title: Cancer BC0159T

description: gene expression data from breast tumor


title: Cancer BC0163T

status: Public on Apr 28 2009

type: RNA

city: Kuala Lumpur

first: Ivyna

middle: PN

last: Bong

state: Kuala Lumpur

address: Jalan Pahang

department: Cancer Research Centre

country: Malaysia

institute: Institute for Medical Research

description: gene expression data from breast tumor

hyb_protocol: Following fragmentation, 35 ug of cRNA were hybridized for 16 hr at 45C on Human U133A GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) and GCOS version 2.0 using Affymetrix default analysis settings. The global trimmed mean signal intensity value were set to ensure the scale factors were in the range of 1.000 – 3.000.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: breast tumor tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNAs

growth_protocol: tissues were collected from the operation theater and immediately stored in liquid nitrogen prior to total RNA isolation.

extract_protocol: total RNAs were extracted using Trizol reagent and purified through Qiagen purification column according to manufacturer's recommendations

tag: tissue

value: breast

tag: histopathological exam

value: infiltrating ductal carcinoma

tag: grade

value: grade 2

tag: age in years

tag: race

value: Chinese


title: Cancer BC0160T

description: gene expression data from breast tumor

value: grade 3

value: Malay


title: Normal BC0160N

description: gene expression data from normal breast tissue

source_name: normal breast tissue

value: normal


title: Normal BC0155N

value: Indian


title: Normal BC0158N


title: Cancer BC0147T

description: gene expression data from breast tumor


title: Cancer BC0156T

description: gene expression data from breast tumor


title: Cancer BC0153T

description: gene expression data from breast tumor


title: Normal BC0156N


title: Cancer BC0158T

description: gene expression data from breast tumor


title: Cancer BC0152T

description: gene expression data from breast tumor

value: grade 1


title: Cancer BC0151T

description: gene expression data from breast tumor


title: Normal BC0152N


title: Cancer BC0142T

description: gene expression data from breast tumor


title: Normal BC0142N


title: Normal BC0153N


title: Cancer BC0155T

description: gene expression data from breast tumor

value: lobular carcinoma


title: Normal BC0147N


title: Cancer BC0138T

description: gene expression data from breast tumor

value: invasive ductal carcinoma


title: Normal BC0151N


title: Normal BC0138N


title: Cancer BC0127T

description: gene expression data from breast tumor

value: ductal carcinoma


title: Normal BC0126N


title: Cancer BC0122T

description: gene expression data from breast tumor


title: Normal BC0122N


title: Cancer BC0117T

description: gene expression data from breast tumor


title: Normal BC0127N


title: Cancer BC0113T

description: gene expression data from breast tumor


title: Normal BC0117N


title: Normal BC0057N


title: Normal BC0113N


title: Normal BC0112N


title: Cancer BC0109T

description: gene expression data from breast tumor


title: Cancer BC0043T

description: gene expression data from breast tumor

value: mucinous carcinoma


title: Normal BC0043N


title: L. lactis µ=0.47h-1 modified MCD medium replicate 2

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

country: France

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

description: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.

hyb_protocol: L. lactis IL1403 specific PCR products were spotted in duplicate on positively charged nylon membranes (4 deposits per spot, Plateforme Génomique, Toulouse). A single PCR per ORF was designed by Eurogentec, PCRs covered about 71 % of each ORF length (mean length 535 bp and final concentration between 40 and 180 µg.ml-1). 2053 ORFs of the 2310 identified on the genome were effectively available. Prior to hybridization, membranes were washed for 5 min in 50 ml of 2X SSPE (SSPE 1X is 0.18 mM NaCl, 1 mM EDTA, and 10 mM phosphate buffer pH 7.2) and prehybridized for 3 h at 68°C in 5 ml of hybridization buffer (5X SSPE, 2 % SDS, 1X Denhardt’s reagent). Labeled cDNA was heated for 10 min at 95°C and immediately cooled at 4°C for 5 min. Membrane hybridization was carried out for 15 h at 68°C with 5 ml of hybridization buffer containing labeled and denatured cDNA. Membranes were then washed 3 times in 50 ml of washing solution (0.5X SSPE, 0.2 % SDS) for 5 min at room temperature and 3 times in 50 ml of preheated washing solution for 20 min at 68°C. Dried membranes were exposed to a phosphoimager screen for 3 days and scanned with a phosphofluoroimager (Storm 860, Molecular Dynamics).

