title: Embryonic Drosophila cells, Kc167 cells, Nup50 DamID

description: Replicates were averaged: 326969 (CH1 = Cy5, CH2 = Cy3), 329735 (CH1 = Cy3, CH2 = Cy5)

data_processing: Scanned images were processed using NimbleScan software (www.nimblegene.com) using automatic alignment and exported as pair files. Further data processing was done using the Ringo software package (J. Toedling, O. Sklyar, T. Krueger, J. J. Fischer, S. Sperling, and W. Huber. Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics, 8:221, 2007.). Data were normalized within arrays using "loess" normalization and between arrays using "Aquantile" and  log2 transformed. Replicates were averaged using mean values. Data was limited to probes mapped on major chromosomes 2L, 2R, 3L, 3R, X and 4 and duplicate and 100 bp spacing probes were removed. Probes corresponding to Nup50 were removed to avoid plasmid derived signals. Data were smoothed using running medians with windowHalfSize = 1000.

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Nup50

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23C. Full length Nup50 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: Embryonic Drosophila cells, Kc167 cells, nucleoplasmic Nup98 DamID

status: Public on Mar 01 2010

type: genomic

city: Amsterdam

first: Maarten

last: Fornerod

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: Replicates were averaged: 5377902 (CH1 = Cy5, CH2 = Cy3), 10252102 (CH1 = Cy3, CH2 = Cy5)

hyb_protocol: Arrays were hybridized in a TECAN hybridization station according to NKI Central Microarray Facility protocol (http://cmfdb.nki.nl/process/protocolView).

scan_protocol: Microarrays are scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at a variable PMT (0-100%) for each channel (Red or Green), a variable resolution (5 or 10 um per pixel) and a suitable scan area.

data_processing: Scanned images were processed using NimbleScan software (www.nimblegene.com) using automatic alignment and exported as pair files. Further data processing was done using the Ringo software package (J. Toedling, O. Sklyar, T. Krueger, J. J. Fischer, S. Sperling, and W. Huber. Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics, 8:221, 2007.). Data were normalized within arrays using "loess" normalization and between arrays using "Aquantile" and  log2 transformed. Replicates were averaged using mean values. Data was limited to probes mapped on major chromosomes 2L, 2R, 3L, 3R, X and 4 and duplicate and 100 bp spacing probes were removed. Probes corresponding to Nup98 were removed to avoid plasmid derived signals. Data were smoothed using running medians with windowHalfSize = 1000.

label: Cy3, Cy5

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Nup98(1-481)

label_protocol: 0.5 µg DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 or Cy5 labelled nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23C. Full Nup98(1-481) was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

tag: cell line

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Plasmid pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: 124246_HB007Z4_8/3/07_12:07_PM

type: RNA

city: Tromsoe

first: Vanessa

last: Dumeaux

address: University of Tromsoe

country: Norway

institute: "The Norwegian Women and Cancer project"

description: NWbAB_ 24

hyb_protocol: Applied Biosystems Chemiluminescence Detection Kit Protocol.

scan_protocol: Applied Biosystems.

data_processing: A total of 304 arrays, including 18 technical replicates, were analyzed. Data analysis was performed using R (http://cran.r-project.org), an open-source-interpreted computer language for statistical computation and graphics, and tools from the Bioconductor project (http://www.bioconductor.org), adapted to our needs. Using R, we set the expression intensity to missing for genes with flagging value > 8191. We filter out samples which had less than 40% probes with a signal to noise ratio (S/N) ≥ 3. When a technical replicate was conducted, the array with the least of probes with S/N ≥ 3 was excluded. Probes which had S/N ≥ 3 in less than 50% of the samples were also filtered out. After samples and spot filtration, we proceed with log transformation, quantile normalization and imputation of missing values using k-nearest neighbourhood method (k=10). A total of 286 arrays and 16,185 probes are analyzed. All significant technical variables in the global Ancova analysis with a multivariate permuted p-value<0.0001 were included in the gene-wise linear model selection (i.e. array lot number, RNA extraction date as random variables, and time between blood collection and storage as fixed variable) and expression values were adjusted for their effects.

label: digoxigenin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Applied Biosystems NanoAmp RT-IVT labeling kit.

growth_protocol: PAXgene™ blood RNA tubes were thawed at room temperature for 4 h.

extract_protocol: PAXgene™ Blood RNA Isolation Kit, according to the manufacturer’s manual.

tag: rnaextraction date

tag: rnacc

tag: amplification date

tag: crnacc

tag: arraylot

tag: smoking status

value: Yes

tag: hormone therapy use

value: No

tag: medication use

tag: fasting status

value: FALSE

tag: days between blood collection and storage

tag: menopausal status

value: post

tag: bmi group

tag: agegroup


title: 122716_HB007W4_12/5/07_2:34_PM

description: NWbAB_ 16


title: HB00B3D_8/30/06_11:37_AM

description:
NWbAB_ 15
Replicate: 1_r2


title: HB00B3N_8/30/06_12:11_PM

description:
NWbAB_ 14
Replicate: 6_r2


title: 123203_HB007W5_12/5/07_12:55_PM

description: NWbAB_ 18


title: 124660_HB007VQ_12/5/07_12:39_PM

description: NWbAB_ 19


title: 126123_HB007W6_12/5/07_2:00_PM

description: NWbAB_ 20


title: 123134_HB007W1_12/5/07_1:45_PM

description: NWbAB_ 17


title: HB004SK_8/23/06_12:14_PM

description:
NWbAB_ 11
Replicate: 10_r2

value: TRUE


title: HB004S0_8/23/06_9:43_AM

description:
NWbAB_ 10
Replicate: 11_r2


title: HB004RZ_8/23/06_10:51_AM

description:
NWbAB_ 12
Replicate: 5_r2


title: HB00B2U_8/30/06_10:46_AM

description:
NWbAB_ 13
Replicate: 13_r2


title: HB009HT_7/6/06_1:04_PM

description: NWbAB_ 6


title: Mock, 2 days recovery, biological replicate 2

city: Vienna

first: Ortrun

last: Mittelsten Scheid

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

description: total RNA

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: gcRMA

label: biotin

organism: Arabidopsis thaliana

label_protocol: standard Affymetrix protocol

growth_protocol: Plants were germinated and grown for three weeks under in vitro conditions under long day light regime at 22oC.

extract_protocol: Qiagen Rneasy

treatment_protocol: Three hours after beginning of the light phase, plants were transferred to 37oC for 30 h, then transferred back to 22oC. Mock controls were kept at 22oC.

tag: tissue

value: seedling


title: HB004RV_8/23/06_11:42_AM

description:
NWbAB_ 9
Replicate: 16_r2


title: Heat, no recovery, biological replicate 2

description: total RNA


title: Cronobacter malonaticus LMG 23826T

city: Nottingham

first: Eva

last: Kucerova

address: Clifton Lane

country: United Kingdom

institute: Nottingham Trent University

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com)

organism: Cronobacter malonaticus

source_name: Genomic DNA

growth_protocol: Trypticase Soy Broth

extract_protocol: Total genomic DNA was isolated using the QIAGEN Genomic-tip 100/G and Genomic DNA Buffer Set (www.1.qiagen.com) with extended cell lysis (1h) and two additional washes of the precipitated DNA. The DNA samples were checked for fragmentation on 0.8% agarose gel and checked for protein and RNA content by spectrophotometry.

tag: strain

tag: strain type

value: Species type strain.

organism: Cronobacter sakazakii ATCC BAA-894

value: ATCC BAA-894

tag: type

value: reference


title: Mock, 2 days recovery, biological replicate 1

description: total RNA


title: Cronobacter dublinensis LMG 23823T

scan_protocol: Standard NimbleGen protocol (www.nimblegen.com)

organism: Cronobacter dublinensis


title: Cronobacter sakazakii ATCC 12868

data_processing: Standard NimbleGen protocol (www.nimblegen.com)

organism: Cronobacter sakazakii

value: Unknown source


title: Cronobacter sakazakii 696

label_protocol: Standard NimbleGen protocol (www.nimblegen.com)

value: NEC II case


title: Cronobacter sakazakii ATCC 29544T

value: ATCC 29544T


title: Cronobacter sakazaki 20

value: Clinical isolate


title: Cronobacter sakazakii 701

value: Fatal NEC III case


title: Heat, 2 days recovery, biological replicate 1

description: total RNA


title: Cronobacter turicensis LMG 23827T

organism: Cronobacter turicensis

value: Species type strain. Meningitis case


title: Heat, 2 days recovery, biological replicate 2

description: total RNA


title: Heat, no recovery, biological replicate 1

description: total RNA


title: Cronobacter muytjensii ATCC 51329T

organism: Cronobacter muytjensii

value: ATCC 51329T


title: Cronobacter sakazakii 767

value: Fatal meningitis case


title: Mock, no recovery, biological replicate 1

description: total RNA


title: 1ng/mL R4 TCDD day 3 Danio rerio 36 embryo

city: Morrisville

first: Patrick

last: Hurban

state: NC

address: 100 Perimeter Park Dr Ste C

department: Scientific Affairs

country: USA

institute: Cogenics, Inc.

hyb_protocol: Hybridizations were conducted according to Agilent recommendations for 22K commercial microarrays.

scan_protocol: Arrays were scanned using the Agilent DNA Microarray scanner using factory settings.

data_processing: Array images were processed using Agilent Feature Extraction Software v8.1.1

organism: Danio rerio

source_name: 1ng/mL R4 TCDD day 3

label_protocol: Total RNA samples were labeled using the Low Input Linear Amplification Kit from Agilent Technologies along with Cy-linked dNTPs from Amersham Biosciences.

growth_protocol: Embryos were incubated in 5 mL danieau in glass scintillation vials, with 15-20 embryos/vial.

extract_protocol: RNA was extracted using Qiagen's RNEasy kit, according to the manufacturer's protocol.

treatment_protocol: Embryos were dosed for 1 hour (from 4 to 5 hours post-fertilization) with 1 ng/mL TCDD in glass scintillation vials, with shaking.

