title: squamous cell carcinoma_biopsy8

status: Public on Oct 31 2014

type: RNA

city: Marseille

first: Celine

last: Mascaux

address: 27 bvd Lei Roure

department: Centre of research for cancer of Marseille

country: France

institute: Aix Marseille University

description: squamous cell carcinoma_biopsy8

hyb_protocol: The labelled cRNAs were hybridized on an Agilent oligonucleotide microarray (Two Colours Whole Human Genome 4x44K arrays, Agilent Technologies) for 17 hours at 60°C in a rotating oven according to the provider’s protocol (Agilent Technologies).

scan_protocol: The signal was read by confocal laser scanning (Agilent Technologies).

data_processing: Grid positioning, spots localization, outliers flagging, fluorescence intensities quantification, background level assessment, correction of the values according to the background followed by linear and Lowess data normalization were all performed according to the default protocol for two colours Agilent customized arrays (GE2_v5_95_Feb07 protocol, Feature Extraction software version 9.5.3.1, Agilent Technologies).

molecule: total RNA

organism: Homo sapiens

source_name: bronchial biopsy

label_protocol: mRNAs were retrotranscribed using a T7 primer coupled with oligo-dT primers and Moloney murine leukaemia virus-reverse transriptase (MMLV-RT). The cDNA was then in vitro transcribed in labelled cRNA by the T7 RNA polymerase with fluorescent nucleotides, Cy5 for samples or Cy3 for reference RNA dyes, by using the Low input RNA Fluorescent Linear Amplification Plus kit (Agilent Technologies). Spike-in RNAs (Agilent Technologies) were included as positive controls to monitor the whole microarray workflow (sample amplification, labelling and microarray processing). For each sample, an amount of 100 ng of total RNA was amplified in parallel with 100 ng of pooled reference RNAs for each experiment with the same Master-Mix.

growth_protocol: During the bronchoscopy, two biopsies were taken with clean forceps in the same area: one for routine histopathology and the second, immediately dropped in Tripure Isolation Reagent on ice, homogenized and frozen at –80°C (Roche Diagnostics, Indianapolis, IN, USA), for molecular studies.

extract_protocol: RNA extraction was performed according to a classical phenol/chloroform protocol as described by the Tripure provider. Twenty µg of glycogen (Roche Diagnostics) was added as carrier and the separation between the organic and the aqueous phase was performed on Phase Lock Gel (Eppendorf, Hamburg, Germany) to optimize the recovery of nucleic acids.

tag: histology

value: squamous cell carcinoma

tag: phenotypical stage

tag: molecular group

tag: smoking status

value: current

tag: gender

value: Male

tag: age

tag: patient

source_name: Pooled total RNA extrated from normal bronchial biopsies from 16 never-smokers

value: never-smokers

tag: tissue

value: normal bronchial mucosa


title: squamous cell carcinoma_biopsy5

description: squamous cell carcinoma_biopsy5


title: squamous cell carcinoma_biopsy12

description: squamous cell carcinoma_biopsy12

value: Female


title: squamous cell carcinoma_biopsy11

description: squamous cell carcinoma_biopsy11


title: squamous cell carcinoma_biopsy9

description: squamous cell carcinoma_biopsy9

value: former


title: squamous cell carcinoma_biopsy4

description: squamous cell carcinoma_biopsy4


title: carcinoma in situ_biopsy9

description: carcinoma in situ_biopsy9

value: carcinoma in situ


title: squamous cell carcinoma_biopsy10

description: squamous cell carcinoma_biopsy10


title: carcinoma in situ_biopsy5

description: carcinoma in situ_biopsy5


title: squamous cell carcinoma_biopsy13

description: squamous cell carcinoma_biopsy13


title: squamous cell carcinoma_biopsy6

description: squamous cell carcinoma_biopsy6


title: squamous cell carcinoma_biopsy14

description: squamous cell carcinoma_biopsy14


title: carcinoma in situ_biopsy13

description: carcinoma in situ_biopsy13


title: carcinoma in situ_biopsy6

description: carcinoma in situ_biopsy6


title: squamous cell carcinoma_biopsy1

description: squamous cell carcinoma_biopsy1


title: carcinoma in situ_biopsy10

description: carcinoma in situ_biopsy10


title: carcinoma in situ_biopsy3

description: carcinoma in situ_biopsy3


title: carcinoma in situ_biopsy7

description: carcinoma in situ_biopsy7


title: carcinoma in situ_biopsy12

description: carcinoma in situ_biopsy12


title: severe dysplasia_biopsy12

description: severe dysplasia_biopsy12

value: severe dysplasia


title: carcinoma in situ_biopsy8

description: carcinoma in situ_biopsy8


title: carcinoma in situ_biopsy4

description: carcinoma in situ_biopsy4


title: squamous cell carcinoma_biopsy2

description: squamous cell carcinoma_biopsy2


title: carcinoma in situ_biopsy1

description: carcinoma in situ_biopsy1


title: squamous cell carcinoma_biopsy7

description: squamous cell carcinoma_biopsy7


title: carcinoma in situ_biopsy2

description: carcinoma in situ_biopsy2


title: squamous cell carcinoma_biopsy3

description: squamous cell carcinoma_biopsy3


title: severe dysplasia_biopsy11

description: severe dysplasia_biopsy11


title: severe dysplasia_biopsy9

description: severe dysplasia_biopsy9


title: severe dysplasia_biopsy5

description: severe dysplasia_biopsy5


title: severe dysplasia_biopsy2

description: severe dysplasia_biopsy2


title: moderate dysplasia_biopsy12

description: moderate dysplasia_biopsy12

value: moderate dysplasia

value: B


title: moderate dysplasia_biopsy10

description: moderate dysplasia_biopsy10


title: severe dysplasia_biopsy6

description: severe dysplasia_biopsy6


title: moderate dysplasia_biopsy9

description: moderate dysplasia_biopsy9


title: carcinoma in situ_biopsy11

description: carcinoma in situ_biopsy11


title: severe dysplasia_biopsy10

description: severe dysplasia_biopsy10


title: severe dysplasia_biopsy8

description: severe dysplasia_biopsy8


title: moderate dysplasia_biopsy11

description: moderate dysplasia_biopsy11


title: severe dysplasia_biopsy7

description: severe dysplasia_biopsy7


title: moderate dysplasia_biopsy5

description: moderate dysplasia_biopsy5


title: severe dysplasia_biopsy4

description: severe dysplasia_biopsy4


title: moderate dysplasia_biopsy6

description: moderate dysplasia_biopsy6


title: moderate dysplasia_biopsy8

description: moderate dysplasia_biopsy8


title: moderate dysplasia_biopsy7

description: moderate dysplasia_biopsy7


title: severe dysplasia_biopsy3

description: severe dysplasia_biopsy3


title: severe dysplasia_biopsy1

description: severe dysplasia_biopsy1


title: moderate dysplasia_biopsy13

description: moderate dysplasia_biopsy13


title: moderate dysplasia_biopsy4

description: moderate dysplasia_biopsy4


title: moderate dysplasia_biopsy2

description: moderate dysplasia_biopsy2


title: moderate dysplasia_biopsy1

description: moderate dysplasia_biopsy1


title: moderate dysplasia_biopsy3

description: moderate dysplasia_biopsy3


title: mild dysplasia_biopsy10

description: mild dysplasia_biopsy10

value: mild dysplasia


title: mild dysplasia_biopsy9

description: mild dysplasia_biopsy9


title: mild dysplasia_biopsy8

description: mild dysplasia_biopsy8


title: mild dysplasia_biopsy13

description: mild dysplasia_biopsy13


title: mild dysplasia_biopsy12

description: mild dysplasia_biopsy12


title: mild dysplasia_biopsy6

description: mild dysplasia_biopsy6


title: mild dysplasia_biopsy4

description: mild dysplasia_biopsy4


title: metaplasia_biopsy14

value: metaplasia


title: metaplasia_biopsy15


title: mild dysplasia_biopsy3

description: mild dysplasia_biopsy3


title: metaplasia_biopsy13


title: mild dysplasia_biopsy7

description: mild dysplasia_biopsy7


title: metaplasia_biopsy9


title: metaplasia_biopsy7


title: mild dysplasia_biopsy11

description: mild dysplasia_biopsy11


title: mild dysplasia_biopsy2

description: mild dysplasia_biopsy2


title: mild dysplasia_biopsy1

description: mild dysplasia_biopsy1


title: metaplasia_biopsy12


title: mild dysplasia_biopsy5

description: mild dysplasia_biopsy5


title: metaplasia_biopsy3


title: metaplasia_biopsy11


title: metaplasia_biopsy6


title: metaplasia_biopsy1


title: metaplasia_biopsy10


title: metaplasia_biopsy4


title: metaplasia_biopsy5


title: metaplasia_biopsy2


title: hyperplasia_biopsy10

value: hyperplasia

value: A


title: hyperplasia_biopsy13


title: hyperplasia_biopsy5


title: hyperplasia_biopsy15


title: hyperplasia_biopsy8


title: hyperplasia_biopsy11


title: hyperplasia_biopsy6


title: hyperplasia_biopsy7


title: hyperplasia_biopsy9


title: hyperplasia_biopsy12


title: normal hypofluorescent_biopsy12

description: normal hypofluorescent_biopsy12

value: normal

value: normal hypofluorescent


title: normal hypofluorescent_biopsy8

description: normal hypofluorescent_biopsy8


title: normal hypofluorescent_biopsy10

description: normal hypofluorescent_biopsy10


title: hyperplasia_biopsy1


title: normal hypofluorescent_biopsy14

description: normal hypofluorescent_biopsy14


title: normal hypofluorescent_biopsy5

description: normal hypofluorescent_biopsy5


title: normal hypofluorescent_biopsy11

description: normal hypofluorescent_biopsy11


title: hyperplasia_biopsy14


title: hyperplasia_biopsy3


title: hyperplasia_biopsy4


title: normal hypofluorescent_biopsy9

description: normal hypofluorescent_biopsy9


title: hyperplasia_biopsy2


title: normal hypofluorescent_biopsy13

description: normal hypofluorescent_biopsy13


title: normal hypofluorescent_biopsy6

description: normal hypofluorescent_biopsy6


title: normal hypofluorescent_biopsy7

description: normal hypofluorescent_biopsy7


title: normal hypofluorescent_biopsy3

description: normal hypofluorescent_biopsy3


title: normal hypofluorescent_biopsy2

description: normal hypofluorescent_biopsy2


title: normal normofluorescent_biospy13

description: normal normofluorescent_biospy13

value: normal normofluorescent


title: normal normofluorescent_biopsy12

description: normal normofluorescent_biopsy12


title: normal hypofluorescent_biospy1

description: normal hypofluorescent_biospy1

value: current


title: normal normofluorescent_biopsy5

description: normal normofluorescent_biopsy5

value: Male


title: normal normofluorescent_biospy9

description: normal normofluorescent_biospy9

value: never-smokers


title: normal normofluorescent_biopsy6

description: normal normofluorescent_biopsy6

value: normal bronchial mucosa


title: normal normofluorescent_biopsy7

description: normal normofluorescent_biopsy7


title: normal normofluorescent_biospy10

description: normal normofluorescent_biospy10


title: normal normofluorescent_biospy11

description: normal normofluorescent_biospy11


title: normal normofluorescent_biopsy4

description: normal normofluorescent_biopsy4

value: Female


title: normal normofluorescent_biopsy3

description: normal normofluorescent_biopsy3

value: former


title: normal normofluorescent_biopsy8

description: normal normofluorescent_biopsy8


title: normal normofluorescent_biopsy2

description: normal normofluorescent_biopsy2


title: normal hypofluorescent_biospy4

description: normal hypofluorescent_biospy4


title: Kitaake_3rd leaf_rep2

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

description: Biological replication 2 of 2

hyb_protocol: Kit: in situ hybridization plus Manufacturer: Agilent Technologies Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner Manufacturer: Agilent Technologies Manual: Agilent Technologies