scan_protocol: Hybridization signals were quantified, assigned to gene names, and statistically treated with the Bioplot software (developed by S. Sokol in Plateforme Génomique, Toulouse, http://biopuce.insa-toulouse.fr/). Local background was removed and signals were normalized by the mean intensity of the membrane.

data_processing: Local background was removed from the raw signals with the Bioplot software (Biochips Platform, INSA Toulouse, France, http://biopuce.insa-toulouse.fr).. Data were normalized by the all spot’s mean with Bioplot software.

organism: Lactococcus lactis

label_protocol: For cDNA synthesis, 10 or 15 µg of total RNA was mixed with 1 µl of random hexamer primers (Sigma Genosys, 500 ng.µl-1), 1 µl of Eurogentec L. lactis open reading frame specific primers (500 ng.µl-1) and sterile water to a final volume of 24 µl. The mixture was heated at 70°C for 5 min and then immediately cooled to 4°C. Reverse transcription was performed for 1 h at 42°C in a total volume of 50 µl, with SuperScriptII reverse transcriptase (300 U, Life Technologies), dithiotreitol (10 mM, Life Technologies), dATP, dGTP, dTTP (0.3 mM each), and [-33P]dCTP (50 µCi, Amersham Biosciences) and 5X first strand buffer (1X, Life Technologies). After 1 h, SuperScriptII reverse transcriptase (100 U) and dCTP (0.1 mM) were added and the reaction performed for one more hour at 42°C. Reaction was stopped by heating (15 min at 70°C), and the remaining RNA was hydrolyzed by RNaseH (2 U, 20 min, 37°C, Life Technologies). Before hybridization, labeled cDNA was purified on Microspin G25 columns (Amersham Biosciences) according to the manufacturer’s instructions.

growth_protocol: see manuscript in preparation Dressaire et al. 2008. Growth rate regulated genes and their wide involvement in the Lactococcus lactis stress responses

extract_protocol: A volume of culture corresponding to 6 mg (dry weight) of cells was frozen immediately in liquid nitrogen. Before cell lysis, each sample was centrifuged (4°C, 5 min, 8000 rpm), washed with 1 ml TE buffer (Tris-HCl 10 mM pH 8, EDTA 1 mM) and resuspended in 500 µl TE buffer. Cells were disrupted at 4 °C (3 cycles of 1 min interspaced by 3 min cooling periods) on a minibead beater (Biospec Products) with glass beads (0.6 g), 50 µl SDS (10 %), and 500 µl phenol (pH 4.7). After centrifugation to eliminate cell debris and phenol (4°C, 25 min, 13000 rpm), half of the aqueous phase containing RNA was extracted with RNeasy midi kit (Qiagen), including the DNase I treatment described in the manufacturer’s instructions. RNA was quantified at 260 and 280 nm and RNA quality was controlled on electrophoresis agarose gel in denaturing conditions.

