [TaqMan MicroRNA Array]

value: resistant

tag: daunorubicin-score

tag: l-asparaginase-score


title: Fat AG1

value: adipose tissue (epididymal)

tag: gender


title: fat Rep1

description: fat

tag: cell type


title: organism part name: V1_GH_Primary Root - rep1

value: PO:0020127 primary root


title: organism part name: V1_GH_Primary Root - rep2


title: pediatric acute lymphoblastic leukemia_3633 [TaqMan MicroRNA Array]

value: sensitive


title: stomach Rep2

description: stomach

source_name: stomach

tag: age

value: stomach Rep2; stomach Rep2; 251508710703A3


title: pediatric acute lymphoblastic leukemia_3543 [TaqMan MicroRNA Array]

source_name: pediatric acute lymphoblastic leukemia

value: B-other


title: organism part name: 6DAS_GH_Primary Root - rep2

description: 6DAS_GH_Primary Root::Primary Root (GH)::6 Days After Sowing (DAS)::This tissue was collected from greenhouse-grown plants. Samples were collected before coleoptiles emerged from the soil surface.

source_name: primary root (organism part name: 6DAS_GH_Primary Root)

value: PO:0007015 radicle emergence


title: pediatric acute lymphoblastic leukemia_3254 [TaqMan MicroRNA Array]


title: organism part name: 6DAS_GH_Primary Root - rep3


title: pediatric acute lymphoblastic leukemia_3144 [TaqMan MicroRNA Array]


title: small_intestine Rep2

value: adult tissue cells

value: male

tag: individual identifier

value: small_intestine Rep2; small_intestine Rep2; 251508710703A1

value: Universale Mouse Reference


title: Control yeast VIN13, biological rep3

city: Stellenbosch

first: Debra

last: Rossouw

state: Western Cape

address: Cnr Neethling and Victoria rd

department: Institute for Wine Biotechnology

country: South Africa

institute: University of Stellenbosch

hyb_protocol: Following fragmentation, 5 ug of labelled fragmented amplified RNA was hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The GeneChips were scanned using the Affymetrix GeneChip® 3000 Scanner 7G. AGCC is used for image acquisition.

data_processing: The cell intensity data was analyzed in Affymetrix Expression Console using the RMA algorithm. The RMA workflow is quantile normalisation with general background correction.

organism: Saccharomyces cerevisiae Vin13

source_name: Yeast VIN13 at day2 of alcoholic fermentation

label_protocol: Following second strand cDNA synthesis (starting material 100ng of total RNA), biotinylated cRNA was prepared in accordance with the Affymetrix 3' Expression protocol .  The expected profile of amplified RNA should be in the range of 250 -5500nt with most of the amplified RNA appearing in the 600-12--nt range. 7.5ug of amplified RNA is required for hybridisation to an array.

growth_protocol: Yeast were inoculated at an OD600 of 0.1 in synthetic wine must in microaerobic fermentation vials. Fermentation was carried out at room temperature.

extract_protocol: RNA was extracted as described using a modified hot-phenol method as described by Abbott et al (2007).

treatment_protocol: Cells were harvested by brief centrifugation and washed prior to extraction.

tag: genotype

value: wild type

tag: time

value: day 2 of alcholic fermentation

tag: replicate


title: Control yeast VIN13, biological rep2


title: muscle  Rep2

description: muscle

source_name: muscle

value: 28 weeks

tag: development stage

value: adult

value: muscle  Rep2; muscle  Rep2; 251508710702A1


title: Control yeast VIN13, biological rep1


title: skin  Rep1

description: skin

source_name: skin

tag: strain

source_name: Universal Mouse Reference 129ES Cell


title: stomach Rep1

description: stomach

value: stomach Rep1; stomach Rep1; 251508710703A2


title: pediatric acute lymphoblastic leukemia_2524 [TaqMan MicroRNA Array]

value: resistant


title: organism part name: 6DAS_GH_Primary Root - rep1

tag: germplasm name

value: Inbred line B73

tag: organism part


title: small_intestine Rep1

value: small_intestine Rep1; small_intestine Rep1; 251508710702A4


title: organism part name: 6DAS_GH_Coleoptile - rep3

description: 6DAS_GH_Coleoptile::Coleoptile (GH)::6DAS::This tissue was collected from greenhouse grown plants. Coleoptiles were harvested from the same plants that were used for collection of 6DAS_GH_Primary Root.

