title: Chinese Female, NA18564, slide 22

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: Japanese Female, NA18997, slide 22

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 NA18997 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: Immortalized cell line, Japanese 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: Japanese

tag: gender

value: female

tag: sample source

value: HapMap

tag: sample type

value: test

source_name: NA10851 reference

value: Caucasian

value: male

value: reference


title: Japanese Female, NA18949, slide 22

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, NA18552, slide 4

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.

source_name: Immortalized cell line, Chinese female

value: Chinese


title: Japanese Female, NA18951, slide 22

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, NA18969, slide 4

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: Japanese Female, NA18973, slide 22

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: Japanese Female, NA18968, slide 4

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, NA18537, slide 22

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, NA18566, slide 22

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: Chinese Female, NA18542, slide 22

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: CEU Female, NA12878, slide 4

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

value: control


title: Japanese Female, NA18969, slide 22


title: Japanese Female, NA18999, slide 4

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 4


title: Chinese Female, NA18537, slide 4


title: Japanese Female, NA18942, slide 22

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: Japanese Female, NA18951, slide 4


title: Chinese Female, NA18526, slide 22

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: Chinese Female, NA18566, slide 4


title: Japanese Female, NA18972, slide 22

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 22

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: Japanese Female, NA18942, slide 4


title: Chinese Female, NA18542, slide 4


title: Chinese Female, NA18547, slide 22

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, NA18973, slide 4


title: Japanese Female, NA18949, slide 4


title: Chinese Female, NA18570, slide 4

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: Chinese Female, NA18570, slide 22


title: Korean Female, AK16, slide 22

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


title: Japanese Female, NA18947, slide 4


title: Korean Female, AK14, slide 22

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, AK12, slide 22

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, AK18, slide 22

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, NA18547, slide 4


title: Korean Female, AK10, slide 22

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: Korean Female, AK18, slide 4


title: Korean Female, AK20, slide 22

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: Chinese Female, NA18592, slide 4

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: Korean Female, AK20, slide 4


title: Korean Female, AK4, slide 22

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: Chinese Female, NA18526, slide 4


title: Chinese Female, NA18592, slide 22


title: Japanese Female, NA18972, slide 4


title: Korean Female, AK8, slide 22

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: Korean Female, AK16, slide 4


title: Korean Female, AK2, slide 22

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: Korean Female, AK6, slide 4

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: YRI Female, NA19240, slide 20

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: Korean Female, AK6, slide 22


title: Korean Female, AK14, slide 4


title: Korean Female, AK10, slide 4


title: Korean Male, AK1, slide 22

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


title: Korean Female, AK4, slide 4


title: Korean Female, AK12, slide 4


title: Chinese Female, NA18552, slide 20

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: Korean Male, AK1, slide 4


title: Korean Female, AK2, slide 4


title: Chinese Female, NA19582, slide 20

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: panicle 1, Zhenshan 97, biological rep2, technical rep2

status: Public on Jan 20 2010

type: RNA

city: Wuhan

first: Weibo

last: Xie

state: Hubei

address: Luoshi Road

department: College of Life Science and Technology

country: China

institute: Huazhong Agricultural University

hyb_protocol: Microarray hybridization were conducted by the CapitalBio Corporation (Beijing, China) according to the Affymetrix standard protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The probe intensity files (.cel files) for expression profiles were read into R. Background correction, quantile normalization and summarization were performed using the RMA method in Bioconductor affy package.

label: biotin

molecule: total RNA

organism: Oryza sativa Indica Group

source_name: developing panicle with length less than 1mm, Zhenshan 97

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Rice seeds were soaked in fresh water until germination. Then the germinated rice seeds were planted in a seed bed in mid-May, and seedling of 20 days old were transplanted to the field and managed according to normal agricultural conditions in the experimental farm of Huazhong Agricultural University, Wuhan, China.

extract_protocol: Total RNA extraction was performed using Trizol, according to the manufacturer's instructions.

treatment_protocol: Untreated.

tag: subspecies

value: indica

tag: variety

value: Zhenshan 97


title: Japanese Female, NA18968, slide 20

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: Japanese Female, NA18997, slide 20

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, NA18969, slide 20

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: CEU Female, NA12878, slide 20

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: Japanese Female, NA18999, slide 20

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: YRI Female, NA19240, slide 3


title: Chinese Female, NA18564, slide 20

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: Japanese Female, NA18999, slide 3


title: Japanese Female, NA18949, slide 20

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, NA18552, slide 3


title: CEU Female, NA12878, slide 3


title: Chinese Female, NA18566, slide 20

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: Japanese Female, NA18968, slide 3


title: Chinese Female, NA18542, slide 20

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: Japanese Female, NA18997, slide 3


title: Japanese Female, NA18969, slide 3


title: Chinese Female, NA18537, slide 20

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: Japanese Female, NA18942, slide 20

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: Chinese Female, NA18564, slide 3


title: Japanese Female, NA18951, slide 20

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: Chinese Female, NA19582, slide 3


title: Korean Female, AK8, slide 4

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: Japanese Female, NA18973, slide 3

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: Japanese Female, NA18973, slide 20


title: Chinese Female, NA18537, slide 3


title: Japanese Female, NA18949, slide 3


title: Chinese Female, NA18526, slide 20

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: Chinese Female, NA18570, slide 20