data_processing:
Software: Feature Extraction
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

organism: Oryza sativa Japonica Group

source_name: 3rd leaf of Kitaake rep2

label_protocol:
Kit: Low amplification kit
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

growth_protocol:
Environment: Green house study
Growth: Pot culture (3x3x5cm)
Growth media: Natural soil of NARO field
Light condition: Natural condition
Temperature: 22±3 °C
Growth stage: Four leaves visible stage

extract_protocol:
Separation: Trimming
Extraction source: Frozen
Extraction source: leaf blades pooled from 5 individual plants
Kit: Qiagen RNeasy Maxi kit
Manufacturer: Qiagen
Manual: Qiagen

tag: cultivar

value: Kitaake

value: Third leaf blade


title: Kitaake_3rd leaf_rep1

description: Biological replication 1 of 2

source_name: 3rd leaf of Kitaake rep1


title: normal normofluorescent_biopsy1

description: normal normofluorescent_biopsy1


title: Hoshinoyume_3rd leaf_rep2

description: Biological replication 2 of 3

source_name: 3rd leaf of Hoshinoyume rep2

value: Hoshinoyume


title: metaplasia_biopsy8

value: B


title: Hoshinoyume_3rd leaf_rep1

description: Biological replication 1 of 3

source_name: 3rd leaf of Hoshinoyume rep1


title: m08442_cho

city: Nashville

first: Kimryn

last: Rathmell

state: TN

address: 2220 Pierce Ave

department: Medicine

country: USA

institute: Vanderbilt

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

organism: Mus musculus

source_name: Mouse Reference

extract_protocol: Total RNA isolated by stratagene

tag: reference

value: Stratagene Mouse Universal Reference

extract_protocol: Qiagen Rneasy Kit

treatment_protocol: all mice were injected with tamoxifen at 6 days to induce Cre recombination, making the Pten loxP/loxP become Pten -/- and Vhl loxP/loxp become Vhl -/-.

tag: sample

value: Mouse 8442

value: Liver and Tumor

tag: strain

value: BALB/c, C57BL/6

tag: genotype/variation

value: CreER; Vhl loxP/loxp; Pten loxP/loxP


title: Hoshinoyume_3rd leaf_rep3

description: Biological replication 3 of 3

source_name: 3rd leaf of Hoshinoyume rep3


title: m08424_cho

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

value: Mouse 8424


title: m08656_cho

value: Mouse 8656


title: m08386_cho

value: Mouse 8386


title: PMA ionomycine stimulated 301167_6p600_1205

city: Jouy en Josas

first: Yu

last: GAO

address: INRA, BAT440

department: Animal Genetics

institute: GABI-GIS

description: The peripheral blood mononuclear cells (PBMCs) from Large White pigs (male) (~57 kg) were isolated by Ficoll-Hypaque density gradient certrifugation at room temperature.

hyb_protocol: 3 ug of labeled cDNA were used for hybridization to SLA Tiling Array with an MAUI hybridization system (BioMicro Systems). After 18 hours at 42oC hybridization, the slides were washed according to the recommended protocol (NimbleGen Arrays User’s Guide: Gene Expression Analysis v3.0) and dried in the ArrayIt Microarray High-Speed Centrifuge for 1 min.

scan_protocol: Arrays were scanned with a GenePix 400B scanner (MDS Inc., Canada) with a resolution of 5 um pixel size.

data_processing: The array images were processed with the NimbleScan v2.5 software (NimbleGen) to align spots, to integrate ID data files and to export reports of spot intensity data. Eight “e generated. For 4 mock-stimulated samples and 4 PMA/ionomycin stimulated samples. The intensity of probes was Log2 transformed and centered (median centered) by slide to normalize data.

organism: Sus scrofa

source_name: PMA ionomycine stimulated

label_protocol: Ten µg of total RNA were reverse transcribed with random primers and oligo(dT), and directly labeled with Cy3 using ChipShotTM Direct Labeling System (Promega, USA). The Cy3-labelled cDNA were purified using ChipShotTM Membrane Clean-Up System (Promega, USA).

extract_protocol: Total RNAs were extracted from stimulated and non stimulated PBMCs using miRNeasy Mini Kit (Qiagen, USA) and purified by on-column digestion of residual DNA with DNase I (Qiagen, USA).

tag: treatment

value: PMA ionomycine stimulated

tag: cell type

value: peripheral blood mononuclear cells

value: Large White


title: Yukara_3rd leaf_rep2

description: Biological replication 2 of 2

source_name: 3rd leaf of Yukara rep2

value: Yukara


title: m08383_cho

value: Mouse 8383


title: m10938 cho_3

value: Mouse 10938

value: CreER; Pten loxP/loxP


title: m10828 cho_4

value: Mouse 10828


title: Control 301159_4c600_1205

description: The peripheral blood mononuclear cells (PBMCs) from Large White pigs (male) (~51 kg) were isolated by Ficoll-Hypaque density gradient certrifugation at room temperature.

source_name: Control

value: Control


title: m10779 cho_2

value: Stratagene Mouse Universal Reference

value: Mouse 10779


title: PMA ionomycine stimulated 301160_4p600_1205

description: The peripheral blood mononuclear cells (PBMCs) from Large White pigs (male) (~55 kg) were isolated by Ficoll-Hypaque density gradient certrifugation at room temperature.


title: m08382_cho

value: Mouse 8382

value: Liver and Tumor


title: Control 301166_6c600_1205

description: The peripheral blood mononuclear cells (PBMCs) from Large White pigs (male) (~53 kg) were isolated by Ficoll-Hypaque density gradient certrifugation at room temperature.


title: NorinNo15_3rd leaf_rep1

description: Biological replication 1 of 3

source_name: 3rd leaf of NorinNo15 rep1

value: Norin No.15

value: Third leaf blade


title: PMA ionomycine stimulated 301162_5p600_1205

description: The peripheral blood mononuclear cells (PBMCs) from Large White pigs (male) (~56 kg) were isolated by Ficoll-Hypaque density gradient certrifugation at room temperature.


title: Control 301161_5c600_1205

description: The peripheral blood mononuclear cells (PBMCs) from Large White pigs (male) (~52 kg) were isolated by Ficoll-Hypaque density gradient certrifugation at room temperature.


title: NorinNo15_3rd leaf_rep2

description: Biological replication 2 of 3

source_name: 3rd leaf of NorinNo15 rep2


title: m08031_cho

value: Mouse 8031

value: BALB/c, C57BL/6

value: CreER; Vhl loxP/loxp; Pten loxP/loxP


title: Control 301157_3c600_1205

description: The peripheral blood mononuclear cells (PBMCs) from Large White pigs (male) (~50 kg) were isolated by Ficoll-Hypaque density gradient certrifugation at room temperature.

value: peripheral blood mononuclear cells


title: Sorachi_3rd leaf_rep3

description: Biological replication 3 of 3

source_name: 3rd leaf of Sorachi rep3

value: Sorachi


title: NorinNo15_3rd leaf_rep3

description: Biological replication 3 of 3

source_name: 3rd leaf of NorinNo15 rep3


title: Sorachi_3rd leaf_rep2

description: Biological replication 2 of 3

source_name: 3rd leaf of Sorachi rep2


title: Mouse 24h PACAP Penumbra (9439_1_4)

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description:
Sample name: 24h Saline Penumbra x PACAP Penumbra
Dye-swap (Cy3/Cy5) 24h PACAP Penumbra x  24h Saline Penumbra

hyb_protocol: hybridization_Kit: Agilent in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Agilent Feature Extraction ver 11.0.1.1

source_name: 24h PACAP Penumbra Cy3

label_protocol: Manual:  Low Input Quick Amp Labeling Kit, Two-Color  (Agilent)

growth_protocol: Animal care and experimental procedures were used as approved by the Institutional Animal Care and Use Committee of Showa University (School of Medicine), Tokyo, Japan. Thirty male mice (C57BL/6J) of 9-weeks-old (25 ~ 35 g body weight) were purchased from Charles River (Kanagawa, Japan). Mice were housed at the Animal Institution in Showa University in acrylic cages (8 mice/cage) maintained at 23 ºC with a standard 12 h light/dark cycle, optimum humidity, and temperature control. Animals were given access to tap water and laboratory chow ad libitum

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: Mice were first anesthetized with 4% sevoflurane (induction) and 2 % sevoflurane (maintenance) in a 30% O2 and 70% N2O gas mixture via a face mask, followed by an incision in the cervical skin, opening of salivary gland, resulting in visualization of the right common carotid artery. A midline cervical incision was made to expose the external carotid artery, and using intraluminal filament technique the PMCAO model was generated. PACAP38 (1 µl containing 1 pmol) or 1 µl of saline (0.9% NaCl, as control) was injected intracerebroventrically, immediately after PMCAO. PACAP38 (Peptide Institute Inc., Osaka, Japan; supplier temperature was -20 ºC) was dissolved at 10-5M concentration by saline, and stored at -80 ºC. PACAP test solution (for injection) was diluted ×10 times with 0.9% NaCl just before use. After injections, the animals were returned to their cages. A total of four groups were prepared

tag: agent

value: PACAP

tag: time

value: Penumbra

source_name: 24h Saline Penumbra Cy5

value: Saline


title: Hayayuki_3rd leaf_rep3

description: Biological replication 3 of 3

source_name: 3rd leaf of Hayayuki rep3

value: Hoayayuki


title: Mouse 24h PACAP Ischemia Core (9439_1_1)

description:
Sample name: 24h Saline Ischemia Core x PACAP Ischemia Core
Dye-swap (Cy3/Cy5) 24h Saline Ischemia Core x 24h PACAP Ischemia Core

source_name: 24h Saline Ischemia Core Cy3

value: saline

value: Ischemia Core

source_name: 24h PACAP Ischemia Core Cy5


title: Hayayuki_3rd leaf_rep2

description: Biological replication 2 of 3

source_name: 3rd leaf of Hayayuki rep2


title: Mouse 6h PACAP Penumbra (9438_1_4)

description:
Sample name: 6h Saline Penumbra x PACAP Penumbra
Dye-swap (Cy3/Cy5) 6h PACAP Penumbra x  6h Saline Penumbra

source_name: 6h PACAP Penumbra Cy3

source_name: 6h Saline Penumbra Cy5


title: PMA ionomycine stimulated 301158_3p600_1205

description: The peripheral blood mononuclear cells (PBMCs) from Large White pigs (male) (~54 kg) were isolated by Ficoll-Hypaque density gradient certrifugation at room temperature.