tag: developmental stage

value: day 3 embryo

tag: treatment

value: 1ng/mL R4 TCDD

source_name: Zebrafish Fibroblast cell line Reference RNA

value: fibroblast cell line


title: Mock, no recovery, biological replicate 2

description: total RNA


title: 1ng/mL R4 TCDD day 4 Danio rerio 38 embryo

source_name: 1ng/mL R4 TCDD day 4

value: day 4 embryo


title: 1ng/mL R4 TCDD day 2 Danio rerio 34 embryo

source_name: 1ng/mL R4 TCDD day 2

value: day 2 embryo


title: 1ng/mL R4 TCDD day 5 Danio rerio 40 embryo

source_name: 1ng/mL R4 TCDD day 5

value: day 5 embryo


title: 1ng/mL R4 DMSO day 4 Danio rerio 37 embryo

source_name: 1ng/mL R4 DMSO day 4

value: 1ng/mL R4 DMSO


title: 1ng/mL R4 DMSO day 5 Danio rerio 39 embryo

source_name: 1ng/mL R4 DMSO day 5


title: 1ng/mL R4 DMSO day 2 Danio rerio 33 embryo

source_name: 1ng/mL R4 DMSO day 2


title: 1ng/mL R4 DMSO day 3 Danio rerio 35 embryo

source_name: 1ng/mL R4 DMSO day 3


title: 1ng/mL R3 TCDD day 3 Danio rerio 26 embryo

source_name: 1ng/mL R3 TCDD day 3

value: 1ng/mL R3 TCDD


title: 1ng/mL R3 TCDD day 4 Danio rerio 28 embryo

source_name: 1ng/mL R3 TCDD day 4


title: Embryonic Drosophila cells, Kc167 cells, nucleoplasmic Nup98 DamID upon ecdysone treatment

description: Replicates were averaged: F256G1 (CH1 = Cy5, CH2 = Cy3), F256G2 (CH1 = Cy3, CH2 = Cy5)

scan_protocol: Microarrays were scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at a variable PMT (0-100%) for each channel at 10 um resolution using a suitable scan area.

data_processing: Images of the expression arrays were analyzed using Agilent Feature Extraction Software version 9.5.1.1. Mean spot intensities were background subtracted and CH1 CH2 ratios log base 2-transformed and normalized within arrays to the median values using "printtiploess" and averaged using "lmFit" using the limma software package (version 3.2.1) taking into account the duplicate spots (ndups =2)(Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, No. 1, Article 3.).

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Nup98(1-481) and treated with ecdysone

label_protocol: Sample labeling was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Nup98(1-481) was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). After electroporation the cells were incubated with 1uM ecdysone

tag: cell line


title: 1ng/mL R4 DMSO day 1 Danio rerio 31 embryo

source_name: 1ng/mL R4 DMSO day 1

value: day 1 embryo


title: 1ng/mL R3 TCDD day 2 Danio rerio 24 embryo

source_name: 1ng/mL R3 TCDD day 2


title: Embryonic Drosophila cells, Kc167 cells, Nup50 DamID after Nup98 RNAi

description: Replicates were averaged: F266J5 (CH1 = Cy5, CH2 = Cy3), F266J6 (CH1 = Cy3, CH2 = Cy5)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Nup50 and treated with Nup98 RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Cells were incubated for 1h with 150 μg/ul Nup98 dsRNA in serum-free medium. After that serum was added to normal concentration (5%). At 48 hrs again 150 g dsRNA was added using the same procedure. Full length Nup50 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells at 72 hrs as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were harvested at 96 hrs.

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Cells were incubated for 1h with 150 μg/ul Nup98 dsRNA in serum-free medium. After that serum was added to normal concentration (5%). At 48 hrs again 150 g dsRNA was added using the same procedure. Dam-only plasmid was transfected into Kc cells at 72 hrs as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were harvested at 96 hrs.


title: 1ng/mL R3 TCDD day 5 Danio rerio 30 embryo

source_name: 1ng/mL R3 TCDD day 5


title: Embryonic Drosophila cells, Kc167 cells, Dam-only DamID upon ecdysone treatment

description: Replicates were averaged: F256G7 (CH1 = Cy5, CH2 = Cy3), F256G8 (CH1 = Cy3, CH2 = Cy5)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam and treated with ecdysone

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Plasmid pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). After electroporation the cells were incubated with 1uM ecdysone


title: Embryonic Drosophila cells, Kc167 cells, Nup98 DamID after white RNAi

description: Replicates were averaged: F266I9 (CH1 = Cy5, CH2 = Cy3), F266J0 (CH1 = Cy3, CH2 = Cy5)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Nup98 and treated with white RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Cells were incubated for 1h with 150 μg/ul white dsRNA in serum-free medium. After that serum was added to normal concentration (5%). At 48 hrs again 150 g dsRNA was added using the same procedure. Full length Nup98 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells at 72 hrs as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were harvested at 96 hrs.

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Cells were incubated for 1h with 150 μg/ul white dsRNA in serum-free medium. After that serum was added to normal concentration (5%). At 48 hrs again 150 g dsRNA was added using the same procedure. Dam-only plasmid was transfected into Kc cells at 72 hrs as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were harvested at 96 hrs.


title: 1ng/mL R3 TCDD day 1 Danio rerio 22 embryo

source_name: 1ng/mL R3 TCDD day 1

source_name: Zebrafish Fibroblast cell line Reference RNA


title: 1ng/mL R4 TCDD day 1 Danio rerio 32 embryo

source_name: 1ng/mL R4 TCDD day 1


title: Embryonic Drosophila cells, Kc167 cells, Nup50 DamID after white RNAi

description: Replicates were averaged: F266J3 (CH1 = Cy5, CH2 = Cy3), F266J4 (CH1 = Cy3, CH2 = Cy5)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Nup50 and treated with white RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Cells were incubated for 1h with 150 μg/ul white dsRNA in serum-free medium. After that serum was added to normal concentration (5%). At 48 hrs again 150 g dsRNA was added using the same procedure. Full length Nup50 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells at 72 hrs as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were harvested at 96 hrs.


title: 1ng/mL R3 DMSO day 5 Danio rerio 29 embryo

source_name: 1ng/mL R3 DMSO day 5

value: 1ng/mL R3 DMSO


title: Embryonic Drosophila cells, Kc167 cells, Nup98 DamID after Nup50 RNAi

description: Replicates were averaged: F266J7 (CH1 = Cy5, CH2 = Cy3), F266I8 (CH1 = Cy3, CH2 = Cy5)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Nup98 and treated with Nup50 RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Cells were incubated for 1h with 150 μg/ul Nup50 dsRNA in serum-free medium. After that serum was added to normal concentration (5%). At 48 hrs again 150 g dsRNA was added using the same procedure. Full length Nup98 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells at 72 hrs as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were harvested at 96 hrs.

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Cells were incubated for 1h with 150 μg/ul Nup50 dsRNA in serum-free medium. After that serum was added to normal concentration (5%). At 48 hrs again 150 g dsRNA was added using the same procedure. Dam-only plasmid was transfected into Kc cells at 72 hrs as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were harvested at 96 hrs.


title: Embryonic Drosophila cells, Kc167 cells, Lam DamID

description: Replicates were averaged: 41900 (CH1 = Cy3, CH2 = Cy5), 48338 (CH1 = Cy5, CH2 = Cy3)

hyb_protocol: Hybridizations were done by NimbleGen, Reykjavik.

scan_protocol: Scans were done by NimbleGen, Reykjavik.

data_processing: Scans were processed by NimbleGen, Reykjavik. Data from pair files were normalized using the Limma software package (Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, No. 1, Article 3.). within arrays using "loess" and between arrays using "Aquantile" and log2-transformed. Log-2 ratios of replicates were averaged by means. Data was limited to chromosome 2L.

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lam

label_protocol: 1 µg DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html) at NimbleGen, Reykjavik.

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23¡C. Full length Lam was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23¡C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: Embryonic Drosophila cells, Kc167 cells, mRNA changes after nucleoplasmic Nup98 overexpression

description: Replicates were averaged: F266D1 (CH1 = Cy5, CH2 = Cy3), F266D2 (CH1 = Cy3, CH2 = Cy5), F266D3 (CH1 = Cy5, CH2 = Cy3), F266D4 (CH1 = Cy3, CH2 = Cy5)

source_name: Embryonic Drosophila cells, Kc167 cells, nucleoplasmic Nup98 overexpression

label_protocol: 1 µg of RNA was labeled with 0.3 µl of ULS-Cy5 or 1 µl of ULS-Cy3 label using the ULS labeling system from Kreatech. Details can be found at the website of the NKI Central Microarray Facility (http://cmfdb.nki.nl/process/protocolView).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Plasmids containing GFP fused to nucleoplasmic Nup98 (1-479) were transfected into the cells by electroporation as described (van Steensel, B., and Henikoff, S. (2000). Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-428.) and expressed for 24 hours. GFP-positive cells were subsequently FACS sorted in PBS.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Contaminating gDNA was degraded using DNaseI (1 unit/µg RNA), 15 min. at room temperature).

treatment_protocol: Cells were stored in Trizol at -80°C.

source_name: Embryonic Drosophila cells, Kc167 cells, white RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Plasmids containing GFP-only (replicates F256D3, F256D4) or GFP fused to nucleoplasmic Nup98 (1-479) (replicates F256D1, F256D2) were transfected into the cells by electroporation as described (van Steensel, B., and Henikoff, S. (2000). Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-428.) and expressed for 24 hours. GFP-positive cells (replicates F256D3, F256D4) or GFP-negative cells (replicates F256D1, F256D2) were subsequently FACS sorted in PBS.


title: 1ng/mL R3 DMSO day 4 Danio rerio 27 embryo

source_name: 1ng/mL R3 DMSO day 4


title: Embryonic Drosophila cells, Kc167 cells, mRNA changes after Nup98 RNAi

description: Replicates were averaged: F266B2 (CH1 = Cy5, CH2 = Cy3), F266B3 (CH1 = Cy3, CH2 = Cy5), F266D9 (CH1 = Cy5, CH2 = Cy3), F266E0 (CH1 = Cy3, CH2 = Cy5)

source_name: Embryonic Drosophila cells, Kc167 cells, Nup98 RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Cells were incubated for 1h with 150 μg/ul Nup98 dsRNA in serum-free medium. After that serum was added to normal concentration (5%). At 48 hrs again 150 g dsRNA was added using the same procedure. At 96 hrs cells were harvested.

