title: Chinese Female, NA18552, slide 21

description: CNV discovery from NA18552 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: test


title: Korean Female, AK16, slide 14

status: Public on Jan 13 2010

type: genomic

city: Seoul

first: Dongwan

last: Hong

address: 28 Yeongeon-dong, Jongno-gu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Genomic Medicine Institute, Seoul National University College of Medicine

description: CNV discovery from AK16 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

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

scan_protocol: Scanned on an Agilent G2505 Scanner.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood cells, Korean female

label_protocol: 1.5ul of genomic DNA fragmented and amplified using random primer. Cy3-dCTP and Cy5-dCTP were incorporated using the BioPrime DNA labelling kit using the manufacturer’s protocol.

growth_protocol: Cell lines were cultured under 10% FBS+standard RPMI media. No antibacterials were used.

extract_protocol: Genomic DNA was extracted using the Gentra DNA extraction kit (Qiagen).

treatment_protocol: Not treated.

tag: population

value: Korean

tag: gender

value: female

tag: sample source

value: anonymous

tag: sample type

source_name: NA10851 reference

value: Caucasian

value: male

value: HapMap

value: reference


title: Japanese Female, NA18999, slide 21

description: CNV discovery from NA18999 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Immortalized cell line, Japanese female

value: Japanese


title: FFPE #1-50 ng rep2

type: RNA

city: San Diego

first: Craig

last: April

state: CA

address: 9885 Towne Centre Drive

country: USA

institute: Illumina, Inc.

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was analyzed using GenomeStudio v1.1

molecule: total RNA

source_name: Human ovarian tumor

label_protocol: Standard Illumina labelling protocol

extract_protocol: RNA was extracted with a modified protocol of the RNeasy FFPE Kit (Qiagen)

value: Female

tag: tissue

value: Ovary


title: FFPE #3-50 ng rep2

description: replicate 2


title: FFPE #4-50 ng rep1

description: replicate 1


title: FFPE #4-50 ng rep2

description: replicate 2


title: Chinese Female, NA19582, slide 21

description: CNV discovery from NA19582 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Immortalized cell line, Chinese female

value: Chinese


title: Korean Female, AK14, slide 14

description: CNV discovery from AK14 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK18, slide 14

description: CNV discovery from AK18 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK12, slide 14

description: CNV discovery from AK12 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: FFPE #3-50 ng rep1

description: replicate 1


title: FFPE #2-50 ng rep1

description: replicate 1


title: Korean Female, AK10, slide 14

description: CNV discovery from AK10 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: FFPE #1-50 ng rep1

description: replicate 1


title: Korean Female, AK8, slide 14

description: CNV discovery from AK8 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: FFPE #4-200 ng rep2

description: replicate 2


title: FFPE #3-200 ng rep2

description: replicate 2


title: Japanese Female, NA18969, slide 21

description: CNV discovery from NA18969 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK2, slide 14

description: CNV discovery from AK2 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18564, slide 21

description: CNV discovery from NA18564 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK6, slide 14

description: CNV discovery from AK6 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Male, AK1, slide 14

description: CNV discovery from AK1 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Blood cells, Korean male

value: control


title: Japanese Female, NA18997, slide 21

description: CNV discovery from NA18997 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18968, slide 21

description: CNV discovery from NA18968 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK4, slide 14

description: CNV discovery from AK4 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18951, slide 21

description: CNV discovery from NA18951 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18973, slide 21

description: CNV discovery from NA18973 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18537, slide 21

description: CNV discovery from NA18537 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: YRI Female, NA19240, slide 13

description: CNV discovery from NA19240 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Immortalized cell line, African Yoruban female

value: African Yoruban


title: Chinese Female, NA18552, slide 1

description: CNV discovery from NA18552 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: FFPE #1-200 ng rep2

description: replicate 2


title: FFPE #4-200 ng rep1

description: replicate 1


title: Chinese Female, NA18552, slide 13


title: Chinese Female, NA19582, slide 13

description: CNV discovery from NA19582 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: FFPE #2-200 ng rep2

description: replicate 2


title: FFPE #2-200 ng rep1

description: replicate 1


title: Chinese Female, NA18542, slide 21

description: CNV discovery from NA18542 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: FFPE #3-200 ng rep1

description: replicate 1


title: Japanese Female, NA18999, slide 13

description: CNV discovery from NA18999 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: FFPE #1 200 ng rep1

description: replicate 1


title: Japanese Female, NA18949, slide 21

description: CNV discovery from NA18949 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18526, slide 21

description: CNV discovery from NA18526 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18968, slide 13


title: Chinese Female, NA18566, slide 21

description: CNV discovery from NA18566 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: CEU Female, NA12878, slide 13

description: CNV discovery from NA12878 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Immortalized cell line, Caucasian female


title: Japanese Female, NA18942, slide 21

description: CNV discovery from NA18942 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: MCF-7 10 pg rep2

description: replicate 2

source_name: Breast Adenocarcinoma (MCF-7) Total RNA (Ambion Cat# AM7846)

extract_protocol: Ambion extraction protocol

tag: cell type

value: Breast Adenocarcinoma (MCF-7)

tag: input

value: 10 pg


title: MCF-7 10 pg rep1

description: replicate 1


title: MCF-7 50 pg rep2

description: replicate 2

value: 50 pg


title: Japanese Female, NA18997, slide 13

value: test


title: MCF-7 250 pg rep2

description: replicate 2


title: Japanese Female, NA18969, slide 13

description: CNV discovery from NA18969 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18570, slide 21

description: CNV discovery from NA18570 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: MCF-7 50 pg rep1

description: replicate 1


title: Japanese Female, NA18972, slide 21

description: CNV discovery from NA18972 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18947, slide 21

description: CNV discovery from NA18947 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: MCF-7 250 pg rep1

description: replicate 1


title: Chinese Female, NA18564, slide 13

description: CNV discovery from NA18564 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: MCF-7 1 ng rep2

description: replicate 2

value: 1 ng


title: Chinese Female, NA18537, slide 13

value: female


title: MCF-7 1 ng rep1

description: replicate 1


title: Japanese Female, NA18951, slide 13

description: CNV discovery from NA18951 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18973, slide 13

description: CNV discovery from NA18973 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK20, slide 21

description: CNV discovery from AK20 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: Korean

value: anonymous


title: MCF-7 5 ng rep1

description: replicate 1

value: 5 ng


title: MCF-7 5 ng rep2

description: replicate 2


title: Chinese Female, NA18547, slide 21

description: CNV discovery from NA18547 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: HapMap

value: Caucasian

value: male


title: Japanese Female, NA18949, slide 13

value: Japanese

value: reference


title: Korean Female, AK14, slide 21

description: CNV discovery from AK14 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK18, slide 21

description: CNV discovery from AK18 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18592, slide 21

description: CNV discovery from NA18592 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: Chinese


title: MCF-7 10 ng rep1

description: replicate 1

value: 10 ng


title: Chinese Female, NA18542, slide 13

description: CNV discovery from NA18542 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: MCF-7 10 ng rep2

description: replicate 2


title: Korean Female, AK12, slide 21

description: CNV discovery from AK12 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK10, slide 21

description: CNV discovery from AK10 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18570, slide 13


title: Japanese Female, NA18942, slide 13


title: Chinese Female, NA18526, slide 13

description: CNV discovery from NA18526 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: MCF-7 50 ng rep1

description: replicate 1

value: 50 ng


title: Chinese Female, NA18566, slide 13

description: CNV discovery from NA18566 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: MCF-7 100 ng rep2

description: replicate 2

value: Breast Adenocarcinoma (MCF-7)


title: Korean Female, AK6, slide 21

description: CNV discovery from AK6 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18972, slide 13


title: Chinese Female, NA18592, slide 13


title: Korean Female, AK4, slide 21

description: CNV discovery from AK4 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK8, slide 21

description: CNV discovery from AK8 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18547, slide 13


title: Korean Female, AK2, slide 21

description: CNV discovery from AK2 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: MCF-7 100 ng rep1

description: replicate 1


title: Korean Female, AK16, slide 21

description: CNV discovery from AK16 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: MCF-7 50 ng rep2

description: replicate 2


title: Japanese Female, NA18947, slide 13

description: CNV discovery from NA18947 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Raji 10 pg rep2

description: replicate 2

source_name: Burkitts Lymphoma (Raji) Total RNA (Ambion Cat# AM7876)

value: Burkitts Lymphoma (Raji)

value: 10 pg


title: Korean Male, AK1, slide 21

description: CNV discovery from AK1 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: control


title: Raji 10 pg rep1

description: replicate 1


title: YRI Female, NA19240, slide 15

description: CNV discovery from NA19240 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: African Yoruban


title: Korean Female, AK20, slide 13

description: CNV discovery from AK20 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: female

value: test


title: CEU Female, NA12878, slide 15

description: CNV discovery from NA12878 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK16, slide 13

value: Korean

value: anonymous


title: Raji 250 pg rep2

description: replicate 2


title: Raji 50 pg rep2

description: replicate 2

value: 50 pg


title: Raji 50 pg rep1

description: replicate 1


title: Raji 250 pg rep1

description: replicate 1


title: Raji 1 ng rep2

description: replicate 2

value: 1 ng


title: Chinese Female, NA19582, slide 15

description: CNV discovery from NA19582 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: HapMap

value: Caucasian

value: male


title: Raji 1 ng rep1

description: replicate 1


title: Korean Female, AK14, slide 13

description: CNV discovery from AK14 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: reference


title: Korean Female, AK12, slide 13


title: Raji 5 ng rep2

description: replicate 2

value: 5 ng


title: Korean Female, AK10, slide 13


title: Korean Female, AK8, slide 13


title: Raji 10 ng rep2

description: replicate 2

value: 10 ng


title: Japanese Female, NA18968, slide 15

description: CNV discovery from NA18968 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: Japanese


title: Raji 5 ng rep1

description: replicate 1

value: Burkitts Lymphoma (Raji)


title: Korean Female, AK4, slide 13


title: Japanese Female, NA18999, slide 15

description: CNV discovery from NA18999 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18997, slide 15

description: CNV discovery from NA18997 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18552, slide 15