source_name: coleoptile (organism part name: 6DAS_GH_Coleoptile)

value: PO:0020033 coleoptile


title: SOK2 overexpressing yeast, biological rep3

source_name: Yeast VIN13 overexpressing transcription factor SOK2 at day2 of fermentation

value: SOK2 overexpressing


title: SOK2 overexpressing yeast, biological rep2


title: SOK2 overexpressing yeast, biological rep1


title: skin  Rep2

description: skin


title: organism part name: 6DAS_GH_Coleoptile - rep2


title: pediatric acute lymphoblastic leukemia_2289 [TaqMan MicroRNA Array]

tag: subtype

value: B-other

value: sensitive


title: muscle  Rep1

description: muscle

value: adult tissue cells

value: muscle  Rep1; muscle  Rep1; 251508710701A4


title: organism part name: 6DAS_GH_Coleoptile - rep1

value: PO:0007015 radicle emergence


title: pediatric acute lymphoblastic leukemia_2575 [TaqMan MicroRNA Array]

tag: patient id


title: organism part name: 24H_Germinating Seed - rep2

description: 24H_Germinating Seed::Germinating Seed::24H after imbibition::Seeds were soaked in Petri dishes containing distilled  water for 12H, allowed to germinate on paper towels for 12H, and immediately frozen in liquid N.

source_name: fruit (organism part name: 24H_Germinating Seed)

value: PO:0007022 inbibition


title: pediatric acute lymphoblastic leukemia_2176 [TaqMan MicroRNA Array]

tag: prednisolone-score


title: organism part name: 24H_Germinating Seed - rep3


title: pediatric acute lymphoblastic leukemia_886 [TaqMan MicroRNA Array]

tag: vincristine-score


title: pediatric acute lymphoblastic leukemia_738 [TaqMan MicroRNA Array]

tag: daunorubicin-score


title: lung  Rep1

description: lung

source_name: lung

value: male

value: Universale Mouse Reference


title: NK cells, mouse 15, day 50

city: San Francisco

first: Charlie

last: Kim

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

hyb_protocol: Pooled reference and sample hybridized in 3x SSC/0.2% SDS as per standard protocols for spotted array hybridization

scan_protocol: Molecular Devices Genepix 4000B scanner at 5 um resolution

source_name: pooled reference amplified RNA from combination of universal mouse reference and samples

label_protocol: 4 ug of aRNA coupled to Cy5 (or Cy3 for common pooled reference aRNA) as per standard protocols

extract_protocol: Total RNA was extracted from FACS-isolated NK cells with the Ambion RNAqueous-Micro kit and amplified with the Ambion Aminoallyl MessageAmp II kit.

treatment_protocol: GFP-lableed NK cells were harvested from MCMV-infected mice and adoptively transferred to naïve C57BL/6 mice. The recipient mice were then infected with MCMV, and NK cells were isolated at various times post-infection for microarray analysis.

tag: sample type

source_name: Amplified total RNA from FACS-isolated NK cells after 50 days infection with MCMV

value: 50 days post-infection

value: NK cell

tag: infection

value: MCMV


title: brain_cortex Rep2

tag: cell type

tag: gender

value: 28 weeks

value: adult

value: Brain's_cortex Rep2; brain_cortex Rep2; 251508710696A1


title: pediatric acute lymphoblastic leukemia_626 [TaqMan MicroRNA Array]

value: resistant

tag: l-asparaginase-score


title: NK cells, mouse 14, day 30

value: pooled reference amplified RNA from combination of universal mouse reference and samples

source_name: Amplified total RNA from FACS-isolated NK cells after 30 days infection with MCMV

value: 30 days post-infection


title: pediatric acute lymphoblastic leukemia_1966 [TaqMan MicroRNA Array]

value: MLL


title: NK cells, mouse 16, day 50


title: organism part name: 24H_Germinating Seed - rep1

value: Inbred line B73


title: pediatric acute lymphoblastic leukemia_1702 [TaqMan MicroRNA Array]

value: sensitive


title: NK cells, mouse 12, day 14

source_name: Amplified total RNA from FACS-isolated NK cells after 14 days infection with MCMV

value: 14 days post-infection


title: pediatric acute lymphoblastic leukemia_1227 [TaqMan MicroRNA Array]


title: Breast cancer_VitaminD_100nM_24h_15C

city: São Paulo

first: Maria Lucia

middle: Hirata

last: Katayama

state: São Paulo

address: Av Dr Arnaldo

department: Radiology and Oncology

country: Brazil

institute: Faculty of Medicine University São Paulo

description: Organotypic culture_ Breast cancer_VitaminD_100nM_15

hyb_protocol: After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)

scan_protocol: GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7

data_processing: Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.

source_name: tissue, breast cancer, vitaminD 100nM, 24h

label_protocol: two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.

extract_protocol:
Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.