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, NA18972, slide 20

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: Chinese Female, NA18542, slide 3


title: Chinese Female, NA18547, slide 20

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, NA18947, slide 20

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: Japanese Female, NA18951, slide 3


title: Chinese Female, NA18566, slide 3


title: Chinese Female, NA18526, slide 3


title: Japanese Female, NA18942, slide 3


title: Chinese Female, NA18570, slide 3


title: Korean Female, AK18, slide 20

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, NA18547, slide 3


title: Japanese Female, NA18947, slide 3


title: Korean Female, AK20, slide 3

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: Korean Female, AK20, slide 20


title: Chinese Female, NA18592, slide 3

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: Korean Female, AK16, slide 20

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: Chinese Female, NA18592, slide 20


title: Korean Female, AK10, slide 20

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: Korean Female, AK8, slide 20


title: Korean Female, AK16, slide 3


title: Korean Female, AK6, slide 20

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, AK14, slide 20

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 3


title: Korean Female, AK12, slide 20

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: YRI Female, NA19240, slide 16

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.


title: Japanese Female, NA18972, slide 3


title: Korean Female, AK2, slide 20

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: Korean Female, AK12, slide 3


title: Korean Female, AK4, slide 20

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 Male, AK1, slide 20

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.


title: Korean Female, AK6, slide 3


title: Korean Female, AK4, slide 3


title: Korean Female, AK2, slide 3


title: Korean Female, AK8, slide 3

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: CEU Female, NA12878, slide 16

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, AK10, slide 3


title: Korean Male, AK1, slide 3


title: YRI Female, NA19240, slide 2


title: Chinese Female, NA18552, slide 16

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: Japanese Female, NA18997, slide 16

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, NA19582, slide 16

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: Japanese Female, NA18999, slide 16

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, NA18537, slide 16

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: Japanese Female, NA18968, slide 16

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: Japanese Female, NA18973, slide 16

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, AK14, slide 3


title: Japanese Female, NA18999, slide 2


title: Chinese Female, NA19582, slide 2


title: CEU Female, NA12878, slide 2


title: Chinese Female, NA18564, slide 16

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: Chinese Female, NA18564, slide 2


title: Japanese Female, NA18968, slide 2


title: Chinese Female, NA18552, slide 2


title: Japanese Female, NA18969, slide 16

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, NA18537, slide 2


title: Japanese Female, NA18997, slide 2


title: Chinese Female, NA18542, slide 16

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: Chinese Female, NA18566, slide 16

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: Japanese Female, NA18949, slide 16

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 16

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, NA18951, slide 2


title: Japanese Female, NA18973, slide 2


title: Japanese Female, NA18947, slide 16

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: Japanese Female, NA18969, slide 2


title: Chinese Female, NA18592, slide 16

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: Japanese Female, NA18942, slide 16

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: Japanese Female, NA18942, slide 2


title: Japanese Female, NA18972, slide 2

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, NA18972, slide 16


title: Chinese Female, NA18526, slide 2

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: Chinese Female, NA18570, slide 16

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: Korean Female, AK18, slide 16

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, NA18566, slide 2


title: Japanese Female, NA18949, slide 2


title: Chinese Female, NA18547, slide 16

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, NA18947, slide 2


title: Korean Female, AK12, slide 16

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, AK20, slide 16

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: Chinese Female, NA18526, slide 16


title: Korean Female, AK20, slide 2


title: Chinese Female, NA18542, slide 2


title: Chinese Female, NA18570, slide 2


title: Chinese Female, NA18592, slide 2


title: Korean Female, AK16, slide 16

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: Chinese Female, NA18547, slide 2


title: Korean Female, AK10, slide 16

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: Korean Female, AK2, slide 16

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: YRI Female, NA19240, slide 9

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.


title: CEU Female, NA12878, slide 9

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: YRI Female, NA19240, slide 1


title: Korean Female, AK14, slide 16

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, AK8, slide 16

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: Korean Male, AK1, slide 16

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.


title: Chinese Female, NA19582, slide 1

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: Chinese Female, NA18537, slide 1

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: Japanese Female, NA18968, slide 1

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: Japanese Female, NA18949, slide 1

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, NA18969, slide 9

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, AK4, slide 16

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 1

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, NA18999, slide 1

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: Korean Female, AK6, slide 16

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, AK18, slide 2

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: Japanese Female, NA18969, slide 1


title: Japanese Female, NA18997, slide 1

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 9


title: CEU Female, NA12878, slide 1


title: Chinese Female, NA19582, slide 9


title: Chinese Female, NA18552, slide 9

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: Chinese Female, NA18542, slide 1

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: Chinese Female, NA18564, slide 1

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: Japanese Female, NA18949, slide 9


title: Chinese Female, NA18566, slide 1

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: Japanese Female, NA18997, slide 9


title: Japanese Female, NA18968, slide 9


title: Chinese Female, NA18537, slide 9


title: Chinese Female, NA18564, slide 9


title: Japanese Female, NA18973, slide 1

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: Japanese Female, NA18973, slide 9


title: Japanese Female, NA18942, slide 1

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: Japanese Female, NA18951, slide 9


title: Chinese Female, NA18526, slide 1

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: Chinese Female, NA18570, slide 1

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, NA18972, slide 1

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, NA18972, slide 9


title: Chinese Female, NA18566, slide 9


title: Chinese Female, NA18592, slide 1

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, NA18547, slide 1

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: Chinese Female, NA18570, slide 9


title: Japanese Female, NA18942, slide 9


title: Japanese Female, NA18947, slide 1

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, NA18592, slide 9


title: Chinese Female, NA18526, slide 9


title: Korean Female, AK18, slide 1


title: Korean Female, AK16, slide 1

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: Korean Female, AK14, slide 1