value: PMA ionomycine stimulated

value: Large White


title: Akage_3rd leaf_rep2

description: Biological replication 2 of 3

source_name: 3rd leaf of Akage rep2

value: Akage


title: Sorachi_3rd leaf_rep1

description: Biological replication 1 of 3

source_name: 3rd leaf of Sorachi rep1


title: Mouse 24h PACAP Ischemia Core (9439_1_2)

description:
Sample name: 24h Saline Ischemia Core x PACAP Ischemia Core
Dye-swap (Cy3/Cy5) 24h PACAP Ischemia Core x  24h Saline Ischemia Core

source_name: 24h PACAP Ischemia Core Cy3

source_name: 24h Saline Ischemia Core Cy5


title: Hayayuki_3rd leaf_rep1

description: Biological replication 1 of 3

source_name: 3rd leaf of Hayayuki rep1


title: m10852 cho_1

source_name: Mouse Reference

value: Stratagene Mouse Universal Reference

value: Mouse 10852

value: Liver and Tumor

value: CreER; Pten loxP/loxP


title: Mouse 6h PACAP Ischemia Core (9438_1_1)

description:
Sample name: 6h Saline Ischemia Core x PACAP Ischemia Core
Dye-swap (Cy3/Cy5) 6h Saline Ischemia Core x 6h PACAP Ischemia Core

source_name: 6h Saline Ischemia Core Cy3

source_name: 6h PACAP Ischemia Core Cy5


title: Mouse 6h PACAP Ischemia Core (9438_1_2)

description:
Sample name: 6h Saline Ischemia Core x PACAP Ischemia Core
Dye-swap (Cy3/Cy5) 6h PACAP Ischemia Core x  6h Saline Ischemia Core

source_name: 6h PACAP Ischemia Core Cy3

source_name: 6h Saline Ischemia Core Cy5


title: Mouse 24h PACAP Penumbra (9439_1_3)

description:
Sample name: 24h Saline Penumbra x PACAP Penumbra
Dye-swap (Cy3/Cy5) 24h Saline Penumbra x 24h PACAP Penumbra

source_name: 24h Saline Penumbra Cy3

source_name: 24h PACAP Penumbra Cy5


title: Akage_3rd leaf_rep1

description: Biological replication 1 of 3

source_name: 3rd leaf of Akage rep1

value: Third leaf blade


title: Akage_3rd leaf_rep3

description: Biological replication 3 of 3

source_name: 3rd leaf of Akage rep3


title: WL711-28DAA_2

city: Mohali

first: Sudhir

middle: P

last: Singh

state: Punjab

address: NABI, C127, Indus Area, Phase8

country: India

description: Developing grain 28 DAA

hyb_protocol: Hybridization of arrays were performed according to Affymetrix protocol described in technical manual.

scan_protocol: The hybridized chips were washed, stained and scanned using GeneChip scanner to generate the CEL files.

data_processing: The expression data was background-adjusted, normalized, and log-transformed perfect match values were obtained using Robust Multi-array Average (RMA) algorithm.

label: Biotin

organism: Triticum aestivum

source_name: Triticum aestivum Cv. WL711

label_protocol: Double stranded cDNA synthesis, In vitro transcription to synthesize biotin labeled cRNA, purification and fragmentation of cRNA were performed according to Affymetrix protocol described in technical manual.

growth_protocol: The two wheat genotypes with contrasting levels of grain mineral concentrations were grown in the experimental field of National Agri-Food Biotechnology Institute (NABI), SAS Nagar (Mohali) Punjab, India (310 m above sea level; Latitude 30° 47' North; Longitude 76° 41' East), using standard protocol. The ears of three plants of each genotype were tagged at anthesis. The spikes were harvested at 14 and 28 DAA

extract_protocol: Developing grains were extracted from the first and second floret of spikelet from the middle portion of the ear. For each sample, three grains were taken for RNA extraction. Total RNA was extracted using TRIzol (Invitrozen) and then purified with RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s protocol. On column DNase (Qiagen) digestion was performed as instructed in the manual.

value: grain

tag: development stage

value: 28 DAA


title: WL711-28DAA_3

institute: National Agri-Food Biotechnology Institu

description: Developing grain 28 DAA


title: WL711-28DAA_1

description: Developing grain 28 DAA


title: IITR26-28DAA_2

description: Developing grain 28 DAA

source_name: Triticum aestivum L. IITR26


title: Yukara_3rd leaf_rep1

description: Biological replication 1 of 2

source_name: 3rd leaf of Yukara rep1

value: Yukara


title: WL711-14DAA_3

description: Developing grain 14 DAA

value: 14 DAA


title: WL711-14DAA_1

description: Developing grain 14 DAA


title: Mouse 6h PACAP Penumbra (9438_1_3)

description:
Sample name: 6h Saline Penumbra x PACAP Penumbra
Dye-swap (Cy3/Cy5) 6h Saline Penumbra x 6h PACAP Penumbra

source_name: 6h Saline Penumbra Cy3

value: Penumbra

source_name: 6h PACAP Penumbra Cy5

value: PACAP


title: IITR26-28DAA_3

description: Developing grain 28 DAA


title: WL711-14DAA_2

description: Developing grain 14 DAA


title: IITR26-14DAA_3

description: Developing grain 14 DAA


title: Human iPS cell derived from N3 fibroblast clone 2

city: kumamoto

first: Makoto

last: Hamasaki

address: honjo 2-2-1

institute: Kumamoto univ

hyb_protocol: Gene chips were hybridized with biotinylated cRNA according to the manufacturer's protocol (Affymetrix). Chips were washed and stained with GeneChip® Fluidics Station 450.

scan_protocol: Scanned with Affymetrix GeneChip®Scanner 3000 7G.

data_processing: Raw CEL files were normalized using the Robust Multichip Average (RMA) method implemented in Genespring GX 12.5 (Agilent).

label: biotin

source_name: Human induced pluripotent stem cell

label_protocol: RNA was amplified, labeled and fragmented  using GeneChip® 3' IVT Express Kit (affymetrix) according to the manufacturer's protocol.

growth_protocol: Human and Chimpanzee iPS cells were maintained on MEFs in a medium containing DMEM/F12, 100mM L-glutamine/2-mercaptoethanol, 20% knockout serum replacement, 1X non-essential aminoacids and 5ng/ml human FGF2. Human dermal fibroblast were maintained in a medium containing DMEM, 10% fetal bovine serum.

extract_protocol: Total RNA was isolated from each cell subset using Sepasol-RNA 1 Super G (nacalai) according to the manufacturer's protocol.

treatment_protocol: Conventional human ES cell cuture method.

value: iPS cell


title: IITR26-28DAA_1

description: Developing grain 28 DAA


title: Human iPS cell derived from N1 fibroblast clone 12


title: IITR26-14DAA_1

description: Developing grain 14 DAA


title: Chimpanzee iPS cell clone 402

organism: Pan troglodytes

source_name: Chimpanzee induced pluripotent stem cell


title: Chimpanzee iPS cell clone 101


title: Human dermal fibroblast from healthy volunteer 1

source_name: Human dermal fibroblast

value: Fibroblast


title: Human dermal fibroblast from healthy volunteer 3


title: IITR26-14DAA_2

description: Developing grain 14 DAA


title: MAP 6wpi-2

city: Seoul

first: Min-Kyoung

last: Shin

address: 1, Gwanak ro, Gwanak gu

country: South Korea

institute: Seoul National University

description: MAP 6-2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R 3.0.2

source_name: mouse spleen_MAP-infected_6wpi

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

extract_protocol: Total RNA was isolated from the spleen of the experimental mice using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice were intraperitoneally inoculated with 300 μL of PBS (control group) or a suspension of MAP ATCC 19698 (3 × 10^7 cells/mouse, MAP-challenged group). Five mice from each group were sampled at 3, 6, and 12weeks post-infection.

tag: strain background

value: female

value: 5 weeks

tag: infected with

value: Mycobacterium avium subsp. Paratuberculosis (MAP)

value: spleen

tag: time point

value: 6 weeks post infection


title: Chimpanzee iPS cell clone 201


title: MAP 12wpi-2

description: MAP 12-2

source_name: mouse spleen_MAP-infected_12wpi

tag: gender

value: 12 weeks post infection


title: MAP 3wpi-2

description: MAP 3-2

source_name: mouse spleen_MAP-infected_3wpi

tag: age

value: 3 weeks post infection


title: MAP 6wpi-1

description: MAP 6-1


title: Con 12wpi-1

description: Con 12-1

source_name: mouse spleen_control_12wpi

value: PBS (control)


title: MAP 3wpi-1

description: MAP 3-1


title: Con 6wpi-1

description: Con 6-1

source_name: mouse spleen_control_6wpi


title: Con 3wpi-2

description: Con 3-2

source_name: mouse spleen_control_3wpi


title: reg1_KOH_10min vs reg1_KCl_10min_Exp_1

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

description: Spots with either a diameter smaller than 120 microm, or fluorescence intensity for Cy3 and Cy5 lower than 100 units, were not considered for further analysis.

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42ºC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 microl of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five microg of salmon sperm DNA was added to the mix before denaturation for 3 min at 95ºC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42ºC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 microm. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices).

data_processing: The GEPAS server (http://gepas3.bioinfo.cipf.es/) was used to preprocess the data (merge replicates). The normalization method we used to generate the data reported in the VALUE columns was the log(2) of the medians of ratios for the non-flagged genes.

organism: Saccharomyces cerevisiae

source_name: reg1 mutant strain in log phase culture

label_protocol: Fluorescent labeled cDNA was prepared from 8 microg of purified total RNA by the indirect dUTP-labeling method using the CyScribe post-labeling kit (GE Healthcare) and oligo(dT) as a primer.

growth_protocol: Grown at 28ºC in 50 ml of YPD rich medium (aprox. pH 5.5) until A660=0.5-0.8. Culture medium was alkalized until pH 8.0 by adding KOH (final concentration 16 mM, from 1 M stock solution). Cells were incubated at 28ºC for 10 min, harvested by rapid filtration, washed with cold water, snap frozen and the dried cells were kept at -80ºC until RNA purification.

extract_protocol: Total RNA purification using the Ambion RiboPure™-Yeast Total RNA Isolation Kit.

treatment_protocol: 16 mM KOH (aprox. pH 8.0) from 10 minutes.

tag: genotype

growth_protocol: Grown at 28ºC in 50 ml of YPD rich medium (aprox. pH 5.5) until A660=0.5-0.8. KCl was added to the medium (16 mM, form 1 M stock solution), and cells Were incubated at 28ºC for 10 min, harvested by rapid filtration, washed with cold water, snap frozen and the dried cells were kept at -80ºC until RNA purification.

treatment_protocol: 16 mM KCl from 10 minutes.


title: reg1 mutant vs wild type_Exp_2

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42ºC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 microl of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five ug of salmon sperm DNA was added to the mix before denaturation for 3 min at 95ºC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42ºC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 microm. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

growth_protocol: Grown at 28ºC in 50 ml of YPD rich medium until A660=0.6. Cells were harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80ºC until RNA purification.

treatment_protocol: Untreated cells

source_name: Wild type strain in log phase culture

value: wild type


title: Con 6wpi-2

description: Con 6-2

tag: tissue


title: MTF+MORAb0003,  rep2

city: Houston

first: Prahlad

last: Ram

state: TEXAS

address: 7435 Fannin Street

institute: UT MD Anderson

description: U133 plus 2.0_561_AS_006_G2_12_20_07

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

scan_protocol: GeneChips were scanned using the Affy GeneArray Scanner 3000, 7G

data_processing: The data were processed and normalized using the BRB Array tools in excel.

