title: Post BR vastus lateralis muscle biopsy: Nu_L2Vpost_2

description: Post BR vastus lateralis muscle biopsy

source_name: Post BR vastus lateralis muscle biopsy

value: vastus lateralis muscle biopsy

tag: pool of equal quantities of cRNA from 18 Pre-BR Soleus or 23 Pre-BR Vastus Lateralis biopsies


title: mstm_KO_1 rep1

status: Public on Feb 13 2009

type: RNA

city: Augusta

first: Han

last: Zhang

state: GA

department: IMMAG

country: USA

institute: Medical College of Georgia

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized using Mean/median scaling normalization and Welch t test  with Array Track v3.3

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Gastric mucosa from Lasp1 knockout

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

extract_protocol: Total RNA was isolated using a Perfect RNA Tissue kit (5 Prime Inc., Gaithersburg, MD) following manufacturer's instructions.

tag: Lasp1 knockout


title: Pre BR vastus lateralis muscle biopsy: Nu_L1Vpre_2

status: Public on Feb 12 2009

city: OTTAWA

first: Angele

last: CHOPARD

state: ONTARIO

address: 451 Smyth road

department: Faculty of Medicine

country: Canada

institute: University of Ottawa

description: Pre BR vastus lateralis muscle biopsy

hyb_protocol: Each individual cRNA sample was Cy3-labeled and mixed with an equal amount of Cy5-labeled reference sample (pool of equal quantities of cRNA from 18 Pre-BR Soleus or 23 Pre-BR Vastus Lateralis biopsies). The mixture was pre-incubated with human Cot-I DNA (Gibco-BRL), yeast tRNA, and polyA RNA, and hybridized onto duplicate microarrays.

scan_protocol: All hybridized arrays were scanned by fluorescence confocal microscopy (Scan array 4000XL, GSI-Lumonics) anda images were quantified using Genepix Pro 5.1.0.19 Extraction Software

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal. Home made (MADSCAN) software was used.

organism: Homo sapiens

source_name: Pre BR vastus lateralis muscle biopsy

label_protocol: 500 ng total RNA was prepared for hybridization using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion). According to the manufacturer, total RNA was reverse transcribed with an oligo-dT primer containing a T7 RNA polymerase promoter, and then converted into double-stranded cDNA. cDNA was used in an in vitro transcription (IVT) reaction in presence of amino-allyl nucleotides. After column purification, the IVT reaction yielded 30-100 µg aminoallyl cRNA. IVT products were labeled either with cyanine 3 or cyanine 5, and fragmented with RNA Fragmentation Reagents (Ambion) into lengths around 100 bases before hybridization.

extract_protocol: Total RNA was extracted from frozen samples with a polytron homogeneizer and the RNeasy Fibrous Tissue Mini kit (Qiagen).

tag: tissue

source_name: reference


title: Pre BR vastus lateralis muscle biopsy: Nu_L2Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Nu_L2Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Nu_L2Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Post BR soleus muscle biopsy: Nu_L2Spost_1

description: Post BR soleus muscle biopsy

source_name: Post BR soleus muscle biopsy

value: soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Nu_L2Spre_2

description: Pre BR soleus muscle biopsy

source_name: Pre BR soleus muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Nu_L1Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Adjacent Tissue 2

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

description: Pair matched to 2T

hyb_protocol: The hybridization was performed using 3DNA array detection system according to the manufacturer’s protocol (Genisphere, PA).

scan_protocol: The arrays were scanned by ScanArray scanner (Perkin-Elmer)

data_processing: Background subtraction and LOWESS normalization of log2 ratio (Cy5/Cy3) using sma R package

source_name: Human placental RNA (reference)

label_protocol: The probe preparation was performed using 3DNA array detection system according to the manufacturer’s protocol (Genisphere, PA) with 20mg of total RNA.

extract_protocol: Total RNA was isolated from frozen tissue according to the manufacturer’s instructions (Qiagen), and quality of the total RNA was judged based on the ratio of 28S/18S RNA after agarose gel electrophoresis.

value: placenta

source_name: Adjacent liver tissue 2N

value: liver


title: mstm_wt_5 rep3

source_name: Gastric mucosa from wild type mice

tag: wild type


title: Post BR vastus lateralis muscle biopsy: Nu_L1Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Nu_L1Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: HCC 36

description: Pair matched to 36N

source_name: HCC 36T

value: hepatocellular carcinoma


title: Pre BR soleus muscle biopsy: Nu_L1Spre_2

description: Pre BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Nu_L1Spre_1

description: Pre BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Nu_L1Spost_1

description: Post BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Nu_L1Spost_2

description: Post BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Nu_K2Spre_2

description: Pre BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Nu_K2Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: Adjacent Tissue 44

description: Pair matched to 44T

source_name: Adjacent liver tissue 44N


title: Pre BR soleus muscle biopsy: Nu_K2Spre_1

description: Pre BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Nu_K1Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Nu_K1Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Nu_K1Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Post BR soleus muscle biopsy: Nu_K1Spost_2

description: Post BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Nu_K1Spre_1

description: Pre BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Nu_K1Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Nu_J2Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Nu_J2Spre_2

description: Pre BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Nu_J2Spost_2

description: Post BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Nu_J2Spre_1

description: Pre BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Nu_J2Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Nu_J2Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Nu_K2Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Nu_J1Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Post BR soleus muscle biopsy: Nu_K1Spost_1

description: Post BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Nu_J2Spost_1

description: Post BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Nu_J1Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Nu_K1Spre_2

description: Pre BR soleus muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Nu_J1Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Nu_J1Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: RA+ OE+KD D2 rep2

city: Singapore

first: Haw Siang

last: Ang

address: 8A Biomedical Grove

country: Singapore

institute: SIgN

hyb_protocol: According to Illumina Protocol

scan_protocol: Illumina BeadScan

data_processing: Data were normalized with cross-correlation method and differential expression was based on the mean of the log2 fold changes. Fold change data presented on the Series.

label: biotin-labeled

source_name: SH-SY5Y mir125b DP & mir125 KD with retinoic acid treatment on day 2

label_protocol: According to Illumina Protocol

growth_protocol: For microarray transcriptome profiling of Sall4- and control shRNA treated cells, cells were transfected with appropriate plasmids and cultured under puromycin selection for 3, 4 or 5 days.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and column-purified with RNeasy kits (Qiagen).

tag: cell line

value: SH-SY5Y cells


title: RA+ OE+KD D2 rep3


title: Pre BR soleus muscle biopsy: Nu_J1Spre_1

description: Pre BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Nu_J2Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Post BR soleus muscle biopsy: Nu_J1Spost_2

description: Post BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Nu_J1Spost_1

description: Post BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Nu_J1Spre_2

description: Pre BR soleus muscle biopsy


title: RA+ OE+KD D2 rep1


title: Pre BR vastus lateralis muscle biopsy: Nu_I2Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: RA+ OE D2 rep2

source_name: SH-SY5Y mir125b DP with retinoic acid treatment on day 2


title: Pre BR vastus lateralis muscle biopsy: Nu_I2Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: RA+ SCR D2 rep3

source_name: SH-SY5Y scrambled control with retinoic acid treatment on day 2


title: Pre BR soleus muscle biopsy: Nu_I2Spre_2

description: Pre BR soleus muscle biopsy


title: RA+ KD D2 rep2

source_name: SH-SY5Y mir125b knockdown with retinoic acid treatment on day 2


title: RA+ KD D2 rep1


title: RA+ OE D2 rep3


title: Pre BR soleus muscle biopsy: Nu_I2Spre_1

description: Pre BR soleus muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Nu_I2Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: RA+ KD D2 rep3


title: Post BR vastus lateralis muscle biopsy: Nu_I2Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: RA+ SCR D2 rep2

source_name: SH-SY5Y scrambled control  with retinoic acid treatment on day 2


title: Post BR soleus muscle biopsy: Nu_I2Spost_1

description: Post BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Nu_I1Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: RA+ OE D2 rep1


title: RA+ SCR D2 rep1


title: RA- OE D4 rep3

source_name: SH-SY5Y mir125b DP without retinoic acid treatment on day 4


title: Post BR vastus lateralis muscle biopsy: Nu_I1Vpost_2

description: Post BR vastus lateralis muscle biopsy

source_name: Post BR vastus lateralis muscle biopsy


title: RA- OE D4 rep1


title: Post BR vastus lateralis muscle biopsy: Nu_I1Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: RA- OE D4 rep2


title: Pre BR vastus lateralis muscle biopsy: Nu_I1Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: RA- OE D2 rep2

source_name: SH-SY5Y mir125b DP without retinoic acid treatment on day 2


title: RA- OE D2 rep3


title: Pre BR soleus muscle biopsy: Nu_I1Spre_2

description: Pre BR soleus muscle biopsy


title: RA- OE D2 rep1


title: RA- SCR D4 rep2

source_name: SH-SY5Y scrambled control without retinoic acid treatment on day 4


title: RA- SCR D4 rep3


title: Pre BR vastus lateralis muscle biopsy: Ex_H2Vpre_2

description: Pre BR vastus lateralis muscle biopsy

source_name: Pre BR vastus lateralis muscle biopsy

source_name: reference


title: Post BR vastus lateralis muscle biopsy: Ex_H2Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Nu_I1Spre_1

description: Pre BR soleus muscle biopsy

source_name: Pre BR soleus muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ex_H2Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: RA- SCR D4 rep1


title: Post BR soleus muscle biopsy: Nu_I1Spost_2

description: Post BR soleus muscle biopsy

source_name: Post BR soleus muscle biopsy


title: RA- SCR D2 rep1

source_name: SH-SY5Y scrambled control  without retinoic acid treatment on day 2


title: Post BR soleus muscle biopsy: Nu_I1Spost_1

description: Post BR soleus muscle biopsy


title: RA- SCR D2 rep2


title: Pre BR soleus muscle biopsy: Ex_H2Spre_2

description: Pre BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ex_G2Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ex_G2Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Ex_H2Spre_1

description: Pre BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ex_H2Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: RA- SCR D2 rep3

source_name: SH-SY5Y scrambled control without retinoic acid treatment on day 2


title: Post BR vastus lateralis muscle biopsy: Ex_G2Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ex_G2Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Post BR soleus muscle biopsy: Ex_G2Spost_1

description: Post BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ex_F2Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ex_F2Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Ex_G2Spre_1

description: Pre BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Ex_F2Spre_1

description: Pre BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Ex_F2Spre_2

description: Pre BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ex_E2Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Ex_G2Spre_2

description: Pre BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Ex_E2Spre_2

description: Pre BR soleus muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ex_E2Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Post BR soleus muscle biopsy: Ex_G2Spost_2

description: Post BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Ex_F2Spost_1

description: Post BR soleus muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ex_E2Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Ex_E2Spre_1

description: Pre BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Ex_F2Spost_2

description: Post BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ex_E2Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Post BR soleus muscle biopsy: Ex_D1Spost_2

description: Post BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ex_D1Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Post BR soleus muscle biopsy: Ex_D1Spost_1

description: Post BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Ex_C1Spre_1

description: Pre BR soleus muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ex_C1Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Ex_C1Spre_2

description: Pre BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Ex_C1Spost_2

description: Post BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ex_C1Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ex_C1Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ex_B1Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ex_D1Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ex_D1Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ex_B1Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ex_A1Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ct_H1Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Post BR soleus muscle biopsy: Nu_I2Spost_2

description: Post BR soleus muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ct_H1Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Ex_A1Spre_2

description: Pre BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ct_H1Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Ex_A1Spre_1

description: Pre BR soleus muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ex_C1Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ct_H1Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Post BR soleus muscle biopsy: Ex_C1Spost_1

description: Post BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Ex_B1Spost_1

description: Post BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Ex_B1Spost_2

description: Post BR soleus muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ex_A1Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ex_A1Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ex_A1Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Post BR soleus muscle biopsy: Ct_H1Spost_2

description: Post BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Ct_H1Spre_1

description: Pre BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Ct_H1Spre_2

description: Pre BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Ct_H1Spost_1

description: Post BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ct_G1Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: THYGYLM18

city: Bellaterra

first: Miguel

last: Perez-Enciso

address: Veterinary School

department: Animal Science

country: Spain

institute: Universitat Autonoma Barcelona

description: Thyroid gland,Youli,male

hyb_protocol: The hybridization was done according to Affymetrix standard protocols.