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, AK20, slide 9

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: Japanese Female, NA18947, slide 9


title: Chinese Female, NA18542, slide 9


title: Patient_61_6hr_NT_rep1

city: Lyon

first: Lars

middle: Petter

last: Jordheim

address: 8 Av Rockefeller

country: France

institute: INSERM U590

description: Gene expression after 6h incubation of human leukemic blasts

hyb_protocol: Cy3-labelled cRNA was fragmented at 60 °C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Whole Human Genome 4 x 44K microarrays (G4112F) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) with default settings, and data extracted by Feature Extraction software, version 9.5.

data_processing: Data were normalized using the quantile method

source_name: Leukemic blasts, 6hr, untreated, repilicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendations and quantified on a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). RNA integrity was verified using the BioAnalyser 2100™ (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Isolated leukemic blasts from AML patients were incubated in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum in presence or absence of 10 µM AS602868 for 6 hours at 37 ºC in a humidified incubator with 5% CO2

tag: cell type

value: leukemic blast

value: f

tag: age


title: Korean Female, AK18, slide 9

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, NA18547, slide 9


title: Korean Female, AK20, slide 1


title: Patient_61_6hr_AS602868_10µM_rep1

description: Gene expression after 6h exposure of human leukemic blasts to 10 µM AS602868

source_name: Leukemic blasts, 6hr, AS602868, 10µM, repilicate 1


title: Korean Female, AK12, slide 1

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 1

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: Patient_60_6hr_NT_rep1


title: Korean Female, AK14, slide 9


title: YRI Female, NA19240, slide 10

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.


title: Korean Female, AK8, slide 1

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: Patient_59_6hr_NT_rep1


title: Patient_60_6hr_AS602868_10µM_rep1


title: Korean Female, AK16, slide 9


title: Korean Female, AK12, slide 9


title: Korean Female, AK6, slide 1

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, AK4, slide 1

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: Chinese Female, NA19582, slide 10

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: Korean Female, AK6, slide 9


title: Korean Female, AK8, slide 9


title: Korean Female, AK4, slide 9


title: Korean Female, AK10, slide 9


title: Patient_58_6hr_NT_rep1


title: Patient_59_6hr_AS602868_10µM_rep1


title: Korean Female, AK2, slide 9

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: Korean Female, AK2, slide 1


title: Chinese Female, NA18552, slide 10

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: CEU Female, NA12878, slide 10

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 Male, AK1, slide 9

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.


title: Patient_58_6hr_AS602868_10µM_rep1


title: Japanese Female, NA18999, slide 10

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: Patient_57_6hr_NT_rep1


title: Patient_57_6hr_AS602868_10µM_rep1


title: Korean Male, AK1, slide 1


title: CEU Female, NA12878, slide 7


title: Patient_56_6hr_NT_rep1


title: Japanese Female, NA18997, slide 10

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 10

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: YRI Female, NA19240, slide 7


title: Japanese Female, NA18969, slide 10

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, AK12, slide 2


title: Korean Female, AK14, slide 2

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: Patient_56_6hr_AS602868_10µM_rep1

description: Gene expression after 6h exposure of human leukemic blasts to 10 µM AS602868


title: DFCI #120 250 pg rep1

city: San Diego

first: Craig

last: April

state: CA

address: 9885 Towne Centre Drive

country: USA

institute: Illumina, Inc.

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
Raw data was analyzed using GenomeStudio v1.1.

Non-normalized data is available in the 'GSE18769_nonorm_nobkgd.txt' file, which is linked to the Series GSE18769 record as a supplementary file.

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).

treatment_protocol: Formalin-fixed, paraffin-embedded.

tag: tissue

value: ovarian tumor

value: DFCI 120

tag: amount


title: Patient_55_6hr_NT_rep1

description: Gene expression after 6h incubation of human leukemic blasts

value: m


title: Chinese Female, NA19582, slide 7

value: female

value: HapMap


title: DFCI #120 1 ng rep2

description: replicate 2

value: 1 ng


title: Chinese Female, NA18564, slide 10

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.

value: test

value: Caucasian

value: male


title: Patient_55_6hr_AS602868_10µM_rep1


title: Korean Female, AK16, slide 2

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: reference


title: Korean Female, AK10, slide 2

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: Korean


title: DFCI #120 250 pg rep2

description: replicate 2


title: Patient_54_6hr_NT_rep1


title: DFCI #120 5 ng rep2

description: replicate 2

value: 5 ng


title: Japanese Female, NA18999, slide 7

value: Japanese


title: Chinese Female, NA18537, slide 10

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.

value: Chinese


title: Korean Female, AK8, slide 2

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: anonymous


title: DFCI #120 10 ng rep2

description: replicate 2

value: 10 ng


title: Patient_54_6hr_AS602868_10µM_rep1

value: leukemic blast


title: Chinese Female, NA18552, slide 7


title: Korean Female, AK4, slide 2

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: DFCI #120 50 ng rep2

description: replicate 2

value: ovarian tumor

value: 50 ng


title: Japanese Female, NA18949, slide 10

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, NA18968, slide 7


title: Japanese Female, NA18969, slide 7


title: Patient_53_6hr_NT_rep1

value: m


title: Japanese Female, NA18997, slide 7

value: female


title: Patient_53_6hr_AS602868_10µM_rep1


title: Korean Female, AK6, slide 2

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.

value: HapMap


title: Korean Female, AK2, slide 2

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 7


title: Japanese Female, NA18973, slide 10

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: DFCI #120 200 ng rep2

description: replicate 2

value: DFCI 120


title: Japanese Female, NA18973, slide 7

value: test


title: Korean Male, AK1, slide 2

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

value: Caucasian


title: Chinese Female, NA18566, slide 10

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.