tag: growth status


title: L. lactis µ=0.47h-1 modified MCD medium replicate 3

tag: strain IL1403


title: Cancer BC0057T

description: gene expression data from breast tumor


title: L. lactis µ=0.47h-1 modified MCD medium replicate 1


title: Cancer BC0126T

description: gene expression data from breast tumor


title: Cancer BC0112T

description: gene expression data from breast tumor

value: intraductal carcinoma


title: Normal BC0087N


title: Cancer BC0051T

description: gene expression data from breast tumor

value: mixed mucinous carcinoma & ductal carcinoma


title: L. lactis µ=0.35h-1 modified MCD medium replicate 3


title: Cancer BC0087T

description: gene expression data from breast tumor


title: L. lactis µ=0.24h-1 modified MCD medium replicate 1


title: Normal BC0051N


title: L. lactis µ=0.35h-1 modified MCD medium replicate 2


title: L. lactis µ=0.35h-1 modified MCD medium replicate 1


title: L. lactis µ=0.24h-1 modified MCD medium replicate 3


title: L. lactis µ=0.09h-1 modified MCD medium replicate 3


title: Cancer BC0170T

description: gene expression data from breast tumor


title: L. lactis µ=0.09h-1 modified MCD medium replicate 2

hyb_protocol: L. lactis IL1403 specific PCR products were spotted in duplicate on positively charged nylon membranes (4 deposits per spot, Plateforme Génomique, Toulouse). A single PCR per ORF was designed by Eurogentec, PCRs covered about 71 % of each ORF length (mean length 535 bp and final concentration between 40 and 180 µg.ml-1). 2053 ORFs of the 2310 identified on the genome were effectively available. Prior to hybridization, membranes were washed for 5 min in 50 ml of 2X SSPE (SSPE 1X is 0.18 mM NaCl, 1 mM EDTA, and 10 mM phosphate buffer pH 7.2) and prehybridized for 3 h at 68°C in 5 ml of hybridization buffer (5X SSPE, 2 % SDS, 1X Denhardt’s reagent). Labeled cDNA was heated for 10 min at 95°C and immediately cooled at 4°C for 5 min. Membrane hybridization was carried out for 15 h at 68°C with 5 ml of hybridization buffer containing labeled and denatured cDNA. Membranes were then washed 3 times in 50 ml of washing solution (0.5X SSPE, 0.2 % SDS) for 5 min at room temperature and 3 times in 50 ml of preheated washing solution for 20 min at 68°C. Dried membranes were exposed to a phosphoimager screen for 3 days and scanned with a phosphofluoroimager (Storm 860, Molecular Dynamics). Hybridization signals were quantified and assigned to gene names with the Bioplot software (developed by S. Sokol in Plateforme Génomique, Toulouse).


title: Cancer BC0171T

description: gene expression data from breast tumor


title: L. lactis µ=0.24h-1 modified MCD medium replicate 2

hyb_protocol: L. lactis IL1403 specific PCR products were spotted in duplicate on positively charged nylon membranes (4 deposits per spot, Plateforme Génomique, Toulouse). A single PCR per ORF was designed by Eurogentec, PCRs covered about 71 % of each ORF length (mean length 535 bp and final concentration between 40 and 180 µg.ml-1). 2053 ORFs of the 2310 identified on the genome were effectively available. Prior to hybridization, membranes were washed for 5 min in 50 ml of 2X SSPE (SSPE 1X is 0.18 mM NaCl, 1 mM EDTA, and 10 mM phosphate buffer pH 7.2) and prehybridized for 3 h at 68°C in 5 ml of hybridization buffer (5X SSPE, 2 % SDS, 1X Denhardt’s reagent). Labeled cDNA was heated for 10 min at 95°C and immediately cooled at 4°C for 5 min. Membrane hybridization was carried out for 15 h at 68°C with 5 ml of hybridization buffer containing labeled and denatured cDNA. Membranes were then washed 3 times in 50 ml of washing solution (0.5X SSPE, 0.2 % SDS) for 5 min at room temperature and 3 times in 50 ml of preheated washing solution for 20 min at 68°C. Dried membranes were exposed to a phosphoimager screen for 3 days and scanned with a phosphofluoroimager (Storm 860, Molecular Dynamics)..


title: TGFbeta treated cells

city: Tsukuba

first: Tomoki

last: Chiba

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Primary osteoblasts cultured under serum-starved condition were treated or untreated with TGF-beta1 for 24 hr.

hyb_protocol: Hybridization was carried out using BD Atlas Glass Hybridizaton Chamber

scan_protocol: Refer to Clonetech BD Atlas standard scan protocol.

data_processing: We carefully selected and focused on a particular gene from the data and confirmed the up-regulation by quantitative RT-PCR. The final processed data used the ratios obtained from qRT-PCR.