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Cells were incubated for 1h with 150 μg/ul white dsRNA in serum-free medium. After that serum was added to normal concentration (5%). At 48 hrs again 150 g dsRNA was added using the same procedure. At 96 hrs cells were harvested.


title: 1ng/mL R3 DMSO day 1 Danio rerio 21 embryo

source_name: 1ng/mL R3 DMSO day 1


title: 1ng/mL R2 TCDD day 4 Danio rerio 18 embryo

source_name: 1ng/mL R2 TCDD day 4

value: 1ng/mL R2 TCDD


title: 1ng/mL R2 TCDD day 5 Danio rerio 20 embryo

source_name: 1ng/mL R2 TCDD day 5


title: 1ng/mL R3 DMSO day 3 Danio rerio 25 embryo

source_name: 1ng/mL R3 DMSO day 3


title: 1ng/mL R2 DMSO day 5 Danio rerio 19 embryo

source_name: 1ng/mL R2 DMSO day 5

value: 1ng/mL R2 DMSO


title: 1ng/mL R3 DMSO day 2 Danio rerio 23 embryo

source_name: 1ng/mL R3 DMSO day 2


title: Embryonic Drosophila cells, Kc167 cells, mRNA changes after Nup50 RNAi

description: Replicates were averaged: F266B0 (CH1 = Cy5, CH2 = Cy3), F266B1 (CH1 = Cy3, CH2 = Cy5), F266C2 (CH1 = Cy5, CH2 = Cy3), F266C3 (CH1 = Cy3, CH2 = Cy5)

source_name: Embryonic Drosophila cells, Kc167 cells, Nup50 RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Cells were incubated for 1h with 150 μg/ul Nup50 dsRNA in serum-free medium. After that serum was added to normal concentration (5%). At 48 hrs again 150 g dsRNA was added using the same procedure. At 96 hrs cells were harvested.


title: 1ng/mL R2 TCDD day 3 Danio rerio 16 embryo

source_name: 1ng/mL R2 TCDD day 3

growth_protocol: Embryos were incubated in 5 mL danieau in glass scintillation vials, with 15-20 embryos/vial.

source_name: Zebrafish Fibroblast cell line Reference RNA


title: 1ng/mL R2 DMSO day 4 Danio rerio 17 embryo

source_name: 1ng/mL R2 DMSO day 4


title: nCEC BP

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

country: Italy

institute: University of Modena and Reggio Emilia

description: circulating endothelial cells (CEC), chronic lymphocytic leukemia (CLL),

hyb_protocol: 825 ng of Cy5-labelled cRNA were mixed with the same amount of Cy3-labeled reference cRNA and then cRNA mixtures were fragmented to an average size of 50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent Technologies). Samples were hybridized for 17 h at 65°C on 4x44K Whole Human Genome Microarray (Agilent Technologies), comprising over 33’000 (60-mer) experimentally validated oligonucleotide probes and then scanned using a confocal laser scanner (Agilent Technologies).

scan_protocol: Fluorescence data were analyzed with Feature Extraction Software v.9.1 (Agilent Technologies).

data_processing: Result data from each scan (Log10 Cy5/Cy3) were imported into the gene expression analysis software Luminator (Rosetta Bio software, Seattle, WA, USA). Two-dimensional clustering analysis was performed using an agglomerative algorithm with an average link heuristics and a correlation with mean subtraction.The identification of genes differentially expressed between subgroups was performed using both Significant Analysis of Microarray (SAM) algorithm with false discovery ratio (FDR)<5% and enhanced Analysis of Variance (ANOVA) with p-value <0.001. To increase the statistical power, the enhanced ANOVA uses as input data both expression level and the estimated technology error associated with the expression level. As a result, the false-positive rate is reduced when the number of replicates is small and, then, sensitivitydetection is increased.

source_name: UHR

label_protocol: Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo alto, CA, USA).

extract_protocol: COMMERCIAL RNA

tag: Universal Human Reference RNA (UHR) (Stratagene, Cedar Creek, TX), consisted of equal amount of total RNA from 10 human cancer cell lines, was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Agilent Technologies) in each experiment.

source_name: nCEC BP

extract_protocol: RNeasy Mini Kit (QIAGEN, Valencia, CA, USA)

tag: CIRCULATING ENDOTHELIAL CELLS FROM HEALTHY CONTROL


title: 1ng/mL R1 TCDD day 4 Danio rerio 8 embryo

source_name: 1ng/mL R1 TCDD day 4

value: 1ng/mL R1 TCDD


title: 1ng/mL R1 TCDD day 3 Danio rerio 6 embryo

source_name: 1ng/mL R1 TCDD day 3


title: 1ng/mL R1 TCDD day 1 Danio rerio 2 embryo

source_name: 1ng/mL R1 TCDD day 1


title: 1ng/mL R1 DMSO day 5 Danio rerio 9 embryo

source_name: 1ng/mL R1 DMSO day 5

value: 1ng/mL R1 DMSO


title: 1ng/mL R2 TCDD day 1 Danio rerio 12 embryo

source_name: 1ng/mL R2 TCDD day 1


title: 1ng/mL R2 DMSO day 2 Danio rerio 13 embryo

source_name: 1ng/mL R2 DMSO day 2


title: 1ng/mL R1 DMSO day 4 Danio rerio 7 embryo

source_name: 1ng/mL R1 DMSO day 4


title: 1ng/mL R1 DMSO day 3 Danio rerio 5 embryo

source_name: 1ng/mL R1 DMSO day 3


title: 1ng/mL R2 TCDD day 2 Danio rerio 14 embryo

source_name: 1ng/mL R2 TCDD day 2


title: 1ng/mL R1 TCDD day 5 Danio rerio 10 embryo

source_name: 1ng/mL R1 TCDD day 5


title: 1ng/mL R2 DMSO day 3 Danio rerio 15 embryo

source_name: 1ng/mL R2 DMSO day 3


title: 1ng/mL R2 DMSO day 1 Danio rerio 11 embryo

source_name: 1ng/mL R2 DMSO day 1


title: 1ng/mL R1 DMSO day 2 Danio rerio 3 embryo

source_name: 1ng/mL R1 DMSO day 2


title: 1ng/mL R1 DMSO day 1 Danio rerio 1 embryo

source_name: 1ng/mL R1 DMSO day 1

source_name: Zebrafish Fibroblast cell line Reference RNA


title: Embryonic Drosophila cells, Kc167 cells, Nucleoplasmic Nup98 DamID

description: Replicates were averaged: 3172 (CH1 = Cy5, CH2 = Cy3), 4017 (CH1 = Cy3, CH2 = Cy5), 4219 (CH1 = Cy5, CH2 = Cy3), 4349 (CH1 = Cy3, CH2 = Cy5)

hyb_protocol: Samples were hybridized to the arrays in a volume of approximately 30 ul (5 mM TRIS, 0.5 mM EDTA, 3X SSC). The following competitors were added: 25 ug DpnI-digested Dam-fusion plasmid DNA, 100 ug yeast tRNA, 20 ug poly (dA-dT). Arrays were washed in four subsequent steps. The respective washing buffers were: 1X SSC/0.03% SDS (arrays were submerged once), 1XSSC (arrays were submerged 15 times), 0.2XSSC (20 minutes), 0.05XSSC (10 minutes).

data_processing: Scan TIFF images were processed with ImaGene 6.0.1 software (BioDiscovery) using automated grid placement with manual control and automated spot adjustment. Measurements were extracted as median spot intensities minus median background intensities. After removal of low quality (ImaGene flags), redundant or ambiguous probes, hybridization data of 9,990 probes was used for analyses, all measured ratios were log base 2-transformed and normalized within arrays to the median values using "printtiploess" and between arrays using "Aquantile" and averaged using "lmFit" using the limma software package (version 3.2.1)(Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, No. 1, Article 3.).

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Nup98(1-576)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23C. Nup98(1-576) was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Plasmid pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: First shYY2

status: Public on Feb 28 2010

city: Boston

first: Emmett

middle: Vance

last: Schmidt

state: MA

address: 55 Fruit St. - GRJ904

department: Tumor Biology

institute: Cancer Research Center at MGH

hyb_protocol: Microarray = Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2

scan_protocol: Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS

data_processing: GCOS MAS 5

source_name: HeLa cells transduced shYY2 control lentivirus.

label_protocol: Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.

extract_protocol: Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.

treatment_protocol: Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.

value: HeLa


title: First shYY1 and shYY2

source_name: HeLa cells transduced shYY1shYY2 control lentivirus.


title: Embryonic Drosophila cells, Kc167 cells, Nup98 DamID

description: Replicates were averaged: 4216 (CH1 = Cy5, CH2 = Cy3), 4343 (CH1 = Cy3, CH2 = Cy5)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Nup98

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23C. Full length Nup98 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: Second shYY1

source_name: HeLa cells transduced shYY1 control lentivirus.


title: Vector control 3

source_name: HeLa cells transduced LKO control lentivirus.


title: Embryonic Drosophila cells, Kc167 cells, Nup50 DamID

description: Replicates were averaged: 2951 (CH1 = Cy5, CH2 = Cy3), 2958 (CH1 = Cy5, CH2 = Cy3), 2908 (CH1 = Cy3, CH2 = Cy5), 2923 (CH1 = Cy3, CH2 = Cy5), 4009 (CH1 = Cy3, CH2 = Cy5), 4222 (CH1 = Cy5, CH2 = Cy3)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Nup50


title: Vector control 1


title: Third shYY1


title: Second shYY2


title: Embryonic Drosophila cells, Kc167 cells, Nup62 DamID

description: Replicates were averaged: 3167 (CH1 = Cy5, CH2 = Cy3), 2922 (CH1 = Cy3, CH2 = Cy5), 4214 (CH1 = Cy5, CH2 = Cy3), 4346 (CH1 = Cy3, CH2 = Cy5)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Nup62


title: Fourth shYY2


title: Third shYY1 and shYY2


title: First shYY1


title: Third shYY2


title: Vector control 2


title: Second shYY1 and shYY2


title: myeloma cells_IGF1_1

city: Leuven

first: Lieven

last: Thorrez

address: Kasteelpark Arenberg 10

country: Belgium

institute: Katholieke Universiteit Leuven

description: myeloma cells IGF1 treated 1

hyb_protocol: Fragmented cRNA was hybridised to mouse 430A arrays (Affymetrix) during 16h at 45 degrees C and 60rpm.

scan_protocol: The arrays were washed and stained in a fluidics station (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: Image files were analysed within GCOS (Affymetrix) and processed using the MAS5 algorithm.

label: Biotin

organism: Mus musculus

source_name: multiple myeloma cells (bone marrow)

label_protocol: Cellular mRNA was reverse transcribed into cDNA (SuperScript Choice System Invitrogen, Carlsbad, CA using oligo-dT primers and a T7 RNA polymerase promoter site). Five microgram of total RNA was used to prepare biotinylated cRNA with the Enzo RNA transcript labeling kit (distributed by Affymetrix, Santa Clara, CA) according to the Genechip expression analysis technical manual 701025 Rev.2. The concentration of labelled cRNA was measured using the NanoDrop ND-1000 spectrophotometer. Labeled cRNA was fragmented in a fragmentation buffer during 35 min at 94 degrees C. The quality of labelled and fragmented cRNA was analysed using the Agilent bioanalyzer 2100.