tag: disease state

value: Breast cancer

tag: agent

value: female

tag: age

tag: histologic type

value: CDI

tag: clinical stage

value: III


title: kidney  Rep1

description: kidney

source_name: kidney

value: adult tissue cells

tag: strain

value: male

tag: development stage

tag: individual identifier

value: kidney  Rep1; kidney  Rep1; 251508710695A1

value: Universale Mouse Reference


title: heart  Rep2

description: heart

source_name: heart

value: 28 weeks

value: adult

value: heart  Rep2; heart  Rep2; 251508710694A4


title: heart  Rep1

description: heart

value: heart  Rep1; heart  Rep1; 251508710694A3


title: Breast cancer_VitaminD_100nM_24h_13C

description: Organotypic culture_ Breast cancer_VitaminD_100nM_13

value: II


title: NK cells, mouse 13, day 30

value: pooled reference amplified RNA from combination of universal mouse reference and samples

tag: time

value: 30 days post-infection

value: NK cell

value: MCMV


title: Breast cancer_VitaminD_100nM_24h_12C

description: Organotypic culture_ Breast cancer_VitaminD_100nM_12

value: Breast cancer

value: I


title: Breast cancer_VitaminD_100nM_24h_11C

description: Organotypic culture_ Breast cancer_VitaminD_100nM_11

value: female

value: CDI


title: NK cells, mouse 11, day 14

value: 14 days post-infection


title: kidney  Rep2

description: kidney

value: adult tissue cells

value: male

value: kidney  Rep2; kidney  Rep2; 251508710695A2


title: pediatric acute lymphoblastic leukemia_929 [TaqMan MicroRNA Array]

source_name: pediatric acute lymphoblastic leukemia

tag: subtype

value: MLL

tag: patient id

tag: prednisolone-score

value: sensitive

value: resistant


title: NK cells, mouse 10, day 14

tag: sample type


title: bladder Rep1

description: bladder

source_name: bladder

value: 28 weeks

value: adult

value: bladder Rep1; bladder Rep1; 251508710695A3

value: Universale Mouse Reference


title: Breast cancer_VitaminD_100nM_24h_6C

description: Organotypic culture_ Breast cancer_VitaminD_100nM_6

value: III


title: liver  Rep2

description: liver

source_name: liver

value: liver  Rep2; liver  Rep2; 251508710694A2


title: NK cells, mouse 8, day 7

value: pooled reference amplified RNA from combination of universal mouse reference and samples

source_name: Amplified total RNA from FACS-isolated NK cells after 7 days infection with MCMV

value: 7 days post-infection

value: NK cell

tag: infection

value: MCMV


title: NK cells, mouse 9, day 7

tag: cell type


title: Breast cancer_VitaminD_0.5nM_24h_15B

description: Organotypic culture_ Breast cancer_VitaminD_0.5nM_15

source_name: tissue, breast cancer, vitaminD 0.5nM, 24h

value: Breast cancer

tag: gender

value: female

value: CDI


title: pediatric acute lymphoblastic leukemia_888 [TaqMan MicroRNA Array]

tag: vincristine-score

tag: daunorubicin-score

tag: l-asparaginase-score


title: bladder Rep2

description: bladder

value: adult tissue cells

value: male

tag: age

value: bladder Rep2; bladder Rep2; 251508710695A4

source_name: Universal Mouse Reference 129ES Cell


title: pediatric acute lymphoblastic leukemia_1191 [TaqMan MicroRNA Array]

value: MLL

value: unknown


title: Breast cancer_VitaminD_0.5nM_24h_12B

description: Organotypic culture_ Breast cancer_VitaminD_0.5nM_12

tag: disease state

tag: agent

tag: histologic type

value: I


title: NK cells, mouse 7, day 7

tag: strain


title: Breast cancer_VitaminD_0.5nM_24h_13B

description: Organotypic culture_ Breast cancer_VitaminD_0.5nM_13

tag: clinical stage

value: II


title: NK cells, mouse 6, day 1.5

source_name: Amplified total RNA from FACS-isolated NK cells after 1.5 days infection with MCMV

tag: time

value: 1.5 days post-infection


title: Breast cancer_VitaminD_0.5nM_24h_11B

description: Organotypic culture_ Breast cancer_VitaminD_0.5nM_11

value: III


title: liver  Rep1

description: liver

value: 28 weeks

tag: development stage

value: adult

tag: individual identifier

value: liver  Rep1; liver  Rep1; 251508710694A1

value: Universale Mouse Reference


title: pediatric acute lymphoblastic leukemia_873 [TaqMan MicroRNA Array]

tag: subtype

tag: patient id

tag: prednisolone-score

value: sensitive

value: resistant


title: pediatric acute lymphoblastic leukemia_788 [TaqMan MicroRNA Array]


title: Breast cancer_VitaminD_0.5nM_24h_6B

description: Organotypic culture_ Breast cancer_VitaminD_0.5nM_6

value: Breast cancer

value: female


title: lung  Rep2

description: lung

tag: cell type

value: adult tissue cells


title: NK cells, mouse 5, day 1.5

tag: sample type

value: pooled reference amplified RNA from combination of universal mouse reference and samples