scan_protocol: Standard Affymetrix protocol

data_processing: Microarray expression data were generated with GeneChip Operating Software (GCOS)

organism: Sus scrofa

source_name: Thyroid gland,Youli,male

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

growth_protocol: Pigs with one month of age were housed simultaneously, fed the same diets during the fattening period, that lasted two months.

extract_protocol: Total RNA was extracted from 100 mg tissue using the RiboPure™ kit (Ambion, Austin, USA) according to the manufacturer’s protocol.

treatment_protocol: At necropsy, samples of 16 tissues were collected, snap frozen in liquid nitrogen and stored at -80 ºC, until de RNA extraction.

value: Thyroid gland

tag: breed

value: Youli

tag: sex

value: male


title: Pre BR vastus lateralis muscle biopsy: Ct_G1Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: THYGYLM20

description: Thyroid gland,Youli,male


title: THYGLWM04

description: Thyroid gland,Youli,female

source_name: Thyroid gland,Youli,female

value: female


title: THYGYLM19

description: Thyroid gland,Youli,male


title: Post BR vastus lateralis muscle biopsy: Ct_G1Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: THYGLWM02

description: Thyroid gland,LargeWhite,male

source_name: Thyroid gland,LargeWhite,male

value: LargeWhite


title: Pre BR soleus muscle biopsy: Ct_G1Spre_1

description: Pre BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Ct_G1Spost_2

description: Post BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ct_F1Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ct_F1Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Post BR soleus muscle biopsy: Ct_G1Spost_1

description: Post BR soleus muscle biopsy


title: THYGIBM24

description: Thyroid gland,LargeWhite,female

source_name: Thyroid gland,LargeWhite,female


title: THYGLWF05

description: Thyroid gland,LargeWhite,female


title: THYGIBF22

description: Thyroid gland,Iberian,male

source_name: Thyroid gland,Iberian,male

value: Iberian


title: THYGDUF14

description: Thyroid gland,Iberian,female

source_name: Thyroid gland,Iberian,female


title: THYGDUM12

description: Thyroid gland,Iberian,female


title: Post BR vastus lateralis muscle biopsy: Ct_G1Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ct_F1Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Ct_F1Spre_1

description: Pre BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Ct_F1Spre_2

description: Pre BR soleus muscle biopsy


title: THYGYLF21

description: Thyroid gland, Duroc, male

source_name: Thyroid gland, Duroc, male

value: Duroc


title: Pre BR vastus lateralis muscle biopsy: Ct_F1Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: THYGLWF06

description: Thyroid gland,LargeWhite,male


title: THYGIBF25

description: Thyroid gland, Duroc, female

source_name: Thyroid gland, Duroc, female


title: THYGIBM23

description: Thyroid gland, Duroc, female


title: THYGDUF13

description: Thyroid gland, Duroc, male


title: THYGDUM15

description: Thyroid gland,Iberian,male


title: Post BR soleus muscle biopsy: Ct_F1Spost_2

description: Post BR soleus muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ct_E1Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ct_E1Vpost_1

description: Post BR vastus lateralis muscle biopsy

source_name: Post BR vastus lateralis muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ct_E1Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ct_E1Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Post BR soleus muscle biopsy: Ct_F1Spost_1

description: Post BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Ct_E1Spre_2

description: Pre BR soleus muscle biopsy


title: HYPTYLM19

description: Hypothalamus,Youli,male

source_name: Hypothalamus,Youli,male

value: Hypothalamus


title: HYPTYLF21

description: Hypothalamus,Youli,female

source_name: Hypothalamus,Youli,female


title: Pre BR vastus lateralis muscle biopsy: Ct_D2Vpre_2

description: Pre BR vastus lateralis muscle biopsy

source_name: Pre BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Ct_E1Spre_1

description: Pre BR soleus muscle biopsy

source_name: reference


title: Pre BR vastus lateralis muscle biopsy: Ct_D2Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: HYPTLWF05

description: Hypothalamus,LargeWhite,female

source_name: Hypothalamus,LargeWhite,female


title: Post BR soleus muscle biopsy: Ct_E1Spost_1

description: Post BR soleus muscle biopsy

source_name: Post BR soleus muscle biopsy


title: HYPTLWM02

description: Hypothalamus,LargeWhite,male

source_name: Hypothalamus,LargeWhite,male


title: HYPTYLM18

description: Hypothalamus,Youli,male


title: Post BR soleus muscle biopsy: Ct_E1Spost_2

description: Post BR soleus muscle biopsy


title: HYPTIBF22

description: Hypothalamus,Iberian,female

source_name: Hypothalamus,Iberian,female


title: HYPTIBM24

description: Hypothalamus,Iberian,male

source_name: Hypothalamus,Iberian,male


title: HYPTLWM04

description: Hypothalamus,LargeWhite,male


title: HYPTIBF25

description: Hypothalamus,Iberian,female


title: HYPTIBM23

description: Hypothalamus,Iberian,male


title: HYPTDUM15

description: Hypothalamus, Duroc, male

source_name: Hypothalamus, Duroc, male


title: HYPTYLM20

description: Hypothalamus,Youli,male


title: HYPTDUM12

description: Hypothalamus, Duroc, male


title: Post BR vastus lateralis muscle biopsy: Ct_D2Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Post BR vastus lateralis muscle biopsy: Ct_D2Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: GONAYLM20

description: Gonad,Youli,male

source_name: Gonad,Youli,male

value: Gonad


title: Pre BR soleus muscle biopsy: Ct_D2Spre_2

description: Pre BR soleus muscle biopsy

source_name: Pre BR soleus muscle biopsy


title: Pre BR soleus muscle biopsy: Ct_D2Spre_1

description: Pre BR soleus muscle biopsy


title: GONAYLM18

description: Gonad,Youli,male


title: Pre BR vastus lateralis muscle biopsy: Ct_C2Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: GONALWM02

description: Gonad,LargeWhite,male

source_name: Gonad,LargeWhite,male


title: GONALWF06

description: Gonad,LargeWhite,female

source_name: Gonad,LargeWhite,female


title: HYPTDUF13

description: Hypothalamus, Duroc, female

source_name: Hypothalamus, Duroc, female


title: GONALWM04

description: Gonad,LargeWhite,male


title: GONAYLM19

description: Gonad,Youli,male


title: HYPTDUF14

description: Hypothalamus, Duroc, female


title: Post BR vastus lateralis muscle biopsy: Ct_C2Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: HYPTLWF06

description: Hypothalamus,LargeWhite,female


title: GONAYLF21

description: Gonad,Youli,female

source_name: Gonad,Youli,female


title: GONAIBM23

description: Gonad,Iberian,male

source_name: Gonad,Iberian,male


title: GONALWF05

description: Gonad,LargeWhite,female


title: GONAIBF22

description: Gonad,Iberian,female

source_name: Gonad,Iberian,female


title: Post BR vastus lateralis muscle biopsy: Ct_C2Vpost_1

description: Post BR vastus lateralis muscle biopsy

source_name: Post BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Ct_G1Spre_2

description: Pre BR soleus muscle biopsy


title: GONADUM12

description: Gonad, Duroc, male

source_name: Gonad, Duroc, male


title: GONAIBF25

description: Gonad,Iberian,female


title: Pre BR soleus muscle biopsy: Ct_C2Spre_1

description: Pre BR soleus muscle biopsy

source_name: reference


title: Pre BR soleus muscle biopsy: Ct_C2Spre_2

description: Pre BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Ct_C2Spost_2

description: Post BR soleus muscle biopsy


title: Lasp1-/- MEFs, rep2

description: Replicate 2 of 3.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using mean/median scaling normalization and Welch t test with array track v3.3.

source_name: mouse embryonic fibroblasts, Lasp1-/-

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

tag: strain

tag: genotype

value: Lasp1 knock out


title: Pre BR vastus lateralis muscle biopsy: Ct_C2Vpre_1

description: Pre BR vastus lateralis muscle biopsy

source_name: Pre BR vastus lateralis muscle biopsy


title: FATBYLM18

description: Backfat,Youli,male

source_name: Backfat,Youli,male

value: Backfat


title: FATBLWM04

description: Backfat,LargeWhite,male

source_name: Backfat,LargeWhite,male


title: Lasp1-/- MEFs, rep3

description: Replicate 3 of 3.


title: Lasp1+/+ MEFs, rep3

description: Replicate 3 of 3.

source_name: mouse embryonic fibroblasts, Lasp1+/+

value: wild type


title: Pre BR vastus lateralis muscle biopsy: Ct_B2Vpre_2

description: Pre BR vastus lateralis muscle biopsy

value: vastus lateralis muscle biopsy


title: GONADUF13

description: Gonad, Duroc, female

source_name: Gonad, Duroc, female


title: FATBYLM19

description: Backfat,Youli,male


title: FATBLWM02

description: Backfat,LargeWhite,male


title: FATBYLF21

description: Backfat,Youli,female

source_name: Backfat,Youli,female


title: FATBYLM20

description: Backfat,Youli,male


title: Lasp1-/- MEFs, rep1

description: Replicate 1 of 3.


title: Lasp1+/+ MEFs, rep2

description: Replicate 2 of 3.


title: Pre BR vastus lateralis muscle biopsy: Ct_B2Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: Lasp1+/+ MEFs, rep1

description: Replicate 1 of 3.