description: CNV discovery from NA18552 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: Chinese


title: Raji 10 ng rep1

description: replicate 1


title: Chinese Female, NA18564, slide 15

description: CNV discovery from NA18564 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK6, slide 13

description: CNV discovery from AK6 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Male, AK1, slide 13

value: control


title: Raji 50 ng rep2

description: replicate 2

value: 50 ng


title: Japanese Female, NA18969, slide 15

description: CNV discovery from NA18969 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: female


title: Korean Female, AK2, slide 13

value: test


title: Japanese Female, NA18973, slide 15

description: CNV discovery from NA18973 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA19582, slide 12


title: Raji 50 ng rep1

description: replicate 1


title: CEU Female, NA12878, slide 12


title: YRI Female, NA19240, slide 12

value: African Yoruban


title: Japanese Female, NA18949, slide 15

description: CNV discovery from NA18949 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18951, slide 15

description: CNV discovery from NA18951 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Raji 100 ng rep1

description: replicate 1


title: Chinese Female, NA18542, slide 15

description: CNV discovery from NA18542 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Raji 100 ng rep2

description: replicate 2


title: Raji intact rep2

description: replicate 2

tag: treatment

value: intact


title: Chinese Female, NA18566, slide 15

description: CNV discovery from NA18566 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Raji degraded rep2

description: replicate 2

value: artificially degraded 95C for 30 minutes


title: Japanese Female, NA18942, slide 15

description: CNV discovery from NA18942 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Raji degraded rep1

description: replicate 1


title: Chinese Female, NA18552, slide 12


title: Japanese Female, NA18999, slide 12


title: Chinese Female, NA18537, slide 15

description: CNV discovery from NA18537 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18570, slide 15

description: CNV discovery from NA18570 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18968, slide 12


title: MCF-7 degraded rep2

description: replicate 2

value: Breast Adenocarcinoma (MCF-7)


title: Raji intact rep1

description: replicate 1


title: MCF-7 intact rep2

description: replicate 2


title: Japanese Female, NA18997, slide 12

value: HapMap


title: Chinese Female, NA18526, slide 15

description: CNV discovery from NA18526 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: Caucasian


title: Chinese Female, NA18537, slide 12

value: male


title: MCF-7 degraded rep1

description: replicate 1


title: Japanese Female, NA18969, slide 12

value: reference


title: MCF-7 intact rep1

description: replicate 1


title: Japanese Female, NA18947, slide 15

description: CNV discovery from NA18947 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18564, slide 12


title: Chinese Female, NA18547, slide 15

description: CNV discovery from NA18547 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18951, slide 12


title: FF lung tumor #3

description: replicate 3

source_name: Lung tumor

growth_protocol: Fresh-Frozen

extract_protocol: Fresh-frozen RNA was extracted with a standard Rneasy Kit (Qiagen); FFPE RNA was extracted with a FormaPure Kit (Agencourt Bioscience Corporation)

treatment_protocol: Fresh-Frozen

value: lung tumor


title: Chinese Female, NA18592, slide 15

description: CNV discovery from NA18592 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18542, slide 12


title: Korean Female, AK16, slide 15

description: CNV discovery from AK16 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: Korean

value: anonymous


title: Japanese Female, NA18949, slide 12

value: Japanese


title: FF lung tumor #4

description: replicate 4


title: Japanese Female, NA18973, slide 12


title: Korean Female, AK14, slide 15

description: CNV discovery from AK14 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK18, slide 15

description: CNV discovery from AK18 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: FF lung tumor #1

description: replicate 1


title: Japanese Female, NA18972, slide 15

description: CNV discovery from NA18972 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Liver of pup exposed to 0.2 mg/kg BW BDE-47 rep5

city: Sherbrooke

first: Alexander

last: Suvorov

state: Quebec

address: 3001, 12e avenue Nord

country: Canada

institute: Université de Sherbrooke

description: individual pup

data_processing: The raw data were pre-processed and normalized with the lumi Bioconductor package

label: biotin

organism: Rattus norvegicus

source_name: rat liver

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

growth_protocol: We obtainedtimed pregnant Wistar rats (250–300 g; Charles River Laboratories, St. Constant, Que., Canada) on gestational day (GD) 14 and housed them individually in plastic cages with sawdust bedding, under regulated temperature (21 ± 2 ° C), relative humidity (50 ± 10%) and a 12-hour light/dark cycle. Food (Rodent chow 5075; Charles River Laboratories) and water were provided ad libitum. All animals received care in compliance with the Guide to the Care and Use of Experimental Animals from the Canadian Council of Animal Care and the protocol was approved by our institutional animal research ethics review board.

extract_protocol: All tissues were snap-frozen in liquid nitrogen, and stored at -80°C until RNA extraction. RNA was extracted with the RNeasy Mini Kit (Qiagen, Maryland, USA) according to the manufacturer’s instructions.

treatment_protocol: Dams were randomly distributed among two groups (3 dams per group) and exposed by caudal injection (0.3 ml/kg body weight) from GD 15 to PND 20 every 5 days (a total of 6 injections/dam). Dams of the control group received vehicle: ethanol 95%, Cremophor EL, and sterile water (1:1:8, v/v); dams of exposed group 1 received 0.002 mg/kg body weight (BW) of BDE-47 in vehicle, and dams of exposed group 2 received 0.2 mg/kg body weight (BW) of BDE-47 in vehicle. Dams and pups were kept together until weaning on PND 21.

tag: sex

value: liver


title: Liver of pup exposed to 0.2 mg/kg BW BDE-47 rep6

description: individual pup


title: Liver of pup exposed to 0.2 mg/kg BW BDE-47 rep4

description: individual pup


title: Chinese Female, NA18566, slide 12

value: Chinese


title: FF lung tumor #2

description: replicate 2


title: Korean Female, AK10, slide 15

description: CNV discovery from AK10 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Liver of pup exposed to 0.2 mg/kg BW BDE-47 rep3

description: individual pup


title: Korean Female, AK12, slide 15

description: CNV discovery from AK12 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: FF lung normal adjacent tumor #4

description: replicate 4

source_name: Normal adjacent lung tumor

value: adjacent lung tumor


title: FF lung normal adjacent tumor #2

description: replicate 2


title: Japanese Female, NA18942, slide 12

value: female


title: Korean Female, AK8, slide 15

description: CNV discovery from AK8 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: test


title: Liver of pup exposed to 0.2 mg/kg BW BDE-47 rep2

description: individual pup


title: Korean Female, AK6, slide 15

description: CNV discovery from AK6 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18570, slide 12


title: Korean Female, AK20, slide 15

description: CNV discovery from AK20 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: FF lung normal adjacent tumor #3

description: replicate 3


title: Chinese Female, NA18526, slide 12


title: Korean Female, AK4, slide 15

description: CNV discovery from AK4 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK2, slide 15

description: CNV discovery from AK2 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18947, slide 12


title: Chinese Female, NA18547, slide 12


title: Liver of pup exposed to 0.002 mg/kg BW BDE-47 rep6

description: individual pup


title: Liver of pup exposed to 0.2 mg/kg BW BDE-47 rep1

description: individual pup


title: FFPE lung tumor #3

description: replicate 3

growth_protocol: Formalin-fixed, paraffin-embedded

treatment_protocol: Formalin-fixed, paraffin-embedded


title: Liver of pup exposed to 0.002 mg/kg BW BDE-47 rep5

description: individual pup


title: Japanese Female, NA18972, slide 12


title: FFPE lung tumor #2

description: replicate 2


title: Liver of pup exposed to 0.002 mg/kg BW BDE-47 rep2

description: individual pup


title: Liver of pup exposed to 0.002 mg/kg BW BDE-47 rep4

description: individual pup


title: FFPE lung tumor #1

description: replicate 1


title: Liver of pup exposed to 0.002 mg/kg BW BDE-47 rep3

description: individual pup


title: FFPE lung normal adjacent tumor #4

description: replicate 4


title: FFPE lung tumor #4

description: replicate 4


title: Liver of pup exposed to 0.002 mg/kg BW BDE-47 rep1

description: individual pup


title: Liver of pup from control group rep6

description: individual pup


title: FF lung normal adjacent tumor #1

description: replicate 1


title: Korean Female, AK20, slide 12


title: FFPE lung normal adjacent tumor #2

description: replicate 2


title: Korean Female, AK16, slide 12


title: FFPE lung normal adjacent tumor #3

description: replicate 3


title: Chinese Female, NA18592, slide 12


title: Korean Male, AK1, slide 15

description: CNV discovery from AK1 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: control


title: FFPE lung normal adjacent tumor #1

description: replicate 1


title: Liver of pup from control group rep3

description: individual pup


title: Liver of pup from control group rep5

description: individual pup


title: reference Sib5_50kXBaI

city: Heidelberg

first: Sandrine

last: Tchatchou

address: Voßstrasse 9

department: Molecular Biology Labor

country: Germany

institute: Universität Frauenklinik Heidelberg

description:
Hybridized to 50K_XbaI
Reference used to generate log2ratio_AB
Genotype Call (SNP call): AA, AB, BB, and NoCall; log2 ratio_AB (total log2 copy number); and Copy Number

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: CNAG 2.0 was applied to all datasets to calculate the raw total log2 copy number (Log2Ratio_AB), selecting the averaging mode performed over 10 SNPs, with the exclusion of min and max values. The total copy number N_AB (i.e., the SNP copy number state) was determined through an HMM estimation.

label: Biotin

source_name: Genomic Instability and Myelodysplasia with Monosomy 7 sample P1_Month 0