extract_protocol: Total RNA was extracted using TRIzol Reagent according to the manufacturer's protocol (Gibco BRL, Carlsbad, CA), followed by a cleanup procedure with RNeasy columns (Qiagen, Cologne, Germany).

treatment_protocol: myeloma cells were treated with IGF-1 (100 ng/ml) for 12h in serum free medium

tag: agent

tag: disease state

value: multiple myeloma

tag: cell type

value: malignant plasma cells


title: myeloma cells control3

description: myeloma cells control3

treatment_protocol: myeloma cells were cultured for 12h in serum free medium without IGF-1

value: control


title: myeloma cells control2

description: myeloma cells control2


title: Honeybee_head_5'LongSAGE

type: SAGE

anchor: MmeI

city: Shanghai

first: Huajun

last: Zheng

address: No.250, Bibo Road

department: Genomic Sequencing Department

country: China

institute: Chinese National Human Genome Center at Shanghai

description: mRNA was purified from total RNA using Micropoly(A)PuristTM mRNA purification kit (Ambion, Cat.No.1919). Clones of 5’ LS library was sequenced with ABI3730.

data_processing: 5’ LS tags extraction and quantifying abundance of each tag were performed using SAGE 2000 software

organism: Apis mellifera

source_name: Drone Head of Apis mellifera

extract_protocol: The bee heads were grinded in liquid nitrogen and total RNA was prepared by using TRIzol reagent (Invitrogen) according to the manufacturer’s protocols.

value: Apis mellifera ligustica

tag: gender

value: Male(Drone)

tag: age

value: 3-14 days

value: head


title: myeloma cells_IGF1_3

description: myeloma cells IGF-1 treated 3


title: Nicotinamide Starve of Mycobacterium bovis Defective for de novo NAD Biosysthesis Replicate 2

status: Public on Feb 24 2010

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

description: effect of nicotinamide starvation in mycobacteria defective for de novo NAD biosynthesis

hyb_protocol: Slide was hybridized for 16 hours at 42 in water bath with volume of 60 uL in solution of standard gene expression hybridization solution, and blocked in standard prehybridization solution. After hybridization, the slide was washed with standard wash protocol. refer to PFGRC protocol SOP#M008

scan_protocol: scanned with PMT voltage adjusted for maximum dynamic range

data_processing: In MIDAS, lowess normalization, standard deviation regularization, in-slide replicate analysis, one bad channel policy set to generous, all flags on

organism: Mycobacterium tuberculosis variant bovis

source_name: whole_organism from Mycobacterium bovis Ravenel Delta nadABC aka mc2 4957

label_protocol: 2 ug total RNA was used as template for reverse transcription with random hexamer primers and aminoallyl-dUTP in a 2:3 ratio to dTTP in the nucleotide mix.  After overnight incubation at 42°C, the reaction was stopped, RNA was hydrolyzed, and unincorporated nucleotides and free amines were removed with the Qiagen MinElute kit as per protocol, with amine-free phosphate wash and elution buffers.  cDNA concentration and purity were measured by Nanodrop.  Cy3 and Cy5 dyes were coupled to the aminoallyl-cDNA, which was then purified using a MinElute kit.  Probe concentration, purity, and dye incorporation were measured by Nanodrop.

growth_protocol: grown with 20mg/L nicotinamide

extract_protocol: Cells are collected by centrifugation and resuspended in 1mL buffer RLT from a Qiagen RNeasy kit.  The suspension is transferred to Fast-Prep Blue Cap tubes and processed for 45 seconds at speed 6.5 in a Fast-Prep apparatus.  After a brief incubation on ice the debris is spun down and the supernatant (~750uL) is removed to a fresh microcentrifuge tube.  525uL absolute ethanol is added and the samples are applied to RNeasy columns in two applications.  At this point the RNA is purified as recommended by the Qiagen protocol.

treatment_protocol: nucleic_acid_extraction: total RNA prep

tag: phenotype

value: requires 0.1mg/L nicotinamide for growth

value: Delta

growth_protocol: grown without 20mg/L nicotinamide


title: myeloma cells control1

description: myeloma cells control1


title: Nicotinamide Starve of Mycobacterium bovis Defective for de novo NAD Biosysthesis Replicate 3


title: Nicotinamide Starve of Mycobacterium bovis Defective for de novo NAD Biosysthesis Replicate 1


title: Nicotinamide Starve of Mycobacterium tuberculosis Defective for de novo NAD Biosysthesis Replicate 3

organism: Mycobacterium tuberculosis

source_name: whole_organism from Mycobacterium tuberculosis CDC1551 Delta nadABC aka mc2 4968

value: requires 0.01mg/L nicotinamide for growth


title: Nicotinamide Starve of Mycobacterium tuberculosis Defective for de novo NAD Biosysthesis Replicate 1


title: Maltose-1-Phosphate Stress Stimulon in Mycobacterium tuberculosis Replicate 3

description: Effect of functional treS in glgE mutant. Phenotype requires 5mM Validamycin.

data_processing: In MIDAS, lowess normalization, standard deviation regularization, in-slide replicate analysis, one bad channel policy set to generous, all flags on. MEV files: Test = Channel B; Reference = Channel A.

source_name: Mycobacterium tuberculosis H37Rv Delta treS Delta glgE pMV361 aka mc27149 pMV361

treatment_protocol: nucleic_acid_extraction: Total RNA Prep

value: whole organism

source_name: Mycobacterium tuberculosis H37Rv Delta treS Delta glgE pMV361::treS aka mc27149 pMV361::treS


title: Maltose-1-Phosphate Stress Stimulon in Mycobacterium tuberculosis Replicate 2


title: Maltose-1-Phosphate Stress Stimulon in Mycobacterium tuberculosis Replicate 1


title: S288C vs. S288C hyb 2_2

status: Public on Feb 14 2010

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

description:
Technical replicate 2 of 2
Slide number: 13672908
Raw data file same as that of GSM424633

hyb_protocol: Yeast cDNA microarrays (Y6.4K7) were hybridized following manufacturer´s suggested protocol (University of Health Network, Canada) with modifications.

scan_protocol: Hybridized and washed arrays were scanned using ScanArray Lite (Perkin-Elmer, USA). Images were processed using GenePix Pro 6.0 (Molecular Devices, USA).

data_processing: Data normalization was performed with the DNMAD tool of the software suite Asterias (http://asterias.bioinfo.cnio.es/). Normalized values represent log2 ratios of test sample over reference sample. L-957, LVCB and EC1118 are test samples, and S288C is the reference sample. Slides 13663786 and 13672908 were S288C self-to-self hybridizations.

label: Alexa fluor 647

organism: Saccharomyces cerevisiae

source_name: Yeast cells

label_protocol: 1 ug of genomic DNA was labeled with the Bioprime Array CGH Genomic Labeling system (Invitrogen, USA) following manufacturer´s protocol with modifications.

growth_protocol: Cells were grown in YPD media (2% glucose, 0.5% yeast extract, 0.5% peptone).

extract_protocol: Genomic DNA was isolated with the DNA Wizard kit (Promega, USA) following manufacturer´s instructions.

value: S288C lab yeast

label: Alexa fluor 555


title: S288C vs. S288C hyb 1_2

description:
Technical replicate 1 of 2
Slide number: 13663786
Raw data file same as that of GSM424631


title: LVCB vs. S288C hyb 1_2

description:
Technical replicate 1 of 2
Slide number: 13672882
Raw data file same as that of GSM424627

value: LVCB wine yeast


title: LVCB vs. S288C hyb 2_1

description:
Technical replicate 2 of 2
Slide number: 13672885
Raw data file same as that of GSM424630


title: LVCB vs. S288C hyb 1_1

description:
Technical replicate 1 of 2
Slide number: 13672882
Raw data file same as that of GSM424628


title: L-957 vs. S288C hyb 2_2

description:
Technical replicate 2 of 2
Slide number: 13672902
Raw data file same as that of GSM424625

value: L-957 wine yeast


title: S288C vs. S288C hyb 1_1

description:
Technical replicate 1 of 2
Slide number: 13663786
Raw data file same as that of GSM424632


title: Nicotinamide Starve of Mycobacterium tuberculosis Defective for de novo NAD Biosysthesis Replicate 2


title: LVCB vs. S288C hyb 2_2

description:
Technical replicate 2 of 2
Slide number: 13672885
Raw data file same as that of GSM424629


title: L-957 vs. S288C hyb 2_1

description:
Technical replicate 2 of 2
Slide number: 13672902
Raw data file same as that of GSM424626


title: EC1118 vs. S288C hyb 2_2

description:
Technical replicate 2 of 2
Slide number: 13672905
Raw data file same as that of GSM424621

value: EC1118 wine yeast


title: S288C vs. S288C hyb 2_1

description:
Technical replicate 2 of 2
Slide number: 13672908
Raw data file same as that of GSM424634


title: myeloma cells_IGF1_2

description: myeloma cells IGF-1 treated 2


title: L-957 vs. S288C hyb 1_2

description:
Technical replicate 1 of 2
Slide number: 13672901
Raw data file same as that of GSM424623


title: FT.1-rep.1

status: Public on Feb 05 2010

city: JOUY EN JOSAS

first: Julien

last: MARUOTTI

address: Domaine de Vilvert

country: France

institute: INRA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: After exported from BeadStudio, data were normalised using lumiExpresso provided in lumi R package

source_name: EpiSC from the epiblast of a fertilized  embryo

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

growth_protocol: EpiSC were maintained on FBS coated dishes in Completely Defined Medium complemented with 20 ng/mL activine A (R&D) and 12 ng/mL bFgF (R&D) according to Brons et al., 2007.

extract_protocol: Total RNA was extracted with the QIAGEN RNeasy minikit followed by DNAse I treatment in accordance with the manufacturer instructions.