value: NK cell

tag: infection

value: MCMV


title: eyes  Rep2

description: eyes

source_name: eyes

tag: gender

value: male


title: pediatric acute lymphoblastic leukemia_656 [TaqMan MicroRNA Array]

value: MLL

tag: vincristine-score

tag: daunorubicin-score

tag: l-asparaginase-score

value: unknown


title: pediatric acute lymphoblastic leukemia_169 [TaqMan MicroRNA Array]


title: NK cells, mouse 3, day 0

source_name: Amplified total RNA from FACS-isolated NK cells after 0 days infection with MCMV

value: 0 days post-infection


title: eyes  Rep1

description: eyes

tag: age


title: NK cells, mouse 4, day 1.5

value: 1.5 days post-infection


title: Breast cancer_Control_24h_15A

description: Organotypic culture_ Breast cancer_Control_15

source_name: tissue, breast cancer, control, 24h

tag: disease state

tag: agent

tag: histologic type

value: CDI

value: III


title: NK cells, mouse 2, day 0

source_name: pooled reference amplified RNA from combination of universal mouse reference and samples

tag: strain

tag: time


title: brain_cortex Rep1

value: 28 weeks

tag: development stage

value: adult

tag: individual identifier

value: Brain's_cortex Rep1; brain_cortex Rep1; 251508710692A1


title: cerebellum Rep1

description: cerebellum

source_name: cerebellum

value: cerebellum Rep1; cerebellum Rep1; 251508710692A3

value: Universale Mouse Reference


title: Breast cancer_Control_24h_12A

description: Organotypic culture_ Breast cancer_Control_12

value: Breast cancer

value: female

tag: clinical stage

value: I


title: Breast cancer_Control_24h_6A

description: Organotypic culture_ Breast cancer_Control_6


title: NK cells, mouse 1, day 0

value: pooled reference amplified RNA from combination of universal mouse reference and samples

value: NK cell


title: Breast cancer_Control_24h_11A

description: Organotypic culture_ Breast cancer_Control_11


title: Breast cancer_Control_24h_13A

description: Organotypic culture_ Breast cancer_Control_13

value: II


title: cerebellum Rep2

description: cerebellum

value: adult tissue cells

value: male

value: cerebellum Rep2; cerebellum Rep2; 251508710692A4


title: EGI-1

status: Public on Feb 10 2011

first: Gard

middle: Olav

last: Thomassen

address: Radiumhospitalet, Rikshospitalet HF

department: Institute for Cancer Research

institute: Rikshospitalet

description: Cancer cell line

hyb_protocol: Hybridized for 16-20 hours using Hybridisation kit from Roche NimbleGen

scan_protocol: Scanned using an Agilent microarray scanner

data_processing: According to related publication; in short, raw data was log2 transformed and normalised by subtracting the median probevalues from each probevalue over each tissue-type

label_protocol: Double stranded cDNA was labelled with Cy3 using One-colour labelling kit from Roche NimbleGen