value: male

value: reference


title: DFCI #120 1 ng rep1

description: replicate 1

value: 1 ng


title: Chinese Female, NA18542, slide 10

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: Patient_52_6hr_NT_rep1


title: Japanese Female, NA18951, slide 10

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.

value: Japanese


title: Japanese Female, NA18942, slide 10

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: Patient_52_6hr_AS602868_10µM_rep1

description: Gene expression after 6h exposure of human leukemic blasts to 10 µM AS602868


title: DFCI #120 10 ng rep1

description: replicate 1


title: DFCI #120 5 ng rep1

description: replicate 1

value: 5 ng


title: Chinese Female, NA18526, slide 10

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: Chinese


title: Patient_51_6hr_NT_rep1

description: Gene expression after 6h incubation of human leukemic blasts


title: Patient_51_6hr_AS602868_10µM_rep1


title: Chinese Female, NA18537, slide 7


title: Patient_50_6hr_NT_rep1

value: f


title: Patient_50_6hr_AS602868_10µM_rep1

value: leukemic blast


title: DFCI #120 200 ng rep1

description: replicate 1

value: ovarian tumor


title: DFCI #120 50 ng rep1

description: replicate 1

value: 50 ng


title: Chinese Female, NA18570, slide 10

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: Patient_49_6hr_NT_rep1


title: Chinese Female, NA18542, slide 7


title: DFCI #129 1 ng rep1

description: replicate 1

value: DFCI 129


title: Japanese Female, NA18947, slide 10

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: female


title: DFCI #129 250 pg rep1

description: replicate 1


title: Patient_49_6hr_AS602868_10µM_rep1


title: Japanese Female, NA18951, slide 7

value: HapMap


title: DFCI #129 5 ng rep2

description: replicate 2


title: Japanese Female, NA18942, slide 7


title: Japanese Female, NA18949, slide 7


title: DFCI #129 50 ng rep2

description: replicate 2


title: Patient_48_6hr_NT_rep1


title: Patient_48_6hr_AS602868_10µM_rep1


title: DFCI #129 10 ng rep2

description: replicate 2

value: 10 ng


title: Chinese Female, NA18592, slide 10

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: test


title: Japanese Female, NA18972, slide 10

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: Chinese Female, NA18526, slide 7


title: Patient_47_6hr_NT_rep1


title: Japanese Female, NA18972, slide 7


title: Chinese Female, NA18566, slide 7


title: DFCI #129 200 ng rep2

description: replicate 2


title: Patient_47_6hr_AS602868_10µM_rep1


title: Chinese Female, NA18547, slide 10

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, AK20, slide 10

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: DFCI #129 250 pg rep2

description: replicate 2


title: Chinese Female, NA18547, slide 7

value: Caucasian

value: male


title: Patient_46_6hr_NT_rep1

value: m


title: Japanese Female, NA18947, slide 7

value: Japanese

value: reference


title: Korean Female, AK18, slide 10

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, AK14, slide 10

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: DFCI #129 1 ng rep2

description: replicate 2

value: 1 ng


title: Chinese Female, NA18592, slide 7

value: Chinese


title: Patient_46_6hr_AS602868_10µM_rep1

value: leukemic blast


title: Korean Female, AK12, slide 10

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: DFCI #129 5 ng rep1

description: replicate 1

value: ovarian tumor

value: 5 ng


title: DFCI #129 10 ng rep1

description: replicate 1

value: DFCI 129


title: Korean Female, AK16, slide 10

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: female


title: Korean Female, AK14, slide 7

value: HapMap


title: Patient_45_6hr_AS602868_10µM_rep1


title: DFCI #129 50 ng rep1

description: replicate 1

value: 50 ng


title: Patient_45_6hr_NT_rep1


title: Korean Female, AK8, slide 10

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: DFCI #129 200 ng rep1

description: replicate 1


title: Patient_44_6hr_NT_rep1

value: f


title: DFCI #121/123 0/100 rep6

description: replicate 6

data_processing:
Raw data was analyzed using GenomeStudio v1.1.

Non-normalized data is available in the 'GSE18767_nonorm_nobkgd.txt' file, which is linked to the Series GSE18767 record as a supplementary file.

tag: cell types

value: DFCI 123

tag: ratio mix


title: Korean Female, AK4, slide 10

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: Korean

value: anonymous

value: Caucasian


title: Patient_44_6hr_AS602868_10µM_rep1


title: Chinese Female, NA18570, slide 7

value: male


title: Patient_43_6hr_NT_rep1

value: m


title: Korean Female, AK18, slide 7

value: reference


title: Korean Female, AK6, slide 10

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, AK20, slide 7


title: Time series time 60 minute after iron repletion, Replicate 3

type: mixed

city: Oak Ridge

first: Yunfeng

last: Yang

address: 1 Bethel Valley Road

department: Biosciences Division

institute: Oak Ridge National Lab

description: Biological replicate 3 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 60 minute

hyb_protocol: The labeled cDNA and gDNA pools were mixed and hybridized simultaneously to the array on UltraGAPS slides (Corning) in a solution containing 5x SSC, 0.1% SDS, and  0.1 mg/mL of herring sperm DNA (Gibco BRL).  The entire process of hybridization, including prehybridization, hybridization, and post-hybridization wash, was performed following the manufacturer's instructions.

scan_protocol: Microarrays were scanned using the confocal laser microscope of the ScanArray Gx Microarray Analysis System (PerkinElmer) at a resolution of 5 Âµm per pixel. Scanning parameters (laser power and photomultiplier tube or PMT gain) were adjusted, so that overall intensities in both fluorescence channels were relatively equal and few spots were saturated.