title: Post BR soleus muscle biopsy: Ct_C2Spost_1

description: Post BR soleus muscle biopsy

source_name: Post BR soleus muscle biopsy

value: soleus muscle biopsy


title: FATBLWF05

description: Backfat,LargeWhite,female

source_name: Backfat,LargeWhite,female


title: FATBLWF06

description: Backfat,LargeWhite,female


title: GONAIBM24

description: Gonad,Iberian,male


title: GONADUF14

description: Gonad, Duroc, female


title: GONADUM15

description: Gonad, Duroc, male


title: FATBIBM24

description: Backfat,Iberian,male

source_name: Backfat,Iberian,male


title: FATBDUM15

description: Backfat, Duroc, male

source_name: Backfat, Duroc, male


title: Post BR vastus lateralis muscle biopsy: Ct_B2Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Ct_B2Spre_2

description: Pre BR soleus muscle biopsy

source_name: Pre BR soleus muscle biopsy


title: FATBIBF25

description: Backfat,Iberian,female

source_name: Backfat,Iberian,female


title: Post BR vastus lateralis muscle biopsy: Ct_B2Vpost_2

description: Post BR vastus lateralis muscle biopsy


title: Pre BR vastus lateralis muscle biopsy: Ct_A2Vpre_2

description: Pre BR vastus lateralis muscle biopsy


title: AHYPYLM20

description: Adenohypophysis,Youli,male

source_name: Adenohypophysis,Youli,male

value: Adenohypophysis


title: FATBIBM23

description: Backfat,Iberian,male


title: FATBIBF22

description: Backfat,Iberian,female


title: Pre BR vastus lateralis muscle biopsy: Ct_A2Vpre_1

description: Pre BR vastus lateralis muscle biopsy


title: FATBDUM12

description: Backfat, Duroc, male


title: FATBDUF13

description: Backfat, Duroc, female

source_name: Backfat, Duroc, female


title: Post BR vastus lateralis muscle biopsy: Ct_A2Vpost_2

description: Post BR vastus lateralis muscle biopsy

source_name: Post BR vastus lateralis muscle biopsy


title: AHYPYLM19

description: Adenohypophysis,Youli,male


title: AHYPLWM04

description: Adenohypophysis,LargeWhite,male

source_name: Adenohypophysis,LargeWhite,male


title: Pre BR soleus muscle biopsy: Ct_B2Spre_1

description: Pre BR soleus muscle biopsy

source_name: reference


title: AHYPYLF21

description: Adenohypophysis,Youli,female

source_name: Adenohypophysis,Youli,female


title: AHYPYLM18

description: Adenohypophysis,Youli,male


title: Post BR vastus lateralis muscle biopsy: Ct_A2Vpost_1

description: Post BR vastus lateralis muscle biopsy


title: Pre BR soleus muscle biopsy: Ct_A2Spre_2

description: Pre BR soleus muscle biopsy


title: AHYPLWM02

description: Adenohypophysis,LargeWhite,male


title: AHYPLWF06

description: Adenohypophysis,LargeWhite,female

source_name: Adenohypophysis,LargeWhite,female


title: FATBDUF14

description: Backfat, Duroc, female


title: AHYPLWF05

description: Adenohypophysis,LargeWhite,female


title: AHYPIBM24

description: Adenohypophysis,Iberian,male

source_name: Adenohypophysis,Iberian,male


title: AHYPIBM23

description: Adenohypophysis,Iberian,male


title: Pre BR soleus muscle biopsy: Ct_A2Spre_1

description: Pre BR soleus muscle biopsy


title: Post BR soleus muscle biopsy: Ct_A2Spost_2

description: Post BR soleus muscle biopsy


title: AHYPIBF25

description: Adenohypophysis,Iberian,female

source_name: Adenohypophysis,Iberian,female


title: AHYPIBF22

description: Adenohypophysis,Iberian,female


title: AHYPDUM15

description: Adenohypophysis, Duroc, male

source_name: Adenohypophysis, Duroc, male


title: Post BR soleus muscle biopsy: Ct_A2Spost_1

description: Post BR soleus muscle biopsy


title: brain met, set2: 4218357021_F1

status: Public on Feb 11 2009

city: Brisbane

first: Leonard

last: Da Silva

address: Herston Road

country: Australia

institute: University of Queensland

description: Illumina's DASL® assay was used for RNA profiling. During the DASL assay gene specific primers with either Cy3 or Cy5 are incorporated into the product which is hybridised. The gene specific primers are produced as a pool which contains both Cy3 and Cy5 within the pool  (therefore some primers for gene 'A' will have Cy3 others will have Cy5). Thus after hybridisation the signal of Cy3 and Cy5 is combined to produce the raw signal (one single raw signal per probe). The DASL assay uses an amended version of Illumina's Goldengate assay which integrates SNPs to determine genotype with either a Cy3 or Cy5. In the case of DASL the sum of the Cy3 and Cy5 is the raw expression of the gene. No independent hybridizations were performed.

hyb_protocol: The labeled PCR products were hybridized to a Sentrix array or Beadchip. Following hybridization, the arrays were scanned with a BeadArray Reader (Illumina) and data was extracted using BeadStudio software (Illumina).

scan_protocol: Following hybridization, the arrays were scanned with a BeadArray Reader (Illumina) and data was extracted using BeadStudio software (Illumina). Samples exhibiting a median hybridization intensity across all probes of <600 (background corrected) were excluded from analysis. Probes with a BeadStudio detection score greater than 0.99 in more than 15 conditions were included.

data_processing: Array data transformation and normalization (per chip normalized to 50th percentile and per gene normalized to median) was done in Genespring® version 7.0 software (Agilent Technologies, Santa Clara, USA). Hierarchical clustering was performed using: Similarity measure; Pearson Correlation and clustering algorithm; Average Linkage. Genes differentially expressed between primary tumors and brain metastases were identified using analysis of variance (ANOVA, p<0.01) or parametric test, variances not assumed equal (Welch t-test, p < 0.005). Up and down regulation was considered for normalized data values that were greater or less than a factor of 2 fold for the conditions compared.

source_name: brain metastases from lung cancer

label_protocol: RNA (250ng) was converted to cDNA through a reverse transcription reaction with biotinylated oligo-d(T)18 and random nonamers. Oligonucleotides (three unique pairs (oligos?) for each of the 512 genes) were annealed to the biotinylated cDNA, the duplexes were bound to streptavidin conjugated paramagnetic particles to remove non-hybridized oligos. The annealed oligos were then extended and ligated (to incorporate an address sequence and primer site) to generate amplifiable products. These products were subjected to PCR amplification using fluorescently labeled (Cy3 and Cy5) primers.

extract_protocol: Three 5μm thick FFPE sections of clinical samples, parental cell line MB-MDA-231 cell line (fixed in paraformoldehyde and embedded in paraffin) and intracranial mouse tumours were cut and de-waxed in two lots of xylene and two lots of 100% ethanol, 10 minutes each. RNA was extracted using the High Pure RNA Paraffin Kit® (Roche Applied Science, Mannheim, Germany) according to the manufacturer’s protocol. RNA was quantified using the NanoDrop® ND-1000 (NanoDrop Technologies, DE, USA).

tag: brain metastases from lung cancer


title: brain met, set2: 4218357035_F1.

source_name: brain metastasis from breast cancer

tag: brain metastasis from breast cancer


title: AHYPDUF13

description: Adenohypophysis, Duroc, female

source_name: Adenohypophysis, Duroc, female


title: brain met, set2: 421835021_D2

source_name: primary breast cancer

tag: primary breast cancer


title: brain met, set2: 4218357021_E2

source_name: brain metastases from breast cancer

tag: brain metastases from breast cancer


title: brain met, set2: 4218357035_D1


title: brain met, set2: 4218357035_A2


title: brain met, set2: 4218357035_H1

source_name: brain metastasis from colonic cancer

tag: brain metastasis from colonic cancer


title: AHYPDUF14

description: Adenohypophysis, Duroc, female


title: brain met, set2: 4218357035_B2

source_name: brain meatstasis from lung cancer

tag: brain meatstasis fro lung cancer


title: brain met, set2: 4218357021_C2


title: AHYPDUM12

description: Adenohypophysis, Duroc, male


title: brain met, set2: 4218357021_B2


title: brain met, set2: 4218357019_E2


title: brain met, set2: 4218357019_C2

source_name: control mice - not treated

tag: MDA-MB-231 parental cell line


title: brain met, set2: 4218357035_G1


title: brain met, set2: 4218357019_B2


title: brain met, set2: 4218357017_H1


title: brain met, set2: 4218357021_C1

source_name: brain metastasis from renal cancer

tag: brain metastasis from renal cancer


title: brain met, set2: 4218357021_G1

source_name: brain metastasis from  breast cancer

tag: brain metastasis from  breast cancer


title: brain met, set2: 4218357017_F1


title: brain met, set2: 4218357017_G1

source_name: mice treated with trastuzumab on the day of injection


title: brain met, set2: 4218357017_E1

source_name: mice treated with anti-neuregulin on the day of brain injection


title: brain met, set2: 4218357017_C2

source_name: mice treated with trastuzumab at week 10 only


title: brain met, set2: 421835035_E1


title: brain met, set2: 4218357017_A2

source_name: mice treated trastuzumab, once a week for two weeks


title: brain met, set2: 4218357017_B2

source_name: mice treated with trastuzumab on the day of brain injection


title: brain met, set2: 421835035_A1


title: brain met, set2: 421835021_H2


title: brain met, set2: 421835035_B1

source_name: brain metastasis from melanoma

tag: brain metastasis from melanoma


title: brain met, set2: 421835035_C1


title: brain met, set2: 421835035_D2


title: brain met, set2: 4218357017_D1


title: brain met, set2: 421835021_F2


title: brain met, set2: 421835019_H2

source_name: brain metastasis from lung cancer

tag: brain metastasis from lung cancer


title: brain met, set2: 421835019_G2


title: brain met, set2: 421835021_A1


title: brain met, set2: 421835021_A2


title: brain met, set2: 421835021_H1

source_name: brain metastasis from prostate cancer

tag: brain metastasis from prostate cancer


title: brain met, set2: 421835021_G2


title: brain met, set2: 421835021_D1

source_name: brain metastasis from breast cancer


title: brain met, set2: 421835021_B1


title: brain met, set2: 421835021_E1


title: brain met, set2: 421835019_F2


title: tud progeny female 96 hr APF - replicate 2

city: Los Angeles

first: Matthew

middle: S

last: Lebo

state: CA

address: 1040 Child's Way

department: Molecular and Copmutational Biology

institute: University of Southern California

hyb_protocol: cDNA samples were then dried and resuspended in formamide (56%), sodium citrate buffer (SSC, 3.37×), SDS (1.12%), Denhardts (5.62×), and Polyadenylic acid potassium salt (0.9 mg/ml; Sigma-Aldrich, St. Louis, MO). Samples were boiled for 2 minutes and then applied to microarray slides underneath a LifterSlip (Erie Scientific, Portsmouth, PA). Microarrays were hybridized at 42◦C for 14-18 hours, then washed in a solution of 1.5% SDS and 1X SSC for 5 minutes, a solution of 0.20X SSC for 5 minutes, and two solutions of 0.05X SSC for 10 minutes each.