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from from peripheral blood mononuclear samples of P1 at different time points

tag: disease state

tag: reference

value: peripheral blood mononuclear cells


title: Korean Female, AK18, slide 12


title: Liver of pup from control group rep2

description: individual pup


title: reference Sib6_50kXBaI

source_name: Genomic Instability and Myelodysplasia with Monosomy 7 sample P1_Month 14


title: P1_Month 27_50kXBaI

description:
Hybridized to 50K_XbaI
Genotype Call (SNP call): AA, AB, BB, and NoCall; log2 ratio_AB (total log2 copy number); and Copy Number

source_name: Genomic Instability and Myelodysplasia with Monosomy 7 sample P1_Month 27

tag: patient

value: patient 1

tag: time

value: Month 27


title: Liver of pup from control group rep1

description: individual pup


title: P1_Month 26_50kXBaI

source_name: Genomic Instability and Myelodysplasia with Monosomy 7 sample P1_Month 26

value: Month 26


title: P1_Month 14_50kXBaI

value: Genomic Instability and Myelodysplasia with Monosomy 7

value: Month 14


title: Korean Female, AK12, slide 12

source_name: Blood cells, Korean female

value: Caucasian

value: male

value: HapMap

value: reference


title: Korean Female, AK14, slide 12

value: Korean

value: anonymous

source_name: NA10851 reference


title: reference Sib6_50kHindIII

description:
Hybridized to 50K_HindIII
Reference used to generate log2ratio_AB
Genotype Call (SNP call): AA, AB, BB, and NoCall; log2 ratio_AB (total log2 copy number); and Copy Number


title: P1_Month 0_50kXBaI

value: Month 0


title: Brain frontal lobes of pup exposed to 0.2 mg/kg BW BDE-47 rep1

description: individual pup

source_name: brain fontal lobes

treatment_protocol: Dams were randomly distributed among three groups (3 dams per group) and exposed by caudal injection (0.3 ml/kg body weight) from GD 15 to PND 20 every 5 days (a total of 6 injections/dam). Dams of the control group received vehicle: ethanol 95%, Cremophor EL, and sterile water (1:1:8, v/v); dams of exposed group 1 received 0.002 mg/kg body weight (BW) of BDE-47 in vehicle, and dams of exposed group 2 received 0.2 mg/kg body weight (BW) of BDE-47 in vehicle. Dams and pups were kept together until weaning on PND 21. One female pup per litter was selected randomly and sacrificed by decapitation on PND 41. Total RNA was extracted from brain frontal lobes of these pups and used for microarray analysis.

value: brain frontal lobe


title: Brain frontal lobes of pup exposed to 0.002 mg/kg BW BDE-47 rep3

description: individual pup

value: female


title: Brain frontal lobes of pup exposed to 0.2 mg/kg BW BDE-47 rep2

description: individual pup


title: Liver of pup from control group rep4

description: individual pup

value: liver


title: Korean Female, AK10, slide 12

value: test


title: reference Sib5_50kHindIII

value: peripheral blood mononuclear cells


title: Brain frontal lobes of pup exposed to 0.002 mg/kg BW BDE-47 rep2

description: individual pup


title: P1_Month 27_50kHindIII

description:
Hybridized to 50K_HindIII
Genotype Call (SNP call): AA, AB, BB, and NoCall; log2 ratio_AB (total log2 copy number); and Copy Number

value: patient 1


title: Korean Female, AK8, slide 12


title: P1_Month 14_50kHindIII


title: Brain frontal lobes of pup exposed to 0.002 mg/kg BW BDE-47 rep1

description: individual pup


title: P1_Month 26_50kHindIII


title: Brain frontal lobes of pup from control group rep3

description: individual pup


title: Brain frontal lobes of pup exposed to 0.2 mg/kg BW BDE-47 rep3

description: individual pup


title: P1_Month 0_50kHindIII


title: Korean Female, AK4, slide 12


title: CEU Female, NA12878, slide 11

description: CNV discovery from NA12878 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: control


title: Korean Female, AK2, slide 12


title: 4ww2m, 1-month-old, control, male

city: Piscataway

first: Jianmin

last: Chen

state: NJ

address: 604 Allison Rd

department: Cell Biology and Neuroscience

institute: Rutgers University

description: littermate of 4wm2m

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Affymetrix GCOS, MAS 5

organism: Mus musculus

source_name: 1-month-old, control, male

label_protocol: Biotin-labeled cRNA was generated using BioArray High Yield RNA Transcription Labeling Kit fro Enzo Diagnostics.

extract_protocol: RNAeasy from Qiagen.

tag: strain

value: kidney

tag: age


title: Korean Male, AK1, slide 12


title: 4ww3m, 1-month-old, control, male

description: littermate of 4wm3m


title: Brain of pup exposed to 0.2 mg/kg BW BDE-47 rep3

description: individual pup

source_name: rat total brain

treatment_protocol: Dams were randomly distributed among three groups (3 dams per group) and exposed by caudal injection (0.3 ml/kg body weight) on GD 15, PND 1 and 5. Dams of the control group received vehicle: ethanol 95%, Cremophor EL, and sterile water (1:1:8, v/v); dams of exposed group 1 received 0.002 mg/kg body weight (BW) of BDE-47 in vehicle, and dams of exposed group 2 received 0.2 mg/kg body weight (BW) of BDE-47 in vehicle. One female pup per litter was selected randomly and sacrificed by decapitation on PND 10. Total RNA was extracted from total brain samples of these pups and used for microarray analysis.

value: brain


title: Brain frontal lobes of pup from control group rep1

description: individual pup


title: 4ww1f, 1-month-old, control, female

description: littermate of 4wm1f

source_name: 1-month-old, control, female


title: Chinese Female, NA19582, slide 11

description: CNV discovery from NA19582 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Immortalized cell line, Chinese female

value: Chinese


title: Brain of pup exposed to 0.2 mg/kg BW BDE-47 rep2

description: individual pup


title: Korean Female, AK6, slide 12

value: Caucasian


title: YRI Female, NA19240, slide 11

description: CNV discovery from NA19240 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Immortalized cell line, African Yoruban female

value: African Yoruban

value: male


title: 4wm2m, 1-month-old, Aprt KO, male

description: littermate of 4ww2m

source_name: 1-month-old, Aprt KO, male


title: Japanese Female, NA18969, slide 11

description: CNV discovery from NA18969 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Immortalized cell line, Japanese female

value: Japanese

value: HapMap

value: reference


title: Brain of pup exposed to 0.2 mg/kg BW BDE-47 rep1

description: individual pup


title: 4wm3m, 1-month-old, Aprt KO, male

description: littermate of 4ww3m


title: Japanese Female, NA18968, slide 11

description: CNV discovery from NA18968 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18552, slide 11

description: CNV discovery from NA18552 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Brain of pup exposed to 0.002 mg/kg BW BDE-47 rep2

description: individual pup


title: Brain frontal lobes of pup from control group rep2

description: individual pup


title: 4wm1f, 1-month-old, Aprt KO, female

description: littermate of 4ww1f

source_name: 1-month-old, Aprt KO, female


title: Japanese Female, NA18997, slide 11

description: CNV discovery from NA18997 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18999, slide 11

description: CNV discovery from NA18999 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18564, slide 11

description: CNV discovery from NA18564 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: OA4, 7-day-old, Aprt KO, male

description: littermate of OA2

source_name: 7-day-old, Aprt KO, male


title: Brain of pup exposed to 0.002 mg/kg BW BDE-47 rep3

description: individual pup


title: OA3, 7-day-old, Aprt KO, female

description: littermate of OA1

source_name: 7-day-old, Aprt KO, female


title: Brain of pup exposed to 0.002 mg/kg BW BDE-47 rep1

description: individual pup


title: Japanese Female, NA18973, slide 11

description: CNV discovery from NA18973 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Brain of pup from control group rep3

description: individual pup


title: OA2, 7-day-old, control, male

description: littermate of OA4

source_name: 7-day-old, control, male


title: Brain of pup from control group rep2

description: individual pup


title: OA1, 7-day-old, control, female

description: littermate of OA3

source_name: 7-day-old, control, female


title: Chinese Female, NA18537, slide 11

description: CNV discovery from NA18537 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Brain of pup from control group rep1

description: individual pup


title: M20, 7-day-old, control, male

description: littermate of M19


title: Chinese Female, NA18566, slide 11

description: CNV discovery from NA18566 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: DS-ALL, BFM data set (SI-DS-ALL-8)

city: Rehovot

first: Libi

last: Hertzberg

address: Herzel 145

country: Israel

institute: Weizmann Institute of Science

description: Gene expression data from pediatric acute leukemia samples at diagnosis

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.

scan_protocol: GeneChips were scanned using the Scan GCS3000Dx.

data_processing: Affymetrix Expression Console (EC) software Version 1.1 was used to median-normalize the data and then apply RMA.

source_name: White blood human cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: No growth protocol used

extract_protocol: Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns

treatment_protocol: White blood cells were isolated through Ficoll-Hypaque density gradient centrifugation

tag: condition

value: Down's syndrome with acute lymphoblastic leukemia

tag: snp dataset

value: IL

tag: gene expression dataset

value: IL, BFM

tag: jak2 r683 mutation

value: normal, wild type

tag: crlf2 mutation

tag: crlf2 fish

tag: crlf2 expression levels (gene expression arrays - log2)

tag: crlf2 expression levels (qrt-pcr - relative to si-ds-all-12)

tag: crlf2 expression levels stratification

value: High/medium

value: white blood cells


title: DS-ALL, BFM data set (SI-DS-ALL-7)

value: No/low

tag: cell type


title: DS-ALL, BFM data set (SI-DS-ALL-6)


title: M19, 7-day-old, Aprt KO, male

description: littermate of M20

tag: tissue

tag: gender


title: M18, 7-day-old, Aprt KO, female

description: littermate of M15

value: female


title: DS-ALL, BFM data set (SI-DS-ALL-5)


title: M15, 7-day-old, control, female

description: littermate of M18

value: kidney


title: M6, 7-day-old, control, female

description: littermate of M2


title: DS-ALL, BFM data set (SI-DS-ALL-4)

value: BFM


title: M4, 7-day-old, Aprt KO, male

description: littermate of M1


title: Japanese Female, NA18951, slide 11

description: CNV discovery from NA18951 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

tag: population

tag: sample source

tag: sample type

value: test


title: Chinese Female, NA18542, slide 11

description: CNV discovery from NA18542 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: Chinese

value: Caucasian


title: M2, 7-day-old, Aprt KO, female

description: littermate of M6

tag: strain


title: DS-ALL, BFM data set (SI-DS-ALL-1)


title: Chinese Female, NA18526, slide 11

description: CNV discovery from NA18526 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: male


title: DS-ALL, BFM data set (SI-DS-ALL-9)


title: Japanese Female, NA18949, slide 11

description: CNV discovery from NA18949 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: Japanese


title: Japanese Female, NA18942, slide 11

description: CNV discovery from NA18942 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: HapMap


title: 7423

status: Public on Jan 12 2010

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII and MspI signals are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167). After intra-array normalization each channel was centered by subtracting background noise (2.5 median absolute deviations from the median of the random probes’ log2 signal for that channel) from its log2-transformed signal intensities. The HpaII/MspI (unmethylated/reference) ratio was then determined for each probe set on array.