data_processing: To determine fluorescence intensity (pixel density) and background intensity, 16-bit TIFF scanned images were analyzed using the software ImaGene version 7.0 (Biodiscovery). The text files from ImaGene were then analyzed using standard procedure as published in Appl Environ Microbiol 2006, 72(8):5578-5588. Specifically, The data files were subjected to Lowess intensity-based normalization and were analyzed further using GeneSpring, version 5.1 (Silicon Genetics, Redwood City, CA). To assess the statistical significance of individual data points, A statistical model incorporating per-gene variance (z values) was used to compute the posterior probability that the expression level of each gene changed in the direction indicated by the mean value. Ratios with |log3(ratio)| > 1 or |z| > 2.0 are considered significant.

organism: Shewanella oneidensis MR-1

source_name: total RNA extracted from MR-1 cells treated with ferrous sulfate for 60 minute

label_protocol: Fluorescently Cy5-labeled cDNA copies of total cellular RNA extracted from MR-1 were prepared by incorporation of fluorescein-labeled nucleotide analogs during a first-strand reverse transcription reaction following the manufacturer's instructions (Invitrogen).

growth_protocol: MR-1 were grown in 100 ml LB medium in 500 ml shake flasks with vigorous shaking at 250–300 rpm

extract_protocol: Total cellular RNAs from MR-1 were isolated using the TRIzol Reagent (Gibco BRL) following manufacturer's instructions. After precipitation, RNA samples were purified with the Qiagen RNeasy Mini kit (Qiagen) following the manufacturer's instructions.

tag: strain

tag: agent

value: ferrous sulfate

tag: time

value: 60 minutes

source_name: total genomic DNA extracted from MR-1 cells grown to stationary phase (reference)

label_protocol: MR-1 genomic DNA (gDNA) was amplified by Klenow following the manufacturer's instructions (Invitrogen), and Cy3 dUTP (Amersham Biosciences) was incorporated into the product. Fluorescein-labeled probes were purified using the Qiaquick PCR purification kit (Qiagen).

extract_protocol: MR-1 cells were lysed by repeated boiling-frozen cycles. DNA were precipitated by isoproposal after succssive extraction with phenol, phenol-chloroform and chloroform


title: Time series time 60 minute after iron repletion, Replicate 4

description: Biological replicate 4 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 60 minute


title: Korean Female, AK2, slide 10

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: Time series time 60 minute after iron repletion, Replicate 2

description: Biological replicate 2 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 60 minute


title: DFCI #121/123 25/75 rep6

description: replicate 6

value: ovarian tumor

value: DFCI 121, DFCI 123


title: Korean Female, AK10, slide 7

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: Korean Female, AK16, slide 7


title: Patient_43_6hr_AS602868_10µM_rep1

description: Gene expression after 6h exposure of human leukemic blasts to 10 µM AS602868

value: leukemic blast


title: Korean Female, AK10, slide 10

value: female


title: YRI Female, NA19240, slide 8

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

value: HapMap

value: control


title: Time series time 60 minute after iron repletion, Replicate 1

description: Biological replicate 1 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 60 minute


title: DFCI #121/123 50/50 rep6

description: replicate 6


title: Patient_42_6hr_NT_rep1

description: Gene expression after 6h incubation of human leukemic blasts

value: f


title: DFCI #121/123 75/25 rep6

description: replicate 6


title: DFCI #121/123 66/33 rep6

description: replicate 6


title: Korean Female, AK8, slide 7

value: test


title: Time series time 40 minute after iron repletion, Replicate 4

description: Biological replicate 4 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 40 minute

source_name: total RNA extracted from MR-1 cells treated with ferrous sulfate for 40 minute

value: 40 minutes


title: Patient_42_6hr_AS602868_10µM_rep1


title: Korean Male, AK1, slide 10

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: Korean

value: anonymous


title: Time series time 40 minute after iron repletion, Replicate 3

description: Biological replicate 3 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 40 minute


title: CEU Female, NA12878, slide 8

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: Caucasian

value: male


title: Chinese Female, NA19582, slide 8

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: Chinese

value: reference


title: Korean Female, AK6, slide 7


title: DFCI #121/123 100/0 rep6

description: replicate 6

value: DFCI 121


title: Time series time 40 minute after iron repletion, Replicate 2

description: Biological replicate 2 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 40 minute

value: ferrous sulfate


title: Time series time 40 minute after iron repletion, Replicate 1

description: Biological replicate 1 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 40 minute


title: DFCI #121/123 33/66 rep6

description: replicate 6

value: ovarian tumor

value: DFCI 121, DFCI 123


title: DFCI #121/123 33/66 rep5

description: replicate 5

value: female


title: Time series time 20 minute after iron repletion, Replicate 3

description: Biological replicate 3 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 20 minute

source_name: total RNA extracted from MR-1 cells treated with ferrous sulfate for 20 minute

value: 20 minutes


title: DFCI #121/123 25/75 rep5

description: replicate 5


title: DFCI #121/123 0/100 rep5

description: replicate 5

value: DFCI 123


title: Japanese Female, NA18999, slide 8

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.

value: Japanese

value: HapMap


title: Korean Female, AK4, slide 7

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: test


title: Korean Male, AK1, slide 7

value: control


title: Chinese Female, NA18552, slide 8

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: DFCI #121/123 50/50 rep5

description: replicate 5


title: Korean Female, AK12, slide 7

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.

value: Korean


title: Time series time 20 minute after iron repletion, Replicate 2

description: Biological replicate 2 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 20 minute


title: Time series time 20 minute after iron repletion, Replicate 1

description: Biological replicate 1 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 20 minute


title: Korean Female, AK2, slide 7

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: anonymous


title: Japanese Female, NA18997, slide 8

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.