organism: Mus musculus

source_name: TGF-treated osteoblastic cells

label_protocol: cDNAs were labeled according to BD Atlas Fluorescent Labeling Kit.

growth_protocol: Primary murine osteoblast cells cultured under serum starved condition (0.2% FBS / alphaMEM)

extract_protocol: TRIZOL reagent

treatment_protocol: Cells were stimulated with 2 ng/ml TGF beta1 for 24hr.

tag: serum-starved TGF-treated osteoblastic cells


title: L. lactis µ=0.09h-1 modified MCD medium replicate 1


title: Normal BC0109N


title: control untreated cells

source_name: serum-starved osteoblastic cells

tag: serum-starved osteoblastic cells untreated with TGF-beta1


title: STAT1 shRNA-transfected STAT1 knockdown SCC61 tumor xenograft, irradiated, technical replicate 2

city: Chicago

first: Sean

middle: Pravin

last: Pitroda

state: IL

address: 5841 South Maryland Avenue, MC 1105

department: Radiation and Cellular Oncology

country: USA

institute: The University of Chicago

description: STAT1 shRNA-transfected STAT1 knockdown SCC61 tumor xenograft, untreated control, pooled sample from 3 independent tumors normalized to total RNA

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99 °C for 5 minutes, then 45 °C for 5 minutes centrifuge at max speed for 1 minute • Transfer 200 μl of hybridization solution to each array, then tape holes and parafilm • Hybridize for 17 hours in 45 °C at 60 rpm • Fluidics washing is FS450_0001

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G using GCOS version 1.4 software with default settings

data_processing: Expression Console software version 1.1

source_name: SCC61 STAT1 knockdown tumor, irradiated

label_protocol: Ribosomal RNA was removed from total RNA extracts using RiboMinus™ Transcriptome Isolation Kit (Invitrogen). Samples were subsequently enzymatically fragmented and biotinylated using GeneChip® Whole Transcript (WT) Sense Target Labeling (Affymetrix).

growth_protocol: The human squamous cell carcinoma SCC61 cell line was stably transfected with a control vector (SCC61 wild-type [WT]) or one expressing a short hairpin RNA to STAT1 (SCC61 knockdown [KD]) and maintained as previously described (Khodarev NN, et al., 2007). Tumor xenografts were established by subcutaneous injection of 10^7 cells in 100 µL of PBS into the right hind limbs of 6-week-old female athymic mice (FCRI-Taconic).

extract_protocol: Frozen tumor xenografts were sectioned into pieces approximately 5 mm^3 in size and soaked overnight in RNAlater-ICE solution (Applied Biosystems-Ambion). Samples were spun, washed in RLT buffer (QIAGEN), and homogenized on ice using a mechanical glass-Teflon homogenizer set at 3,000 rpm. Further purification was performed using TRIzol reagent (Invitrogen Life Sciences) as previously described (Khodarev NN et al., 2002). The quality of samples was assessed using gel electrophoresis in 1.8% agarose and spectrophotometry.

treatment_protocol: Ionizing radiation (IR) was delivered in 5 Gy fractions over six consecutive days (total 30 Gy) when tumors reached an average size of 160 mm^3 using a Philips RT 250 X-ray generator with a dose rate of 1.65 Gy/min. When tumor volume reached 1,000 mm^3, mice were euthanized by using CO2 followed by cervical dislocation. Tumors were excised, snap-frozen in liquid nitrogen, and stored at -80 °C until RNA extraction.

tag: genotype

value: STAT1 knockdown

tag: cell line


title: L. lactis exponential phase ILV5 medium replicate 1

scan_protocol: Dried membranes were exposed to a phosphoimager screen for 3 days and scanned with a phosphofluoroimager (Storm 860, Molecular Dynamics). Hybridization signals were quantified and assigned to gene names with the Bioplot software (developed by S. Sokol in Plateforme Génomique, Toulouse). After background removal, spots with intensities below the detection limit, defined as the mean intensity of “empty” spots, were removed.