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

growth_protocol: 1) cells plated in folate-free medium (7 days), 2) cells plated in medium with physiological levels of folic acid (2-10 nm) (7 days), 3) cells with physiological levels of folic acid (7 days) and 003 antibody (24 hours), 4) cells with physiologic levels of folic acid (7 days) and control 004 antibody (24 hours).; 5) cells with physiological levels of folic acid (7 days) and MORAb003 antibody (24 hours)

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

treatment_protocol: MORAb-003 or control antibody for 24 hours

tag: cell line

value: epithelial ovarian cancer cells

tag: exposed to

value: folic acid for 7 days and MORAb003 antibody for 24hrs


title: MTF+MORAb0003,  rep1

description: U133 plus 2.0_561_AS_006_12_20_07


title: MTF+MORAb0003,  rep3

description: U133 plus 2.0_561_AS_006_G3_12_21_07


title: MAP 12wpi-1

description: MAP 12-1


title: reg1 mutant vs wild type_Exp_1


title: Con 3wpi-1

description: Con 3-1


title: 5-MTF+003 24hrs,  rep1

description: U133 plus 2.0_561_AS_003_12_20_07

value: folic acid for 7 days and 003 antibody for 24hrs


title: 5-MTF+004,  rep2

description: U133 plus 2.0_561_AS_005_G2_12_20_07

value: folic acid for 7 days and 004 control antibody for 24hrs


title: 5-MTF+004,  rep3

description: U133 plus 2.0_561_AS_005_G3_12_21_07


title: reg1_KOH_10min vs reg1_KCl_10min_Exp_2


title: 5-MTF+003 24hrs,  rep2

description: U133 plus 2.0_561_AS_003_G2_12_20_07


title: WT liver 24 month repl. 2

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 Gene Chip Arrays.

scan_protocol: Washing and staining was performed in Affymetrix fluidics station 450 with the recommended programm. Arrays were scanned on a GCS 3000.

data_processing: The data were analysed Affymetrix Expression Console 1.0. Background correction, normalization and probe summarization was performed with RMA.

source_name: ataxin-2 wildtype, liver, 24 month

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix One-Cycle protocol from 1000 ng total RNA.

growth_protocol: C57/Bl6 Mice were housed in Type II L cages (365x207x140 mm, floor area 530 cm2; IVC-based)at an environmental temperature 20-24°C, humidity: 55±10%and under 12/12 h light/dark cycle with food and water ad libitum.

extract_protocol: RNA  was extracted by using RNeasy Midi Kit (Qiagen) following manufacturers instructions for animal tissues.

treatment_protocol: not applicable

value: liver

value: ataxin-2 wild type

value: 24 month


title: WT liver 24 month repl. 1


title: 5-MTF,  rep2

description: U133 plus 2.0_561_AS_002_G2_12_20_07

value: media with folic acid for 7 days


title: 1205Lu original monolayer (OM)

city: Rehovot

first: Yuval

last: Levy Peretz

state: Israel

address: pob 12

country: Israel

institute: Hebrew Un

description:
OM
Sample1

hyb_protocol: Cy3-labeled cRNA (1.65 micrograms) was hybridized to the Agilent 4 x 44K Whole Genome Array for 17 hours at 65 ºC and washed according to manufacturer’s protocol.

scan_protocol: Hybridized slides were scanned at 5µm resolution on the Agilent Microarray Scanner and fluorescent intensities of hybridization signals were extracted using the Agilent Feature Extraction software.

data_processing: gProcessedSignal data from Agilent Feature Extraction v9.5

source_name: human melanoma cell line derived from mouse lung metastasis

label_protocol: 50-200 ng of total cellular RNA was amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (cat. no. 5190-2305) following  the manufacturer's protocol.

growth_protocol: Sample 1 (OM): Cells were grown for 14 days in RPMI-1640/10% FCS/37°C/5% CO2.  Sample 2 (MB): Cells were grown as melanoma bodies for 14 days in hESC media (DMEM F-12/20% Knock Out (KO) serum replacement) 37°C/5% CO2. Sample 3 (NM): Cells were grown as melanoma bodies for 14 days in hESC media followed by 10 days in RPMI-1640/10% FCS. Residual 3D melanoma bodies were removed before preparing RNA.

extract_protocol: RNA was isolated using RNAqueous-4PCR Kit (cat. no. AM1914, Life  Technologies, Carlsbad, California) according to the manufacturer's protocol.

tag: cell line source

value: human melanoma cells

tag: cell subtype

value: original monolayer (OM)

value: xenograft lung metastasis driven from cell line WM793


title: 1205Lu new monolayer derived from MBs (NM)

description:
NM
Sample3

value: new monolayer derived from MBs (NM)


title: 5-MTF+003 24hrs,  rep3

description: U133 plus 2.0_561_AS_003_G3_12_21_07


title: 5-MTF,  rep1

description: U133 plus 2.0_561_AS_002_12_20_07


title: 5-MTF,  rep3

description: U133 plus 2.0_561_AS_002_G3_12_21_07


title: Con 12wpi-2

description: Con 12-2

value: female

value: 5 weeks

value: spleen


title: WT liver 24 month repl. 3

tag: genotype/variation


title: KO liver 24 month repl. 4

source_name: ataxin-2 knock-out, liver, 24 month

value: ataxin-2 knock out


title: KO liver 24 month repl. 2


title: 1205Lu Melanoma stem cell-like bodies (MB)

description:
MB
Sample2

value: Melanoma stem cell-like bodies (MB)


title: no MTF,  rep2

description: U133 plus 2.0_561_AS_001_G2_12_20_07

source_name: SKOV3ip1_no MTF

value: epithelial ovarian cancer cells

value: folate-free medium for 7 days


title: no MTF,  rep3

description: U133 plus 2.0_561_AS_001_G3_12_21_07


title: KO liver 24 month repl. 3


title: WT midbrain 24 month repl. 4

source_name: ataxin-2 wildtype, midbrain, 24 month

value: midbrain


title: no MTF,  rep1

description: U133 plus 2.0_561_AS_001_12_20_07


title: WT midbrain 24 month repl. 3


title: KO liver 24 month repl. 1


title: WT liver 24 month repl. 4


title: JSA patient_10

city: Zagreb

first: Fran

last: Borovecki

address: Salata 2

department: Center for Translational anc Clinical Research

country: Croatia

institute: University of Zagreb School of Medicine

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: JSA

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

extract_protocol: From each study participant 7.5 mL of venous blood was collected using three PAXgene™ tubes for stabilization of whole blood RNA (3x2.5mL=7.5mL).  Total RNA was isolated from whole blood using a RNA isolation kit (PaxGene, Preanalytix) according to the manufacturer's instructions.

tag: age (yrs)

tag: diagnosis

value: enthesitis-related arthritis

tag: hla status

value: whole blood


title: JSA patient_11


title: WT midbrain 24 month repl. 2

value: ataxin-2 wild type


title: KO midbrain 24 month repl. 4

source_name: ataxin-2 knock-out, midbrain, 24 month

value: 24 month


title: KO midbrain 24 month repl. 3


title: JSA patient_9

value: male


title: Cornea_fungal_keratitis_rep8

city: London

first: Jaya

middle: Devi

last: Chidambaram

address: Keppel Street

department: Clinical Research Department

country: United Kingdom

institute: London School of Hygiene and Tropical Medicine

hyb_protocol: Standard Illumina HT12 v4 beadchip hybridization protocol

data_processing:
Raw data were analysed in Lumi in R in three subsets according to the following pairwise comparisons: Bacterial keratitis v Controls; Fungal keratitis v Controls; Bacterial v Fungal keratitis. For each pair, non-expressed probes were filtered out (using detection call function, any probe with detection p-value>0.01 in all samples was considered as non-expressed). Data were then transformed using Variance Stabilising Transformation, and then quantile normalised. Hierarchical clustering (agglomerative with complete linkage) revealed 3 samples as outliers (M50, M80, M73) so these were excluded from all analyses. Differential expression analysis: After exclusion of M50, M73 & M80, the remaining 27 samples were used in the pairwise comparisons. Mean log2 signal intensities of each probe within in each group (Bacterial keratitis, Fungal keratitis, Controls) were used to generate log2 fold change. Significance testing of comparisons was performed using empirical Bayes moderated t-test with false discovery rate adjusted p-values (performed in Limma in R). Probes with fdr-adjusted p-value <0.05 and fold change >= 2 or <0.5 were considered differentially expressed. Network co-expression analysis was performed using data from the 27 samples (M50, M73 & M80 excluded) which were VST transformed and quantiled normalised as one group, and then a pearson correlation coefficient calculated between each probe in each sample. Network graph generated using probes that had pearson correlation coefficient of >=0.9, with each probe as a node and connections between probes as the correlation.
Non-normalised data: Illumina beadstudio calculated summarized expression level (AVG_Signal), detection p-value (Detection pval), bead replicates standard error (BEAD_STDERR), no. of beads (Avg_NBEADS); Normalised data: quantile normalized log2 signal intensity and detection p-value
Normalizations performed with Bacterial v Control, Fungal v Control and Bacterial v Fungal are available on the series level.

source_name: cornea

label_protocol: Biotinylated cRNA were prepared with the Target Amp Nano-g Biotin a-RNA labeling kit (EpiCenter Biotechnologies, Wisconsin, USA)

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

value: cornea

tag: organism cultured from ulcer

value: Fusarium species


title: Cornea_normal_rep13

value: Normal non-infected tissue


title: JSA patient_8


title: Cornea_bacterial_keratitis_rep8

value: Streptococcus pneumoniae


title: Cornea_bacterial_keratitis_rep7

value: Pseudomonas aeruginosa


title: Cornea_bacterial_keratitis_rep4

description: No normalized data available for this sample. This sample was found to be an outlier in hierarchical clustering analysis and so was excluded before normalization of all remaining samples.


title: JSA patient_5

value: female


title: WT midbrain 24 month repl. 1


title: KO midbrain 24 month repl. 1


title: JSA patient_4


title: WT cerebellum 24 month repl. 4

source_name: ataxin-2 wildtype, cerebellum, 24 month

value: cerebellum


title: KO midbrain 24 month repl. 2

value: ataxin-2 knock out


title: Bacterial keratitis rep6


title: Cornea_normal_rep12


title: JSA patient_6


title: Cornea_bacterial_keratitis_rep5


title: Cornea_fungal_keratitis_rep9

value: Aspergillus terreus


title: Cornea_normal_rep10


title: Cornea_normal_rep8


title: Cornea_normal_rep9


title: JSA patient_7


title: WT cerebellum 24 month repl. 3


title: JSA patient_3


title: Cornea_fungal_keratitis_rep7


title: JSA patient_2


title: WT cerebellum 24 month repl. 2


title: JSA patient_1


title: Cornea_bacterial_keratitis_rep3


title: Cornea_fungal_keratitis_rep4


title: Cornea_fungal_keratitis_rep6


title: WT cerebellum 24 month repl. 1


title: KO cerebellum 24 month repl. 4

source_name: ataxin-2 knock-out, cerebellum, 24 month


title: 5-MTF+004,  rep1

description: U133 plus 2.0_561_AS_005_12_20_07

tag: cell type

value: epithelial ovarian cancer cells

value: folic acid for 7 days and 004 control antibody for 24hrs


title: Cornea_normal_rep7


title: control sample_4

source_name: Control

value: healthy


title: KO cerebellum 24 month repl. 2


title: Cornea_bacterial_keratitis_rep2


title: KO cerebellum 24 month repl. 3


title: Cornea_fungal_keratitis_rep2

value: Aspergillus flavus


title: Cornea_normal_rep6


title: Cornea_normal_rep5


title: Cornea_fungal_keratitis_rep1


title: KO cerebellum 24 month repl. 1


title: Cornea_fungal_keratitis_rep3

value: Lasio diplodia


title: control sample_2

value: whole blood


title: control sample_3


title: Cornea_normal_rep4


title: control sample_1


title: genomic DNA from great saphenous vein 6

type: genomic

city: Tomsk

first: Anton

middle: Vladimirovich

last: Markov

state: Tomskaya oblast

address: Nab. Ushaiki, 10

country: Russia

institute: Research Institute of Medical Genetics

description: normal tissue of great saphenous vein, patient 6

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

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

data_processing: BeadStudio software v3.2, R 3.0.1 (Bioconductor v2.14, 'lumi' package)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: great saphenous vein 6

label_protocol: Standard Illumina Protocol

extract_protocol: Tissue samples were homogenized and digested with proteinase K, DNA from tissue and whole blood samples was extracted using standard phenol/chloroform method