tag: embryo stage

value: pre-streak/early streak

tag: embryo morphology

value: normal


title: EC1118 vs. S288C hyb 1_2

description:
Technical replicate 1 of 2
Slide number: 13663782
Raw data file same as that of GSM424619


title: L-957 vs. S288C hyb 1_1

description:
Technical replicate 1 of 2
Slide number: 13672901
Raw data file same as that of GSM424624


title: NT.1-rep.3

source_name: EpiSC from the epiblast of a somatic cell nuclear transfer  embryo


title: NT-LE-rep.1

value: Large Extra-embryonic ectoderm


title: EC1118 vs. S288C hyb 2_1

description:
Technical replicate 2 of 2
Slide number: 13672905
Raw data file same as that of GSM424622


title: FT.2-rep.2


title: NT.1-rep.2


title: NT-LE-rep.2


title: FT.2-rep.3


title: NT.2-rep.1


title: FT.3-rep.2


title: FT.1-rep.2


title: Mouse_ESC_Pcl2_shRNA_sample 1

city: Toronto

first: William

middle: L

last: Stanford

state: Ontario

address: 164 College St

department: IBBME

country: Canada

institute: University of Toronto

description: Total RNA was extracted from Pcl2 mismatch controls and one Pcl2 shRNA clone with RNeasy columns (Qiagen). RNA quality was tested using an Agilent Bioanalyzer before performing standard cDNA synthesis (Invitrogen Superscript) and in vitro transcription (IVT) (Enzo IVT kit). 10 ug of RNA was used for IVT and 15 ug of cRNA was used for hybridization (EukGEWS2v4 kit) to the Mouse Genome 430 2.0 GeneChip. Scanning was performed using the Affymetrix GeneChip Scanner 3000 and analysis done using GCOS1.4 to obtain signal-log ratios of the control to the sample. Hybridizations of three biological replicates for both the control and Pcl2 shRNA clone were performed.

scan_protocol: Affymetrix GeneChip Scanner 3000

source_name: Undifferentiated mouse embryonic stem cells

label_protocol: Enzo IVT kit

growth_protocol: R1 ESCs were cultured at 37°C and 5% CO2, in ESC media consisting of Dulbecco modified eagle serum (DMEM) supplemented with 15% FBS (North Bio, Lot SF30408), 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine (all from Gibco), 1000 U/mL leukemia inhibitory factor (LIF) (ESGRO, from Chemicon, batch 11061065) and 100 µM b-mercaptoethanol (Sigma).  Differentiation media consisted of either ESC media without LIF, or ESC media without LIF and supplemented with 0.1 uM retinoic acid.  Selection media consisted of ESC media supplemented with 150 ug/mL G418 (Gibco).  ESCs were passaged every two days at a ratio of 1:5 by washing with PBS (Gibco), dissociating with 0.05% trypsin (Gibco) for 5 minutes at 37ÃÂ°C and resuspending in ESC media. Media was changed daily.

extract_protocol: Qiagen RNeasy column purification

treatment_protocol: Cells were stably expressing Pcl2 shRNA.

value: R1 mouse embryonic stem cells stably transfected with Pcl2 shRNA sequence


title: FT.3-rep.3


title: FT.2-rep.1


title: EC1118 vs. S288C hyb 1_1

description:
Technical replicate 1 of 2
Slide number: 13663782
Raw data file same as that of GSM424620


title: FT.1-rep.3


title: Mouse_ESC_Pcl2_mismatch_control_sample 1

treatment_protocol: Cells were stably expressing shRNA mismatch control sequence for comparision with Pcl2 shRNA knockdown cells.

value: R1 mouse embryonic stem cells stably transfected with shRNA mismatch control sequence


title: NT.2-rep.2


title: NT.2-rep.3


title: KO_431

status: Public on Feb 04 2010

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from Ugcg-deficient mouse liver

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Manufacturer's recommended protocols. Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 3.2, from SAS. Gene expression profiling was performed using arrays of mouse430_2 -type from Affymetrix. A Custom CDF Version 12 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: liver KO 431

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

extract_protocol: mRNA was isolated according to Chomczynski, P. & Sacchi, N. (1987) Anal. Biochem. 162, 156–159

tag: genotype/variation

value: Ugcg-deficient


title: FT.3-rep.1

tag: strain


title: WT_428

description: Gene expression data from wildtype mouse liver

source_name: liver WT 428

value: wildtype


title: WT_430

source_name: liver WT 430


title: NT-LE-rep.3


title: NT.1-rep.1


title: Mouse_ESC_Pcl2_shRNA_sample 2

growth_protocol: R1 ESCs were cultured at 37°C and 5% CO2, in ESC media consisting of Dulbecco modified eagle serum (DMEM) supplemented with 15% FBS (North Bio, Lot SF30408), 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine (all from Gibco), 1000 U/mL leukemia inhibitory factor (LIF) (ESGRO, from Chemicon, batch 11061065) and 100 µM b-mercaptoethanol (Sigma).  Differentiation media consisted of either ESC media without LIF, or ESC media without LIF and supplemented with 0.1 uM retinoic acid.  Selection media consisted of ESC media supplemented with 150 ug/mL G418 (Gibco).  ESCs were passaged every two days at a ratio of 1:5 by washing with PBS (Gibco), dissociating with 0.05% trypsin (Gibco) for 5 minutes at 37°C and resuspending in ESC media. Media was changed daily.


title: Mouse_ESC_Pcl2_shRNA_sample 3


title: Mouse_ESC_Pcl2_mismatch_control_sample 2


title: KO_429

source_name: liver KO 429


title: WT_426

source_name: liver WT 426


title: Mouse_ESC_Pcl2_mismatch_control_sample 3


title: KO_427

source_name: liver KO 427


title: gastric adenoma, case27

status: Public on Feb 01 2010

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

country: Japan

institute: Oita university, Faculty of Medicine

description: Non-neoplastic tissue in the same patient was used as the source of control DNA.

hyb_protocol: Samples were dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65℃ for 40 h.

scan_protocol: Microarrays were scanned using Microarray scanner (Agilrny Technologies) at a pixel resolution size of 5μm.

data_processing:
Microarray images were analyzed using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies). The log2ratio of Cy5 (tumor) to Cy3 (Control) was normalized by the Centralization Algorithm in DNA Analytics. Aberrant regions were determined by the ADM-2 algorithm at a threshold of 12.0 in DNA Analytics. To detect gains and losses, we set the values of parameters for aberration filters as: minimum number of probes in region 2, minimum absolute average log2ratio for region 0.263034, maximum number of aberrant regions 10000, and percentage penetrance per feature 0. We set the value of the minimum absolute average log2ratio at 0.263034 to detect regions showing a change in the averaged copy number equal to or more than 1.2-fold (log2(1.2)=0.263034).

A summary of the aberrations in the gastric adenomas as determined by the ADM-2 algorithm is available in the 'GSE19574_aberrations.txt' file, which is linked to the Series GSE19574 record as a supplementary file.

source_name: gastric adenoma : FFPE sample

label_protocol: Agilent Genomic DNA Labeling Kit Plus (Agilent).

extract_protocol: Standard proteinase K-digestion method.

treatment_protocol: Samples were formalin-fixed paraffin-embedded (FFPE) tissues.

value: female

tag: tissue

value: gastric adenoma

source_name: non-neoplastic gastric mucosa : FFPE sample

value: non-neoplastic gastric mucosa


title: gastric adenoma, case40

value: male


title: gastric adenoma, case39


title: gastric adenoma, case35


title: gastric adenoma, case37


title: Liver Non-Tumor Tissue LCS-106B

status: Public on Dec 01 2010

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description: No additional information.

hyb_protocol: Hybridization Protocol Other: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Scanning Protocol for HT Arrays Other: GeneChips were scanned using GeneChip® HT Array Plate Scanner by Affymetrix.

data_processing:
Data Processing Protocol
Calculation Method: The CEL files from the two Affymetrix series were combined using the matchprobes package in the R programming environment. Thereafter, the RMA method in the R affy package was used to obtain probe set expression summaries.

label_protocol:
Biotinylated cRNA Labeling for HT Arrays
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, For HT Array Plates Using the GeneChip® Array Station, P/N 702063 Rev. 2, Affymetrix).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was isolated from microdissected fresh frozen tissues using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol. RNA integrity for each sample was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: Tissue

value: Liver Non-Tumor Tissue

tag: Disease state

value: Hepatocellular carcinoma (HCC)

tag: Individual


title: gastric adenoma, case30


title: gastric adenoma, case22


title: gastric CIS, case20

scan_protocol: Microarrays were scanned using Microarray scanner (Agilent Technologies) at a pixel resolution size of 5μm.

data_processing:
Microarray images were analyzed using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies). The log2ratio of Cy5 (tumor) to Cy3 (Control) was normalized by the Centralization Algorithm in DNA Analytics. Aberrant regions were determined by the ADM-2 algorithm at a threshold of 12.0 in DNA Analytics. To detect gains and losses, we set the values of parameters for aberration filters as: minimum number of probes in region 2, minimum absolute average log2ratio for region 0.263034, maximum number of aberrant regions 10000, and percentage penetrance per feature 0. We set the value of the minimum absolute average log2ratio at 0.263034 to detect regions showing a change in the averaged copy number equal to or more than 1.2-fold (log2(1.2)=0.263034).

A summary of the aberrations in the gastric CISs as determined by the ADM-2 algorithm is available in the 'GSE19566_aberrations.txt' file, which is linked to the Series GSE19566 record as a supplementary file.

source_name: gastric CIS : FFPE sample

value: gastric carcinoma in situ


title: gastric CIS, case19


title: gastric adenoma, case38


title: gastric adenoma, case36


title: gastric adenoma, case31


title: gastric adenoma, case34


title: gastric adenoma, case33


title: gastric adenoma, case32


title: gastric adenoma, case26


title: gastric adenoma, case29


title: gastric adenoma, case28


title: gastric CIS, case16


title: gastric CIS, case17


title: gastric adenoma, case25


title: gastric adenoma, case24


title: gastric adenoma, case21


title: gastric CIS, case15


title: gastric CIS, case14


title: gastric CIS, case12


title: gastric CIS, case7


title: gastric CIS, case9


title: gastric CIS, case8


title: gastric adenoma, case23


title: gastric CIS, case13


title: gastric CIS, case11


title: gastric CIS, case10


title: gastric CIS, case18


title: Line27859 peel of red fruit, biological rep 2

city: Kisarazu

first: Koh

last: Aoki

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Department of Biotechnology Research

institute: Kazusa DNA Research Institute

description: Gene expression data from Line27859 red fruit peel

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: Scanned GeneChip images were analyzed using Microarray Suite version 5.0.1 (Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Solanum lycopersicum

source_name: Line27859 peel of red fruit (approximately 50-55 days after anthesis)

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

growth_protocol: Solanum lycopersicum Line 27859 was grown in the field under natural photo-period condition from March to July, 2006 in Gunma prefecture, Japan.