source_name: AML blast cells

label_protocol: Random 9-mers pre-labeled with either Cy3 or Cy5

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

tag: digestion

tag: age

tag: fab

value: NN

value: Intermediate

value: Neg

tag: tri 8

tag: complex

tag: other

tag: normal karyotype

value: Pos

tag: nras

tag: kras

tag: cebpa

value: HpaII


title: Japanese Female, NA18947, slide 11

description: CNV discovery from NA18947 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: reference


title: 7418


title: 7419

value: Complex

value: Poor


title: 7413


title: 7421


title: 7420


title: Japanese Female, NA18972, slide 11

description: CNV discovery from NA18972 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: female


title: 7416


title: 7408


title: 7412

value: Good


title: 7414


title: 7406


title: 7326

value: Other


title: 7407


title: 7328


title: M1, 7-day-old, control, male

description: littermate of M4

value: kidney


title: 7402


title: 7324


title: 7411


title: 7320


title: Korean Female, AK16, slide 11

description: CNV discovery from AK16 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Blood cells, Korean female

value: Korean

value: anonymous

value: test


title: Chinese Female, NA18570, slide 11

description: CNV discovery from NA18570 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: Chinese

source_name: NA10851 reference

value: Caucasian

value: male


title: 7318

value: NN

value: Intermediate


title: 7325

value: Neg

value: Pos


title: 7403

value: HpaII


title: Korean Female, AK20, slide 11

description: CNV discovery from AK20 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: HapMap

value: reference


title: 7316

value: female


title: 7317

value: RAEB-t

value: Poor


title: Korean Female, AK6, slide 11

description: CNV discovery from AK6 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK12, slide 11

description: CNV discovery from AK12 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: 7315

value: Good


title: Chinese Female, NA18547, slide 11

description: CNV discovery from NA18547 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK8, slide 11

description: CNV discovery from AK8 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: Korean


title: 7313


title: Korean Male, AK1, slide 11

description: CNV discovery from AK1 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Blood cells, Korean male

value: anonymous

value: control


title: 7311


title: 7314

value: Other


title: 7310


title: Korean Female, AK10, slide 11

description: CNV discovery from AK10 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: test

value: Caucasian


title: Korean Female, AK4, slide 11

description: CNV discovery from AK4 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: male


title: 7309

value: NN

value: Intermediate


title: 7323

value: trisomy 8

value: Neg

value: Pos


title: 7308

value: HpaII


title: Chinese Female, NA18592, slide 11

description: CNV discovery from NA18592 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: Chinese

value: female

value: HapMap

value: reference


title: 7312

value: RAEB

value: MDS complex

value: Poor


title: 7304

value: Other


title: 7306

value: ND


title: 7319


title: 7305


title: 7307

value: Complex


title: Korean Female, AK18, slide 11

description: CNV discovery from AK18 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: Korean

value: anonymous

value: test

value: Caucasian

value: male


title: 7303

value: RAEB-t

value: MDS -Y

value: Intermediate

value: Neg

value: Pos


title: Korean Female, AK2, slide 11

description: CNV discovery from AK2 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

value: female

value: HapMap

value: reference


title: 7302

value: HpaII


title: Korean Female, AK14, slide 11

description: CNV discovery from AK14 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: 7273

value: Good


title: 7301

value: NN


title: 7185


title: 7186

value: failure

value: ND


title: 7178


title: 7169


title: 7188


title: 7177

value: MDS -7(q)

value: Poor

value: Polymorfisme


title: 7187

value: male


title: 7176


title: 7168


title: 7183


title: 7172


title: 7180


title: 7166

value: Other


title: 7161


title: 7151


title: 7150


title: 7148


title: 7154


title: 7147


title: 7146


title: 7139


title: 7137


title: 7134


title: 7322


title: 7142


title: 7136


title: 7143


title: 7114


title: 7117


title: 7131


title: 7118


title: 7122


title: 7115


title: 7124


title: 7121


title: 7119


title: 7125


title: 7084

value: no data


title: 7081


title: 7076

value: Intermediate


title: 7077

value: RAEB

value: Neg


title: 7079

value: Pos


title: 7071


title: 7116


title: 7145

value: female


title: 7070


title: 7067


title: 7074


title: 7073


title: 7062


title: 7072


title: 7059


title: 7058


title: 6947


title: 7052


title: 6887


title: 6891


title: 7051


title: 6945

value: trisomy 8


title: 6975

value: HpaII


title: 6882


title: 6889

value: Good


title: 6881


title: 6735

value: NN


title: 6458


title: 6717


title: 6457


title: 7075


title: 6462


title: 6463


title: 6456


title: 6454


title: 7167


title: 7127


title: 6379


title: 6455


title: 6450


title: 6449


title: 6453


title: 6374


title: 6378


title: 6448

value: RAEB-t


title: 6376


title: 6375

value: Complex


title: 6371


title: 6365


title: 6363


title: 6364


title: 6373

value: MDS complex


title: 6357

value: Poor


title: 6243


title: 6372


title: 6247


title: 6241

value: Polymorfisme


title: 6370


title: 6240


title: 6356


title: 6238


title: 6359

value: male


title: 5361


title: 6237


title: 5360


title: 5358


title: 5364


title: 5359


title: 5365


title: 5357


title: 6239


title: 5354

value: Other


title: 5356


title: 5352


title: 5355


title: 6236


title: 5362


title: 5353


title: 5291


title: 5351


title: 5349


title: 5289


title: 5363


title: 5348


title: 5288


title: 5286


title: 5283


title: 4341


title: 4342


title: 5282


title: 4340


title: 4337

value: onbekeNA

value: onbekend


title: 5287

value: Intermediate


title: 4339

value: RAEB

value: Neg


title: 4338

value: Pos


title: 3492

value: female


title: 4335

value: HpaII


title: 3484


title: 4336


title: 3483


title: 4334


title: 4333


title: 3329

value: Good


title: 3481


title: 3491

value: NN


title: 3330

value: trisomy 8


title: 3331


title: 3493


title: 5350


title: 3489


title: 3332


title: 3328


title: 3323


title: 3316


title: 3327


title: 3311


title: 3321


title: 3313


title: 3320


title: 3314

value: Complex


title: 3312


title: 3318


title: 3310


title: 3309


title: 2765


title: 3308


title: 2757

value: ND


title: 2767

value: failure


title: 2764


title: 2756


title: 2771


title: 2752

value: Polymorfisme


title: 2751


title: 2754

value: male


title: 2753


title: 2762


title: 2747

value: Poor


title: 2672


title: Liver_BPN_Rep2

city: Rahway

first: Oscar

last: Puig

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

institute: Merck Research Laboratories

description: Liver from genetically hypertensive blood pressure high (BPH), normotensiveblood pressure normal (BPN), and hypotensive blood pressure low (BPL) inbred mouse strains.

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45oC with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

source_name: Liver

label_protocol:
Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.
The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: Liver

tag: condition

value: BPN


title: 2748

value: Intermediate


title: Liver_BPN_Rep4

tag: tissue


title: 2686

tag: gender


title: Liver_BPN_Rep5


title: 2749


title: 2769


title: 2668


title: Liver_BPN_Rep3


title: 2670


title: Liver_BPLo_Rep5

value: BPLo


title: 2666

value: Neg


title: Liver_BPN_Rep1


title: Liver_BPLo_Rep3


title: 2664

value: Pos


title: 2647


title: Liver_BPLo_Rep4


title: Liver_BPLo_Rep2


title: 2549


title: Liver_BPLo_Rep1


title: 2327

value: female


title: 2326

value: HpaII


title: Liver_BPHi_Rep4

value: BPHi


title: Liver_BPHi_Rep1


title: 2307

value: Good


title: 2306

value: NN


title: 5290


title: 2301


title: Kidney_BPN_Rep5

description: Kidney from genetically hypertensive blood pressure high (BPH), normotensiveblood pressure normal (BPN), and hypotensive blood pressure low (BPL) inbred mouse strains.

source_name: Kidney

value: Kidney


title: Liver_BPHi_Rep2


title: 2300


title: 2305


title: Liver_BPHi_Rep3


title: Liver_BPHi_Rep5


title: Kidney_BPN_Rep4


title: Kidney_BPN_Rep3


title: Kidney_BPLo_Rep5


title: Kidney_BPN_Rep2


title: 2292

value: trisomy 8


title: 2299

value: Other


title: Kidney_BPN_Rep1


title: 2297

value: ND


title: 2296

value: male


title: 2291


title: 2293


title: Kidney_BPLo_Rep2


title: Kidney_BPLo_Rep4


title: Kidney_BPLo_Rep1


title: 2290


title: Kidney_BPHi_Rep5


title: 2287


title: Kidney_BPHi_Rep4


title: Kidney_BPHi_Rep1


title: 2286


title: 2284


title: Heart_BPN_Rep4

description: Heart from genetically hypertensive blood pressure high (BPH), normotensiveblood pressure normal (BPN), and hypotensive blood pressure low (BPL) inbred mouse strains.