data_processing: Local background was removed from the raw signals with the Bioplot software (Biochips Platform, INSA Toulouse, France, http://biopuce.insa-toulouse.fr). Spots with intensities below the detection threshold were discarded. Detection threshold was defined as the mean intensity plus two standard deviations of empty spots. Data were normalized by the all spot’s mean with Bioplot software.

source_name: L. lactis IL1403 exponential phase

label_protocol: For cDNA synthesis, 10 µg of total RNA was mixed with 1 µl of random hexamer primers (Sigma Genosys, 500 ng.µl-1), 1 µl of Eurogentec L. lactis open reading frame specific primers (500 ng.µl-1) and sterile water to a final volume of 24 µl. The mixture was heated at 70°C for 5 min and then immediately cooled to 4°C. Reverse transcription was performed for 1 h at 42°C in a total volume of 50 µl, with SuperScriptII reverse transcriptase (300 U, Life Technologies), dithiotreitol (10 mM, Life Technologies), dATP, dGTP, dTTP (0.3 mM each), and [-33P]dCTP (50 µCi, Amersham Biosciences) and 5X first strand buffer (1X, Life Technologies). After 1 h, SuperScriptII reverse transcriptase (100 U) and dCTP (0.1 mM) were added and the reaction performed for one more hour at 42°C. Reaction was stopped by heating (15 min at 70°C), and the remaining RNA was hydrolyzed by RNaseH (2 U, 20 min, 37°C, Life Technologies). Before hybridization, labeled cDNA was purified on Microspin G25 columns (Amersham Biosciences) according to the manufacturer’s instructions.

tag: growth status exponential


title: Control vector-transfected STAT1 wild-type SCC61 tumor xenograft, irradiated, technical replicate 1

description: Control vector-transfected STAT1 wild-type SCC61 tumor xenograft, untreated control, pooled sample from 3 independent tumors normalized to total RNA

source_name: SCC61 STAT1 wild-type tumor, irradiated

value: STAT1 wild-type


title: STAT1 shRNA-transfected STAT1 knockdown SCC61 tumor xenograft, untreated control, technical replicate 1

source_name: SCC61 STAT1 knockdown tumor, untreated control


title: L. lactis exponential phase ILV5 medium replicate 3

description: Dried membranes were exposed to a phosphoimager screen for 3 days and scanned with a phosphofluoroimager (Storm 860, Molecular Dynamics). Hybridization signals were quantified and assigned to gene names with the Bioplot software (developed by S. Sokol in Plateforme Génomique, Toulouse). After background removal, spots with intensities below the detection limit, defined as the mean intensity of “empty” spots, were removed.


title: STAT1 shRNA-transfected STAT1 knockdown SCC61 tumor xenograft, untreated control, technical replicate 2


title: L. lactis exponential phase ILV5 medium replicate 2


title: GBM_Cell Line_6

city: Cambridge

first: Talal

middle: M.

last: Fael Al-Mayhani

state: Cambridgeshire

address: Forvie Site, Robinson Way

department: Clinical Neurosciences

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Standard Illumina hybridization protocol by Centre for Microarray Resources at the department of Pathology of the University of Cambridge, UK

scan_protocol: Standard Illumina scan protocol by Centre for Microarray Resources at the department of Pathology of the University of Cambridge, UK

data_processing: Robust spline normalization

source_name: GBM

growth_protocol: GBM cell lines were derived from excised GBM tumours and cultured under serum-free conditions with EGF and FGF. Full details of the derivation and culture protocol have been described by Fael Al-Mayhani et al, 2009

extract_protocol: RNA was extracted using Qiagen RNAeasy kit

treatment_protocol: Full details of the cell lines culture prior RNA extraction have been described by Fael Al-Mayhani et al, 2009

value: GBM


title: L. lactis 1.6h after norvaline addition ILV5 medium replicate 3

source_name: L. lactis IL1403 1.6h after norvaline addition

tag: 1.6h after norvaline addition


title: L. lactis 1.6h after norvaline addition ILV5 medium replicate 2


title: GBM_Cell Line_7


title: Hues63

status: Public on Apr 27 2009

type: genomic

city: La Jolla

first: Kun

last: Zhang

state: CA

address: 9500 Gilman Drive, MC0412

department: Bioengineering

institute: University of California at San Diego

description: Digital DNA methylation analysis of stem cell reprogramming by targeted bisulfite sequencing