extract_protocol: Fruit peel and flesh were separated using razor blade. Total RNA was extracted from the tissues by an acid guanidinium thiocyanate-phenol-chloroform method (Chomczynski, P. and Sacchi, N. 1987, Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction, Anal Biochem, 162, 156-159). Sugars were further removed by sodium acetate-precipitation method (Tsugane, T., Watanabe, M., Yano, K., Sakurai, N., Suzuki, H. and Shibata, D. 2005, Expressed sequence tags of full-length cDNA clones from the miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom, Plant Biotechnol., 22, 161-165).

value: fruit exocarp

value: Approximately 50-55 days after anthesis

tag: cultivar


title: gastric CIS, case6


title: gastric CIS, case4


title: Momotaro8 flesh of red fruit, biological rep 1

description: Gene expression data from Momotaro8 red fruit flesh

source_name: Momotaro8 flesh of red fruit (approximately 50-55 days after anthesis)

growth_protocol: Solanum lycopersicum cultivar House MomotaroⓇ (Takii & Co, Ltd., Kyoto, Japan) was grown in the green house under natural photo-period condition from March to July, 2006 in Chiba prefecture, Japan.

value: fruit pericarp and endocarp

value: Momotaro 8 (Takii)


title: Line27859 peel of red fruit, biological rep 3


title: gastric CIS, case5


title: Momotaro8 flesh of red fruit, biological rep 3


title: Momotaro8 peel of red fruit, biological rep 3

description: Gene expression data from Momotaro8 red fruit peel

source_name: Momotaro8 peel of red fruit (approximately 50-55 days after anthesis)


title: Momotaro8 peel of red fruit, biological rep 1


title: Momotaro8 peel of red fruit, biological rep 4


title: Momotaro8 peel of red fruit, biological rep 2


title: gastric CIS, case3


title: gastric CIS, case2


title: Momotaro8 flesh of red fruit, biological rep 4


title: Line27859 peel of red fruit, biological rep 1


title: Line27859 peel of mature green fruit, biological rep 3

description: Gene expression data from Line27859 mature green fruit peel

source_name: Line27859 peel of mature green fruit (approximately 40 days after anthesis)

value: Approximately 40 days after anthesis


title: Line27859 peel of mature green fruit, biological rep 2


title: Momotaro8 flesh of red fruit, biological rep 2


title: Line27859 peel of mature green fruit, biological rep 1


title: gastric CIS, case1


title: Line27859 flesh of red fruit, biological rep 3

description: Gene expression data from Line27859 red fruit flesh

source_name: Line27859 flesh of red fruit (approximately 50-55 days after anthesis)


title: Line27859 flesh of red fruit, biological rep 1


title: Line27859 flesh of red fruit, biological rep 2


title: Line27859 flesh of mature green fruit, biological rep 2

description: Gene expression data from Line27859 mature green fruit flesh

source_name: Line27859 flesh of mature green fruit (approximately 40 days after anthesis)


title: Aft flesh of red fruit, biological rep 3

description: Gene expression data from Aft red fruit flesh

source_name: Aft mutant (LA1996) flesh of red fruit (approximately 50-55 days after anthesis)

growth_protocol: Monogenic mutant tomato, Anthocyanin fruit (Aft, LA1996), was provided by C. M. Rick Tomato Genetic Resource Center (University of California, Davis, CA, U.S.A.), and was grown in the green house under natural photo-period condition from March to July, 2006 in Chiba prefecture, Japan.

value: Anthocyanin fruit (Aft) LA1996


title: Aft flesh of red fruit, biological rep 2


title: Aft peel of red fruit, biological rep 2

description: Gene expression data from Aft red fruit peel

source_name: Aft mutant (LA1996) peel of red fruit (approximately 50-55 days after anthesis)


title: Line27859 flesh of mature green fruit, biological rep 1


title: Aft flesh of mature green fruit, biological rep 1

description: Gene expression data from Aft mature green fruit flesh

source_name: Aft mutant (LA1996) flesh of mature green fruit (approximately 40 days after anthesis)


title: Aft peel of mature green fruit, biological rep 3

description: Gene expression data from Aft mature green fruit peel

source_name: Aft mutant (LA1996) peel of mature green fruit (approximately 40 days after anthesis)


title: Aft peel of red fruit, biological rep 1


title: Micro-Tom peel of red fruit, biological rep 1

description: Gene expression data from Micro-Tom red fruit peel

source_name: Micro-Tom peel of red fruit (approximately 45-48 days after anthesis)

growth_protocol: Seeds of cultivated tomato (S. lycopersicum cv. Micro-Tom) were sawn in the pots (500 ml) filled with mixture of vermiculite and Powersoil (1 to 1 mixing ratio, Kureha Chemical Ind., Tokyo, Japan, and Kanto Hiryou Ind., Saitama, Japan, respectively) and kept in a controlled room at 25C. After 4 days of germination, they were grown with a photoperiod of 16 hr light (7000 lux) and 8 hr dark at 25C. Hyponex (Hyponex Ltd., Osaka, Japan) at 1000-fold dilution was applied to plants once a week as a nutrient.

value: Approximately 45-48 days after anthesis

value: Micro-Tom


title: Aft flesh of red fruit, biological rep 1


title: Aft peel of mature green fruit, biological rep 2


title: Line27859 flesh of mature green fruit, biological rep 3


title: Aft flesh of mature green fruit, biological rep 2


title: Aft peel of red fruit, biological rep 3


title: Aft peel of mature green fruit, biological rep 1


title: Micro-Tom peel of orange fruit, biological rep 2

description: Gene expression data from Micro-Tom orange fruit peel

source_name: Micro-Tom peel of orange fruit (approximately 38-40 days after anthesis)

value: Approximately 38-40 days after anthesis


title: Micro-Tom peel of yellow fruit, biological rep 2

description: Gene expression data from Micro-Tom yellow fruit peel

source_name: Micro-Tom peel of yellow fruit (approximately 35 days after anthesis)

value: Approximately 35 days after anthesis


title: Micro-Tom peel of yellow fruit, biological rep 1


title: Aft flesh of mature green fruit, biological rep 3


title: Micro-Tom peel of red fruit, biological rep 3


title: Micro-Tom peel of red fruit, biological rep 2


title: Micro-Tom peel of orange fruit, biological rep 1


title: Micro-Tom peel of mature green fruit, biological rep 3

description: Gene expression data from Micro-Tom mature green fruit peel

source_name: Micro-Tom peel of mature green fruit (approximately 30 days after anthesis)

value: Approximately 30 days after anthesis


title: Micro-Tom peel of mature green fruit, biological rep 1


title: Micro-Tom peel of mature green fruit, biological rep 2


title: Micro-Tom flesh of red fruit, biological rep 2

description: Gene expression data from Micro-Tom red fruit flesh

source_name: Micro-Tom flesh of red fruit (approximately 45-48 days after anthesis)


title: Micro-Tom flesh of red fruit, biological rep 3


title: Micro-Tom flesh of orange fruit, biological rep 2

description: Gene expression data from Micro-Tom orange fruit flesh

source_name: Micro-Tom flesh of orange fruit (approximately 38-40 days after anthesis)


title: Micro-Tom flesh of red fruit, biological rep 1


title: Micro-Tom flesh of mature green fruit, biological rep 1

description: Gene expression data from Micro-Tom mature green fruit flesh

source_name: Micro-Tom flesh of mature green fruit (approximately 30 days after anthesis)


title: Micro-Tom all leaves from 5-week-old plant, biological rep 2

description: Gene expression data from all leaves of 5-week-old Micro-Tom plant

source_name: Micro-Tom all leaves (including petiole) of 5-week-old plant

value: leaf

value: 5 weeks after germination


title: Micro-Tom flesh of yellow fruit, biological rep 1

description: Gene expression data from Micro-Tom yellow fruit flesh

source_name: Micro-Tom flesh of yellow fruit (approximately 35 days after anthesis)


title: Micro-Tom cotyledon of 3-week-old plant, biological rep2

description: Gene expression data from Micro-Tom cotyledon

source_name: Micro-Tom 3-week-old cotyledon

value: cotyledon

value: 3 weeks after germination


title: Micro-Tom flesh of mature green fruit, biological rep 2


title: Micro-Tom hypocotyl of 3-week-old-plant, biological rep2

description: Gene expression data from Micro-Tom hypocotyl

source_name: Micro-Tom 3-week-old hypocotyl

value: hypocotyl


title: Micro-Tom third leaves of 3-week-old plant, biological rep 1

description: Gene expression data from Micro-Tom 3rd leaf

source_name: Micro-Tom blade of the third leaf (counted from the basal end) of 3-week-old plant


title: Micro-Tom flesh of mature green fruit, biological rep 3


title: Micro-Tom all leaves from 5-week-old plant, biological rep 1


title: Micro-Tom all leaves from 3-week-old plant, biological rep 1

description: Gene expression data from all leaves of 3-week-old Micro-Tom plant

source_name: Micro-Tom all leaves (including petiole) of 3-week-old plant


title: Micro-Tom all leaves from 3-week-old plant, biological rep 3


title: Micro-Tom 5Wroot, biological rep3

description: Gene expression data from Micro-Tom root

source_name: Micro-Tom 5-week-old root

growth_protocol: Seed of Solanum lycopersicum cv Micro-Tom were sawn in the pots (500 ml) filled with vermiculite, and kept in a controlled room at 25C in the dark. After 4 days of germination, plants were grown with a photoperiod of 16 hr light (7000 lux) and 8 hr dark at 25C. Hyponex (Hyponex Ltd., Osaka, Japan) at 1000-fold dilution was applied to plants once a week as a nutrient.

value: root


title: Micro-Tom flesh of yellow fruit, biological rep 2


title: Micro-Tom all leaves from 3-week-old plant, biological rep 2


title: Micro-Tom cotyledon of 3-week-old plant, biological rep1


title: Micro-Tom hypocotyl of 3-week-old-plant, biological rep1


title: Micro-Tom third leaves of 3-week-old plant, biological rep 2


title: Micro-Tom 5Wroot, biological rep1


title: 16wk, F vs RBC2, Replicate 9

city: East Lansing

first: Kelly

middle: R

last: Sporer

state: MI

address: 3365 Anthony Hall

department: Food Science and Human Nutrition

institute: Michigan State University

description: 16wk market weight bird F line versus RBC2 line comparison, replicate 9 of 10.