tag: parient id

value: Male

tag: sample type

value: great saphenous vein


title: genomic DNA from coronary atherosclerotic plaque 6

description: advanced atherosclerotic plaque of right coronary artery, patient 6

source_name: atherosclerotic plaque of right coronary artery 6


title: Cornea_bacterial_keratitis_rep1

value: cornea


title: WT liver 12 month repl. 3

source_name: ataxin-2 wildtype, liver, 12 month

value: liver

value: ataxin-2 wild type

value: 12 month


title: Cornea_normal_rep3

value: Normal non-infected tissue


title: WT liver 12 month repl. 4


title: genomic DNA from whole blood 6

description: sample of whole blood, patient 6

source_name: whole blood 6


title: Cornea_fungal_keratitis_rep5

value: Fusarium species


title: genomic DNA from internal mammary artery 6

description: normal tissue of internal mammary artery, patient 6

source_name: internal mammary artery 6

value: internal mammary artery


title: WT liver 12 month repl. 1


title: Cornea_normal_rep2


title: WT liver 12 month repl. 2


title: genomic DNA from internal mammary artery 5

description: normal tissue of internal mammary artery, patient 5

source_name: internal mammary artery 5


title: Metaplastic Carcinoma META65

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

description: Metaplastic Carcinoma

hyb_protocol: As per manufacturer (Illumina)

scan_protocol: As per manufacturer (Illumina)

data_processing: Raw data were subjected to variance-stabilizing transformation and robust-spline normalization using the lumi package (2.14.1) in R (3.0.2)

source_name: Metaplastic Carcinoma META65

label_protocol: As per manufacturer (Illumina)

extract_protocol: RNA was extracted using the Qiagen DNA RNA  Tissue kit

tag: phenotype

value: triple-negative

value: Spindle cell carcinoma


title: Metaplastic Carcinoma META64

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META64

value: Carcinoma with heterologous elements - Matrix producing


title: Metaplastic Carcinoma META56

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META56


title: genomic DNA from coronary atherosclerotic plaque 5

description: advanced atherosclerotic plaque of right coronary artery, patient 5

source_name: atherosclerotic plaque of right coronary artery 5

tag: gender


title: Metaplastic Carcinoma META60

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META60


title: Cornea_normal_rep1


title: KO liver 12 month repl. 4

source_name: ataxin-2 knock-out, liver, 12 month

value: ataxin-2 knock out

tag: age


title: KO liver 12 month repl. 3


title: Metaplastic Carcinoma META57

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META57


title: Metaplastic Carcinoma META53

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META53


title: Metaplastic Carcinoma META62

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META62

value: Carcinoma with heterologous elements


title: genomic DNA from great saphenous vein 5

description: normal tissue of great saphenous vein, patient 5

source_name: great saphenous vein 5


title: Cornea_normal_rep11

source_name: cornea


title: Metaplastic Carcinoma META58

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META58


title: Metaplastic Carcinoma META59

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META59


title: KO liver 12 month repl. 1


title: genomic DNA from whole blood 5

description: sample of whole blood, patient 5

source_name: whole blood 5


title: WT liver 6 month repl. 4

source_name: ataxin-2 wildtype, liver, 6 month

value: 6 month


title: Metaplastic Carcinoma META45

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META45


title: KO liver 12 month repl. 2


title: Metaplastic Carcinoma META55

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META55


title: genomic DNA from internal mammary artery 4

description: normal tissue of internal mammary artery, patient 4

source_name: internal mammary artery 4


title: Metaplastic Carcinoma META49

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META49


title: Metaplastic Carcinoma META47

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META47


title: genomic DNA from coronary atherosclerotic plaque 4

description: advanced atherosclerotic plaque of right coronary artery, patient 4

source_name: atherosclerotic plaque of right coronary artery 4


title: WT liver 6 month repl. 2


title: Metaplastic Carcinoma META44

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META44


title: Metaplastic Carcinoma META43

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META43


title: genomic DNA from great saphenous vein 4

description: normal tissue of great saphenous vein, patient 4

source_name: great saphenous vein 4


title: genomic DNA from whole blood 4

description: sample of whole blood, patient 4

source_name: whole blood 4


title: WT liver 6 month repl. 3


title: Metaplastic Carcinoma META52

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META52

value: Spindle cell carcinoma with areas of chondroid differentiation (Carcinoma with heterologous elements)


title: Metaplastic Carcinoma META42

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META42

value: Carcinoma with squamous features


title: WT liver 6 month repl. 1


title: Metaplastic Carcinoma META41

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META41


title: Metaplastic Carcinoma META46

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META46


title: Metaplastic Carcinoma META37

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META37


title: Metaplastic Carcinoma META40

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META40


title: Metaplastic Carcinoma META39

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META39


title: genomic DNA from great saphenous vein 3

description: normal tissue of great saphenous vein, patient 3

source_name: great saphenous vein 3

value: Male


title: genomic DNA from internal mammary artery 3

description: normal tissue of internal mammary artery, patient 3

source_name: internal mammary artery 3


title: Metaplastic Carcinoma META36

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META36


title: genomic DNA from coronary atherosclerotic plaque 3

description: advanced atherosclerotic plaque of right coronary artery, patient 3

source_name: atherosclerotic plaque of right coronary artery 3


title: Metaplastic Carcinoma META34

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META34


title: KO liver 6 month repl. 4

source_name: ataxin-2 knock-out, liver, 6 month


title: genomic DNA from whole blood 3

description: sample of whole blood, patient 3

source_name: whole blood 3

value: whole blood


title: Metaplastic Carcinoma META33

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META33


title: KO liver 6 month repl. 2


title: KO liver 6 month repl. 1


title: KO liver 6 month repl. 3


title: Metaplastic Carcinoma META32

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META32


title: genomic DNA from internal mammary artery 2

description: normal tissue of internal mammary artery, patient 2

source_name: internal mammary artery 2


title: WT midbrain 6 month repl. 3

source_name: ataxin-2 wildtype, midbrain, 6 month

value: midbrain


title: Metaplastic Carcinoma META31

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META31


title: genomic DNA from great saphenous vein 2

description: normal tissue of great saphenous vein, patient 2

source_name: great saphenous vein 2

value: great saphenous vein


title: WT midbrain 6 month repl. 4

value: ataxin-2 wild type


title: Metaplastic Carcinoma META30

description: Metaplastic Carcinoma

source_name: Metaplastic Carcinoma META30


title: Hypo-A2/12_serotonin 100ug/ml-4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: G145_G07_20_177_5HT1_4.CEL (h177_sero100)

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.26.6).

source_name: cell line HypoA-2/12, exposed to 100ug/ml serotonin, 24 h exposure, repliclate 4

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Murine derived hypothalamic neuronal cell lines hypoE-46 and hypoA2/12 (CELLutions Biosystems Inc. Canada) were grown and maintained in DMEM supplemented with 10% heat-inactivated fetal calf serum, 100 units/ml penicillin and 100μg/ml streptomycin at 37 C under  5.0% CO2.

extract_protocol: Total RNA was isolated using TrIzol (Life Technologies) according to manyfacturer's protocol. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Cells were grown in monolayers to 90% confluency. Then medium was replaced by serum-free DMEM containing penicillin and streptomycin. After 4 hours, cells were exposed to serotonin.

value: hypothalamic neuronal cells

value: serotonin unresponsive


title: Hypo-A2/12_serotonin 100ug/ml-1

description: G145_F07_17_177_5HT1_1.CEL (h177_sero100)

source_name: cell line HypoA-2/12, exposed to 100ug/ml serotonin, 24 h exposure, repliclate 1


title: genomic DNA from whole blood 2

description: sample of whole blood, patient 2

source_name: whole blood 2


title: WT midbrain 6 month repl. 1


title: Hypo-A2/12_control-4

description: G145_F05_16_177_m4.CEL (h177_control)

source_name: cell line HypoA-2/12, control, 24 h exposure, repliclate 4


title: KO midbrain 6 month repl. 4

source_name: ataxin-2 knock-out, midbrain, 6 month


title: genomic DNA from coronary atherosclerotic plaque 2

description: advanced atherosclerotic plaque of right coronary artery, patient 2

source_name: atherosclerotic plaque of right coronary artery 2


title: Low count WBC R0413_13904467

description: Total RNA was extraction from whole blood sample using PAXgene blood RNA kit. The reference RNA sample was prepared by pooling of total RNAs from different porcine tissues (brain, heart, muscle, skin, liver, kidney, lung, spleen, nodes, thymus, Peyer's patches, testis, epididymis, uterus, ovary, fetus (3 weeks), Peripheral Blood Mononuclear Cell (PBMC) stimulated with the mixture of Phorbol Myristate Acetate (PMA) and ionomycin, PBMC stimulated with conA, and PBMC stimulated with phytohemagglutinin (PHA)).

hyb_protocol: 750 ng each of Cy3-labeled and Cy5-labeled cDNA targets were combined and the value of mixture was adjusted to 200 ul using water. Labeled cDNA targets mixture was denatured at 95oC for 2 min. 200 ul of 2X hybridization buffer (Agilent Technologies, Germany) was added and centrifuge. 400 ul of the mixture was applied to a single microarray with Agilent cover slip. Microarrays were incubated at 60oC using Agilent DNA Microarray Hybridization Oven for 17 h.

scan_protocol: The slides were scanned using Agilent DNA Microarray Scanner. Data from each array was collected with GenePixTM Pro software V6.0 (MDS Inc., Canada).

data_processing: Data were preceded using within-array loess normalization method. The empirical eBayes method was applied to identify the significance of differential expression in each group. The false discovery rate (FDR) was controlled using the method of Benjamini and Hochberg as implemented in Limma. Significant changes in gene expression were limited to FDR < 0.05.

label_protocol: Cy3 or Cy5 was incorporated into each total RNA sample (5 ug) using ChipShotTM Direct Labeling System (Promega) and the CyDye-labelled cDNA was purified by ChipShotTM.

value: blood

value: Low count WBC

source_name: Reference RNA

value: Reference RNA (mixture samples)


title: KO midbrain 6 month repl. 3


title: Low count WBC R0355_13904466

extract_protocol: Total RNA was extraction from whole blood sample using PAXgene blood RNA kit. The reference RNA sample was prepared by pooling of total RNAs from different porcine tissues (brain, heart, muscle, skin, liver, kidney, lung, spleen, nodes, thymus, Peyer's patches, testis, epididymis, uterus, ovary, fetus (3 weeks), Peripheral Blood Mononuclear Cell (PBMC) stimulated with the mixture of Phorbol Myristate Acetate (PMA) and ionomycin, PBMC stimulated with conA, and PBMC stimulated with phytohemagglutinin (PHA)).