data_processing:
Reads were aligned to captured target sequences. CpG methylation levels were extracted from mapped reads. The resulting values are real numbers ranging from 0 to 1, which correspond to completely unmethylated and completely methylated.
Annotation track file (bed) and raw read file (seq) are attached. The full set of raw sequence data with quality information was not supplied.
Format of the attached BED file is as follows:
Column 1: chromosome
Column 2: chromosome_start of CpG
Column 3: chromosome_end of CpG
Column 4: methylation level [0-1]; 0=completely unmethylated, 1=completely methylated
Column 5: sequencing depth at the CpG site
Column 6: strand, ignored since the reads from both strands were combined
Column 7: chromosome_start, same as Column 2
Column 8: chromosome_end, same as Column 3
Column 9: pesudo color, red is methylated, and green is unmethylated

molecule: genomic DNA

source_name: Embyonic stem cells

growth_protocol: Fibroblasts were cultured with DMEM with 10% FBS; hES cells and hybrid stem cells were cultured on MEF with hES media; iPS cells were cultured with protocols described in (Maherali et al. Cell Stem Cell 3:340-5; Park et al. Nature 451:141-6; Yu et al. Science 318:1917-20).

extract_protocol:
Genomic DNAs were extracted with Qiagen DNeasy kit, and converted by Zymo Research DNA Methylation Gold Kit
library strategy: USER-S1-Ligation
library selection: Padlock capture

tag: Cell line:HuES

tag: Cell type:Embyonic stem cells


title: Control vector-transfected STAT1 wild-type SCC61 tumor xenograft, irradiated, technical replicate 2


title: GBM_Cell Line_5


title: STAT1 shRNA-transfected STAT1 knockdown SCC61 tumor xenograft, irradiated, technical replicate 1


title: L. lactis 1.6h after norvaline addition ILV5 medium replicate 1


title: GBM_Cell Line_2


title: GBM_Cell Line_8


title: GBM_Cell Line_4


title: Control vector-transfected STAT1 wild-type SCC61 tumor xenograft, untreated control, technical replicate 1

source_name: SCC61 STAT1 wild-type tumor, untreated control


title: GBM_Cell Line_1


title: Control vector-transfected STAT1 wild-type SCC61 tumor xenograft, untreated control, technical replicate 2


title: Hues42


title: Hues12


title: P5R2 H3K4me2 ID96063b

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

description: Chip-chip Pax5-/-Rag2-/- pro-B cells H3K4me2

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: log2(Signal Cy5/Signal Cy3) - tukey.biweight(Signal Cy5/Signal Cy3)

source_name: H3K4me2 ChIP DNA from Pax5-/- Rag2-/- pro-B cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium.

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

treatment_protocol: Pax5-/- Rag2-/- pro-B cells are an established cell line.

tag: age

value: cell line

value: pro-B cells

tag: strain

tag: antibody

tag: type

value: ChIP

source_name: Input DNA from Pax5-/- Rag2-/- pro-B cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: see chanel 1

extract_protocol: see chanel 1

treatment_protocol: see chanel 1

value: Input


title: P5R2 H3K4me3 ID91992b

description: Chip-chip Pax5-/-Rag2-/- pro-B cells H3K4me3

source_name: H3K4me3 ChIP DNA from Pax5-/- Rag2-/- pro-B cells

tag: tissue


title: RAG H3K4me2 ID90982b

description: Chip-chip Rag2-/- pro-B cells H3K4me2

source_name: H3K4me2 ChIP DNA from Rag2-/- pro-B cells

growth_protocol: Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells.

treatment_protocol: Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice.

value: 5 days in culture

source_name: Input DNA from Rag2-/- pre-B cells


title: BW25113 CP4-57-deficient strain at OD=0.5 LB 37C

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from  planktonic cells of E. coli K-12 CP4-57-deficient strain at OD=0.5 in LB at 37ºC.