hyb_protocol: Fragmented, Cy3-coupled aRNA was mixed with its Cy5-coupled partner, and the mixtures were brought to 110 μL with 68°C SlideHyb 1 (Ambion, Inc.) and incubated at 68°C for 5 min. These dye-coupled mixtures were then hybridized to oligonucleotide microarrays (described previously) for 18 h in a GeneTac Hybridization Station (Genomic Solutions, Ann Arbor, MI) using the following conditions: 54°C for 18 h, followed by a medium-stringency wash at 42°C (2X SSC, 0.1% SDS), a high-stringency wash (0.2X SSC, 0.1% SDS) at 22°C, and a wash with postwash buffer (0.2X SSC) at 22°C. Arrays were then rinsed in 2X SSC and Nanopure H2O, dried by centrifugation at 500 × g for 5 min.

scan_protocol: Scanned with a GenePix 4000B (Molecular Devices, Sunnyvale, CA) scanner. Image analysis was performed using GenePix Pro 6.0, and spot intensities were exported as GPR files.

data_processing: Fluorescence intensity data was normalized for dye intensity bias using the LOESS procedure of the normalizeWithinArray function of the Bioconductor R software LIMMA (Smyth 2004).

organism: Meleagris gallopavo

source_name: Turkey pectoralis major muscle, F, 16-week market age bird

label_protocol: Total RNA for use in microarrays was amplified using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Inc.) per manufacturer instructions. Briefly, 2 μg total RNA was incubated with T7 Oligo(dT) primer for 10 min at 70°C then reverse transcribed into cDNA at 42°C for 2 h. Second strand synthesis was performed at 16°C for 2 h. Double-stranded cDNA was then purified, and in vitro transcription was performed at 37°C for 4 h. Amplified RNA (aRNA) was purified and quantified using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA). For the dye coupling procedure, 10 μg aRNA was coupled to either Cy3 or Cy5 fluorescent dye (GE Healthcare, Piscataway, NJ) in the dark at room temperature for 1 hour until the reaction was quenched by the addition of 4M hydroxylamine. Dye-coupled aRNA was purified and quantified, then 5 μg was fragmented to 60-200 nucleotide segments using RNA Fragmentation Reagents (Ambion, Inc.) at 70°C for 15 min in preparation for microarray hybridization.

extract_protocol: Total RNA extracted using TRIReagent (Molecular Research Center, Cincinnati, OH) following manufacturer's instructions. RNA integrity and concentration was determined using an Agilent 2100 Bioanlyzer (Santa Clara, CA).

value: pectoralis major muscle

tag: line

value: F (selected from RBC2 line for increased 16wk body weight)

value: 16-week market age bird

source_name: Turkey pectoralis major muscle, RBC2, 16-week market age bird

value: RBC2 (randombred control line representative of 1967 commercial turkey)


title: 16wk, F vs RBC2, Replicate 10

description: 16wk market weight bird F line versus RBC2 line comparison, replicate 10 of 10.


title: 16wk, F vs RBC2, Replicate 8

description: 16wk market weight bird F line versus RBC2 line comparison, replicate 8 of 10.


title: Micro-Tom flesh of orange fruit, biological rep 1

value: fruit pericarp and endocarp


title: Micro-Tom all leaves from 5-week-old plant, biological rep 3


title: 16wk, F vs RBC2, Replicate 4

description: 16wk market weight bird F line versus RBC2 line comparison, replicate 4 of 10.


title: Micro-Tom 5Wroot, biological rep2


title: 16wk, F vs RBC2, Replicate 5

description: 16wk market weight bird F line versus RBC2 line comparison, replicate 5 of 10.


title: 1d, F vs RBC2, Replicate 8

description: 1d post-hatch chick F line versus RBC2 line comparison, replicate 8 of 10.

source_name: Turkey pectoralis major muscle, RBC2, 1-day post-hatch chick

value: 1-day post-hatch chick

source_name: Turkey pectoralis major muscle, F, 1-day post-hatch chick


title: 1d, F vs RBC2, Replicate 5

description: 1d post-hatch chick F line versus RBC2 line comparison, replicate 5 of 10.


title: 1d, F vs RBC2, Replicate 10

description: 1d post-hatch chick F line versus RBC2 line comparison, replicate 10 of 10.


title: 16wk, F vs RBC2, Replicate 3

description: 16wk market weight bird F line versus RBC2 line comparison, replicate 3 of 10.


title: 16wk, F vs RBC2, Replicate 6

description: 16wk market weight bird F line versus RBC2 line comparison, replicate 6 of 10.


title: 1d, F vs RBC2, Replicate 3

description: 1d post-hatch chick F line versus RBC2 line comparison, replicate 3 of 10.


title: 16wk, F vs RBC2, Replicate 7

description: 16wk market weight bird F line versus RBC2 line comparison, replicate 7 of 10.


title: 18de, F vs RBC2, Replicate 9

description: 18d embryo F line versus RBC2 line, replicate 9 of 10.

source_name: Turkey pectoralis major muscle, F, 18-day embryo

value: 18-day embryo

source_name: Turkey pectoralis major muscle, RBC2, 18-day embryo


title: 16wk, F vs RBC2, Replicate 2

description: 16wk market weight bird F line versus RBC2 line comparison, replicate 2 of 10.


title: 18de, F vs RBC2, Replicate 10

description: 18d embryo F line versus RBC2 line, replicate 10 of 10.


title: 1d, F vs RBC2, Replicate 4

description: 1d post-hatch chick F line versus RBC2 line comparison, replicate 4 of 10.


title: 1d, F vs RBC2, Replicate 6

description: 1d post-hatch chick F line versus RBC2 line comparison, replicate 6 of 10.


title: 16wk, F vs RBC2, Replicate 1

description: 16wk market weight bird F line versus RBC2 line comparison, replicate 1 of 10.


title: 1d, F vs RBC2, Replicate 7

description: 1d post-hatch chick F line versus RBC2 line comparison, replicate 7 of 10.


title: 1d, F vs RBC2, Replicate 1

description: 1d post-hatch chick F line versus RBC2 line comparison, replicate 1 of 10.


title: 1d, F vs RBC2, Replicate 9

description: 1d post-hatch chick F line versus RBC2 line comparison, replicate 9 of 10.


title: 18de, F vs RBC2, Replicate 6

description: 18d embryo F line versus RBC2 line, replicate 6 of 10.


title: 18de, F vs RBC2, Replicate 5

description: 18d embryo F line versus RBC2 line, replicate 5 of 10.


title: 18de, F vs RBC2, Replicate 7

description: 18d embryo F line versus RBC2 line, replicate 7 of 10.


title: 18de, F vs RBC2, Replicate 8

description: 18d embryo F line versus RBC2 line, replicate 8 of 10.


title: 1d, F vs RBC2, Replicate 2

description: 1d post-hatch chick F line versus RBC2 line comparison, replicate 2 of 10.


title: 18de, F vs RBC2, Replicate 4

description: 18d embryo F line versus RBC2 line, replicate 4 of 10.


title: 18de, F vs RBC2, Replicate 3

description: 18d embryo F line versus RBC2 line, replicate 3 of 10.


title: 18de, F vs RBC2, Replicate 2

description: 18d embryo F line versus RBC2 line, replicate 2 of 10.


title: RBC2, 1d vs 16wk, Replicate 3

description: RBC2 line 1d chick versus 16wk market age bird comparison, replicate 3 of 10.


title: RBC2, 1d vs 16wk, Replicate 5

description: RBC2 line 1d chick versus 16wk market age bird comparison, replicate 5 of 10.


title: 18de, F vs RBC2, Replicate 1

description: 18d embryo F line versus RBC2 line, replicate 1 of 10.


title: RBC2, 18de vs 1d, Replicate 9

description: RBC2 line 18d embryo versus 1d chick comparison, replicate 9 of 10.


title: RBC2, 1d vs 16wk, Replicate 6

description: RBC2 line 1d chick versus 16wk market age bird comparison, replicate 6 of 10.


title: RBC2, 1d vs 16wk, Replicate 1

description: RBC2 line 1d chick versus 16wk market age bird comparison, replicate 1 of 10.


title: RBC2, 18de vs 1d, Replicate 10

description: RBC2 line 18d embryo versus 1d chick comparison, replicate 10 of 10.


title: RBC2, 18de vs 1d, Replicate 1

description: RBC2 line 18d embryo versus 1d chick comparison, replicate 1 of 10.


title: RBC2, 1d vs 16wk, Replicate 8

description: RBC2 line 1d chick versus 16wk market age bird comparison, replicate 8 of 10.


title: RBC2, 18de vs 1d, Replicate 5

description: RBC2 line 18d embryo versus 1d chick comparison, replicate 5 of 10.


title: RBC2, 1d vs 16wk, Replicate 7

description: RBC2 line 1d chick versus 16wk market age bird comparison, replicate 7 of 10.


title: RBC2, 1d vs 16wk, Replicate 4

description: RBC2 line 1d chick versus 16wk market age bird comparison, replicate 4 of 10.


title: RBC2, 18de vs 1d, Replicate 2

description: RBC2 line 18d embryo versus 1d chick comparison, replicate 2 of 10.


title: RBC2, 1d vs 16wk, Replicate 2

description: RBC2 line 1d chick versus 16wk market age bird comparison, replicate 2 of 10.


title: RBC2, 18de vs 1d, Replicate 8

description: RBC2 line 18d embryo versus 1d chick comparison, replicate 8 of 10.


title: RBC2, 18de vs 1d, Replicate 3

description: RBC2 line 18d embryo versus 1d chick comparison, replicate 3 of 10.


title: F, 1d vs 16wk, Replicate 8

description: F line 1d chick versus 16wk market age bird comparison, replicate 8 of 10.


title: RBC2, 18de vs 1d, Replicate 7

description: RBC2 line 18d embryo versus 1d chick comparison, replicate 7 of 10.


title: kidney_PKD2mut_d6 biol_rep2

description: kidney tissue were frozen immediately in liquid nitrogen and then stored at -80oC to be later processed for RNA analysis

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 3.2, from SAS. Gene expression profiling was performed using arrays of rat 230_2 -type from Affymetrix. A Custom CDF Version 12 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

organism: Rattus norvegicus

source_name: kidney_PKD2mut_d6 biol_rep2

extract_protocol: 15-50mg from the frozen kidney tissues were used to extract total RNA from the WT and PKD2(1-703) rats using the RNeasy® Mini (QIAGEN, City, Germany) or Midi (QIAGEN) kit depending on the weight of the tissue obtained. Tissues were grinded in 1.5ml eppendorf tubes using a pestle. Total RNA was extracted according to the manufacturer’s instructions.

value: Sprague Dawley

tag: genome/variation

value: PKD2 mutant transgenic [TGR (CMV-hPKD2/1-703)]

value: kidney

tag: sex

value: male

tag: age (after birth)


title: RBC2, 1d vs 16wk, Replicate 9

description: RBC2 line 1d chick versus 16wk market age bird comparison, replicate 9 of 10.