title: WT midbrain 6 month repl. 2


title: Hypo-A2/12_serotonin 100ug/ml-3

description: G145_G05_19_177_5H1_3.CEL (h177_sero100)

source_name: cell line HypoA-2/12, exposed to 100ug/ml serotonin, 24 h exposure, repliclate 3


title: Hypo-A2/12_control-3

description: G145_E09_15_177_m3_2.CEL (h177_control)

source_name: cell line HypoA-2/12, control, 24 h exposure, repliclate 3


title: Low count WBC R0316_13904229


title: genomic DNA from whole blood 1

description: sample of whole blood, patient 1

source_name: whole blood 1


title: genomic DNA from great saphenous vein 1

description: normal tissue of great saphenous vein, patient 1

source_name: great saphenous vein 1


title: Hypo-E46_serotonin 1ug/ml-4

description: G145_D09_12_138_5HT2_4.CEL (h138_sero100)

source_name: cell line HypoE-46, exposed to 1ug/ml serotonin, 24 h exposure, repliclate 4

value: serotonin sensitive


title: Low count WBC R0303_13904460


title: Hypo-A2/12_control-2

description: G145_E07_14_177_m2.CEL (h177_control)

source_name: cell line HypoA-2/12, control, 24 h exposure, repliclate 2


title: WT cerebellum 6 month repl. 4

source_name: ataxin-2 wildtype, cerebellum, 6 month

value: cerebellum


title: genomic DNA from internal mammary artery 1

description: normal tissue of internal mammary artery, patient 1

source_name: internal mammary artery 1

value: internal mammary artery


title: Hypo-A2/12_control-1

description: G145_E05_13_177_m1.CEL (h177_control)

source_name: cell line HypoA-2/12, control, 24 h exposure, repliclate 1


title: Low count WBC R0196_13904224


title: Hypo-E46_serotonin 1ug/ml-3

description: G145_D07_11_138_5HT2_3.CEL (h138_sero100)

source_name: cell line HypoE-46, exposed to 1ug/ml serotonin, 24 h exposure, repliclate 3


title: Hypo-A2/12_serotonin 100ug/ml-2

description: G145_F09_18_177_5HT1_2.CEL (h177_sero100)

source_name: cell line HypoA-2/12, exposed to 100ug/ml serotonin, 24 h exposure, repliclate 2


title: WT cerebellum 6 month repl. 3


title: WT cerebellum 6 month repl. 1


title: Low count WBC R0107_13904469


title: Low count WBC R0078_13904464


title: genomic DNA from coronary atherosclerotic plaque 1

description: advanced atherosclerotic plaque of right coronary artery, patient 1

source_name: atherosclerotic plaque of right coronary artery 1


title: KO cerebellum 6 month repl. 3

source_name: ataxin-2 knock-out, cerebellum, 6 month

value: ataxin-2 knock out


title: KO midbrain 6 month repl. 1

value: 6 month


title: High count WBC R0441_13904228

value: High count WBC


title: KO cerebellum 6 month repl. 4


title: KO midbrain 6 month repl. 2


title: WT cerebellum 6 month repl. 2


title: Hypo-E46_serotonin 1ug/ml-1

description: G145_C09_09_138_5HT2_1.CEL (h138_sero100)

source_name: cell line HypoE-46, exposed to 1ug/ml serotonin, 24 h exposure, repliclate 1


title: Hypo-E46_serotonin 100ug/ml-3

description: G145_C05_07_138_5HT1_3.CEL (h138_sero1)

source_name: cell line HypoE-46, exposed to 100ug/ml serotonin, 24 h exposure, repliclate 3


title: KO cerebellum 6 month repl. 1


title: Low count WBC R0180_13904472


title: Hypo-E46_serotonin 100ug/ml-1

description: G145_B07_05_138_5HT1_1.CEL (h138_sero1)

source_name: cell line HypoE-46, exposed to 100ug/ml serotonin, 24 h exposure, repliclate 1


title: High count WBC R0282_13904225

source_name: Reference RNA


title: KO cerebellum 6 month repl. 2


title: High count WBC R0105_13904226


title: Hypo-E46_serotonin 100ug/ml-4

description: G145_C07_08_138_5HT1_4.CEL (h138_sero1)

source_name: cell line HypoE-46, exposed to 100ug/ml serotonin, 24 h exposure, repliclate 4


title: KO midbrain 12 month repl. 4

source_name: ataxin-2 knock-out, midbrain, 12 month

value: 12 month


title: Hypo-E46_control-3

description: G145_A09_03_138_m3.CEL (h138_control)

source_name: cell line HypoE-46, control, 24 h exposure, repliclate 3


title: High count WBC R0266_13904227


title: KO midbrain 12 month repl. 3


title: High count WBC R0245_13904221


title: Hypo-E46_control-1

description: G145_A05_01_138_m1.CEL (h138_control)

source_name: cell line HypoE-46, control, 24 h exposure, repliclate 1


title: KO midbrain 12 month repl. 1


title: Hypo-E46_serotonin 100ug/ml-2

description: G145_B09_06_138_5HT1_2.CEL (h138_sero1)

source_name: cell line HypoE-46, exposed to 100ug/ml serotonin, 24 h exposure, repliclate 2


title: KO midbrain 12 month repl. 2


title: Hypo-E46_control-2

description: G145_A07_02_138_m2.CEL (h138_control)

source_name: cell line HypoE-46, control, 24 h exposure, repliclate 2


title: High count WBC R0028_13904461


title: Hypo-E46_serotonin 1ug/ml-2

description: G145_D05_10_138_5HT2_2.CEL (h138_sero100)

source_name: cell line HypoE-46, exposed to 1ug/ml serotonin, 24 h exposure, repliclate 2


title: Hypothalamus_Control_d14-4

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.26.6).).

source_name: hypothalamus, control, replicate 4

growth_protocol: Male C57BL/6 mice (Criffa, Barcelona, Spain), approximately 20 g, were placed on a standard ad libitum diet (Panlab, Barcelona, Spain) and had free access to water. Animals were individually housed one week before the start of the experiment in a climate-controlled room (12:12 dark-light cycle with a constant room temperature of 21 ±1 C).The mice were placed on a standard ad libitum diet based on AIN93M formulation and had free access to tap water.

extract_protocol: Total RNA from the hypothalamus was isolated using the RNeasy Lipid tissue kit (Qiagen, Venlo, The Netherlands). RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Lewis Lung carcinoma cells were obtained from exponential tumours. Under general anaesthesia, 0.5x10^6 cells were  injected intramuscular in the hind leg.  Four groups were included:  C, Control mice sacrificed at day 14 ;  TB-10, Tumour-bearing mice sacrificed at day 10; TB-14 Tumour-bearing mice sacrificed at day 14, and TB-17, Tumour-bearing mice sacrificed at day 17. At the day of section, mice were anesthetized with a ketamine/xylazine mixture (i.p.; Imalgene® and Rompun® respectively). After sacrifice, hypothalamus were removed, frozen in liquid nitrogen and stored at -80 C.

tag: strain

tag: Sex

value: male

value: hypothalamus


title: High count WBC R0133_13904468

tag: tissue


title: WT midbrain 12 month repl. 4

source_name: ataxin-2 wildtype, midbrain, 12 month

value: midbrain


title: WT midbrain 12 month repl. 3


title: High count WBC R0384_13904470


title: Hypothalamus_TumorBearing_d14-7

source_name: hypothalamus, Tumour-bearing, sacrificed at day 14 after inoculation, replicate 7


title: WT midbrain 12 month repl. 1


title: Hypothalamus_Control_d14-2

source_name: hypothalamus, control, replicate 2


title: Hypothalamus_TumorBearing_d14-6

source_name: hypothalamus, Tumour-bearing, sacrificed at day 14 after inoculation, replicate 6


title: Hypothalamus_TumorBearing_d17-6

source_name: hypothalamus, Tumour-bearing, sacrificed at day 17 after inoculation, replicate 6


title: WT midbrain 12 month repl. 2


title: KO cerebellum 12 month repl. 4

source_name: ataxin-2 knock-out, cerebellum, 12 month


title: KO cerebellum 12 month repl. 2


title: KO cerebellum 12 month repl. 3


title: WT cerebellum 12 month repl. 4

source_name: ataxin-2 wildtype, cerebellum, 12 month


title: Hypothalamus_TumorBearing_d14-5

source_name: hypothalamus, Tumour-bearing, sacrificed at day 14 after inoculation, replicate 5


title: Hypothalamus_Control_d14-3

source_name: hypothalamus, control, replicate 3


title: Hypothalamus_TumorBearing_d14-4

source_name: hypothalamus, Tumour-bearing, sacrificed at day 14 after inoculation, replicate 4


title: KO cerebellum 12 month repl. 1


title: Hypothalamus_TumorBearing_d17-5

source_name: hypothalamus, Tumour-bearing, sacrificed at day 17 after inoculation, replicate 5


title: WT cerebellum 12 month repl. 2


title: Low count WBC R0036_13904465

source_name: Reference RNA


title: WT cerebellum 12 month repl. 3


title: WT cerebellum 12 month repl. 1


title: Hypothalamus_TumorBearing_d10-5

source_name: hypothalamus, Tumour-bearing, sacrificed at day 10 after inoculation, replicate 5


title: Hypothalamus_TumorBearing_d17-4

source_name: hypothalamus, Tumour-bearing, sacrificed at day 17 after inoculation, replicate 4


title: Hypothalamus_TumorBearing_d10-4

source_name: hypothalamus, Tumour-bearing, sacrificed at day 10 after inoculation, replicate 4


title: Hypothalamus_TumorBearing_d10-3

source_name: hypothalamus, Tumour-bearing, sacrificed at day 10 after inoculation, replicate 3


title: Hypothalamus_Control_d14-1

source_name: hypothalamus, control, replicate 1


title: Hypothalamus_TumorBearing_d14-3

source_name: hypothalamus, Tumour-bearing, sacrificed at day 14 after inoculation, replicate 3


title: Hypothalamus_TumorBearing_d14-2

source_name: hypothalamus, Tumour-bearing, sacrificed at day 14 after inoculation, replicate 2


title: single cell profile of retinal Muller Glial Cell 5w RD A6

city: Boston

first: Karin

last: Roesch

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description: rd1 mice carry a mutation in the b subunit of cGMP PDE.

hyb_protocol: Affymetrix

scan_protocol: Affymetrix, Genechip Affymetrix Scanner 7G

data_processing: The Affymetrix MAS5.0 algorithm was used to normalize data.

source_name: RD1 single retinal Muller Glial Cell, 5w

label_protocol: Ten micrograms of each single cell cDNA was digested with Dnase I for 13 minutes at 37C. Heated to 99C for 15 minutes and biotin labeled using Biotin N6 ddATP (Enzo Biosciences) and TdT (Roche) at 37C for 1.5 hours.

extract_protocol: Retinas were dissociated with papain, single Muller Glial cells were isolated with a micropipette based on their distinct morphology and expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40). Total mRNAs were reverse transcribed using Superscript II (Invitrogen) in combination with an oligo dT primer. CDNAs were tailed with poly As using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

value: FVB

value: retina

tag: developmental stage


title: single cell profile of retinal Muller Glial Cell 5w RD B1


title: single cell profile of retinal Muller Glial Cell 5w RD A8


title: Hypothalamus_TumorBearing_d17-2

source_name: hypothalamus, Tumour-bearing, sacrificed at day 17 after inoculation, replicate 2


title: Hypothalamus_TumorBearing_d17-3

source_name: hypothalamus, Tumour-bearing, sacrificed at day 17 after inoculation, replicate 3


title: Hypothalamus_TumorBearing_d14-1

source_name: hypothalamus, Tumour-bearing, sacrificed at day 14 after inoculation, replicate 1


title: single cell profile of retinal Muller Glial Cell 5 w RD1 A1


title: Hypothalamus_TumorBearing_d17-1

source_name: hypothalamus, Tumour-bearing, sacrificed at day 17 after inoculation, replicate 1


title: single cell profile of retinal Muller Glial Cell 5 w RD1 A5


title: single cell profile of retinal Muller Glial Cell P13 RD1 B1

source_name: RD1 single retinal Muller Glial Cell, P13


title: single cell profile of retinal Muller Glial Cell P13 RD1 B3


title: Hypothalamus_TumorBearing_d10-2

source_name: hypothalamus, Tumour-bearing, sacrificed at day 10 after inoculation, replicate 2


title: High count WBC R0377_13904222


title: single cell profile of retinal Muller Glial Cell P13 RD1 A1


title: Hypo-E46_control-4

description: G145_B05_04_138_m4.CEL (h138_control)

source_name: cell line HypoE-46, control, 24 h exposure, repliclate 4

tag: cell line

value: hypothalamic neuronal cells


title: single cell profile of retinal Muller Glial Cell P13 RD1 A4


title: Blood_Test3_3

description: Test3 003

hyb_protocol: Following fragmentation, 1.65 μg of labeled cRNA was hybridized to the Agilent expression microarray according to the protocols provided by manufacturer.

scan_protocol: The arrays were scanned using the Agilent Technologies G2600D SG12494263 (Agilent Technologies, Inc.).