growth_protocol: Standard conditions

extract_protocol: TRIzol

value: Bilde duct cancer cell line

tag: cell line


title: J82

description: Cancer cell line

tag: cell type

value: Bladder cancer cell line


title: HUCCT1

description: Cancer cell line


title: SW480

description: Cancer cell line

value: Colon cancer cell line


title: BT-20

description: Cancer cell line

value: Breast cancer cell line


title: scaBER

description: Cancer cell line

source_name: scaBER

value: scaBER


title: RKO

description: Cancer cell line

source_name: RKO

value: RKO


title: SK-ChA-1

description: Cancer cell line


title: SNU-1

description: Cancer cell line

value: Gastric cancer cell line


title: KMBC

description: Cancer cell line

source_name: KMBC

value: Cholangiocarcinoma cell line

value: KMBC


title: TFK-1

description: Cancer cell line


title: LS1034

description: Cancer cell line


title: 5637

description: Cancer cell line


title: ZR-751

description: Cancer cell line


title: HT29

description: Cancer cell line


title: Mz-ChA-1

description: Cancer cell line

value: Gall bladder carcinoma cell line


title: MCF-7

description: Cancer cell line


title: Mz-ChA-2

description: Cancer cell line


title: SW48

description: Cancer cell line


title: Colo320

description: Cancer cell line


title: LS174T

description: Cancer cell line


title: HCT116

description: Cancer cell line


title: KATOIII

description: Cancer cell line

source_name: KATOIII

value: KATOIII


title: TCCSUP

description: Cancer cell line

source_name: TCCSUP

value: TCCSUP


title: ALA

description: Cancer cell line

source_name: ALA

value: ALA


title: AGS

description: Cancer cell line

source_name: AGS

value: AGS


title: Hs578T

description: Cancer cell line


title: Caki-2

description: Cancer cell line

value: Kidney cancer cell line


title: HTC15

description: Cancer cell line


title: THP-1

description: Cancer cell line

value: Leukemia cell line


title: RS4-11

description: Cancer cell line


title: ACHN

description: Cancer cell line

source_name: ACHN

value: ACHN


title: Mono-Mac6

description: Cancer cell line


title: MV4-11

description: Cancer cell line


title: 697

description: Cancer cell line


title: ST8814

description: Cancer cell line

value: Malignant peripheral nerve sheat tumour cell line


title: REH

description: Cancer cell line

source_name: REH

value: REH


title: Panc1

description: Cancer cell line

value: Pancreas cancer cell line


title: RCH-ACV

description: Cancer cell line

source_name: RCH-ACV

value: RCH-ACV


title: STS26T

description: Cancer cell line


title: NCI-H226

description: Cancer cell line

value: Lung cancer cell line


title: K562

description: Cancer cell line


title: NCI-N87

description: Cancer cell line


title: SK.OV-3

description: Cancer cell line

value: Ovary cancer cell line


title: ES-2

description: Cancer cell line


title: A-549

description: Cancer cell line


title: NCI-H23

description: Cancer cell line


title: NCI-H460

description: Cancer cell line


title: Caki-1

description: Cancer cell line


title: OV-90

description: Cancer cell line


title: HPAF-II

description: Cancer cell line

source_name: HPAF-II

value: HPAF-II


title: exposure to Al

city: Padua

first: Karina

last: Fincati

address: V.le G. Colombo, 3

department: Department of Biology, University of Padua

country: Italy

institute: CNR-Institute for Biomedical Technologies

description: In all hybridizations SH-SY5Y  cell  culture was used as control for direct comparison to the experimental  conditions: expoure to AB, AB-Aal or Al

hyb_protocol: Labeled aRNA was dissolved in 90 ul of hybridization buffer, denaturated at 90ºC for 3 min and applied directly to microarray slides. Microarray hybridization was carried out in an ArrayBooster Hybridization Station. The reaction was carried out overnight at 42ºC. Posthybridization washing was performed according to the microarray slides manufacturer’s instructions.

scan_protocol: The microarrays slides were scanned using a GenePix 4000B laser scanner  and images were processed using Genepix 6.0 software.

data_processing: Data analysis  were performed using Acuity 4.0 software. Initial results were normalized using Lowess algorithm and filtered to exclude extreme outliers and flags. We also excluded any spots that had no detectable response on all slides. The log-ratios of expression were calculated as the base 2 logarithm of the ratios of background-corrected intensity medians of red dye over green dye intensities. In order to obtain a single expression value for each gene, the internal replicates (1 to 14) were plotted versus the technical replicates (6 for exposure to AB and 2 for exposure to Al and AB-Al complex). The X-Y scatterplot confirmed that the data were generally reproducible but we observed the presence of extreme outliers values. Then we excluded the outliers and the values of spots replicates within and among arrays were averaged using a trimmed mean. We excluded any spot that had no detectable response in all three treatments.

label: Alexa Fluor 555, Alexa Fluor 649

source_name: human neuroblastoma cells culture

label_protocol: 1 ug of total RNA was amplified following the SuperscriptTM Indirect RNA Amplification System Kit (InvitrogenTM): total RNA was reverse transcribed into single-stranded complementary DNA (cDNA) using oligo(dT) primer containing a T7 promoter and Superscript III reverse transcriptase. RNase H was then added together with E. coli DNA polymerase I and E. coli DNA ligase, followed by a short incubation in order to achieve synthesis of the second-strand cDNA. The purified double-strand cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7-RNA polymerase. This step generated antisense RNA (aRNA) molecules complementary to the original mRNA targets, incorporating amino-allyl UTP (aa-UTP) into the aRNA. 10 ug of purified aRNA was coupled with Alexa Fluor 555 or Alexa Fluor 647 dyes (Invitrogen) according to the manufacturer’s instructions.

growth_protocol: SH-SY5Y human neuroblastoma cells were purchased from ECACC. SH-SY5Y human neuroblastoma cells were maintained in Dulbecco’s modified Eagle’s medium (1: 1) with L-Glutamine and 15 mM Hepes at 37 °C with 5% CO2 in a humidified atmosphere (90 % humidity). The medium was replaced every 2 days. Penicillin (100 units/ml) and streptomycin (100 ug/ml), 15 % fetal bovine serum, and MEM non-essential amino acids (100x) were added to the medium. 0.25% Trypsin-EDTA solution and phosphate buffered saline (PBS) were obtained from Sigma Aldrich. SHSY5Y cells were plated onto 6-well plates.

extract_protocol: Total RNA of SH-SY5Y human neuroblastoma cells exposed to AB,  AB-metal complexes (AB-Al) and Al was isolated using the Qiagen RNA/DNA Mini Kit following the manufacturer’s instructions.