title: F, 1d vs 16wk, Replicate 9

description: F line 1d chick versus 16wk market age bird comparison, replicate 9 of 10.


title: RBC2, 18de vs 1d, Replicate 6

description: RBC2 line 18d embryo versus 1d chick comparison, replicate 6 of 10.


title: Liver Non-Tumor Tissue LCS-004B

description: No additional information.

organism: Homo sapiens

value: Liver Non-Tumor Tissue

value: Hepatocellular carcinoma (HCC)


title: kidney_PKD2mut_d6 biol_rep3

source_name: kidney_PKD2mut_d6 biol_rep3


title: F, 1d vs 16wk, Replicate 10

description: F line 1d chick versus 16wk market age bird comparison, replicate 10 of 10.


title: RBC2, 1d vs 16wk, Replicate 10

description: RBC2 line 1d chick versus 16wk market age bird comparison, replicate 10 of 10.


title: kidney_PKD2mut_d0 biol_rep3

source_name: kidney_PKD2mut_d0 biol_rep3


title: kidney_PKD2mut_d6 biol_rep1

source_name: kidney_PKD2mut_d6 biol_rep1


title: F, 1d vs 16wk, Replicate 6

description: F line 1d chick versus 16wk market age bird comparison, replicate 6 of 10.


title: F, 1d vs 16wk, Replicate 5

description: F line 1d chick versus 16wk market age bird comparison, replicate 5 of 10.


title: F, 1d vs 16wk, Replicate 4

description: F line 1d chick versus 16wk market age bird comparison, replicate 4 of 10.


title: F, 1d vs 16wk, Replicate 2

description: F line 1d chick versus 16wk market age bird comparison, replicate 2 of 10.


title: F, 1d vs 16wk, Replicate 3

description: F line 1d chick versus 16wk market age bird comparison, replicate 3 of 10.


title: F, 18de vs 1d, Replicate 9

description: F line 18d embryo versus 1d chick comparison, replicate 9 of 10.


title: kidney_SD_d0 biol_rep2

source_name: kidney_SD_d0 biol_rep2

value: wild type


title: F, 1d vs 16wk, Replicate 1

description: F line 1d chick versus 16wk market age bird comparison, replicate 1 of 10.


title: RBC2, 18de vs 1d, Replicate 4

description: RBC2 line 18d embryo versus 1d chick comparison, replicate 4 of 10.


title: F, 18de vs 1d, Replicate 8

description: F line 18d embryo versus 1d chick comparison, replicate 8 of 10.


title: F, 18de vs 1d, Replicate 6

description: F line 18d embryo versus 1d chick comparison, replicate 6 of 10.


title: kidney_SD_d0 biol_rep3

source_name: kidney_SD_d0 biol_rep3


title: F, 18de vs 1d, Replicate 7

description: F line 18d embryo versus 1d chick comparison, replicate 7 of 10.


title: F, 1d vs 16wk, Replicate 7

description: F line 1d chick versus 16wk market age bird comparison, replicate 7 of 10.


title: F, 18de vs 1d, Replicate 4

description: F line 18d embryo versus 1d chick comparison, replicate 4 of 10.


title: kidney_SD_d0 biol_rep1

description: kidney tissue were frozen immediately in liquid nitrogen and then stored at -80oC to be later processed for RNA analysis

source_name: kidney_SD_d0 biol_rep1


title: F, 18de vs 1d, Replicate 3

description: F line 18d embryo versus 1d chick comparison, replicate 3 of 10.


title: kidney_PKD2mut_d24 biol_rep2

source_name: kidney_PKD2mut_d24 biol_rep2


title: kidney_PKD2mut_d24 biol_rep3

source_name: kidney_PKD2mut_d24 biol_rep3


title: kidney_PKD2mut_d0 biol_rep2

source_name: kidney_PKD2mut_d0 biol_rep2


title: F, 18de vs 1d, Replicate 1

description: F line 18d embryo versus 1d chick comparison, replicate 1 of 10.


title: kidney_PKD2mut_d24 biol_rep1

source_name: kidney_PKD2mut_d24 biol_rep1


title: F, 18de vs 1d, Replicate 5

description: F line 18d embryo versus 1d chick comparison, replicate 5 of 10.


title: F, 18de vs 1d, Replicate 2

description: F line 18d embryo versus 1d chick comparison, replicate 2 of 10.


title: kidney_SD_d24 biol_rep3

source_name: kidney_SD_d24 biol_rep3


title: Self-self validation array

description: RBC2 line 18d embryo-Cy5 versus the same RBC2 18d embryo sample-Cy3.

hyb_protocol: Fragmented, Cy3-coupled aRNA was mixed with its Cy5-coupled partner, and the mixtures were brought to 110 μL with 68°C SlideHyb 1 (Ambion, Inc.) and incubated at 68°C for 5 min.  These dye-coupled mixtures were then hybridized to oligonucleotide microarrays (described previously) for 18 h in a GeneTac Hybridization Station (Genomic Solutions, Ann Arbor, MI) using the following conditions: 54°C for 18 h, followed by a medium-stringency wash at 42°C (2X SSC, 0.1% SDS), a high-stringency wash (0.2X SSC, 0.1% SDS) at 22°C, and a wash with postwash buffer (0.2X SSC) at 22°C.  Arrays were then rinsed in 2X SSC and Nanopure H2O, dried by centrifugation at 500 × g for 5 min.

label_protocol: Total RNA for use in microarrays was amplified using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Inc.) per manufacturer instructions.  Briefly, 2 μg total RNA was incubated with T7 Oligo(dT) primer for 10 min at 70°C then reverse transcribed into cDNA at 42°C for 2 h.  Second strand synthesis was performed at 16°C for 2 h.  Double-stranded cDNA was then purified, and in vitro transcription was performed at 37°C for 4 h.  Amplified RNA (aRNA) was purified and quantified using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA).  For the dye coupling procedure, 10 μg aRNA was coupled to either Cy3 or Cy5 fluorescent dye (GE Healthcare, Piscataway, NJ) in the dark at room temperature for 1 hour until the reaction was quenched by the addition of 4M hydroxylamine.  Dye-coupled aRNA was purified and quantified, then 5 μg was fragmented to 60-200 nucleotide segments using RNA Fragmentation Reagents (Ambion, Inc.) at 70°C for 15 min in preparation for microarray hybridization.

extract_protocol: Total RNA extracted using TRIReagent (Molecular Research Center, Cincinnati, OH) following manufacturer's instructions.  RNA integrity and concentration was determined using an Agilent 2100 Bioanlyzer (Santa Clara, CA).

value: RBC2 (random bred, genetically unimproved line)


title: Repeat Dye Swap 2 validation array

description: F line 1d post-hatch chick-Cy3 versus F line 18d embryo-Cy5, repeated same hybridization as "Dye Swap 2".


title: Organs control rep2

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

description: qRT-PCR

scan_protocol: The amplification products were obtained and analysed in a Rotor-gene 2000 machine (RCorbett Research, Sydney, Australia ).

data_processing: Data were processed with Microsoft Excel. Normalization was done using the mean of three independent RPLO genes.

label: FAM

source_name: Organs, control, replicate 2

label_protocol: Probes were labeled with FAM

growth_protocol: Zebrafishes were grown at 25 ºC and then acclimated to 14 ºC for 7 days

extract_protocol: RNA was prepared using the Rneasy Micro Kit (QIAGEN)

treatment_protocol: Zebrafishes were infected with VHSV or mock (control) and incubated at 14 ºC for 2 days

value: spleen, head kidney and liver


title: Organs control rep1

description: qRT-PCR

source_name: Organs, control, replicate 1


title: Dye Swap 2 validation array

description: F line 1d post-hatch chick-Cy3 versus F line 18d embryo-Cy5, dye assignments reverse of "Dye Swap 1".

source_name: Turkey pectoralis major muscle, F, 1-day post-hatch chick


title: Organs control rep3

description: qRT-PCR

source_name: Organs, control, replicate 3


title: Dye Swap 1 validation array

description: F line 18d embryo-Cy3 versus F line 1d post-hatch chick-Cy5.

source_name: Turkey pectoralis major muscle, F, 18-day embryo


title: Organs VHSV rep3

description: qRT-PCR

source_name: Organs, 2d after VHSV infection, replicate 3


title: Organs VHSV rep2

description: qRT-PCR

source_name: Organs, 2d after VHSV infection, replicate 2


title: kidney_PKD2mut_d0 biol_rep1

source_name: kidney_PKD2mut_d0 biol_rep1


title: Organs VHSV rep1

description: qRT-PCR

source_name: Organs, 2d after VHSV infection, replicate 1


title: kidney_SD_d24 biol_rep1

source_name: kidney_SD_d24 biol_rep1


title: kidney_SD_d24 biol_rep2

source_name: kidney_SD_d24 biol_rep2


title: Fins control rep5

description: qRT-PCR

source_name: Fins, control, replicate 5

value: fins


title: Fins control rep4

description: qRT-PCR

source_name: Fins, control, replicate 4


title: F, 18de vs 1d, Replicate 10

description: F line 18d embryo versus 1d chick comparison, replicate 10 of 10.

value: pectoralis major muscle


title: Fins control rep6

description: qRT-PCR

source_name: Fins, control, replicate 6


title: kidney_SD_d6 biol_rep3

source_name: kidney_SD_d6 biol_rep3


title: Fins control rep3

description: qRT-PCR

source_name: Fins, control, replicate 3


title: Fins control rep2

description: qRT-PCR

source_name: Fins, control, replicate 2


title: Fins control rep1

description: qRT-PCR

source_name: Fins, control, replicate 1


title: kidney_SD_d6 biol_rep2

source_name: kidney_SD_d6 biol_rep2


title: Fins VHSV rep6

description: qRT-PCR

source_name: Fins, 2d after VHSV infection, replicate 6


title: Fins VHSV rep5

description: qRT-PCR

source_name: Fins, 2d after VHSV infection, replicate 5


title: kidney_SD_d6 biol_rep1

source_name: kidney_SD_d6 biol_rep1


title: Fins VHSV rep1

description: qRT-PCR

source_name: Fins, 2d after VHSV infection, replicate 1


title: Fins VHSV rep4

description: qRT-PCR

source_name: Fins, 2d after VHSV infection, replicate 4


title: Fins VHSV rep2

description: qRT-PCR

source_name: Fins, 2d after VHSV infection, replicate 2


title: Fins VHSV rep3

description: qRT-PCR

source_name: Fins, 2d after VHSV infection, replicate 3