value: Caucasian


title: Japanese Female, NA18968, slide 8

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: male


title: Chinese Female, NA18537, slide 8

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.

value: Chinese


title: Japanese Female, NA18969, slide 8

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: reference


title: Time series time 10 minute after iron repletion, Replicate 4

description: Biological replicate 4 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 10 minute

source_name: total RNA extracted from MR-1 cells treated with ferrous sulfate for 10 minute

value: 10 minutes


title: DFCI #121/123 66/33 rep5

description: replicate 5


title: Time series time 10 minute after iron repletion, Replicate 3

description: Biological replicate 3 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 10 minute

value: ferrous sulfate


title: Time series time 20 minute after iron repletion, Replicate 4

description: Biological replicate 4 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 20 minute


title: DFCI #121/123 100/0 rep5

description: replicate 5

value: ovarian tumor

value: DFCI 121


title: Chinese Female, NA18564, slide 8

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.

value: female


title: Time series time 10 minute after iron repletion, Replicate 2

description: Biological replicate 2 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 10 minute


title: DFCI #121/123 0/100 rep4

description: replicate 4


title: Time series time 10 minute after iron repletion, Replicate 1

description: Biological replicate 1 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 10 minute


title: DFCI #121/123 75/25 rep5

description: replicate 5

value: DFCI 121, DFCI 123


title: YRI Female, NA19240, slide 24

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: DFCI #121/123 33/66 rep4

description: replicate 4


title: Japanese Female, NA18949, slide 8

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: CEU Female, NA12878, slide 24

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: HapMap


title: DFCI #121/123 25/75 rep4

description: replicate 4


title: Japanese Female, NA18951, slide 8

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.

value: test


title: Time series time 5 minute after iron repletion, Replicate 4

description: Biological replicate 4 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 5 minute

source_name: total RNA extracted from MR-1 cells treated with ferrous sulfate for 5 minute

value: 5 minutes


title: Time series time 5 minute after iron repletion, Replicate 3

description: Biological replicate 3 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 5 minute


title: Chinese Female, NA18542, slide 8

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: DFCI #121/123 50/50 rep4

description: replicate 4


title: Time series time 5 minute after iron repletion, Replicate 2

description: Biological replicate 2 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 5 minute


title: DFCI #121/123 66/33 rep4

description: replicate 4


title: Japanese Female, NA18973, slide 8

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.

source_name: Immortalized cell line, Japanese female


title: Chinese Female, NA18552, slide 24

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.

source_name: NA10851 reference


title: Chinese Female, NA18566, slide 8

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.

source_name: Immortalized cell line, Chinese female


title: Time series time 5 minute after iron repletion, Replicate 1

description: Biological replicate 1 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 5 minute


title: Japanese Female, NA18942, slide 8

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: Japanese Female, NA18999, slide 24

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 24

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: Time series time 1 minute after iron repletion, Replicate 4

description: Biological replicate 4 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 1 minute

source_name: total RNA extracted from MR-1 cells treated with ferrous sulfate for 1 minute

value: 1 minutes


title: DFCI #121/123 100/0 rep4

description: replicate 4


title: DFCI #121/123 0/100 rep3

description: replicate 3

value: DFCI 123


title: Chinese Female, NA18526, slide 8

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: DFCI #121/123 75/25 rep4

description: replicate 4


title: Time series time 1 minute after iron repletion, Replicate 3

description: Biological replicate 3 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 1 minute


title: Chinese Female, NA18570, slide 8

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: male


title: Japanese Female, NA18968, slide 24

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, NA19582, slide 24

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: Chinese


title: Time series time 1 minute after iron repletion, Replicate 2

description: Biological replicate 2 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 1 minute


title: Japanese Female, NA18973, slide 24

value: reference


title: DFCI #121/123 33/66 rep3

description: replicate 3


title: DFCI #121/123 25/75 rep3

description: replicate 3


title: Chinese Female, NA18564, slide 24

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: Japanese Female, NA18947, slide 8

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, NA18547, slide 8

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 24

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: DFCI #121/123 50/50 rep3

description: replicate 3


title: Time series time 1 minute after iron repletion, Replicate 1

description: Biological replicate 1 from MR-1 sample after iron repletion by treatment with ferrous sulfate for 1 minute


title: Korean Female, AK20, slide 8

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.

source_name: Blood cells, Korean female

value: Korean

value: anonymous


title: Japanese Female, NA18972, slide 8

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: Time series time 60 minute after iron depletion, Replicate 4

description: Biological replicate 4 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 60 minute

source_name: total RNA extracted from MR-1 cells treated with iron chelator for 60 minute

value: iron chelator

value: 60 minutes


title: Chinese Female, NA18592, slide 8

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: female


title: Japanese Female, NA18969, slide 24

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: Time series time 60 minute after iron depletion, Replicate 3

description: Biological replicate 3 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 60 minute


title: Chinese Female, NA18537, slide 24

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: DFCI #121/123 66/33 rep3

description: replicate 3

value: ovarian tumor

value: DFCI 121, DFCI 123


title: Japanese Female, NA18949, slide 24

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: Time series time 60 minute after iron depletion, Replicate 1

description: Biological replicate 1 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 60 minute


title: DFCI #121/123 100/0 rep3

description: replicate 3

value: DFCI 121


title: DFCI #121/123 75/25 rep3

description: replicate 3


title: Time series time 40 minute after iron depletion, Replicate 4

description: Biological replicate 4 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 40 minute

source_name: total RNA extracted from MR-1 cells treated with iron chelator for 40 minute

value: 40 minutes


title: DFCI #121/123 0/100 rep2

description: replicate 2


title: Korean Female, AK14, slide 8

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: test

value: HapMap


title: Chinese Female, NA18566, slide 24

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: Time series time 40 minute after iron depletion, Replicate 3

description: Biological replicate 3 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 40 minute


title: Time series time 60 minute after iron depletion, Replicate 2

description: Biological replicate 2 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 60 minute


title: Time series time 40 minute after iron depletion, Replicate 2

description: Biological replicate 2 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 40 minute


title: DFCI #121/123 33/66 rep2

description: replicate 2


title: Korean Female, AK16, slide 8

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: Chinese Female, NA18570, slide 24