source_name: Heart

value: Heart


title: Heart_BPN_Rep3


title: Kidney_BPHi_Rep3


title: Kidney_BPHi_Rep2


title: 2288

value: Poor


title: Heart_BPN_Rep5

value: BPN


title: 2289

value: Intermediate


title: Heart_BPN_Rep2


title: 2279


title: Heart_BPN_Rep1


title: Heart_BPLo_Rep4

value: BPLo


title: Heart_BPLo_Rep5


title: 2282

value: Neg


title: 2276

value: Pos


title: 2285

value: female


title: 2283

value: HpaII


title: Heart_BPLo_Rep3


title: Heart_BPLo_Rep2


title: 2280


title: 2273

value: MspI


title: 2275

value: Polymorfisme


title: 2268

value: NN


title: 2278


title: 2274


title: Heart_BPLo_Rep1


title: 2267

value: Good


title: Heart_BPHi_Rep4

value: BPHi


title: Heart_BPHi_Rep2


title: Heart_BPHi_Rep3


title: Heart_BPHi_Rep5


title: 2265


title: Heart_BPHi_Rep1


title: 2261


title: 2271


title: AORTA_BPN_Rep14

description: Aorta from genetically hypertensive blood pressure high (BPH), normotensiveblood pressure normal (BPN), and hypotensive blood pressure low (BPL) inbred mouse strains.

source_name: Aorta

label_protocol:
Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.
The reverse transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cDNA.

value: Aorta


title: 2259

value: Complex


title: AORTA_BPN_Rep15


title: AORTA_BPN_Rep12


title: 2256

value: male


title: AORTA_BPN_Rep13


title: 2257


title: Aorta_BPL_Rep29

value: BPL


title: AORTA_BPN_Rep11


title: 2255

value: Poor

value: ND


title: Aorta_BPL_Rep28


title: 2260

value: Intermediate


title: 2254


title: 2250


title: Aorta_BPL_Rep27


title: 2253


title: Aorta_BPL_Rep26


title: Aorta_BPL_Rep24


title: 2247

value: Other


title: 2248

value: Neg


title: Aorta_BPL_Rep22


title: Aorta_BPL_Rep21


title: Aorta_BPL_Rep23


title: 2245

value: Pos


title: 2246


title: Aorta_BPL_Rep25


title: Aorta_BPH_Rep9

value: BPH


title: 2244

value: trisomy 8

value: HpaII


title: 2249

value: MspI

value: female


title: 2242


title: Cardiac_RV_WT2_Rep3

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

description: Single-color chemiluminescent signals were quantified, corrected for background and spatially normalized. Applied Biosystems Expression System software was used to extract assay signal, and assay signal to noise ratio values from the micro-array images. Bad spots flagged by the software were removed from the analysis.

hyb_protocol: Each micro-array was first prehybridized at 55C for 1 hr in hybridization buffer with blocking reagent, after which 13 microg of labeled cRNA was hybridized to each array in a 1.5mL volume at 55C for 16 hr. After hybridization, the arrays were washed with hybridization wash buffer and chemiluminescence rinse buffer.

scan_protocol: Chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer's protocol.

data_processing: The raw signal of the set of genes was log transformed and quantile-normalized across arrays, and genes were further filtered by standard expression array signal to noise threshold (S/N greater than 3 in at least one sample).

label: Digoxigenin-UTP

source_name: cardiac right ventricle free wall

label_protocol: Digoxigenin-UTP labeled cRNA was generated from 1 microg of total RNA using Applied Biosystems Chemiluminescent RT-IVT labeling kit according to manufacturer's instructions.

extract_protocol: Total RNA was isolated from tissue samples from mice aged 10 to 12 weeks, using the Nucleospin RNA II kit according to manufacturer's instructions (Clontech). RNA quality was assessed using the Agilent 2100 Bioanalyzer, and RNA concentration was measured by spectrophotometry (Nanodrop).

value: cardiac right ventricle free wall

value: FVB/NJ

value: 12 weeks

value: Male

tag: transgene

value: wild-type


title: 2243

value: male

value: Good


title: 2241

value: NN


title: 2237

value: Poor


title: Aorta_BPH_Rep7

value: Aorta


title: Cardiac_RV_MUT2_Rep3


title: Aorta_BPH_Rep8


title: Cardiac_RV_MUT2_Rep1

scan_protocol: Chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer’s protocol.

label_protocol: Digoxigenin-UTP labeled cRNA was generated from 1 microg of total RNA using Applied Biosystems Chemiluminescent RT-IVT labeling kit according to manufacturer’s instructions.

extract_protocol: Total RNA was isolated from tissue samples from mice aged 10 to 12 weeks, using the Nucleospin RNA II kit according to manufacturer’s instructions (Clontech). RNA quality was assessed using the Agilent 2100 Bioanalyzer, and RNA concentration was measured by spectrophotometry (Nanodrop).


title: 2240

value: Intermediate

value: Neg


title: Aorta_BPH_Rep5

value: BPH


title: Aorta_BPH_Rep3


title: Cardiac_RV_WT2_Rep2


title: Aorta_BPH_Rep11


title: 2238

value: Pos


title: Cardiac_RV_MUT2_Rep2


title: Cardiac_RV_WT2_Rep1


title: 2236

value: ND

value: HpaII


title: Cardiac_RV_WT_Rep3


title: Aorta_BPH_Rep2


title: Aorta_BPH_Rep10


title: 2239

value: MspI

value: female


title: Aorta_BPH_Rep6


title: Cardiac_RV_WT_Rep1

value: cardiac right ventricle free wall


title: 2234

value: Other


title: Cardiac_RV_WT_Rep2

value: 12 weeks

value: Male


title: Cardiac_RV_MUT_Rep1


title: spleen-baclofen-5day-rep 8

city: groton

first: Petra

last: Koza-Taylor

state: CT

address: Eastern Point Road

institute: Pfizer

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol.

scan_protocol: The microarrays were scanned on a GeneChip Scanner 3000 according to standard procedures.

data_processing: RNA expression data were analyzed using the “affy” and “limma” packages of the Bioconductor suite of microarray analysis tools available for the R statistical environment (Gentleman, 2005; Gentleman et al., 2004; Irizarry et al., 2003; R Development Core Team, 2007).  Robust Microarray Analysis (RMA) background correction and quantile normalization were used to generate microarray expression values.  An overall linear model was fit to the data for all sample groups and specific contrasts of interest were evaluated to generate raw p-values for each probe set on the expression array (Smyth, 2004).  The Benjamini-Hochberg False Discovery Rate (FDR) method was then used to correct for multiple testing effects.  Probe sets were considered to have changed qualitatively in a specific comparison if an adjusted p-value of 0.05 was obtained, their average expression intensity was above 150 in either treatment group, and they had an absolute fold change greater than 1.3.

label_protocol: The Affymetrix GeneChip One-Cycle labeling kit was used for labeling according to the manufacturer's protocol.

extract_protocol: RNA from bone marrow was isolated using Paxgene Bone Marrow as described by the manufacturere (Qiagen). RNA from the liver and spleen was isolated using Qiagen mini columns as recomemended by the manufacturer.

value: Spleen

tag: treatment

value: Baclofen

tag: time

value: 5 day


title: Cardiac_RV_MUT_Rep3

tag: strain


title: Cardiac_RV_MUT_Rep2


title: 2235

tag: digestion

value: Good


title: spleen-baclofen-5day-rep 7


title: spleen-baclofen-5day-rep 6


title: 2229

tag: age

value: male


title: 2230

tag: fab

value: NN

value: Intermediate

value: Polymorfisme


title: MenadioneT8 biological replicate 2

city: Maastricht

first: Jacob

middle: Jan

last: Briede

address: PO Box 616

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

description:
ch1: MenadioneT8 biological replicate 2
ch2: ControlT8 biological replicate 2

hyb_protocol: Hybridization according to Agilent instructions.

scan_protocol: Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 and Cy5 were excited at wavelengths of 532 and 635 nm, respectively. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 587 (Cy3) and 705 (Cy5) for replicates 1 and 2, and 628 (Cy3) and 560 (Cy5) for replicates 3 and 4, based on automatic establishment of ideal scan settings. The images obtained (resolution 5 micron, 16 bit tiff image) were processed with Imagene 8.0.1 software (Biodiscovery, El Segundo, USA) to measure mean signal intensities for spots and local backgrounds followed by a quality control in Microsoft Excel.

data_processing: Data preparations were performed in GeneSight software (BioDiscovery) and included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), LOWESS normalization, log (base=2) transformations.

source_name: Caco-2 (Human colonic adenocarcinoma cells)

label_protocol: The Two-Color Microarray-Based Gene Expression Analysis kit from Agilent Technologies (Amstelveen, The Netherlands) was used to generate Cyanine (Cy) labelled cRNA according to the manufacturer’s protocol.

growth_protocol: Caco-2 cell cultures were transferred weekly by trypsinization and incubated at 37 ºC in a humidified incubator containing 5% CO2

extract_protocol: RNA was isolated from TRIzol® suspended cells according to the manufacturer’s protocol with minor modifications, followed by a clean up, using an RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) with DNase treatment.

treatment_protocol: Caco-2 cells were treated for 0.08, 0.25, 0.5, 1, 2, 4, 8, 16, or 24h with 20 mM H2O2 or 100 mM menadione. Controls were none-exposed time-matched samples from caco-2 cells

tag: cell line

tag: agent

value: Menadione

value: 8 h

value: control (non-exposed)


title: MenadioneT24 biological replicate 2

description:
ch1: MenadioneT24 biological replicate 2
ch2: ControlT24 biological replicate 2


title: 2228

value: MspI

value: Neg

value: Pos

tag: tri 8

tag: complex

tag: other

value: HpaII


title: spleen-baclofen-5day-rep 4


title: MenadioneT4FD biological replicate 2

description:
ch1: MenadioneT4FD biological replicate 2
ch2: ControlT4FD biological replicate 2

value: 4 h


title: MenadioneT16 biological replicate 2

description:
ch1: MenadioneT16 biological replicate 2
ch2: ControlT16 biological replicate 2


title: spleen-baclofen-5day-rep 5


title: MenadioneT16FD biological replicate 2

description:
ch1: MenadioneT16FD biological replicate 2
ch2: ControlT16FD biological replicate 2


title: 2226

value: Other

tag: normal karyotype

tag: nras

tag: kras


title: MenadioneT4 biological replicate 2

description:
ch1: MenadioneT4 biological replicate 2
ch2: ControlT4 biological replicate 2


title: MenadioneT8FD biological replicate 2

description:
ch1: MenadioneT8FD biological replicate 2
ch2: ControlT8FD biological replicate 2