treatment_protocol: The day after this plating, the culture medium was replaced with the same medium with 2 % FBS containing AB or AB-metal complexes at 0.5 uM peptide concentration. The cells were incubated with different AB or AB-metal complexes for 24h. The cell treatment was also performed in the presence of metals (Al) at a concentration 10-fold higher than the peptide concentration.

tag: treatment

value: aluminum

label: Alexa Fluor 555, Alexa Fluor 647

source_name: human neuroblastoma cells exposed to Al

value: untreated


title: TPC1

description: Cancer cell line

value: Thyroidea cancer cell line


title: Ovcar-3

description: Cancer cell line


title: A13B, mock vs. GATA6 shRNA

first: Christine

last: Iacobuzio Donahue

address: 1550 Orleans Street, CRB2 Rm 343

institute: Johns Hopkins

description: dye swap replicate 1

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

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

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

source_name: A13B, mock

label_protocol: 0.4ug of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Lentiviral infected cells were GFP sorted to >90% purity, and plated in DMEM media supplemented with 10% FBS and antibiotics. Cells were grown to 80% confluence and then total RNA extracted.

extract_protocol: Qiagen Rneasy Kits

value: mock shRNA

source_name: A13B, GATA6 shRNA

value: GATA6 shRNA


title: 768-0

description: Cancer cell line


title: exposure to AB-Al complex

label: Alexa Fluor 555, Alexa Fluor 648

value: B-amyloid aluminum complex

source_name: human neuroblastoma cells exposed to AB-Al complex


title: A13B, GATA6 vs. mock shRNA

description: dye swap replicate 2

source_name: A13B, GATA6

source_name: A13B, mock shRNA


title: AsPC1, GATA6 vs. mock shRNA

description: dye swap replicate 2

source_name: AsPC1, GATA6

source_name: AsPC1, mock shRNA


title: Lama-84

description: Cancer cell line


title: Liver metastsis 18

city: Uppsala

first: Katarina

last: Edfeldt

address: Akademiska Sjukhuset

department: Surgical Sciences

country: Sweden

institute: Uppsala University

hyb_protocol: The hybridizations were done manually and Standard Operation Procedure; SOP 003 Hybridization onto oligo or cDNA Microarrays were followed. http://www.biotech.kth.se/molbio/microarray/protocols.html

scan_protocol: The slides were scanned in the Aglient DNA Microarray Scanner and in GenePix 5.1, Axon Instruments, were used for image analysis. (http://www.moleculardevices.com/Products/Software/GenePix-Pro.html)

data_processing: After removal of bad quality spots (if less than 70% of foreground pixels were below background intensity plus 2 SDs in both channels or if the difference between ratio of medians and regression ratio exceeded 20% in one of the channels), analysis of the gene expression data was carried out in the freely available statistical computing language R (http://www.r-project.org) using a package available from the Bioconductor project (www.bioconductor.org). The raw data was normalized using the LOWESS method (Yang, Dudoit et al. 2002). In order to search for differentially expressed genes between groups, an empirical Bayes moderated t test was applied, using the Limma package (Smyth 2004). To address the problem of multiple testing, the p-values were adjusted using the Benjamini and Hochberg method (Benjamini 1995).

source_name: Liver metastasis

label_protocol: For labeling of the total RNA samples a Standard Operation Procedure; SOP 002 Indirect labeling of cDNA using aminoallyl modified nucleotides was used. http://www.biotech.kth.se/molbio/microarray/protocols.html

extract_protocol: Total RNA was extracted using TriZol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Sections from all the tumors were stained with Mayer´s hematoxylin and histopathologically evaluated, and the tissue used contained at least 80 % of neoplastic cells. When needed, the tumor was macroscopically resected from excessive stroma tissue, blood vessels, bowel mucosa, lymphoid and liver tissue. Quality and quantity of the extracted RNA was assessed by Aglient 2100 Bioanalyzer (Aglient Technologies, Santa Clara, CA, USA). One lymph node metastases were contaminated with < 5 % of lymphatic tissue (LNmet9181).

treatment_protocol: Tumors were snap frozen in liquid nitrogen and kept at -70°C until used.

value: Associated lymph node metastasis 18

source_name: Universal Human Reference RNA, Agilent Technologies, USA. A mix of 10 human cell lines.

tag: sample type

value: reference


title: Liver metastsis 16

tag: associated primary tumor no


title: BxPc-3

description: Cancer cell line


title: sw1116.l15.2

city: Goettingen

first: Melanie

last: Spitzner

address: Robert-Koch-Str. 40

department: Department of General and Visceral Surgery

institute: Georg-August-University Goettingen

description: Cell line: SW1116; Medium: L-15; SF2: 0.68

hyb_protocol: Subsequently, 1.65 µg of labeled cRNA per sample was fragmentized and hybridized overnight to a 4x44k gene expression microarray (Agilent Technologies).  After a washing step the arrays were scanned on an Agilent DNA microarray scanner G2505B (Agilent Technologies) at 5 micron resolution.  Scanned image files were visually inspected for artifacts and subsequently analyzed.