scan_protocol: All arrays were scanned using the GenePix 4100A scanner and GenePix Pro 5.0 software from Axon Instruments (Molecular Diagnostics, Sunnyvale, CA).

data_processing: Visual inspection of the microarray images filtered out florescence most likely not due to labeled cDNA binding; the data from these array elements was discarded. Array elements were only considered for further analysis if at least one channel (Cy3 or Cy5) had greater than 75% of the pixels with intensity values one standard deviation above background levels. All microarray normalization and statistical analyses were performed using the limma package of BioConductor in the program R.

organism: Drosophila melanogaster

source_name: tud progeny female 96 hr APF

label_protocol: cDNAs were directly labeled with Cy5 or Cy3 during the reverse transcription reaction; 30µg of total RNA was used as a starting template. The reverse transcription reaction was performed for two hours at 42◦C using the following reagents (values in parentheses are final molarity or final concentration): oligo dT primer (Operon, 3.75 μM), dithiothreitol (Invitrogen, 10 mM), First Strand Buffer (Invitrogen, 1×), dNTPs minus dTTP (Invitrogen, 0.5 mM), dTTP (Invitrogen, 50 μM), Cy-labeled dUTP (Perkin-Elmer, 0.625 nM), and Superscript II reverse transcriptase (Invitrogen, 10 U/μL). The reaction was stopped and RNA was hydrolyzed by a 20 minute incubation at 65◦C with NaOH (167 mM) and EDTA (83 mM). After neutralizing by adding HEPES buffer (pH8.0; 294 mM) and sodium acetate (pH5.2; 228 mM), cDNA samples were purified (Gel-Purification Kit, Qiagen, Valencia, CA).

extract_protocol: RNA was isolated from ~30 pupae by homogenization and extraction using the TRIzol® protocol (Invitrogen, Carlsbad, CA) and resuspended in 20µL diethylpyrocarbonate (DEPC)-treated H2O.

treatment_protocol: Female tud progeny were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 96 hours and then snap frozen in liquid nitrogen.

tag: Strain

value: tud Progeny

tag: Gender

value: Female

tag: Age

value: 96 hr APF

tag: Tissue

value: Whole Body

source_name: Reference

extract_protocol: RNA was isolated from the entire batch by homogenization and extraction using the TRIzol(R) protocol (Invitrogen, Carlsbad, CA) and 30 ug were resuspended in 20µL diethylpyrocarbonate (DEPC)-treated H2O.

treatment_protocol: Male and female flies of all pupal stages were collected and snap frozen in liquid nitrogen.

value: Canton S

value: Male and Female

value: All pupal stages


title: tud progeny female 96 hr APF - replicate 3


title: tud progeny female 72 hr APF - replicate 3

source_name: tud progeny female 72 hr APF

treatment_protocol: Female tud progeny were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 72 hours and then snap frozen in liquid nitrogen.

value: 72 hr APF


title: tud progeny female 72 hr APF - replicate 2


title: brain met, set1: 1596969007_G2

source_name: brain metastasis

tag: brain metastasis


title: brain met, set1: 1596969007_F1


title: brain met, set1: 1596969007_E1


title: tud progeny female 72 hr APF - replicate 1


title: tud progeny female 48 hr APF - replicate 3

source_name: tud progeny female 48 hr APF

treatment_protocol: Female tud progeny were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours and then snap frozen in liquid nitrogen.

value: 48 hr APF


title: brain met, set1: 1596969007_C1


title: tud progeny female 24 hr APF - replicate 2

source_name: tud progeny female 24 hr APF

treatment_protocol: Female tud progeny were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 24 hours and then snap frozen in liquid nitrogen.

value: 24 hr APF


title: tud progeny female 48 hr APF - replicate 2

value: 46 hr APF


title: tud progeny female 24 hr APF - replicate 1


title: brain met, set1: 1447331_R008_C011

source_name: primary breast cancer


title: tud progeny female 0 hr APF - replicate 3

source_name: tud progeny female 0 hr APF

treatment_protocol: Female tud progeny were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4 and immediately snap frozen in liquid nitrogen.

value: 0 hr APF


title: tud progeny female 48 hr APF - replicate 1


title: brain met, set1: 1447331_R007_C010


title: brain met, set1: 1447331_R007_C007


title: tud progeny female 0 hr APF - replicate 1


title: tud progeny male 96 hr APF - replicate 2

source_name: tud progeny male 96 hr APF

treatment_protocol: Male tud progeny were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 96 hours and then snap frozen in liquid nitrogen.

value: Male


title: tud progeny male 96 hr APF - replicate 3


title: tud progeny female 0 hr APF - replicate 2


title: brain met, set1: 1447331_R007_C002


title: tud progeny male 96 hr APF - replicate 1


title: tud progeny male 72 hr APF - replicate 3

source_name: tud progeny male 72 hr APF

treatment_protocol: Male tud progeny were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 72 hours and then snap frozen in liquid nitrogen.


title: tud progeny male 72 hr APF - replicate 1


title: tud progeny male 72 hr APF - replicate 2


title: brain met, set1: 1447331_R006_C011


title: brain met, set1: 1447331_R007_C001


title: tud progeny male 48 hr APF - replicate 3

source_name: tud progeny male 48 hr APF

treatment_protocol: Male tud progeny were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours and then snap frozen in liquid nitrogen.


title: tud progeny female 24 hr APF - replicate 3


title: brain met, set1: 1447331_R006_C010


title: brain met, set1: 1447331_R006_C008


title: tud progeny male 0 hr APF - replicate 3

source_name: tud progeny male 0 hr APF

treatment_protocol: Male tud progeny were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4 and immediately snap frozen in liquid nitrogen.


title: brain met, set1: 1447331_R006_C004


title: tud progeny male 48 hr APF - replicate 2


title: brain met, set1: 1447331_R007_C011


title: tud progeny male 24 hr APF - replicate 2

source_name: tud progeny male 24 hr APF

treatment_protocol: Male tud progeny were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 24 hours and then snap frozen in liquid nitrogen.


title: tud progeny male 24 hr APF - replicate 1


title: Wild type female 96 hr APF - replicate 2

source_name: Wild type female 96 hr APF

treatment_protocol: Female flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 96 hours and then snap frozen in liquid nitrogen.


title: tud progeny male 0 hr APF - replicate 2


title: tud progeny male 0 hr APF - replicate 1


title: tud progeny male 24 hr APF - replicate 3


title: brain met, set1: 1447331_R006_C002


title: brain met, set1: 1447331_R006_C003


title: Wild type female 96 hr APF - replicate 3


title: brain met, set1: 1447331_R006_C007


title: Wild type female 72 hr APF - replicate 2

source_name: Wild type female 72 hr APF

treatment_protocol: Female flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 72 hours and then snap frozen in liquid nitrogen.


title: Wild type female 96 hr APF - replicate 1


title: Wild type female 72 hr APF - replicate 3


title: Wild type female 72 hr APF - replicate 1


title: Wild type female 24 hr APF - replicate 3

source_name: Wild type female 24 hr APF

treatment_protocol: Female flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 24 hours and then snap frozen in liquid nitrogen.


title: Wild type female 48 hr APF - replicate 3

source_name: Wild type female 48 hr APF

treatment_protocol: Female flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours and then snap frozen in liquid nitrogen.


title: Wild type female 0 hr APF - replicate 3

source_name: Wild type female 0 hr APF

treatment_protocol: Female flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4 and immediately snap frozen in liquid nitrogen.


title: brain met, set1: 1447331_R006_C001


title: Wild type male 96 hr APF - replicate 3

source_name: Wild type male 96 hr APF

treatment_protocol: Male flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 96 hours and then snap frozen in liquid nitrogen.

source_name: Reference


title: Wild type female 48 hr APF - replicate 2


title: Wild type male 96 hr APF - replicate 1


title: brain met, set1: 1447331_R005-C001

source_name: brain metastasis


title: Wild type female 24 hr APF - replicate 1


title: Wild type female 0 hr APF - replicate 2


title: Wild type female 48 hr APF - replicate 1


title: Wild type female 24 hr APF - replicate 2


title: brain met, set1: 1447331_R005_C010


title: brain met, set1: 1447331_R005_C007


title: Wild type female 0 hr APF - replicate 1


title: Wild type male 48 hr APF - replicate 3

source_name: Wild type male 48 hr APF

treatment_protocol: Male flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours and then snap frozen in liquid nitrogen.


title: brain met, set1: 1447331_R005_C011


title: Wild type male 96 hr APF - replicate 2

treatment_protocol: Male and female flies of all pupal stages were collected and snap frozen in liquid nitrogen.


title: SKMEL28-901-timecourse-24HRS

city: New York

first: Christine

middle: Anne

last: Pratilas

state: NY

address: 1275 York Avenue

department: Molecular Pharmacology

institute: Memorial Sloan-Kettering Cancer Center

description: Gene expression data at 24hrs after MEK inhibition in V600E BRAF-mutant cells

hyb_protocol: 10ug of labeled and fragmented cRNA were hybridized onto a U133A 2.0 expression array (Affymetrix)

scan_protocol: Gene chips were scanned using a high-numerical aperture and flying objective (FOL) lens in the GS300 scanner (Affymetrix) and quantified using GeneChip Operating Software ver1.4 (GCOS, Affymetrix).

data_processing: Cell line and xenograft data were analyzed with the Affymetrix GeneChip Operating Software v1.4 using default settings, timecourse data were analyzed with RMA

source_name: SkMel-28, PD0325901-treated, 24hrs

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol from 2ug total RNA.

growth_protocol: Cell lines growing under standard culture conditions in the presence of 10% fetal bovine serum, were treated at 70-80% confluence; mice were treated once subcutaneous tumors reached an average volume of 150mm3

extract_protocol: Cells were harvested on ice eight hours after treatment. Mice were sacrificed and subcutaneous tumors were excised eight hours after treatment. Total cellular RNA was extracted using the Qiagen Rneasy mini kit.

treatment_protocol: Cells in culture were treated with 50nM PD0325901 or DMSO 0.1%. Mice were treated with a single oral dose of PD0325901 25mg/kg or vehicle alone.