data_processing:
Array data export processing and analyses were performed using Agilent Feature Extraction v11.0.1.1 (Agilent Technologies, Inc.).
Array probes were filtered by p < 0.05 (similar to the signal to noise ratio) in at least 50% of samples. Array probes were transformed by logarithm and normalized by quantile method. Statistical significance of the expression data was determined using the local pooled error (LPE) test and fold change in which the null hypothesis was that no difference exists among groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

organism: Bos taurus

source_name: Peripheral Blood_IS900-PCR positive

label_protocol: Labeled cRNA was prepared from 5 μg total RNA according to the manufacturer’s instructions using the Agilent’s Quick Amp Labeling Kit (Agilent Technologies, Inc.).

extract_protocol: The total RNA was isolated from blood of the cattle according to the manufacturer's instructions using a PAXGene blood RNA kit (PreAnalytiX/Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The cattles were evaluated for disease status by a commercial ELISA (IDEXX Laboratories, Inc., Westbrook, ME, USA) for the detection of MAP-specific antibodies and for IS900 and ISMap02 by fecal PCR. Blood samples from the cattle were immediately collected into PAXGene Blood RNA tubes (PreAnalytiX/Qiagen, Hilden, Germany).

value: female

tag: sample group

value: IS900-PCR positive, MAP-ELISA positive

value: Peripheral Blood


title: Blood_Test3_2

description: Test3 002


title: single cell profile of retinal Muller Glial Cell P13 RD1 B4

tag: genotype/variation


title: Hypothalamus_TumorBearing_d10-1

source_name: hypothalamus, Tumour-bearing, sacrificed at day 10 after inoculation, replicate 1


title: single cell profile of retinal Muller Glial Cell P13 congFVB A5

description: Congenic FVB mice (Jackson Laboratories stock number 4828l, FVB.129P2-Pde6b+Tyrc-ch/AntJ; Bar Harbor, ME)

source_name: WT single retinal Muller Glial Cell, P13

value: wildtype


title: Metaplastic Carcinoma META65

description: Metaplastic Carcinoma META65

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: Raw data were analyzed using the CRMAv2 algorithm in the aroma.affymetrix package.

source_name: Metaplastic Carcinoma META65

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted using the Qiagen DNA Blood and Tissue kit

value: triple-negative

value: Spindle cell carcinoma


title: Metaplastic Carcinoma META64

description: Metaplastic Carcinoma META64

source_name: Metaplastic Carcinoma META64

value: Carcinoma with heterologous elements - Matrix producing


title: Metaplastic Carcinoma META58

description: Metaplastic Carcinoma META58

source_name: Metaplastic Carcinoma META58

value: Carcinoma with heterologous elements


title: Metaplastic Carcinoma META62

description: Metaplastic Carcinoma META62

source_name: Metaplastic Carcinoma META62


title: Blood_Test3_1

description: Test3 001


title: Blood_Test2_3

description: Test2 003

source_name: Peripheral Blood_IS900-PCR negative

value: IS900-PCR negative, MAP-ELISA positive


title: Metaplastic Carcinoma META59

description: Metaplastic Carcinoma META59

source_name: Metaplastic Carcinoma META59


title: single cell profile of retinal Muller Glial Cell P13 congFVB A4


title: Metaplastic Carcinoma META60

description: Metaplastic Carcinoma META60

source_name: Metaplastic Carcinoma META60


title: Blood_Test2_2

description: Test2 002


title: single cell profile of retinal Muller Glial Cell P13 congFVB A3


title: Metaplastic Carcinoma META57

description: Metaplastic Carcinoma META57

source_name: Metaplastic Carcinoma META57


title: Metaplastic Carcinoma META55

description: Metaplastic Carcinoma META55

source_name: Metaplastic Carcinoma META55


title: Metaplastic Carcinoma META53

description: Metaplastic Carcinoma META53

source_name: Metaplastic Carcinoma META53


title: single cell profile of retinal Muller Glial Cell 25 weeks Rhodko A5

description: Rhodopsin knockout (Rhod-ko) mice are deleted in the rod-specific Rhodopsin gene

source_name: Rhod-ko single retinal Muller Glial Cell, 25 wks

value: Rhod-ko

value: 25 wks


title: NRASQ61R_off_resistant_tumor_7

first: Guo

last: Chen

state: TX

department: Melanoma Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

description:
TRE-NRAS-IRES-Cre + Tet-off
03331-01

hyb_protocol: Biotinylated cRNA was loaded onto Illumina Sentrix Beadchip Array MouseRef-8 V2.0 arrays, hybridized at 58ºC in an Illumina Hybridization Oven (Cat# 198361, Illumina) for 17 hours, washed and incubated with straptavidin-Cy3.

scan_protocol: Arrays were dried and scanned with BeadArray Reader (Illumina, CA) under standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization in GenomeStudio (Illumina, CA).

source_name: Melanoma,NRASQ61R off,resistant tumor #7

label_protocol: Biotinylated cRNA was generated using Illumina® TotalPrep™ RNA Amplification Kit (AMIL1791, Life technologies) following manufactuer's instructions.

growth_protocol: Newborn DCT-TVA;Ink4a/Arf lox/lox mice were injected subcutaneously with viral producing cells expressing Tet-off and TRE-NRASQ61RIRES-Cre, to express mutant NRAS and inactivate both p16Ink4a and p19Arf, specifically in melanocytes of these mice.While TVA-negative;Ink4a/Arf lox/lox mice infected with both Tet-off and TRE-NRASQ61R-IRES-Cre viruses as well as DCT-TVA-postitive;Ink4a/Arf lox/lox mice infected with only TRE-NRASQ61R-IRES-Cre viruses remained tumor free for the duration of the study (n = 20), 72% of the DCT-TVA-postitive;Ink4a/Arf lox/lox mice infected with both Tet-off and TRE-NRASQ61R-IRES-Cre viruses developed tumors at the site of injection (n = 46).

extract_protocol: Total RNA was extracted using mirVanaTM RNA extracrion kit (AM1560, Life technologies) following manufactuer's instructions.

treatment_protocol: To determine whether down-regulation of NRAS expression in Tet-off and TRE-NRASQ61R-IRES-Cre initiated melanomas results in tumor regression, tumors were induced in DCT-TVA;Ink4a/Arf lox/lox mice by subcutaneous injection of Tet-off and TRE-NRASQ61R-IRES-Cre containing viruses at birth. Tumor development and growth was monitored daily. When tumors reached 1,000 mm3, one cohort of tumor-bearing mice was given Dox containing food to suppress NRASQ61R and Cre expression while a separate cohort of tumor bearing mice received standard feed.

value: resistant to NRAS withdrawal

value: melanoma

tag: treatment

value: NRASQ61R Off


title: Metaplastic Carcinoma META56

description: Metaplastic Carcinoma META56

source_name: Metaplastic Carcinoma META56

tag: diagnosis


title: single cell profile of retinal Muller Glial Cell 25 weeks Rhodko A2


title: NRASQ61R_off_resistant_tumor_6

description:
TRE-NRAS-IRES-Cre + Tet-off
03330-00

source_name: Melanoma,NRASQ61R off,resistant tumor #6


title: NRASQ61R_off_resistant_tumor_5

description:
TRE-NRAS-IRES-Cre + Tet-off
03270-10

source_name: Melanoma,NRASQ61R off,resistant tumor #5


title: Blood_Test2_1

description: Test2 001


title: Metaplastic Carcinoma META47

description: Metaplastic Carcinoma META47

source_name: Metaplastic Carcinoma META47


title: single cell profile of retinal Muller Glial Cell 25 weeks Rhodko A3


title: Metaplastic Carcinoma META45

description: Metaplastic Carcinoma META45

source_name: Metaplastic Carcinoma META45


title: single cell profile of retinal Muller Glial Cell 25 weeks Rhodko A4


title: Blood_Test1_1

description: Test1 001

source_name: Peripheral Blood_IS900-PCR positive

value: IS900-PCR positive, MAP-ELISA negative


title: Metaplastic Carcinoma META49

description: Metaplastic Carcinoma META49

source_name: Metaplastic Carcinoma META49


title: single cell profile of retinal Muller Glial Cell 25 weeks Rhodko A1

value: retina


title: Metaplastic Carcinoma META52

description: Metaplastic Carcinoma META52

source_name: Metaplastic Carcinoma META52

value: Spindle cell carcinoma with areas of chondroid differentiation (Carcinoma with heterologous elements)


title: Blood_Test1_2

description: Test1 002

value: female


title: Metaplastic Carcinoma META42

description: Metaplastic Carcinoma META42

source_name: Metaplastic Carcinoma META42

value: Carcinoma with squamous features


title: Metaplastic Carcinoma META41

description: Metaplastic Carcinoma META41

source_name: Metaplastic Carcinoma META41


title: single cell profile of retinal Muller Glial Cell 8w Rhodko 8

source_name: Rhod-ko single retinal Muller Glial Cell, 8 wks

value: 8 wks


title: single cell profile of retinal Muller Glial Cell 8w Rhodko 7


title: Metaplastic Carcinoma META40

description: Metaplastic Carcinoma META40

source_name: Metaplastic Carcinoma META40


title: NRASQ61R_off_resistant_tumor_4

description:
TRE-NRAS-IRES-Cre + Tet-off
03194-01

source_name: Melanoma,NRASQ61R off,resistant tumor #4


title: Blood_CON_2

description: Control 002

source_name: Peripheral Blood_IS900-PCR negative

value: IS900-PCR negative, MAP-ELISA negative

value: Peripheral Blood


title: NRASQ61R_off_resistant_tumor_2

description:
TRE-NRAS-IRES-Cre + Tet-off
02908-00

source_name: Melanoma,NRASQ61R off,resistant tumor #2


title: Blood_CON_3

description: Control 003


title: mc2155+pMind  vs mc2155+pMind+6189 replicate 4

city: Dunedin

first: Htin Lin

last: Aung

state: Otago

address: 720 Cumberland Street

department: Microbiology and Immunology

country: New Zealand

institute: University of Otago

description: Biological replicate 4 of 4.

hyb_protocol: Hybrization performed according to SOP M008 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

scan_protocol: Scanned Genepix 4000A scanner .  Images were quantified using Spotfinder (TIGR).

data_processing: Total normalization and LOWESS normalization with MIDAS software (TIGR). Raw data file: IA corresponds to Cy3 and IB corresponds to Cy5.

organism: Mycolicibacterium smegmatis

source_name: Batch culture HdB 10 mM glycerol

label_protocol: 10 µg of total RNA were reverse transcribed and labelled in a two step protocol according to SOP M007 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

growth_protocol: strains were grown in 400 ml of Hartmans de Bont (HdB) minimal medium supplemented with 10 mM glycerol in 2 l flasks at 37°C with agitation (200 rpm). Wild-type and Dcrp1 strains were grown to an optical density (600nm) of 0.4. Cells were then harvestedfor RNA extraction. For overexpression, strains were grown in 400 ml of Hartmans de Bont (HdB) minimal medium supplemented with 10 mM glycerol and hygromycin B (50 μg/ml) in 2 l flasks at 37°C with agitation (200 rpm). Strains HLA102(pMind+Crp2) and wild-type strain (pMind) were grown to an optical density (600nm) of ~0.3. Protein expression was then induced with tetracycline (20 ng/ml). Cells were then harvested after 3 h post-induction for RNA extraction.