scan_protocol: Agilent DNA microarray scanner G2505B, 5 micron resolution

data_processing: Median signal intensities from the Feature Extraction Software were converted to log2 and quantile normalized using the R package “limma”.

source_name: colorectal cancer cell line

label_protocol: 800 ng of total RNA were reverse-transcribed, amplified and labeled with Cy3 using the Low RNA Input Linear Amplification Kit, PLUS (Agilent Technologies).  After purification, the cRNA yield and integration of cyanine 3-CTP was measured using a spectrophotometer.  cRNA with a specific activity > 9.0 pmol/µg was excluded from further experiments.

growth_protocol: Twelve human colorectal cancer cell lines were obtained from the American Type Culture Collection (ATCC, Manassas, VA): Caco-2, HT-29, LS411N, LS513, LS1034, SW403, SW480, SW620, SW837, SW1116, SW1463, and WiDr.  All lines were cultured in their recommended medium (Invitrogen, Karlsruhe, Germany), supplemented with fetal bovine serum (Pan, Aidenbach, Germany) and 2mM L-glutamine (BioWhittaker, Verviers, Belgium).  Periodically, mycoplasma contamination was excluded by PCR, and cell line cross-contamination was excluded by short tandem repeat profiling.

extract_protocol: Total RNA was isolated using the RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions, including a DNase treatment step.  Nucleic acid quantity, quality and purity were determined using NanoDrop ND-1000 spectrophotometer (Peqlab, Erlangen, Germany) and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  Only RNA samples with a RNA integrity number > 9.5 were considered for further analysis.

treatment_protocol: No treatment prior to expression profiling analysis.