tag: Genotype

value: BRAF mutant, V600E


title: Wild type male 48 hr APF - replicate 1


title: Wild type male 72 hr APF - replicate 2

source_name: Wild type male 72 hr APF

treatment_protocol: Male flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 72 hours and then snap frozen in liquid nitrogen.


title: Wild type male 24 hr APF - replicate 3

source_name: Wild type male 24 hr APF

treatment_protocol: Male flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 24 hours and then snap frozen in liquid nitrogen.


title: Wild type male 72 hr APF - replicate 3


title: brain met, set1: 1447331_R005_C006


title: SKMEL28-901-timecourse-8HRS

description: Gene expression data at 8hrs after MEK inhibition in V600E BRAF-mutant cells

source_name: SkMel-28, PD0325901-treated, 8hrs


title: brain met, set1: 1447331_R005_C004

source_name: primary breast cancer


title: Wild type male 48 hr APF - replicate 2


title: brain met, set1: 1447331_R005_C008


title: SKMEL28-901-timecourse-2HRS

description: Gene expression data at 2hrs after MEK inhibition in V600E BRAF-mutant cells

source_name: SkMel-28, PD0325901-treated, 2hrs


title: SKMEL28-901-timecourse-0HRS

description: Gene expression data at 0hrs in V600E BRAF-mutant cells

source_name: SkMel-28, untreated, 0hrs


title: brain met, set1: 1447331_R004_C011


title: M7-xeno-901

description: Gene expression data from V600E BRAF-mutant xenograft tumor treated with MEK inhibitor

source_name: SkMel-28 xenograft, PD0325901-treated


title: brain met, set1: 1447331_R004_C007


title: brain met, set1: 1447331_R005_C002


title: brain met, set1: 1447331_R004_C010


title: M10-xeno-901


title: brain met, set1: 1447331_R004_c005


title: brain met, set1: 1447331_R004_C006


title: Wild type male 0 hr APF - replicate 1

source_name: Wild type male 0 hr APF

treatment_protocol: Male flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4 and imediately snap frozen in liquid nitrogen.


title: Wild type male 24 hr APF - replicate 1


title: B7-xeno-901

description: Gene expression data from RTK-activated xenograft tumor treated with MEK inhibitor

source_name: BT474 xenograft, PD0325901-treated

value: HER2 amplification


title: Wild type male 0 hr APF - replicate 3


title: M5-xeno-vehicle

description: Gene expression data from V600E BRAF-mutant xenograft tumor treated with vehicle

source_name: SkMel-28 xenograft, vehicle-treated


title: M2-xeno-vehicle


title: brain met, set1: 1447331_R003-C003


title: XX dsx null 48 hr APF pupae - whole body - replicate 2

source_name: Female CS 48 hr APF pupae

treatment_protocol: XX dsx and female flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours and then snap frozen in liquid nitrogen.

source_name: XX dsx null intersexual 48 hr APF pupae

value: dsx D+R3 / dsx M+R15

value: XX intersexual


title: Wild type male 24 hr APF - replicate 2


title: brain met, set1: 1447331_R004_C004


title: brain met, set1: 1447331_R004_C003


title: Wild type male 0 hr APF - replicate 2


title: B4-xeno-vehicle

description: Gene expression data from RTK-activated xenograft tumor treated with vehicle

source_name: BT474 xenograft, vehicle-treated


title: B1-xeno-vehicle


title: XX dsx null 48 hr APF pupae - whole body - replicate 4


title: XX dsx null 48 hr APF pupae - whole body - replicate 3


title: brain met, set1: 1447331_R004_C001


title: B5-xeno-901


title: brain met, set1: 1447331_R003_C007


title: XY dsx null 48 hr APF pupae - whole body - replicate 3

source_name: XY dsx null intersexual 48 hr APF pupae

treatment_protocol: XY dsx and male flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours and then snap frozen in liquid nitrogen.

value: XY intersexual

source_name: Male CS 48 hr APF pupae


title: XX dsx null 48 hr APF pupae - whole body - replicate 1

value: Female


title: XY dsx null 48 hr APF pupae - whole body - replicate 2


title: brain met, set1: 1447331_R003_C010

source_name: brain metastasis


title: XY dsx null 48 hr APF pupae - whole body - replicate 4


title: Wild type male 72 hr APF - replicate 1

source_name: Reference


title: brain met, set1: 1447331_R003_C008


title: SKMEL28-901

description: Gene expression data from V600E BRAF-mutant cell line upon treatment with MEK inhibitor

source_name: SkMel-28 cell line, PD0325901-treated, 8hrs


title: brain met, set1: 1447331_R003_C005


title: SKMEL28-DMSO

description: Gene expression data from V600E BRAF-mutant cell line upon treatment with DMSO

source_name: SkMel-28 cell line, DMSO-treated, 8hrs


title: brain met, set1: 1447331_R003_C004


title: brain met, set1: 1447331_R003_C006


title: SKMEL5-DMSO

source_name: SkMel-5 cell line, DMSO-treated, 8hrs


title: brain met, set1: 1447331_R002_C011


title: XY dsx null 48 hr APF pupae - whole body - replicate 1


title: SKMEL19-901

source_name: SkMel-19 cell line, PD0325901-treated, 8hrs


title: SKMEL1-DMSO

source_name: SkMel-1 cell line, DMSO-treated, 8hrs


title: SKMEL19-DMSO

source_name: SkMel-19 cell line, DMSO-treated, 8hrs


title: SKMEL5-901

source_name: SkMel-5 cell line, PD0325901-treated, 8hrs


title: tra 48 hr APF pupae - whole body - replicate 2

treatment_protocol: XX tra and female flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours and then snap frozen in liquid nitrogen.

source_name: XX tra pseudomale 48 hr APF pupae

value: tra/Df

value: XX Pseudomale


title: brain met, set1: 1447331_R003_C002


title: dsxD 48 hr APF pupae - whole body - replicate 4

hyb_protocol: cDNA samples were then dried and resuspended in formamide (56%), sodium citrate buffer (SSC, 3.37×), SDS (1.12%), Denhardts (5.62×), and Polyadenylic acid potassium salt (0.9 mg/ml; Sigma-Aldrich, St. Louis, MO).  Samples were boiled for 2 minutes and then applied to microarray slides underneath a LifterSlip (Erie Scientific, Portsmouth, PA).  Microarrays were hybridized at 42◦C for 14-18 hours, then washed in a solution of 1.5% SDS and 1X SSC for 5 minutes, a solution of 0.20X SSC for 5 minutes, and two solutions of 0.05X SSC for 10 minutes each.

data_processing: Visual inspection of the microarray images filtered out florescence most likely not due to labeled cDNA binding; the data from these array elements was discarded.  Array elements were only considered for further analysis if at least one channel (Cy3 or Cy5) had greater than 75% of the pixels with intensity values one standard deviation above background levels.  All microarray normalization and statistical analyses were performed using the limma package of BioConductor in the program R.

source_name: XX dsxD pseudomale 48 hr APF pupae

label_protocol: cDNAs were directly labeled with Cy5 or Cy3 during the reverse transcription reaction; 30µg of total RNA was used as a starting template.  The reverse transcription reaction was performed for two hours at 42◦C using the following reagents (values in parentheses are final molarity or final concentration): oligo dT primer (Operon, 3.75 μM), dithiothreitol (Invitrogen, 10 mM), First Strand Buffer (Invitrogen, 1×), dNTPs minus dTTP (Invitrogen, 0.5 mM), dTTP (Invitrogen, 50 μM), Cy-labeled dUTP (Perkin-Elmer, 0.625 nM), and Superscript II reverse transcriptase (Invitrogen, 10 U/μL).  The reaction was stopped and RNA was hydrolyzed by a 20 minute incubation at 65◦C with NaOH (167 mM) and EDTA (83 mM).  After neutralizing by adding HEPES buffer (pH8.0; 294 mM) and sodium acetate (pH5.2; 228 mM), cDNA samples were purified (Gel-Purification Kit, Qiagen, Valencia, CA).

treatment_protocol: XX dsxD and female flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours and then snap frozen in liquid nitrogen.

value: dsxD / dsx M+R15

value: Whole Body

value: Canton S


title: brain met, set1: 1447331_R003_C001


title: brain met, set1: 1447331_R002_C008


title: brain met, set1: 1447331_R002_C007


title: SKMEL1-901

source_name: SkMel-1 cell line, PD0325901-treated, 8hrs


title: dsxD 48 hr APF pupae - whole body - replicate 1

source_name: Female CS 48 hr APF pupae


title: dsxD 48 hr APF pupae - whole body - replicate 2


title: brain met, set1: 1447331_R002_C006


title: HT29-DMSO

source_name: HT29 cell line, DMSO-treated, 8hrs


title: tra 48 hr APF pupae - whole body - replicate 3


title: tra 48 hr APF pupae - whole body - replicate 1


title: brain met, set1: 1447331_R002_C010


title: brain met, set1: 1447331_R002_C003


title: HT29-901

source_name: HT29 cell line, PD0325901-treated, 8hrs


title: MALME3M-901

source_name: Malme-3M cell line, PD0325901-treated, 8hrs


title: MALME3M-DMSO

source_name: Malme-3M cell line, DMSO-treated, 8hrs


title: tudor progeny 48 hr APF pupae - whole body - replicate 4

source_name: Male tudor progeny 48 hr APF pupae

treatment_protocol: Male and female flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours and then snap frozen in liquid nitrogen.