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

value: wild-type + pMind

value: wild-type + pMind +6189


title: Metaplastic Carcinoma META43

description: Metaplastic Carcinoma META43

source_name: Metaplastic Carcinoma META43

value: triple-negative

value: Carcinoma with heterologous elements


title: single cell profile of retinal Muller Glial Cell 8w Rhodko 3

value: Rhod-ko


title: NRASQ61R_off_resistant_tumor_1

description:
TRE-NRAS-IRES-Cre + Tet-off
03179-00

source_name: Melanoma,NRASQ61R off,resistant tumor #1


title: NRASQ61R_off_resistant_tumor_3

description:
TRE-NRAS-IRES-Cre + Tet-off
03182-01

source_name: Melanoma,NRASQ61R off,resistant tumor #3


title: Metaplastic Carcinoma META36

description: Metaplastic Carcinoma META36

source_name: Metaplastic Carcinoma META36

value: Carcinoma with heterologous elements - Matrix producing


title: Metaplastic Carcinoma META39

description: Metaplastic Carcinoma META39

source_name: Metaplastic Carcinoma META39


title: Blood_Test1_3

description: Test1 003


title: mc2155+pMind  vs mc2155+pMind+6189 replicate 2

description: Biological replicate 2 of 4.


title: single cell profile of retinal Muller Glial Cell 8w Rhodko 1


title: Blood_CON_1

description: Control 001


title: Metaplastic Carcinoma META34

description: Metaplastic Carcinoma META34

source_name: Metaplastic Carcinoma META34


title: mc2155 vs.Dcrp1 replicate 4

description: Biological replicate 4 of 4.

value: wild-type


title: mc2155 vs.Dcrp1 replicate 2

description: Biological replicate 2 of 4.


title: single cell profile of retinal Muller Glial Cell WT MG3

description: C57/BL6 mice

source_name: WT single retinal Muller Glial Cell, adult

value: wildtype

value: >25 wks


title: mc2155 vs.Dcrp1 replicate 3

description: Biological replicate 3 of 4.


title: NRASQ61R_control_tumor

description:
NRAS-IRES-Cre
02573-10

source_name: Melanoma,NRASQ61R on,control

value: control

value: melanoma

value: NRASQ61R On


title: single cell profile of retinal Muller Glial Cell WT MG15

description: C57/BL6 mice

value: retina


title: single cell profile of retinal Muller Glial Cell 8w Rhodko 2


title: HPPL with Grhl2

city: Sapporo

first: Naoki

last: Tanimizu

address: S1, W17, Chuou-ku

institute: Sapporo Medical University

hyb_protocol: The fluorescently labeled samples were hybridized overnight to miRXplore Microarrays using the a-HybTM Hybridization Station. The miRXplore Universal Reference (UR) provided by Miltenyi Biotec was used as the control. The control samples are labedled with fluorescent dye Hy3TM and experimental samples are labeled with Hy5TM.

scan_protocol: Fluorescence signals of the hybridized miRXploreTM Microarrays were detected using a laser scanner from Agilent (Agilent Technologies).

data_processing: Mean signal and mean local background intensities were obtained for each spot of the microarray images using the ImaGene software (Biodiscovery). Qualified sopts were analyzed with the PIQOR Analyzer Software. The PIQOR Analyzer allows automated data processing of the raw data text files derived from teh ImaGene software. THis includes background subtraction to obtain the net sigal intensity, data normalization, and calculation of the Hy5/Hy3 ratios.

source_name: HPPL, a liver progenitor cell line, derived from E14.5 Dlk1+ hepatoblast

label_protocol: Sample labeling was performed according to the undisclosed miRXploreTM User manual.

growth_protocol: HPPL were cultured in DMEM/F12 containg FBS, Dex, EGF, HGF, ITS, and Nicontinamide as previously reported (Tanimizu et al . JCS 2003)

extract_protocol: RNA was extraceted according to the manufacture's instruction of Qiagen miRNeasy kit.

treatment_protocol: When cells became confluent, RNA was extraceted.

value: HPPL

tag: infection

source_name: miRXplore Universal Reference

tag: source

value: miRXplore Universal Reference


title: HPPL with Neo

value: pMXsNeo


title: Myoblasts treated with follistatin-rep4

city: Warsaw

first: Zofia

last: Wicik

state: mazovia

address: Pawinskiego 5

department: Department of Human Epigenetics

country: Poland

institute: Mossakowski Medical Research Center

description:
FS vs. CTRL-4
Biological replicate 4 of 4. Control: myoblasts cells, untreated, harvested after 6 day of differentiation. Dye swap.

hyb_protocol: The cRNA was fragmented and hybridized to Agilent-014868 Whole Mouse Genome Oligonucleotide Microarray (4 × 44K slide format) at 37 ºC for 17 hours (Version 5.7, March 2008).

scan_protocol: After washing, the slides were scanned with a DNA microarray Agilent Technologies Scanner G2505C US10353 and images were processed with the Feature Extraction Software version 10.7.3.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 014868_D_F_20110406) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data were processed using GeneSpring GX (Agilent).

source_name: C2C12 myoblasts, 6 day of differentiation in [10%HS/24h/6d]

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double-stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent Technologies Version 5.7, March 2008). All microarrays were dye-swaps (test sample labeled with Cy3, control sample labeled with Cy5).

growth_protocol: C2C12 myoblasts were conducted in proliferation medium with DMEM/10% FBS (Gibco Invitrogen Co.) till 80% confluence. Next, myoblasts were differentiated during 6 days in DMEM/2% HS (Gibco Invitrogen Co.)

extract_protocol: Total RNA was extracted from the cells with RNeasy (Qiagen). The quality of the total RNA was examined by 2100 Bioanalyzer (Agilent).

treatment_protocol: Differentiating myoblasts were treated for every 24h with: 200 ng/ml FS (Recombinant Human Follistatin 288- R&D, USA). Control cells were untreated during 6 days.

tag: cell type

value: myoblasts

tag: days of differentiation

source_name: C2C12 myoblasts, 6 day of differentiation in [10%HS+200 ng/ml FS/24h/6d]

value: 200 ng/ml follistatin/24h


title: Metaplastic Carcinoma META37

description: Metaplastic Carcinoma META37

source_name: Metaplastic Carcinoma META37

value: Carcinoma with squamous features


title: single cell profile of retinal Muller Glial Cell WT MG16

description: C57/BL6 mice


title: Myoblasts treated with follistatin-rep2

description:
FS vs. CTRL-2
Biological replicate 2 of 4. Control: myoblasts cells, untreated, harvested after 6 day of differentiation. Dye swap.


title: mc2155+pMind  vs mc2155+pMind+6189 replicate 1

description: Biological replicate 1 of 4.

value: wild-type + pMind

value: wild-type + pMind +6189


title: single cell profile of retinal Muller Glial Cell WT MG1

description: C57/BL6 mice


title: Myoblasts treated with follistatin-rep3

description:
FS vs. CTRL-3
Biological replicate 3 of 4. Control: myoblasts cells, untreated, harvested after 6 day of differentiation. Dye swap.


title: single cell profile of retinal Muller Glial Cell WT MG22

description: C57/BL6 mice


title: mc2155 vs.Dcrp1 replicate 1

description: Biological replicate 1 of 4.


title: Myoblasts treated with follistatin-rep1

description:
FS vs. CTRL-1
Biological replicate 1 of 4. Control: myoblasts cells, untreated, harvested after 6 day of differentiation. Dye swap.


title: p110 alpha-overexpressing Max-null ESCs  Dox (+)

status: Public on Oct 30 2014

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

description: sample 18

hyb_protocol: Labelled samples were hybridized to the microarrays according to the manufacturer’s protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was preformed as described elsewhere. (Irizarry et al, Nucleic Acids Res 31, e15, 2003)

data_processing: The data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al.  Nucleic Acids Res  31(4): e15, 2003) via R/Bioconductor 2.7 affy package using default analysis settings.

source_name: p110 alpha-overexpressing Max-null ESCs Dox-treated

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

growth_protocol: ERRTcH3 ESCs, Max-null ESCs and their derivatives overexpressing the indicated cDNAs (c-Myc, N-Myc or p110 alpha) were culture under conventional ESC medium with LIF and serum. Wild-type ERRTcH3 ESCs were also cultured under 2i condition as indicated.

extract_protocol: Total RNAs were prepared using TRIzol reagent from Invitrogen (15596-026).

treatment_protocol: ERRTcH3 ESCs and their derivatives were treated with or without LY294002, while Max-null ESCs and their derivatives were treated with or without doxycycline

tag: strain background

value: male

value: EBRTcH3 embryonic stem cells (ESCs)

value: p110 alpha-overexpressing Max-null

tag: treated with

value: Dox


title: c-Myc(T58A)-overexpressing EBRTcH3 ESCs LY294002-treated (day 5)

description: sample 13

source_name: c-Myc(T58A)-overexpressing ESCs LY294002-treated for 5 days

tag: gender

value: LY294002 for 5 days


title: Max-null ESCs Dox-treated (day 6)

description: sample 16

source_name: Max-null ESCs Dox-treated for 6 days

value: Max-null

value: Dox for 6 days


title: Max-null ESCs Dox-treated (day 4)

description: sample 15

source_name: Max-null ESCs Dox-treated for 4 days

value: Dox for 4 days


title: c-Myc(wild)-overexpressing EBRTcH3 ESCs LY294002-treated (day 2)

description: sample 9

source_name: c-Myc(wild)-overexpressing ESCs LY294002-treated for 2 days

value: c-Myc(wild)-overexpressing

value: LY294002 for 2 days


title: Max-null ESCs Dox-untreated

description:
sample 14
Reference sample for sample 15 and 16 (Max-null ESCs treated with Dox for 4 or 6 days)

source_name: Max-null ESCs Dox-untreated

value: none (untreated control)


title: c-Myc(wild)overexpressing EBRTcH3 ESCs LY294002-treated (day 5)

description: sample 12

source_name: c-Myc(wild)-overexpressing ESCs LY294002-treated for 5 days


title: c-Myc(T58A)-overexpressing EBRTcH3 ESCs LY294002-treated (day 2)

description: sample 10

source_name: c-Myc(T58A)-overexpressing ESCs LY294002-treated for 2 days


title: p110 alpha-overexpressing Max-null ESCs  Dox (-)

description:
sample 17
Reference sample for sample 18 (p110 alpha-overexpressing Max-null ESCs treated with Dox)

source_name: p110 alpha-overexpressing Max-null ESCs Dox-untreated


title: EBRTcH3 EBRTcH3 ESCs LY294002-treated (day 2)

description: sample 8

source_name: EBRTcH3 ESCs LY294002-treated for 2 days


title: c-Myc(T58A)-overexpressing EBRTcH3 ESCs LY294002 untreated

description:
sample 7
Reference sample for sample 10 and 13 (N-Myc overexpressing EBRTcH3 treated with LY294002 for 2 or 5 days)

source_name: c-Myc(T58A)-overexpressing ESCs LY294002 untreated


title: EBRTcH3 ESCs LY294002-treated (day 5) ver2

description: sample 11

source_name: EBRTcH3 ESCs LY294002-treated for 5 days


title: EBRTcH3 ESCs 2i and LY294002 (day 5)-treated

description: sample 4

source_name: EBRTcH3 ESCs 2i and LY294002-treated


title: EBRTcH3 ESCs LY294002 untreated ver2

description:
sample 5
Reference sample for sample 8 and 11 (EBRTcH3 treated with LY294002 for 2 or 5 days)

source_name: EBRTcH3 ESCs LY294002 untreated


title: Metaplastic Carcinoma META31

description: Metaplastic Carcinoma META31

source_name: Metaplastic Carcinoma META31

tag: phenotype

value: triple-negative

value: Carcinoma with heterologous elements - Matrix producing


title: c-Myc(wild)-overexpressing EBRTcH3 ESCs LY294002 untreated

description:
sample 6
Reference sample for sample 9 and 12 (c-Myc overexpressing EBRTcH3 treated with LY294002 for 2 or 5 days)

source_name: c-Myc(wild)-overexpressing ESCs LY294002 untreated


title: EBRTcH3 ESCs 2i-treated but LY294002-untreated

description:
sample 3
Reference sample for sample 4 (EBRTcH3 treated with 2i and LY294002)


title: EBRTcH3 ESCs LY294002-treated (day 5)

description: sample 2


title: EBRTcH3 ESCs LY294002 untreated

description:
sample 1
Reference sample for sample 2 (EBRTcH3 treated with LY294002 for 5 days)