title: 2227

value: female

tag: cebpa


title: MenadioneT2FD biological replicate 2

description:
ch1: MenadioneT2FD biological replicate 2
ch2: ControlT2FD biological replicate 2

value: 2 h


title: spleen-vehicle-5day-rep 4

tag: tissue

value: Spleen

value: Vehicle

value: 5 day


title: MenadioneT24FD biological replicate 2

description:
ch1: MenadioneT24FD biological replicate 2
ch2: ControlT24FD biological replicate 2


title: MenadioneT2 biological replicate 2

description:
ch1: MenadioneT2 biological replicate 2
ch2: ControlT2 biological replicate 2


title: 2224

tag: gender

value: male


title: MenadioneT1 biological replicate 2

description:
ch1: MenadioneT1 biological replicate 2
ch2: ControlT1 biological replicate 2

value: 1 h


title: spleen-baclofen-5day-rep 3

tag: treatment

value: Baclofen


title: MenadioneT0.5FD biological replicate 2

description:
ch1: MenadioneT0.5FD biological replicate 2
ch2: ControlT0.5FD biological replicate 2

value: Menadione

tag: time


title: spleen-vehicle-5day-rep 3

tag: strain


title: MenadioneT1FD biological replicate 2

description:
ch1: MenadioneT1FD biological replicate 2
ch2: ControlT1FD biological replicate 2


title: spleen-baclofen-5day-rep 2


title: MenadioneT0.25FD biological replicate 2

description:
ch1: MenadioneT0.25FD biological replicate 2
ch2: ControlT0.25FD biological replicate 2


title: 2223

tag: digestion

value: Intermediate

value: ND


title: MenadioneT0.25 biological replicate 2

description:
ch1: MenadioneT0.25 biological replicate 2
ch2: ControlT0.25 biological replicate 2

value: control (non-exposed)


title: H2O2T24FD biological replicate 2

description:
ch1: H2O2T24FD biological replicate 2
ch2: ControlT24FD biological replicate 2


title: spleen-vehicle-5day-rep 2


title: MenadioneT0.5 biological replicate 2

description:
ch1: MenadioneT0.5 biological replicate 2
ch2: ControlT0.5 biological replicate 2


title: 2215

value: MspI

tag: age

value: Good

value: Neg


title: 2220

tag: fab

value: Pos

value: Polymorfisme

value: HpaII


title: H2O2T8FD biological replicate 2

description:
ch1: H2O2T8FD biological replicate 2
ch2: ControlT8FD biological replicate 2

tag: cell line

value: 8 h


title: 2219

value: female


title: H2O2T24 biological replicate 2

description:
ch1: H2O2T24 biological replicate 2
ch2: ControlT24 biological replicate 2

tag: agent


title: H2O2T16 biological replicate 2

description:
ch1: H2O2T16 biological replicate 2
ch2: ControlT16 biological replicate 2


title: spleen-baclofen-1day-rep 3

value: Spleen

value: 1 day


title: spleen-baclofen-1day-rep 4


title: MenadioneT0.08 biological replicate 2

description:
ch1: Menadione T=0.08 biological replicate 2
ch2: Control T=0.08 biological replicate 2


title: spleen-vehicle-5day-rep 1

value: Vehicle

value: 5 day


title: H2O2T4 biological replicate 2

description:
ch1: H2O2T4 biological replicate 2
ch2: ControlT4 biological replicate 2

value: 4 h


title: 2216

value: NN

tag: tri 8


title: MenadioneT0.08FD biological replicate 2

description:
ch1: MenadioneT0.08FD biological replicate 2
ch2: ControlT0.08FD biological replicate 2

value: Menadione


title: spleen-vehicle-1day-rep 4


title: spleen-baclofen-5day-rep 1

value: Baclofen


title: 2214

value: Intermediate

tag: complex


title: 2218

value: MspI

value: male

tag: other


title: 2217

value: trisomy 8

value: Neg

tag: normal karyotype

value: ND


title: H2O2T16FD biological replicate 2

description:
ch1: H2O2T16FD biological replicate 2
ch2: ControlT16FD biological replicate 2

value: control (non-exposed)


title: H2O2T4FD biological replicate 2

description:
ch1: H2O2T4FD biological replicate 2
ch2: ControlT4FD biological replicate 2


title: H2O2T8 biological replicate 2

description:
ch1: H2O2T8 biological replicate 2
ch2: ControlT8 biological replicate 2

value: 8 h


title: H2O2T2 biological replicate 2

description:
ch1: H2O2T2 biological replicate 2
ch2: ControlT2 biological replicate 2

value: 2 h


title: spleen-vehicle-1day-rep 3

value: Spleen


title: 2210

value: Good

value: Pos

tag: nras

value: HpaII


title: H2O2T2FD biological replicate 2

description:
ch1: H2O2T2FD biological replicate 2
ch2: ControlT2FD biological replicate 2


title: spleen-vehicle-1day-rep 2

value: Vehicle

value: 1 day


title: H2O2T1 biological replicate 2

description:
ch1: H2O2T1 biological replicate 2
ch2: ControlT1 biological replicate 2

value: 1 h


title: 2209

value: female

value: Other

tag: kras


title: H2O2T1FD biological replicate 2

description:
ch1: H2O2T1FD biological replicate 2
ch2: ControlT1FD biological replicate 2


title: H2O2T0.5FD biological replicate 2

description:
ch1: H2O2T0.5FD biological replicate 2
ch2: ControlT0.5FD biological replicate 2


title: 2208

value: MspI

tag: cebpa


title: H2O2T0.25FD biological replicate 2

description:
ch1: H2O2T0.25FD biological replicate 2
ch2: ControlT0.25FD biological replicate 2


title: spleen-baclofen-1day-rep 1

tag: tissue

value: Baclofen


title: H2O2T0.25 biological replicate 2

description:
ch1: H2O2T0.25 biological replicate 2
ch2: ControlT0.25 biological replicate 2


title: H2O2T0.08FD biological replicate 2

description:
ch1: H2O2T0.08FD biological replicate 2
ch2: ControlT0.08FD biological replicate 2


title: H2O2T0.08 biological replicate 2

description:
ch1: H2O2 T=0.08 biological replicate 2
ch2: Control T=0.08 biological replicate 2


title: H2O2T0.5 biological replicate 2

description:
ch1: H2O2T0.5 biological replicate 2
ch2: ControlT0.5 biological replicate 2


title: 2204

tag: gender

value: male


title: 2206

value: NN

value: Intermediate

value: Neg


title: astrocyte_a_syn_24h_rep3

first: Seung-Jae

last: Lee

address: 1 Hwayang-dong, Gwangjin-Gu

institute: Konkuk university

description: Scanned raw data ([.tiff] image files and [.csv] probe location info. files) were processed with a R package, 'Beadarray'.

hyb_protocol: 750ng of amplified cRNA was hybridized to RatRef-12 expression beadchip (Illumina, San Diego, CA) for 16 hours.

scan_protocol: The hybridized array was detected with streptavidin-Cy3 (Amersham Biosciences, UK) and scanned with the BeadArray Reader (Illumina).

data_processing: The column VALUE in the table was obtained by quantile normalization of log2(SIGNAL-BACKGROUND) and used for all the analysis (Bolstad, B. M., Irizarry R. A., Astrand, M., and Speed, T. P. (2003), A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19, 185-193).

source_name: astrocytes treated for 24h with a-synuclein containing conditioned media

label_protocol: RNA samples were labeled according to the chip manufacturers recommended protocols. In brief, 500ng of high-quality total RNA was amplified and labeled with TotalPrep amplification kit (Ambion, Austin, TX). Total RNA was reverse transcribed with oligo(dT) primer, and second strand was synthesized. Purified cDNA was in-vitro transcribed with T7 polymerase to generate antisense RNA copies of each mRNA in a sample. Biotin-UTP are incorporated into cRNA during the in-vitro transcription.

extract_protocol: QIAGEN RNeasy, according to manufacturer

tag: Primary astrocytes were obtained from 1-day old Sprague Dawley rats as previously described in Shin et al. (2001), Immunostimulation of rat primary astrocytes decreases intracellular ATP level. Brain Res., 902, 198-204.


title: bone marrow-baclofen-5day-rep 7

source_name: bone marrow-baclofen-5day

value: Bone Marrow

tag: treatment

tag: time

value: 5 day


title: astrocyte_a_syn_24h_rep2


title: 2207

tag: digestion

value: Poor


title: astrocyte_lacZ_24h_rep3

source_name: astrocytes treated for 24h with lacZ containing conditioned media


title: 2203

tag: age


title: spleen-baclofen-1day-rep 2

tag: strain

value: Spleen


title: bone marrow-baclofen-5day-rep 6


title: spleen-vehicle-1day-rep 1


title: astrocyte_lacZ_24h_rep2


title: astrocyte_a_syn_6h_rep3

source_name: astrocytes treated for 6h with a-synuclein containing conditioned media


title: astrocyte_a_syn_24h_rep1


title: astrocyte_a_syn_6h_rep2


title: 2200

tag: fab

value: Good

value: Pos


title: bone marrow-baclofen-5day-rep 5


title: bone marrow-baclofen-5day-rep 8


title: astrocyte_lacZ_6h_rep3

source_name: astrocytes treated for 6h with lacZ containing conditioned media


title: astrocyte_a_syn_6h_rep1


title: bone marrow-baclofen-5day-rep 4


title: astrocyte_lacZ_24h_rep1


title: astrocyte_lacZ_6h_rep2


title: astrocyte_lacZ_6h_rep1


title: Pe7F_rep3_Array4

city: college park

first: Carlos Alberto

last: Machado

state: MD

department: department of biology

institute: University of Maryland

description: Global gene expression of 7-day-old virgin adults

hyb_protocol: Agilent’s protocols

scan_protocol: Agilent’s protocols

data_processing: Performed in HDBStat: data is normalized by flagging out bad spots, filtering unexpressed genes (average raw intensity across all the samples <50), negative and positive Agilent controls, and then normalized with Chip Mean and log2 transformation.