value: tudor progeny

source_name: Female tudor progeny 48 hr APF pupae


title: COLO205-901

source_name: Colo-205 cell line, PD0325901-treated, 8hrs


title: brain met, set1: 1447331_R002_C004

source_name: brain metastasis


title: brain met, set1: 1447331_R001_C011


title: tudor progeny 48 hr APF pupae - whole body - replicate 3

value: 48 hr APF


title: tudor progeny 48 hr APF pupae - whole body - replicate 2

value: whole body


title: brain met, set1: 1447331_R003_C011

source_name: primary breast cancer


title: SKBR3-901

description: Gene expression data from RTK-activated cell line upon treatment with MEK inhibitor

source_name: SkBr3 cell line, PD0325901-treated, 8hrs


title: brain met, set1: 1447331_R001_C007


title: Berlin 48 hr APF pupae - whole body - replicate 4

source_name: Male Berlin 48 hr APF pupae

value: Berlin

source_name: Female Berlin 48 hr APF pupae


title: brain met, set1: 1447331_R001_C006


title: brain met, set1: 1447331_R001_C010


title: Berlin 48 hr APF pupae - whole body - replicate 3


title: brain met, set1: 1447331_R001_C005


title: tudor progeny 48 hr APF pupae - whole body - replicate 1


title: A431-DMSO

description: Gene expression data from RTK-activated cell line upon treatment with DMSO

source_name: A431 cell line, DMSO-treated, 8hrs

value: EGFR amplification


title: A431-901

source_name: A431 cell line, PD0325901-treated, 8hrs


title: Canton S 48 hr APF pupae - whole body - replicate 4

source_name: Male CS 48 hr APF pupae

value: Canton-S

value: Male


title: brain met, set1: 1447331_R001_C003


title: brain met, set1: 1447331_R001_C004


title: BT474-DMSO

source_name: BT474 cell line, DMSO-treated, 8hrs

value: HER2 amplification


title: Berlin 48 hr APF pupae - whole body - replicate 1


title: Berlin 48 hr APF pupae - whole body - replicate 2


title: BT474-901

source_name: BT474 cell line, PD0325901-treated, 8hrs


title: Canton S 48 hr APF pupae - whole body - replicate 3

source_name: Female CS 48 hr APF pupae


title: brain met, set1: 1447331_R001_C002


title: Canton S 48 hr APF pupae - whole body - replicate 2

value: Whole body


title: Canton S 48 hr APF pupae - whole body - replicate 1


title: H1650-901

source_name: NCI-H1650 cell line, PD0325901-treated, 8hrs

value: EGFR mutant, del E746-A750


title: SKBR3-DMSO

source_name: SkBr3 cell line, DMSO-treated, 8hrs


title: MDA468-901

source_name: MDA-468 cell line, PD0325901-treated, 8hrs


title: H1650-DMSO

source_name: NCI-H1650 cell line, DMSO-treated, 8hrs


title: dsxD 48 hr APF pupae - whole body - replicate 3

source_name: XX dsxD pseudomale 48 hr APF pupae


title: MDA468-DMSO

source_name: MDA-468 cell line, DMSO-treated, 8hrs


title: Normal NO029

status: Public on Feb 10 2009

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression data from human normal kidney tissue and human kidney tumor tissues.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with custom CDF environments created by the MBNI - The version 6 entrez gene ID CDF was used.

label: R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml  ( we use 6 ul per reaction )

source_name: Homo Sapiens

label_protocol: 10 ug of Qiagen-purified total RNA

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

tag: disease state

value: Normal

tag: tissue

value: kidney


title: Normal NO045


title: COLO205-DMSO

source_name: Colo-205 cell line, DMSO-treated, 8hrs

value: BRAF mutant, V600E


title: tra 48 hr APF pupae - whole body - replicate 4

source_name: XX tra pseudomale 48 hr APF pupae

value: tra/Df

value: XX Pseudomale

value: Female


title: Normal NO012


title: Normal NO009


title: Normal NO006


title: Normal NO005


title: brain met, set1: 1447331_R002_C002

source_name: brain metastasis


title: Normal NO096


title: Normal NO076


title: Normal NO041


title: H3 K27me3 ChIP in HSF6 cells

type: genomic

first: Wei

last: Xie

address: 611 Young Dr. East, Boyer Hall Rm 332, UCLA

institute: UCLA

description: H3 K27me3 IP vs. input

hyb_protocol: Hybridization was done according to manufacturer's protocol.

scan_protocol: Scanning was done according to manufacturer's protocol.

data_processing:
Data was processed first using Agilent Feature Extraction, and then using Agilent ChIP-Analytics software v1.3, which produced one file that combined the hybridization data from Agilent Human Promoter ChIP-on-Chip Set 244K Microarrays 1 and 2. Data was not used directly from Feature Extraction.
The IP and Input channels were normalized after both inter- and intra- array normalization according to manufacturer's instructions.

molecule: genomic DNA

source_name: H3 K27me3 IP, HSF6 cells

label_protocol: Labeling was performed according to manufacturer's protocol.

extract_protocol: Chromatin was isolated using standard procedures and an immunoprecipitation was performed using an antibody against H3 K27me3. DNA was then extracted using standard protocols.

tag: cell line

value: cultured human embryonic stem cell line HSF6

source_name: H3 K27me3 Input, HSF6 cells

extract_protocol: Genomic DNA was isolated using standard procedures without immunoprecipitations.


title: Clear cell renal carcinoma CC124

value: clear cell renal cell carcinoma

value: kidney tumor


title: Normal NO052


title: Normal NO050


title: Normal NO027


title: Light smoker 2, biological rep2

status: Public on Aug 28 2009

city: Washington

first: Jinguo

last: Chen

state: DC

address: 3800 Reservoir Road NW

department: Cancer Genetics and Epidemiology

institute: Georgetown University Lombardi Cancer Center

description: Gene expression data from light smoker

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent Scanner 3000.

data_processing: The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.

source_name: Human PBMC from smokers who smoked 7 cig/last 24h, 12.25 pack-years

growth_protocol: no culture in vitro

extract_protocol: Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.

treatment_protocol: Subjects were recruited through local print advertising, and screened for eligibility.  Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts).  Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.

tag: age

tag: gender

tag: race

value: white


title: Clear cell renal carcinoma CC123


title: H3 K56Ac ChIP in ARPE cells

description: H3 K56Ac IP vs. input

source_name: H3 K56Ac IP, ARPE cells

extract_protocol: Chromatin was isolated using standard procedures and an immunoprecipitation was performed using an antibody against H3 K56Ac. DNA was then extracted using standard protocols.

value: cultured somatic cell line ARPE

source_name: H3 K56Ac Input, ARPE cells


title: H3 K56Ac ChIP in HSF6 cells

description: H3 K56Ac IP vs. input

source_name: H3 K56Ac IP, HSF6 cells

source_name: H3 K56Ac Input, HSF6 cells


title: Clear cell renal carcinoma CC081


title: H3 K56Ac ChIP in BJ cells

description: H3 K56Ac IP vs. input

source_name: H3 K56Ac IP, BJ cells

value: cultured somatic cell line BJ

source_name: H3 K56Ac Input, BJ cells


title: Clear cell renal carcinoma CC059


title: Clear cell renal carcinoma CC010


title: H3 K27me3 ChIP in ARPE cells

description: H3 K27me3 IP vs. input

source_name: H3 K27me3 IP, ARPE cells

source_name: H3 K27me3 Input, ARPE cells


title: Clear cell renal carcinoma CC048


title: Clear cell renal carcinoma CC015


title: Clear cell renal carcinoma CC033


title: Clear cell renal carcinoma CC011


title: 16h anti-CD40 siRNA versus control replicate 2 dye swap

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

description: 16h time point, biological replicate 2 of 2. Technical replicate 2 of 2, with dye reversal. HUVEC cells treated with anti-CD40 siRNA activated by D1.1 T lymphocytes overexpressing the CD40L (CD40 ligand) compared to same transfected with control siRNA.

hyb_protocol: Two biological replicate experiments were performed, each comparing msiRNA-2-transfected with siRNA-2-transfected HUVEC. Each experimental pair of labelled samples was co-hybridized on two separate microarrays with dye swapping to correct for dye bias effects. Thus, up to four microarray hybridizations were processed for each of three EC-D1.1 Jurkat cell co-incubation time points, totalling 12 array datasets.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization using 0.3 as the span parameter with reduced weights in control and poor quality spots, followed by scaling across chips. An Empirical Bayes B statistic was computed taking into account dye swapping and the probes were ranked according to B value, although given the small number of replicates it was only taken as a ranking measure. Differentially expressed genes were chosen, unless otherwise stated, using as cut off criteria a Bayesian atatistic (B rank) percentile above 95% and absolute fold change (|FC|) above 1.2 in at least one of the time points. Moreover, we applied the following quality filter: GenePix flag status found in 6 of the 12 hybridizations and normalized background subtracted intensity in at least one of the two channels above 250 in at least 2 of the 4 hybridizations for each time point.

source_name: human umbilical vein endothelial cells (HUVEC)

label_protocol: 500 ng of total RNA were reverse transcribed, amplified, labelled by in vitro transcription using the Low Input Linear Amplification Kit (Agilent 5184-3523), and hybridized following the manufacturer’s instructions (SSC wash Agilent 60-mer oligo microarray processing protocol, Version 4.1, April 2004).

growth_protocol: HUVEC were maintained in endothelial growth medium EGM-Bullet kit (Clonetics-Cambrex, Walkersville, MD) at 37ºC in a 5% CO2 atmosphere. siRNA-transfected HUVEC were stimulated by co-incubation with Jurkat D1.1 (CD154+) cells (American Type Culture Collection (ATCC), Manassas, VA) (CRL-10915) (1:10 ratio) at 4, 10 or 16 h prior to analysis. At 48 h post-transfection, the co-cultures were extensively washed with warm PBS to release the attached Jurkat D1.1 cells from the HUVEC monolayer. Residual Jurkat D1.1 contamination of HUVEC monolayers was estimated to be less than 0.5% by flow cytometry (data not shown).

extract_protocol: Total RNA  from treated HUVEC were extracted using the RNeasy RNA Isolation kit (Qiagen) and incubated with RNase-free DNase I (Ambion, Austin, TX) following manufacturer's instructions. RNA quantification was performed through a Nanodrop spectrophotometer, and their quality was assessed using the Bioanalyzer 2100 nanoelectrophoresis Lab-on-a–chip system (Agilent, Wilmington, DE). All RNAs used had RIN (RNA integrity number) ranging between 9.3 and 10, and 28S/18S ratios between 1.67 and 2.07.

treatment_protocol: The siRNA duplex targeting human CD40 (siRNA-2) and its corresponding mismatched siRNA control (msiRNA-2) were chemically synthesized (Qiagen, Hilden, Germany). Specific sequences and characterization of their silencing effect in HUVEC have already been described [PMID: 15315968]. Incorporation of the siRNAs into exponentially growing HUVEC (passage 3-4) was achieved by electroporation using an ECM 830 Electropulse Generator System (BTX, San Diego, CA). Briefly, 400 µl of cell suspension containing 2x10E6 cells and 100 nM of siRNA in siPORT siRNA Electroporation Buffer (Ambion, Austin, TX), a low-conductivity electroporation pulse medium, were transferred into a 4-mm electroporation cuvette (BTX), incubated 10 min at 4 ºC, and pulsed for 70 msec at 160V. The electroporation parameters were previously optimized using a FITC-labeled siRNA, reaching 80-90% transfection efficiencies. After electroporation, ECs were recovered in the cuvette for 10 min at room temperature (RT) and transferred into a culture dish with 10 ml of pre-warmed complete growth medium.

tag: HUVEC transfected with anti-CD40 siRNA-2 for 48 hours, activated by co-culture with Jurkat D1.1 T cells (CD40L+) during the last 16 hours

tag: HUVEC transfected with control msiRNA-2 for 48 hours, activated by co-culture with Jurkat D1.1 T cells (CD40L+) during the last 16 hours


title: 16h anti-CD40 siRNA versus control replicate 1

description: 16h time point, biological replicate 1 of 2. Technical replicate 1 of 2. HUVEC cells treated with anti-CD40 siRNA activated by D1.1 T lymphocytes overexpressing the CD40L (CD40 ligand) compared to same transfected with control siRNA.