tag: medium

tag: rep


title: caco2.rpmi.2

description: Cell line: Caco-2; Medium: RPMI

value: RPMI


title: caco2.rpmi.1

description: Cell line: Caco-2; Medium: RPMI


title: KU812

description: Cancer cell line

value: Leukemia cell line


title: AsPC1, mock vs. GATA6 shRNA

description: dye swap replicate 1

source_name: AsPC1, mock

source_name: AsPC1, GATA6 shRNA


title: widr.mem.2

description: Cell line: WiDr; Medium: MEM; SF2: 0.4

value: WiDr

value: MEM


title: Liver metastsis 14


title: Liver metastsis 13


title: sw620.l15.1

description: Cell line: SW620; Medium: L-15; SF2: 0.46


title: ls513.rpmi.1

description: Cell line: LS513; Medium: RPMI; SF2: 0.59


title: sw837.l15.2

description: Cell line: SW837; Medium: L-15; SF2: 0.71


title: Lymph node metastasis 19

source_name: Lymph node metastasis


title: Liver metastsis 15


title: Liver metastsis 12


title: Liver metastsis 11


title: sw480.rpmi.4

description: Cell line: SW480; Medium: RPMI


title: ls411n.rpmi.1

description: Cell line: LS411N; Medium: RPMI; SF2: 0.28


title: ht29.mccoy.2

description: Cell line: HT-29; Medium: McCoy's; SF2: 0.81

value: McCoy's


title: Lymph node metastasis 18

tag: gender

value: Female

tag: carcinoid syndrome

value: No

tag: ki67 proliferation index

tag: age at diagnosis

tag: radically operated

value: Yes

tag: disease status

value: Stable


title: T265

description: Cancer cell line

value: Malignant peripheral nerve sheat tumour cell line


title: TERA2

description: Cancer cell line

value: Germ cell cancer cell line


title: PaCa-2

description: Cancer cell line

value: Pancreas cancer cell line


title: ls411n.rpmi.3


title: sw403.l15.3

description: Cell line: SW403; Medium: L-15; SF2: 0.76


title: Lymph node metastasis 17


title: Lymph node metastasis 15


title: 2102Ep

description: Cancer cell line


title: sw620.l15.3


title: sw480.l15.2

description: Cell line: SW480; Medium: L-15; SF2: 0.55


title: sw403.l15.1


title: Lymph node metastasis 13


title: Lymph node metastasis 12


title: sw480.rpmi.1

description: Cell line: SW480; Medium: RPMI


title: NCCIT

description: Cancer cell line

source_name: NCCIT

value: NCCIT


title: Lymph node metastasis 10


title: sw1116.l15.1


title: caco2.mem.2

description: Cell line: Caco-2; Medium: MEM; SF2: 0.58


title: sw837.rpmi.2

description: Cell line: SW837; Medium: RPMI


title: Lymph node metastasis 11


title: sw620.l15.2


title: Lymph node metastasis 8


title: HEC-1-A

description: Cancer cell line

value: Uterus cancer cell line


title: ls1034.rpmi.2

description: Cell line: LS1034; Medium: RPMI; SF2: 0.59


title: AN3CA

description: Cancer cell line


title: RL-95-2

description: Cancer cell line


title: Lymph node metastasis 7


title: KLE

description: Cancer cell line

source_name: KLE

value: KLE


title: sw837.rpmi.3

description: Cell line: SW837; Medium: RPMI


title: Lymph node metastasis 5


title: ls513.rpmi.3


title: Lymph node metastasis 4


title: sw1463.l15.2

description: Cell line: SW1463; Medium: L-15; SF2: 0.56


title: Lymph node metastasis 2


title: Lymph node metastasis 9


title: sw480.rpmi.2

description: Cell line: SW480; Medium: RPMI


title: Primary tumor 17

source_name: Primary tumor

value: Male


title: Lymph node metastasis 1

value: reference


title: Lymph node metastasis 3


title: sw480.l15.1


title: Cigarette smoke extract-chronically treated OKF6 cells

type: genomic

first: wenyue

last: sun

address: 1550 Orleans street, Rm 574A

department: Otolaryngology Head and Neck Surgery

institute: Johns Hopkins Medical Institutions

description: Cigarette Smoke Extract-chronically treated OKF6 cells

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their DNA Array Fluidics Station 450 Protocol.

scan_protocol: Image analysis by GeneChip Operating Software (GCOS) 1.4 at manufacturer's settings.

data_processing:
All CEL files were analyzed in Affy's GeneChip Sequence Analysis Software, GSEQ, using its "Resequencing Algorithm Version 2", for 8 um arrays.  The results of this process are saved as CHP files (containing processed base calls). Analysis was conducted using the recommendations from Affy's Mitochondrial Resequencing Array 2.0 Supporting Documentation on their Support page (http://www.affymetrix.com/support/technical/byproduct.affx?product=humitoreseq) following algorithm parameter settings recommendations 3.1:

- Genome Model = Diploid. Selection of the diploid genome model will enable the detection of heteroplasmy.
- Quality Score Threshold (QST) = 3. The QST parameter was selected to provide the highest performance in terms of overall base calling accuracy and call rates.

FASTA files were exported from GSEQ using proceedures fully described in the gseq_user_guide.pdf, from Affy's webpage. In short, Affy's GSEQ Toolbar provides an "Export -> FASTA"  function (alternatively the [FASTA] button) with two options.

The "Whole sequence" option was used to create the submitted file named "SDas051408_Whole_Sequence.txt".
The "SNP flanking sequence" option was used to create "SDas051408_FASTA_Export.txt".

The base calls (from .CHP files) are provided in the file named "SDas051408_TableData.txt".

molecule: genomic DNA

source_name: OKF6 cells, chronic cigarette extract treatment for 7 months

label_protocol: GeneChip CustomSeq Resequencing Assay Kit

growth_protocol: The cell line was expanded and passaged in keratinocyte serum-free medium (Gibco/Invitrogen; 10725-018). This medium was supplemented with BPE (25 ug/ml), epidermal growth factor (0.2 ng/ml), CaCl2(0.4 mM) and 1% penicillin-streptomycin. Both the cells treated with CSE and passaged cells were cultured in 37 °C humidified air incubators with 5% CO2. All cell lines were grown in 35mm dishes.

extract_protocol: phenol/chloroform extraction

treatment_protocol: Research-grade cigarettes, 2R4F, from the Kentucky Tobacco Research and Development Center at the University of Kentucky were smoked to 0.25 cm above the filter. 100% CSE was prepared by bubbling smoke from one cigarette into 1 ml of PBS. Each puff was 2 seconds long at a rate 35ml/second. This extract was then filtered using a .22um filter from BD biosciences filter. Each dilution was done by volume in media. Treatment concentration was .1%.

value: oral immortal keratinocyte, treated for 7 months


title: ls513.rpmi.2

value: RPMI


title: sw1463.l15.1


title: Primary tumor 16

value: Progressive


title: Primary tumor 19

value: Deceased


title: Control OKF6 cells

description: Control human oral immortal OKF6 cells

source_name: OKF6 cells, passaged for 7 months

value: oral immortal keratinocyte, passaged 7 months


title: Primary tumor 14

value: Female


title: sw837.l15.3


title: widr.mem.1

description: Cell line: WiDr; Medium: MEM; SF2: 0.4

value: WiDr

value: MEM


title: ht29.mccoy.1

value: McCoy's


title: Primary tumor 15

value: Yes

value: No

value: Stable


title: sw403.l15.2


title: Primary tumor 13


title: TERA1

description: Cancer cell line

value: Germ cell cancer cell line


title: Primary tumor 12


title: Primary tumor 9


title: Primary tumor 11


title: Primary tumor 10


title: sw837.l15.1


title: widr.mem.3

description: Cell line: WiDr; Medium: MEM; SF2: 0.4


title: sw1463.l15.3