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: Korean Female, AK12, slide 8

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: DFCI #121/123 25/75 rep2

description: replicate 2


title: Japanese Female, NA18942, slide 24

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: Chinese Female, NA18542, slide 24

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: Japanese Female, NA18972, slide 24

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: Korean Female, AK18, slide 8

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, AK10, slide 8

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: Time series time 40 minute after iron depletion, Replicate 1

description: Biological replicate 1 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 40 minute


title: DFCI #121/123 50/50 rep2

description: replicate 2


title: DFCI #121/123 66/33 rep2

description: replicate 2


title: Time series time 20 minute after iron depletion, Replicate 4

description: Biological replicate 4 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 20 minute

source_name: total RNA extracted from MR-1 cells treated with iron chelator for 20 minute

value: 20 minutes


title: Time series time 20 minute after iron depletion, Replicate 3

description: Biological replicate 3 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 20 minute


title: Korean Female, AK4, slide 8

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: Caucasian


title: Korean Female, AK8, slide 8

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: male


title: Time series time 20 minute after iron depletion, Replicate 2

description: Biological replicate 2 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 20 minute


title: DFCI #121/123 100/0 rep2

description: replicate 2


title: Chinese Female, NA18526, slide 24

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: Chinese


title: Chinese Female, NA18592, slide 24

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: reference


title: Korean Female, AK20, slide 24

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


title: Chinese Female, NA18547, slide 24

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: Time series time 20 minute after iron depletion, Replicate 1

description: Biological replicate 1 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 20 minute


title: DFCI #121/123 75/25 rep2

description: replicate 2


title: YRI Female, NA19240, slide 23

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: control


title: DFCI #121/123 0/100 rep1

description: replicate 1

value: DFCI 123


title: Korean Female, AK2, slide 8

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: anonymous


title: Chinese Female, NA19582, slide 23

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: Korean Female, AK18, slide 24


title: Time series time 10 minute after iron depletion, Replicate 4

description: Biological replicate 4 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 10 minute

source_name: total RNA extracted from MR-1 cells treated with iron chelator for 10 minute

value: iron chelator

value: 10 minutes


title: Japanese Female, NA18947, slide 24

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: Japanese


title: Korean Male, AK1, slide 8

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


title: Korean Female, AK14, slide 24

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: DFCI #121/123 50/50 rep1

description: replicate 1

source_name: Human ovarian tumor

value: ovarian tumor

value: DFCI 121, DFCI 123


title: Time series time 10 minute after iron depletion, Replicate 3

description: Biological replicate 3 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 10 minute

source_name: total genomic DNA extracted from MR-1 cells grown to stationary phase (reference)


title: DFCI #121/123 33/66 rep1

description: replicate 1


title: DFCI #121/123 66/33 rep1

description: replicate 1


title: DFCI #121/123 25/75 rep1

description: replicate 1


title: Korean Female, AK16, slide 24

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: test

value: HapMap


title: Time series time 10 minute after iron depletion, Replicate 2

description: Biological replicate 2 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 10 minute


title: Korean Female, AK12, slide 24

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.

value: Caucasian


title: Korean Female, AK6, slide 8

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.

value: male


title: Japanese Female, NA18999, slide 23

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: CEU Female, NA12878, slide 23

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: DFCI #121/123 75/25 rep1

description: replicate 1


title: Korean Female, AK10, slide 24

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: Time series time 10 minute after iron depletion, Replicate 1

description: Biological replicate 1 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 10 minute


title: Time series time 5 minute after iron depletion, Replicate 3

description: Biological replicate 3 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 5 minute

source_name: total RNA extracted from MR-1 cells treated with iron chelator for 5 minute

value: 5 minutes


title: DFCI #121/123 100/0 rep1

description: replicate 1

value: DFCI 121


title: Time series time 5 minute after iron depletion, Replicate 2

description: Biological replicate 2 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 5 minute


title: Korean Female, AK8, slide 24

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

value: reference


title: Japanese Female, NA18997, slide 23

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 23

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: MCF-7 100 ng IVT-based rep2

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

label: biotin-streptavidin Cy3

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

label_protocol: Standard Illumina labelling protocol

extract_protocol: Ambion extraction protocol

value: IVT-based


title: Korean Female, AK6, slide 24


title: Time series time 5 minute after iron depletion, Replicate 4

description: Biological replicate 4 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 5 minute


title: Raji 100 ng IVT-based rep2

description: replicate 2

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


title: MCF-7 100 ng IVT-based rep1

description: replicate 1


title: Chinese Female, NA18552, slide 23

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: Time series time 1 minute after iron depletion, Replicate 4

description: Biological replicate 4 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 1 minute

source_name: total RNA extracted from MR-1 cells treated with iron chelator for 1 minute

value: 1 minutes


title: Time series time 1 minute after iron depletion, Replicate 3

description: Biological replicate 3 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 1 minute


title: Korean Female, AK4, slide 24

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: female

value: anonymous

source_name: NA10851 reference


title: Raji 100 ng IVT-based rep1

description: replicate 1


title: Chinese Female, NA18564, slide 23

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.