title: H3 K9Ac ChIP in BJ cells

description: H3 K9Ac IP vs. input

source_name: H3 K9Ac IP, BJ cells

extract_protocol: Chromatin was isolated using standard procedures and an immunoprecipitation was performed using an antibody against H3 K9Ac. DNA was then extracted using standard protocols.

source_name: H3 K9Ac Input, BJ cells


title: 10h anti-CD40 siRNA versus control replicate 2 dye swap

description: 10h time point, biological replicate 2 of 2. Technical replicate 2 of 2, with dye reversal. HUVEC cells treated with anti-CD40 siRNA activated by D1.1 T lymphocytes overexpressing the CD40L (CD40 ligand) compared to same transfected with control siRNA.

tag: HUVEC transfected with anti-CD40 siRNA-2 for 48 hours, activated by co-culture with Jurkat D1.1 T cells (CD40L+) during the last 10 hours

tag: HUVEC transfected with control msiRNA-2 for 48 hours, activated by co-culture with Jurkat D1.1 T cells (CD40L+) during the last 10 hours


title: 16h anti-CD40 siRNA versus control replicate 1 dye swap

description: 16h time point, biological replicate 1 of 2. Technical replicate 2 of 2, with dye reversal. HUVEC cells treated with anti-CD40 siRNA activated by D1.1 T lymphocytes overexpressing the CD40L (CD40 ligand) compared to same transfected with control siRNA.


title: H3 K4me3 ChIP in ARPE cells

description: H3 K4me3 IP vs. input

source_name: H3 K4me3 IP, ARPE cells

extract_protocol: Chromatin was isolated using standard procedures and an immunoprecipitation was performed using an antibody against H3 K4me3. DNA was then extracted using standard protocols.

source_name: H3 K4me3 Input, ARPE cells


title: H3 K9Ac ChIP in HSF6 cells

description: H3 K9Ac IP vs. input

source_name: H3 K9Ac IP, HSF6 cells

source_name: H3 K9Ac Input, HSF6 cells


title: H3 K4me3 ChIP in HSF6 cells

description: H3 K4me3 IP vs. input

source_name: H3 K4me3 IP, HSF6 cells

source_name: H3 K4me3 Input, HSF6 cells


title: H3 K4me3 ChIP in BJ cells

description: H3 K4me3 IP vs. input

source_name: H3 K4me3 IP, BJ cells

source_name: H3 K4me3 Input, BJ cells


title: H3 K27me3 ChIP in BJ cells

description: H3 K27me3 IP vs. input

source_name: H3 K27me3 IP, BJ cells

source_name: H3 K27me3 Input, BJ cells


title: H3 K4me3 ChIP in HSF1 cells

description: H3 K4me3 IP vs. input

source_name: H3 K4me3 IP, HSF1 cells

value: cultured human embryonic stem cell line HSF1

source_name: H3 K4me3 Input, HSF1 cells


title: H3 K56Ac ChIP in HSF1 cells

description: H3 K56Ac IP vs. input

source_name: H3 K56Ac IP, HSF1 cells

source_name: H3 K56Ac Input, HSF1 cells


title: 10h anti-CD40 siRNA versus control replicate 1

description: 10h time point, biological replicate 1 of 2. Technical replicate 1 of 2. HUVEC cells treated with anti-CD40 siRNA activated by D1.1 T lymphocytes overexpressing the CD40L (CD40 ligand) compared to same transfected with control siRNA.

source_name: human umbilical vein endothelial cells (HUVEC)


title: H3 K9Ac ChIP in HSF1 cells

description: H3 K9Ac IP vs. input

source_name: H3 K9Ac IP, HSF1 cells

source_name: H3 K9Ac Input, HSF1 cells


title: 4h anti-CD40 siRNA versus control replicate 2 dye swap

description: 4h time point, biological replicate 2 of 2. Technical replicate 2 of 2, with dye reversal. HUVEC cells treated with anti-CD40 siRNA activated by D1.1 T lymphocytes overexpressing the CD40L (CD40 ligand) compared to same transfected with control siRNA.

tag: HUVEC transfected with anti-CD40 siRNA-2 for 48 hours, activated by co-culture with Jurkat D1.1 T cells (CD40L+) during the last 4 hours

tag: HUVEC transfected with control msiRNA-2 for 48 hours, activated by co-culture with Jurkat D1.1 T cells (CD40L+) during the last 4 hours


title: 10h anti-CD40 siRNA versus control replicate 1 dye swap

description: 10h time point, biological replicate 1 of 2. Technical replicate 2 of 2, with dye reversal. HUVEC cells treated with anti-CD40 siRNA activated by D1.1 T lymphocytes overexpressing the CD40L (CD40 ligand) compared to same transfected with control siRNA.


title: 4h anti-CD40 siRNA versus control replicate 2

description: 4h time point, biological replicate 2 of 2. Technical replicate 1 of 2. HUVEC cells treated with anti-CD40 siRNA activated by D1.1 T lymphocytes overexpressing the CD40L (CD40 ligand) compared to same transfected with control siRNA.


title: 4h anti-CD40 siRNA versus control replicate 1 dye swap

description: 4h time point, biological replicate 1 of 2. Technical replicate 2 of 2, with dye reversal. HUVEC cells treated with anti-CD40 siRNA activated by D1.1 T lymphocytes overexpressing the CD40L (CD40 ligand) compared to same transfected with control siRNA.


title: Glucose-limited chemostat in absence of PAA strain DS17690 -2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

hyb_protocol: Probe preparation and Target hybridization Double stranded cDNA synthesis was carried out using 10 ug of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labeling using the GeneChip® IVT labeling Kit (Affymetrix). Finally, labeled cRNA was purified (GeneChip® Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridized to the P. chrysogenum MicroArrays (a proprietary GeneChip®, DSM_PENa520255F) at 45 °C for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.

data_processing: Data analysis Acquisition and quantification of array images were performed using Affymetrix GeneChip® Operating Software (GCOS version 1.2). CHP file targeted at 100.

label: SAPE (Streptavidin Phycoerythrin)

organism: Penicillium chrysogenum

source_name: Chemostat culture

growth_protocol:
Chemostat cultivation Aerobic glucose-limited chemostat cultivation was performed at 25 °C in 3 - L turbine stirred bioreactors (Applikon, Schiedam, The Netherlands) with a working volume of 1.8 L. The pH was maintained at 6.5 via automated addition of 2 M NaOH (ADI 1030 biocontroller, Applikon, Schiedam, The Netherlands). The fermenter was sparged with air at a flow rate of 0.9 L•min-1 using a Brooks mass-flow controller (Brooks Instruments, Hatfield, USA) and stirred at 750 rpm. The dissolved-oxygen concentration was continuously monitored with an oxygen electrode (Applisens, Schiedam, The Netherlands). Continuous cultivation was initiated after 50-60 hours of batch cultivation. The feed medium was supplied continuously by a peristaltic pump (Masterflex, Cole Parmer, USA) and the dilution rate was set at 0.03 h-1 for all chemostat experiments. Effluent was removed discontinuously by means of a special overflow device, which has been described previously (Harris, D.M., et al. Enzymic analysis of NADPH metabolism in Penicillium chrysogenum: presence of a mitochondrial NADPH dehydrogenase in beta-lactam-producing cultures. Metab. Eng. 8, 91-101 (2006)). The time interval between effluent removals was fixed in such a way that each time approximately 1 % of the culture volume was removed. To prevent excessive foaming, silicone antifoam (10 % vol/vol, BDH) was discontinuously added at timed intervals.
Media The mineral medium was set at pH 5.5 with KOH pellets and contained per liter of demineralised water 7.5 g glucose, 3.5 g (NH4)2SO4, 0.8 g KH2PO4, 0.5 g MgSO4•7H2O, 10 mL of a trace element solution. The trace element solution contained 15 g•L-1 Na2EDTA•2H2O, 0.5 g•L-1 Cu2SO4•5H2O, 2 g•L-1 ZnSO4•7H2O, 2 g•L-1 MnSO4•H2O, 4 g•L-1 FeSO4•7H2O, and 0.5 g•L-1 CaCl2•2H2O and was set at pH 6.0 by adding NaOH pellets. Glucose was heat-sterilized separately (110 °C) and added to the medium in a concentration of 7.5 g•L-1. After filter sterilization and during the chemostat experiments the medium vessel was mixed continuously by a magnetic stirrer.

extract_protocol: Sampling and RNA extraction procedures 60 mL of culture broth was sampled and rapidly filtered over a glass fiber filter (Type A/E, Pall Life Sciences, East Hills, USA). The filter with mycelium was wrapped in aluminum foil, quenched in liquid nitrogen and subsequently stored at -80 °C until further use. For total RNA extraction half of the pellet was grounded by mortar and pestle under constant cooling with liquid nitrogen. The powder was dissolved in 5 mL of Trizol reagent (Invitrogen) and 1 mL chloroform (Sigma) and mixed well. The two phases were separated by centrifugation (4600 g, 15 minutes). Total RNA was isolated using a phenol-chloroform extraction method, which consisted of two extraction steps in acid-phenol/chloroform/isoamyl alcohol (5:1, pH 4.8, Ambion), followed by a chloroform extraction step. Each time the phases were separated by centrifugation (4600 g, 15 minutes). Total RNA was precipitated for 30 minutes at -20°C in 96% ethanol and 0.3 M sodium acetate. The RNA was collected by centrifugation at 23000 g for 15 minutes and dissolved in RNAse free H2O.

treatment_protocol: Liquid nitrogen quenching

tag: Penicillium chrysogenum DS17690 Penicillin G high producing prototrophic strain (Harris, D.M., et al. Enzymic analysis of NADPH metabolism in Penicillium chrysogenum

value: presence of a mitochondrial NADPH dehydrogenase in beta-lactam-producing cultures. Metab. Eng. 8, 91-101 (2006). DS17690 is derived from the strain improvement program of DSM after several classical mutagenesis rounds and is an offspring of the sequenced Wisconsin 54-1255 strain.


title: H3 K9Ac ChIP in ARPE cells

description: H3 K9Ac IP vs. input

source_name: H3 K9Ac IP, ARPE cells

source_name: H3 K9Ac Input, ARPE cells


title: Glucose-limited chemostat in presence of PAA strain DS50661 -3

hyb_protocol: Probe preparation and Target hybridization Double stranded cDNA synthesis was carried out using 10 ug of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labeling using the GeneChip® IVT labeling Kit (Affymetrix). Finally, labeled cRNA was purified (GeneChip® Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridized to the P. chrysogenum  MicroArrays (a proprietary GeneChip®, DSM_PENa520255F) at 45 °C for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.