organism: Drosophila persimilis

source_name: whole body, 7-day-old adult, female, replicate 3

label_protocol: Fluorescent cRNA was synthesized from 200 ng of total RNA using Agilent’s low-RNA input fluorescent linear amplification kit following manufacturer's protocols (Agilent Technologies). Labelled RNAs were cleaned with RNeasy columns (Qiagen), and cRNA yields were quantified on a NanoDrop spectrophotometer. Two separate labeling reactions per sample were pooled and hybridized to the arrays following Agilent’s protocols.

growth_protocol: flies were reared on cornmeal/yeast medium and maintained at 20°C with a 12:12-h light/dark cycle.

extract_protocol: flies were instantly frozen in liquid nitrogen and stored in TRIZOL (Invitrogen) at -80°C. RNA was isolated using TRIZOL from at least 40 individuals. RNA quantity and quality were separately measured on a NanoDrop spectrophotometer (Thermo Scientific) and a Bioanalyzer 2100 (Agilent Technologies). High-quality samples (260/280>1.85; 260/230>1.7) from all lines of each species were pooled in equal amounts and further purified using the RNeasy kit (Qiagen).

value: whole body

value: Female


title: bone marrow-vehicle-5day-rep 4

source_name: bone marrow-vehicle-5day

value: Vehicle


title: bone marrow-baclofen-5day-rep 3


title: bone marrow-baclofen-5day-rep 2


title: bone marrow-vehicle-5day-rep 3


title: 2198

source_name: AML blast cells

value: HpaII


title: Pe7F_rep2_Array3

source_name: whole body, 7-day-old adult, female, replicate 2


title: 2202

value: female


title: Pe7M_rep1_Array3

source_name: whole body, 7-day-old adult, male, replicate 1

value: Male


title: Pe7M_rep2_Array4

source_name: whole body, 7-day-old adult, male, replicate 2


title: Pe7F_rep1_Array1

source_name: whole body, 7-day-old adult, female, replicate 1


title: bone marrow-vehicle-5day-rep 2


title: 2195

value: MspI


title: Pe7M_rep3_Array1

source_name: whole body, 7-day-old adult, male, replicate 3


title: Pb7M_2_rep1_Array1

organism: Drosophila pseudoobscura bogotana


title: 2193


title: Pb7M_2_rep3_Array2


title: 2197

value: male


title: Pb7M_2_rep2_Array4


title: 2192

value: NN


title: bone marrow-baclofen-5day-rep 1

value: Baclofen


title: Pb7F_rep3_Array4


title: bone marrow-vehicle-5day-rep 1


title: Pb7F_rep2_Array3


title: 2194

value: Intermediate

value: Neg


title: bone marrow-baclofen-1day-rep 4

source_name: bone marrow-baclofen-1day

value: Bone Marrow

value: 1 day


title: 2191

value: M?

value: ND


title: Ps7M_rep2_Array2

organism: Drosophila pseudoobscura


title: Pb7F_rep1_Array3


title: Ps7M_rep3_Array1


title: Ps7M_rep4_Array3


title: 2188

value: trisomy 8

value: Pos


title: MenadioneT24 biological replicate 1

description:
ch1: MenadioneT24 biological replicate 1
ch2: ControlT24 biological replicate 1

tag: cell line

tag: agent

value: Menadione

value: control (non-exposed)


title: 2190

value: Poor

tag: tri 8

tag: complex

value: HpaII


title: bone marrow-baclofen-1day-rep 3


title: bone marrow-vehicle-1day-rep 4

source_name: bone marrow-vehicle-1day

value: Vehicle


title: MenadioneT24FD biological replicate 1

description:
ch1: MenadioneT24FD biological replicate 1
ch2: ControlT24FD biological replicate 1


title: MenadioneT16FD biological replicate 1

description:
ch1: MenadioneT16FD biological replicate 1
ch2: ControlT16FD biological replicate 1


title: Ps7F_rep3_Array3

value: whole body

value: Female


title: bone marrow-vehicle-1day-rep 3


title: 2186

value: MspI

value: male

tag: other

tag: normal karyotype


title: 2189

value: Good

tag: nras

tag: kras

value: Polymorfisme


title: MenadioneT8FD biological replicate 1

description:
ch1: MenadioneT8FD biological replicate 1
ch2: ControlT8FD biological replicate 1

value: 8 h


title: MenadioneT8 biological replicate 1

description:
ch1: MenadioneT8 biological replicate 1
ch2: ControlT8 biological replicate 1


title: 2187

value: female

value: NN

value: Intermediate

value: Neg

tag: cebpa


title: bone marrow-baclofen-1day-rep 2

tag: tissue

value: Bone Marrow

value: Baclofen

value: 1 day


title: Ps7F_rep1_Array3

tag: gender


title: Ps7F_rep2_Array1


title: bone marrow-vehicle-1day-rep 2

tag: treatment


title: MenadioneT4 biological replicate 1

description:
ch1: MenadioneT4 biological replicate 1
ch2: ControlT4 biological replicate 1

value: Menadione

tag: time

value: 4 h

value: control (non-exposed)


title: bone marrow-baclofen-1day-rep 1


title: MenadioneT2FD biological replicate 1

description:
ch1: MenadioneT2FD biological replicate 1
ch2: ControlT2FD biological replicate 1

value: 2 h


title: MenadioneT16 biological replicate 1

description:
ch1: MenadioneT16 biological replicate 1
ch2: ControlT16 biological replicate 1


title: MenadioneT1FD biological replicate 1

description:
ch1: MenadioneT1FD biological replicate 1
ch2: ControlT1FD biological replicate 1

value: 1 h


title: MenadioneT4FD biological replicate 1

description:
ch1: MenadioneT4FD biological replicate 1
ch2: ControlT4FD biological replicate 1


title: 2183

tag: digestion

value: MspI

value: Pos

value: HpaII


title: MenadioneT0.5FD biological replicate 1

description:
ch1: MenadioneT0.5FD biological replicate 1
ch2: ControlT0.5FD biological replicate 1


title: MenadioneT0.5 biological replicate 1

description:
ch1: MenadioneT0.5 biological replicate 1
ch2: ControlT0.5 biological replicate 1


title: 2185

tag: age


title: MenadioneT2 biological replicate 1

description:
ch1: MenadioneT2 biological replicate 1
ch2: ControlT2 biological replicate 1


title: 2181


title: bone marrow-vehicle-1day-rep 1

tag: strain

value: Vehicle


title: liver-baclofen-5day-rep 6

value: Liver

value: 5 day


title: MenadioneT0.25 biological replicate 1

description:
ch1: MenadioneT0.25 biological replicate 1
ch2: ControlT0.25 biological replicate 1


title: MenadioneT0.25FD biological replicate 1

description:
ch1: MenadioneT0.25FD biological replicate 1
ch2: ControlT0.25FD biological replicate 1


title: liver-baclofen-5day-rep 7


title: H2O2T24FD biological replicate 1

description:
ch1: H2O2T24FD biological replicate 1
ch2: ControlT24FD biological replicate 1


title: 2182

value: female

tag: fab

value: trisomy 8


title: 2179

value: NN

value: Intermediate

value: Neg

value: ND


title: MenadioneT0.08FD biological replicate 1

description:
ch1: Menadione T=0.08FD biological replicate 1
ch2: Control T=0.08FD biological replicate 1

tag: cell line

value: Menadione


title: MenadioneT1 biological replicate 1

description:
ch1: MenadioneT1 biological replicate 1
ch2: ControlT1 biological replicate 1

tag: agent


title: liver-baclofen-5day-rep 8

value: Baclofen


title: 2199

value: male

tag: tri 8


title: MenadioneT0.08 biological replicate 1

description:
ch1: Menadione T=0.08h biological replicate 1
ch2: Control T=0.08h biological replicate 1

value: control (non-exposed)


title: H2O2T24 biological replicate 1

description:
ch1: H2O2T24 biological replicate 1
ch2: ControlT24 biological replicate 1


title: 2177

tag: complex


title: liver-baclofen-5day-rep 4


title: liver-baclofen-5day-rep 5


title: 2176

tag: other


title: liver-vehicle-5day-rep 4


title: H2O2T16 biological replicate 1

description:
ch1: H2O2T16 biological replicate 1
ch2: ControlT16 biological replicate 1


title: liver-baclofen-5day-rep 3


title: H2O2T16FD biological replicate 1

description:
ch1: H2O2T16FD biological replicate 1
ch2: ControlT16FD biological replicate 1


title: 1747

tag: normal karyotype


title: H2O2T8FD biological replicate 1

description:
ch1: H2O2T8FD biological replicate 1
ch2: ControlT8FD biological replicate 1

value: 8 h


title: H2O2T4 biological replicate 1

description:
ch1: H2O2T4 biological replicate 1
ch2: ControlT4 biological replicate 1

value: 4 h


title: H2O2T0.5FD biological replicate 1

description:
ch1: H2O2T0.5FD biological replicate 1
ch2: ControlT0.5FD biological replicate 1


title: 2173

value: MspI

value: Other

value: Pos

tag: nras


title: H2O2T1FD biological replicate 1

description:
ch1: H2O2T1FD biological replicate 1
ch2: ControlT1FD biological replicate 1

value: 1 h


title: 2175

tag: kras

value: HpaII


title: H2O2T8 biological replicate 1

description:
ch1: H2O2T8 biological replicate 1
ch2: ControlT8 biological replicate 1


title: 2170

value: Good

tag: cebpa


title: 1595

value: female


title: liver-vehicle-5day-rep 3

tag: tissue

value: Liver

value: Vehicle

value: 5 day


title: liver-baclofen-5day-rep 1


title: 2172

tag: gender

value: NN

value: Intermediate

value: Neg


title: liver-vehicle-5day-rep 1

tag: treatment


title: 1766

value: male


title: H2O2T2FD biological replicate 1

description:
ch1: H2O2T2FD biological replicate 1
ch2: ControlT2FD biological replicate 1

tag: time

value: 2 h

value: control (non-exposed)


title: liver-baclofen-1day-rep 4

value: Baclofen

value: 1 day


title: 2171

tag: digestion

value: MspI

value: Other


title: liver-vehicle-5day-rep 2


title: H2O2T2 biological replicate 1

description:
ch1: H2O2T2 biological replicate 1
ch2: ControlT2 biological replicate 1