source_name: Immortalized cell line, Chinese female


title: Korean Female, AK2, slide 24

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: Time series time 1 minute after iron depletion, Replicate 2

description: Biological replicate 2 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 1 minute

value: iron chelator


title: Chinese Female, NA18537, slide 23

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: MCF-7 100 ng WG-DASL rep2

description: replicate 2

value: WG-DASL


title: YRI Female, NA19240, slide 14

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

value: control


title: Time series time 1 minute after iron depletion, Replicate 1

description: Biological replicate 1 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 1 minute


title: Japanese Female, NA18969, slide 23

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: test


title: Raji 100 ng WG-DASL rep2

description: replicate 2


title: Korean Male, AK1, slide 24

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: Caucasian

value: HapMap


title: Japanese Female, NA18973, slide 23

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.

value: male


title: CEU Female, NA12878, slide 14

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: Time series time 5 minute after iron depletion, Replicate 1

description: Biological replicate 1 from MR-1 sample after iron depletion by treatment with iron chelator 2,2'-dipyridyl for 5 minute

value: 5 minutes


title: Time series time 0 before iron depletion, Replicate 4

description: Biological replicate 4 of control sample of MR-1, grown to mid-log phase, untreated.

source_name: total RNA extracted from MR-1 cells grown to mid-log phase


title: MCF-7-100 ng WG-DASL rep1

description: replicate 1


title: Time series time 0 before iron depletion, Replicate 3

description: Biological replicate 3 of control sample of MR-1, grown to mid-log phase, untreated.


title: Chinese Female, NA19582, slide 14

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: Raji 100 ng WG-DASL rep1

description: replicate 1


title: R/M 10/90 rep1

description: replicate 2

source_name: Burkitts Lymphoma (Raji) Total RNA (Ambion Cat# AM7876); Breast Adenocarcinoma (MCF-7) Total RNA (Ambion Cat# AM7846)

value: Burkitts Lymphoma (Raji) and Breast Adenocarcinoma (MCF-7)


title: Japanese Female, NA18949, slide 23

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: reference


title: Time series time 0 before iron depletion, Replicate 1

description: Biological replicate 1 of control sample of MR-1, grown to mid-log phase, untreated.


title: R/M 10/90 rep2

description: replicate 1


title: Chinese Female, NA18542, slide 23

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: Chinese Female, NA18552, slide 14

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: Chinese Female, NA18570, slide 23

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 14

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: Japanese Female, NA18969, slide 14


title: Japanese Female, NA18942, slide 23

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: Chinese Female, NA18566, slide 23

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: Japanese Female, NA18997, slide 14

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, NA18526, slide 23

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, NA18972, slide 23

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: Chinese Female, NA18564, slide 14

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: Chinese Female, NA18537, slide 14

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: Time series time 0 before iron depletion, Replicate 2

description: Biological replicate 2 of control sample of MR-1, grown to mid-log phase, untreated.


title: R/M 25/75 rep2

description: replicate 2


title: Japanese Female, NA18973, slide 14

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, NA18547, slide 23

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: R/M 33/66 rep1

description: replicate 2


title: R/M 50/50 rep1

description: replicate 2


title: R/M 33/66 rep2

description: replicate 1


title: R/M 25/75 rep1

description: replicate 1


title: Japanese Female, NA18951, slide 23

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: R/M 66/33 rep1

description: replicate 2


title: Japanese Female, NA18949, slide 14

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: R/M 50/50 rep2

description: replicate 1


title: Korean Female, AK20, slide 23

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.

source_name: Blood cells, Korean female

value: Korean


title: Chinese Female, NA18592, slide 23

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: Korean Female, AK16, slide 23

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: Korean Female, AK18, slide 23

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, NA18542, slide 14

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: R/M 75/25 rep1

description: replicate 2


title: R/M 66/33 rep2

description: replicate 1


title: Japanese Female, NA18947, slide 23

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: Japanese Female, NA18999, slide 14

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: R/M 75/25 rep2

description: replicate 1


title: Chinese Female, NA18566, slide 14

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: Korean Female, AK14, slide 23

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: R/M 90/10 rep2

description: replicate 2


title: R/M 90/10 rep1

description: replicate 1


title: Korean Female, AK10, slide 23

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: R/M 0/100 rep2

description: replicate 2

value: Breast Adenocarcinoma (MCF-7)


title: Chinese Female, NA18526, slide 14

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: female


title: Japanese Female, NA18947, slide 14


title: R/M 100/0 rep2

description: replicate 2

value: Burkitts Lymphoma (Raji)

value: 100% Raji


title: R/M 0/100 rep1

description: replicate 1


title: Korean Female, AK4, slide 23

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: anonymous


title: Korean Female, AK2, slide 23

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: Korean Female, AK12, slide 23

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: Japanese Female, NA18972, slide 14

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: Korean Female, AK8, slide 23

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: Japanese Female, NA18942, slide 14

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: Chinese Female, NA18570, slide 14

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: R/M 100/0 rep1

description: replicate 1


title: Korean Female, AK20, slide 14

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: Chinese Female, NA18547, slide 14

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: Chinese Female, NA18592, slide 14

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: CEU Female, NA12878, slide 21

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 Male, AK1, slide 23

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.


title: Korean Female, AK6, slide 23

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: YRI Female, NA19240, slide 21

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: FFPE #2-50 ng rep2

description: replicate 2

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

value: Female

value: Ovary