growth_protocol:
Chemostat cultivation Aerobic glucose-limited chemostat cultivation was performed at 25 °C in 3 - L turbine stirred bioreactors (Applikon, Schiedam, The Netherlands) with a working volume of 1.8 L. The pH was maintained at 6.5 via automated addition of 2 M NaOH (ADI 1030 biocontroller, Applikon, Schiedam, The Netherlands). The fermenter was sparged with air at a flow rate of 0.9 L•min-1 using a Brooks mass-flow controller (Brooks Instruments, Hatfield, USA) and stirred at 750 rpm. The dissolved-oxygen concentration was continuously monitored with an oxygen electrode (Applisens, Schiedam, The Netherlands). Continuous cultivation was initiated after 50-60 hours of batch cultivation. The feed medium was supplied continuously by a peristaltic pump (Masterflex, Cole Parmer, USA) and the dilution rate was set at 0.03 h-1 for all chemostat experiments. Effluent was removed discontinuously by means of a special overflow device, which has been described previously (Harris, D.M., et al. Enzymic analysis of NADPH metabolism in Penicillium chrysogenum: presence of a mitochondrial NADPH dehydrogenase in beta-lactam-producing cultures. Metab. Eng. 8, 91-101 (2006)). The time interval between effluent removals was fixed in such a way that each time approximately 1 % of the culture volume was removed. To prevent excessive foaming, silicone antifoam (10 % vol/vol, BDH) was discontinuously added at timed intervals.
Media The mineral medium was set at pH 5.5 with KOH pellets and contained per liter of demineralised water 7.5 g glucose, 3.5 g (NH4)2SO4, 0.8 g KH2PO4, 0.5 g MgSO4•7H2O, 10 mL of a trace element solution. The trace element solution contained 15 g•L-1 Na2EDTA•2H2O, 0.5 g•L-1 Cu2SO4•5H2O, 2 g•L-1 ZnSO4•7H2O, 2 g•L-1 MnSO4•H2O, 4 g•L-1 FeSO4•7H2O, and 0.5 g•L-1 CaCl2•2H2O and was set at pH 6.0 by adding NaOH pellets. Production of penicillinG was induced by adding 0.58 g•L-1 phenylacetic acid (PAA) to the medium. The appropriate amount of PAA was dissolved in demineralised water. After the pH was set to 5.5 with KOH pellets, the PAA solution was autoclaved for 40 min at 121 °C. All other components were dissolved in demineralised water and added to the PAA solution in the medium vessel via filter sterilization with a sterile 0.2 µm capsule filter (Supor®DCF™; Pall Corporation, East Hills, USA). Glucose was heat-sterilized separately (110 °C) and added to the medium in a concentration of 7.5 g•L-1. After filter sterilization and during the chemostat experiments the medium vessel was mixed continuously by a magnetic stirrer.

tag: Penicillium chrysogenum DS50661 lacks the penicillin biosynthesis cluster and was constructed from DS17690

tag: To enable studies on the genome-wide impact of penicillin-G biosynthesis in Penicillium chrysogenum, penicillin gene clusters (pcbAB-pcbC-penDE) were removed from the penicillin-G high-producing strain P. chrysogenum DS17690. Since the beta-lactam gene amplifications are in direct repeats of a larger amplified region on the same chromosome spontaneous recombinations between different repeats can result in loss of gene cluster copies. Spontaneous recombinations were induced via protoplast formation and subsequent sporulation of regenerating colonies 27 random isolates were selected for Southern analysis to estimate the relative gene copy numbers of the penicillin biosynthesis gene pcbC and the single-copy niaA gene. The same strains were tested for penicillin-V production in shake-flask cultures grown on mineral medium with the side-chain precursor phenoxyacetic acid. All strains with reduced pcbC:niaA ratio's also showed reduced penicillin-V titres. One selected st  rain was subjected to a second round of protoplast formation and screening. Again, 27 random isolates were selected and analysed. Several putative single-copy penicillin gene cluster candidates (indicated by arrows in Figure 1, panel B) were identified based on a similar pcbC:niaA ratio to that of the single-copy Wisconsin54-1255 strain [8,27,55,78]. Three of these strains were tested in for penicillin-V production, with the parental P. chrysogenum DS17690 parent, the intermediate parent DS47274, the laboratory strain Wisconsin54-1255 and a non-producing isolate of the latter strain, npe10, as controls. All three isolates showed a drastically reduced penicillin-V titre, comparable to that of the single-copy strain Wisconsin54-1255. It was therefore assumed that these three isolates are derivatives of P. chrysogenum DS17690 that carry a single copy of the penicillin biosynthesis gene cluster. To delete the last remaining copy of the penicillin gene cluster, a double homologous recom  b  ination strategy was applied. Sequences adjacent to the beta-lactam biosynthetic gene cluster (3' from the pcbAB gene and 3' from the penDE gene) were used as homologous flanking sequences to target the amdS selection marker to this locus and to delete the entire 17 kb region containing the cluster of beta-lactam biosynthetic genes (pcbAB-pcbC-penDE) in the same integration event. Homologous integration by double crossover will generate transformants able to use acetamide as the sole carbon source (due to the presence of the amdS gene) but unable to produce any penicillins. Moreover, genomic DNA of strains that have undergone a successful double crossover should not hybridise to beta-lactam gene specific probes. Of 27,076 transformants tested, 22 (0.08%) gave no inhibition zone when overlaid with a penicillin sensitive E. coli strain and were selected for further analyses. All 22 putative mutants were negative in the diagnostic PCR for the beta-lactam biosyn  thetic gene penDE. Two of these strains gave no signal for amdS, suggesting that they had spontaneously lost marker gene. Southern analysis of the obtained P. chrysogenum strains was subsequently carried out. As a probe an internal DNA fragment of 300 nucleotides from the pcbAB sequence was amplified. All strains with intact penicillin-gene amplicon sequences (i.e. the industrial parent strain as well as the 1 amplicon copy strain) show an 8.1 kb DNA hybridising fragment. Putative beta-lactam cluster free DS17690 derivatives showed no hybridisation with the probe. To confirm their inability to biosynthesise beta-lactams all 22 mutants were inoculated in liquid mineral medium with phenylacetic acid as precursor. Indeed, none of the mutants was capable of producing penicillin-G . It was concluded that all 22 strains are derivatives of the P. chrysogenum DS17690 strain in which all copies of the penicillin gene cluster have been deleted. Isolate DS50661 was used as cluster-free strain in this study


title: Glucose-limited chemostat in presence of PAA strain DS50661 -1

scan_protocol: Probe preparation and Target hybridization Double stranded cDNA synthesis was carried out using 10 ug of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labeling using the GeneChip® IVT labeling Kit (Affymetrix). Finally, labeled cRNA was purified (GeneChip® Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridized to the P. chrysogenum  MicroArrays (a proprietary GeneChip®, DSM_PENa520255F) at 45 °C for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.


title: H3 K27me3 ChIP in HSF1 cells

description: H3 K27me3 IP vs. input

source_name: H3 K27me3 IP, HSF1 cells

source_name: H3 K27me3 Input, HSF1 cells


title: Glucose-limited chemostat in absence of PAA strain DS17690 -3

scan_protocol: Probe preparation and Target hybridization Double stranded cDNA synthesis was carried out using 10 ug of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labeling using the GeneChip® IVT labeling Kit (Affymetrix). Finally, labeled cRNA was purified (GeneChip® Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridized to the P. chrysogenum MicroArrays (a proprietary GeneChip®, DSM_PENa520255F) at 45 °C for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.


title: Glucose-limited chemostat in presence of PAA strain DS17690 -4

label_protocol: Probe preparation and Target hybridization Double stranded cDNA synthesis was carried out using 10 ug of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labeling using the GeneChip® IVT labeling Kit (Affymetrix). Finally, labeled cRNA was purified (GeneChip® Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridized to the P. chrysogenum  MicroArrays (a proprietary GeneChip®, DSM_PENa520255F) at 45 °C for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.


title: Glucose-limited chemostat in absence of PAA strain DS17690 -1


title: Glucose-limited chemostat in presence of PAA strain DS17690 -3


title: Glucose-limited chemostat in presence of PAA strain DS50661 -2


title: Glucose-limited chemostat in presence of PAA strain DS17690 -2


title: Glucose-limited chemostat in presence of PAA strain DS17690 -1


title: Sample 70: treated with frankincense oil for 3 hrs

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

hyb_protocol: cRNA was hybridized overnight on Illumina human Ref-8 version 3 BeadChips.  Microarray chips were washed to high stringency and labeled with streptavidin -Cy3 (Amersham Biosciences, Piscataway, NJ) prior to scanning on an Illumina BeadArray Reader.

scan_protocol: Microarrays were scanned on an Illumina BeadArray Reader.

data_processing: Initial intensity values were obtained using with Illumina Bead Studio software with background subtraction. For normalization, negative values were replaced with 1, and all values were quantile normalized using Matlab software.

source_name: Bladder transitional cell carcinoma J82 was obtained from ATCC (HTB-1; Manassas, VA)

label_protocol: 250 ng of RNA from a single cell culture from each time point was labeled using the Illumina Total Prep RNA Amplification Kit following manufacturer’s directions (Ambion, Austin. TX)

growth_protocol: J82 cells were maintained MEM medium supplemented with 10% FBS, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 2% MEM vitamin solution, and 100 units/ml penicillin-, and 100 µg/ml streptomycin.

extract_protocol: Total RNA was isolated at 3 hours following exposure to frankincense oil using RNeasy® Mini total RNA isolation kit based on manufacture’s procedures.

treatment_protocol: Cells untreated or Cells treated with 1/1000 dilution of frankincense oil (Young Living EWssential Oil, Lehi, Utah) for 1 hr prior to RNA extraction

tag: J86 cell line treated with frankincense oil for 3 hrs


title: Sample 69: treated with frankincense oil for 2 hrs

extract_protocol: Total RNA was isolated at 2 hours following exposure to frankincense oil using RNeasy® Mini total RNA isolation kit based on manufacture’s procedures.

tag: J86 cell line treated with frankincense oil for 2 hrs


title: Clear cell renal carcinoma CC076

source_name: Homo Sapiens

tag: disease state


title: Sample 67: treated with frankincense oil for 0.5 hr

scan_protocol: Microarrays were scanned on an Illumina BeadArray Reader

extract_protocol: Total RNA was isolated at 0.5 hours following exposure to frankincense oil using RNeasy® Mini total RNA isolation kit based on manufacture’s procedures.

treatment_protocol: Cells treated with 1/1000 dilution of frankincense oil (Young Living EWssential Oil, Lehi, Utah) for 0.5 hrs prior to RNA extraction

tag: J86 cell line treated with frankincense oil for 0.5 hr