title: H2O2T1 biological replicate 1

description:
ch1: H2O2T1 biological replicate 1
ch2: ControlT1 biological replicate 1

value: 1 h


title: liver-baclofen-5day-rep 2


title: H2O2T0.5 biological replicate 1

description:
ch1: H2O2T0.5 biological replicate 1
ch2: ControlT0.5 biological replicate 1


title: H2O2T0.25FD biological replicate 1

description:
ch1: H2O2T0.25FD biological replicate 1
ch2: ControlT0.25FD biological replicate 1


title: liver-vehicle-1day-rep 3


title: H2O2T0.08 biological replicate 1

description:
ch1: H2O2 T=0.08h biological replicate 1
ch2: Control T=0.08h biological replicate 1


title: liver-vehicle-1day-rep 2


title: H2O2T0.25 biological replicate 1

description:
ch1: H2O2T0.25 biological replicate 1
ch2: ControlT0.25 biological replicate 1


title: H2O2T0.08FD biological replicate 1

description:
ch1: H2O2 T=0.08FD biological replicate 1
ch2: Control T=0.08FD biological replicate 1


title: 1448

tag: age

value: Pos

value: HpaII


title: 1432

value: female


title: 1188

value: Poor


title: liver-baclofen-1day-rep 3

tag: strain

value: Liver


title: liver-baclofen-1day-rep 1


title: liver-baclofen-1day-rep 2


title: 1174

tag: fab

value: Polymorfisme


title: spleen-vehicle-2hours-rep 7

status: Public on Jan 11 2010

description: B6C3F1 Mouse

value: Spleen

value: control

value: 2 hours


title: H2O2T4FD biological replicate 1

description:
ch1: H2O2T4FD biological replicate 1
ch2: ControlT4FD biological replicate 1

tag: cell line

value: 4 h


title: 1316

value: male

value: NN

value: Intermediate

value: Neg


title: spleen-vehicle-2hours-rep 8

description: B6C3F1 Mouse


title: spleen-hypoxia-2hours-rep 6

description: B6C3F1 Mouse

value: reduced oxygen


title: spleen-vehicle-2hours-rep 5

description: B6C3F1 Mouse


title: spleen-hypoxia-2hours-rep 7

description: B6C3F1 Mouse


title: spleen-hypoxia-2hours-rep 5

description: B6C3F1 Mouse


title: spleen-vehicle-2hours-rep 6

description: B6C3F1 Mouse


title: spleen-hypoxia-2hours-rep 3

description: B6C3F1 Mouse


title: spleen-hypoxia-2hours-rep 4

description: B6C3F1 Mouse


title: spleen-hypoxia-2hours-rep 2

description: B6C3F1 Mouse


title: spleen-hypoxia-2hours-rep 8

description: B6C3F1 Mouse


title: 1299

value: MspI


title: Ischemic heart failure, Left Ventricle, sample 15

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: Ischemic heart failure, Left Ventricle

hyb_protocol: Affymetrix Standard Protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Affymetrix Power Tools version 1.0.12. Antigenomic background correction were applied to probe intensities, gene level expression were summarized using the Robust Multichip Average (RMA) method.

source_name: Ischemic heart failure, Left Ventricle

label_protocol: RNA was labeled by random priming using Affymetrix Whole Transcript and used to probe Affymetrix GeneChip Human Exon 1.0 ST (HuEx) Arrays.

extract_protocol: RNA was extracted with Trizol (Invitrogen) and further purified on RNeasy columns (Qiagen) with on column DNase digestion. RNA quality was checked on an Experion bio-analyzer (Bio-Rad).

tag: clinical diagnosis

value: Ischemic Heart Failure


title: spleen-vehicle-2hours-rep 4

description: B6C3F1 Mouse


title: spleen-vehicle-2hours-rep 1

description: B6C3F1 Mouse


title: bone marrow-hypoxia-2hours-rep 3

description: B6C3F1 Mouse

source_name: bone marrow-hypoxia-2hours

value: Bone Marrow


title: spleen-hypoxia-2hours-rep 1

description: B6C3F1 Mouse


title: Ischemic heart failure, Left Ventricle, sample 12

description: Ischemic heart failure, Left Ventricle


title: spleen-vehicle-2hours-rep 3

description: B6C3F1 Mouse


title: bone marrow-vehicle-2hours-rep 3

description: B6C3F1 Mouse

source_name: bone marrow-vehicle-2hours


title: bone marrow-hypoxia-2hours-rep 2

description: B6C3F1 Mouse


title: bone marrow-hypoxia-2hours-rep 4

description: B6C3F1 Mouse


title: liver-vehicle-2hours-rep 7

description: B6C3F1 Mouse


title: Ischemic heart failure, Left Ventricle, sample 14

description: Ischemic heart failure, Left Ventricle


title: bone marrow-vehicle-2hours-rep 2

description: B6C3F1 Mouse


title: bone marrow-hypoxia-2hours-rep 1

description: B6C3F1 Mouse


title: liver-vehicle-2hours-rep 8

description: B6C3F1 Mouse


title: liver-vehicle-2hours-rep 6

description: B6C3F1 Mouse


title: liver-hypoxia-2hours-rep 8

description: B6C3F1 Mouse


title: liver-vehicle-2hours-rep 5

description: B6C3F1 Mouse


title: bone marrow-vehicle-2hours-rep 1

description: B6C3F1 Mouse


title: Ischemic heart failure, Left Ventricle, sample 13

description: Ischemic heart failure, Left Ventricle


title: Ischemic heart failure, Left Ventricle, sample 1

description: Ischemic heart failure, Left Ventricle


title: Normal left ventricular function, Left Ventricle, sample 15

value: Normal


title: Ischemic heart failure, Left Ventricle, sample 10

description: Ischemic heart failure, Left Ventricle


title: Ischemic heart failure, Left Ventricle, sample 11

description: Ischemic heart failure, Left Ventricle


title: Ischemic heart failure, Left Ventricle, sample 3

description: Ischemic heart failure, Left Ventricle


title: Ischemic heart failure, Left Ventricle, sample 9

description: Ischemic heart failure, Left Ventricle


title: Ischemic heart failure, Left Ventricle, sample 5

description: Ischemic heart failure, Left Ventricle


title: Ischemic heart failure, Left Ventricle, sample 2

description: Ischemic heart failure, Left Ventricle


title: 322

value: female

value: Other

value: Pos

tag: tri 8

value: HpaII


title: Ischemic heart failure, Left Ventricle, sample 7

description: Ischemic heart failure, Left Ventricle


title: Ischemic heart failure, Left Ventricle, sample 8

description: Ischemic heart failure, Left Ventricle


title: spleen-vehicle-2hours-rep 2

description: B6C3F1 Mouse

value: Spleen


title: Ischemic heart failure, Left Ventricle, sample 4

description: Ischemic heart failure, Left Ventricle


title: Ischemic heart failure, Left Ventricle, sample 6

description: Ischemic heart failure, Left Ventricle


title: liver-vehicle-2hours-rep 3

description: B6C3F1 Mouse

value: Liver

value: control


title: liver-hypoxia-2hours-rep 2

description: B6C3F1 Mouse

value: 2 hours


title: liver-hypoxia-2hours-rep 5

description: B6C3F1 Mouse


title: liver-vehicle-2hours-rep 2

description: B6C3F1 Mouse


title: liver-vehicle-2hours-rep 1

description: B6C3F1 Mouse


title: liver-vehicle-2hours-rep 4

description: B6C3F1 Mouse


title: liver-hypoxia-2hours-rep 4

description: B6C3F1 Mouse


title: spleen-2BE-7days-rep 5

description: B6C3F1 Mouse

data_processing: RNA expression data were analyzed using the Affymetrix and lpackages of the Bioconductor suite of microarray analysis tools available for the R statistical environment (Gentleman, 2005; Gentleman et al., 2004; Irizarry et al., 2003; R Development Core Team, 2007).  Robust Microarray Analysis (RMA) background correction and quantile normalization were used to generate microarray expression values.  An overall linear model was fit to the data for all sample groups and specific contrasts of interest were evaluated to generate raw p-values for each probe set on the expression array (Smyth, 2004).  The Benjamini-Hochberg False Discovery Rate (FDR) method was then used to correct for multiple testing effects.  Probe sets were considered to have changed qualitatively in a specific comparison if an adjusted p-value of 0.05 was obtained, their average expression intensity was above 150 in either treatment group, and they had an absolute fold change greater than 1.3.

value: 7 days


title: liver-hypoxia-2hours-rep 1

description: B6C3F1 Mouse


title: liver-hypoxia-2hours-rep 7

description: B6C3F1 Mouse


title: liver-hypoxia-2hours-rep 3

description: B6C3F1 Mouse


title: liver-hypoxia-2hours-rep 6

description: B6C3F1 Mouse


title: Normal left ventricular function, Left Ventricle, sample 14


title: liver-vehicle-1day-rep 1

value: Vehicle

value: 1 day


title: Normal left ventricular function, Left Ventricle, sample 12


title: Normal left ventricular function, Left Ventricle, sample 13


title: Normal left ventricular function, Left Ventricle, sample 11


title: Normal left ventricular function, Left Ventricle, sample 7


title: spleen-vehicle-7days-rep 5

description: B6C3F1 Mouse


title: Normal left ventricular function, Left Ventricle, sample 9


title: Normal left ventricular function, Left Ventricle, sample 10


title: spleen-2BE-7days-rep 2

description: B6C3F1 Mouse


title: Normal left ventricular function, Left Ventricle, sample 4


title: spleen-vehicle-7days-rep 3

description: B6C3F1 Mouse


title: spleen-2BE-7days-rep 4

description: B6C3F1 Mouse


title: spleen-vehicle-7days-rep 4

description: B6C3F1 Mouse


title: spleen-vehicle-7days-rep 2

description: B6C3F1 Mouse


title: Normal left ventricular function, Left Ventricle, sample 6


title: bone marrow-2BE-7days-rep 4

description: B6C3F1 Mouse

source_name: bone marrow-2BE-7days