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS)

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS)

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: When OD=0.5 , planktonic cells were collected and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: RAG H3K9ac ID95879b

description: Chip-chip Rag2-/- pro-B cells H3K9ac

source_name: H3K9ac ChIP DNA from Rag2-/- pro-B cells


title: Hues6-BJ-Hybrid1

source_name: Hybrid stem cells

tag: Cell type:Hybrid stem cells


title: P5R2 H3K9ac ID87920b

description: Chip-chip Pax5-/-Rag2-/- pro-B cells H3K9ac

source_name: H3K9ac ChIP DNA from Pax5-/- Rag2-/- pro-B cells


title: TYML-PRB ERID _R5020_6h_ReplicateC_146

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

description: Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

hyb_protocol: Slides were pre-hybridized in prewarmed 5X SCC, 0.1% SDS and 0.1% BSA at 42ºC for 45 min, rinsed under milliQ water and spun dry using a centrifuge for 5 min at 1500 rpm. Labeled samples were redissolved in 42ºC prewarmed 12 microliter of Hybridization buffer A (50% formamide, 6X SSC, 0.5% SDS and 5X Denhardt’s applied to a glass coverslip, covered with the spotted glass slide. Arrays were incubated in a corning hybridization chamber for 18 hr at 42ºC in a humid environment (In Slide Out oven, Boeckel). Arrays were washed at room temperature using an orbital shaker for 10 min with a high stringency wash buffer (0.1X SSC, 0.1% SDS), twice for 10 min with a low stringency wash buffer (0.1X SSC), rinsed for 5 min in milliQ water and spun dry for 5 min at 1500 rpm using a centrifuge.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing:
Raw data were processed using LIMMA, a microarray statistical analysis package of Bioconductor (http://www.bioconductor.org, Dudoit et al. 2003) that runs in the R programming environment (Gentleman et al. 2004, Wettenhall et al. 2004). Gene intensities were locally background subtracted using Normexp, taking mean of channel intensities and the median of background intensities. Spots with intensities smaller than two times the local background in both dye filter channels (Cy3 or Cy5), as well as control spots, were excluded from normalization and are left blank.
Expression ratios were calculated as R/G, where R and G are the red and green color intensities, respectively. Ratios were transformed to logarithm base 2. Locally weighted linear regression (Lowess) analysis was used as a normalization method. We applied a local Lowess to each print-tip group or subgrid to correct any systematic spatial variation on the array, between spotting needles or variability on slide surface, by adjusting the mean of the Log2Ratio values in each subgrid to zero. We adjust the variance across all subgrids with a scaling factor for normalization, applying a smoothing factor f=0.2 to each subgrid in order to homogenize the variance of the log2Ratio within each print-tip. Normalized Log2Ratios across all arrays were scaled so that every array has the same median intensity and same absolute standard deviation, in order to give the same weight to every gene on the array.
After normalization, replicated spots of the same gene were average.

source_name: TYML-PRB ERID human breast cancer cell line

label_protocol:
Linear T7-oligodT mediated mRNA amplification (described by Van Gelder et al. 1990 and Eberwine et al. 1992)
3 microgram of the in vitro amplified aRNA samples were reverse transcribed with 4 microliter 5X first strand buffer, 2 microliter 0.1 M DTT, 0.4 microliter low dT-dNTP mix (25 mM dA, dC, dG, 10 mM dT), 1.5 microliter Superscript II (Invitrogen) and 2 microliter 25 mM Cy3-dUTP or Cy5-dUTP (Amersham). The reaction was incubated at 42ºC for 2 hr, chilled on ice and quick spun to bring down condensation. To stop the reaction 1 microliter 1 M NaOH/20 mM EDTA, was added followed by 80 microliter MilliQ-H20 and 10 microliter 3M NaOAc pH 5. Labeled samples were purified with Quiaquick PCR purification columns (Qiagen) and eluted twice with 50 microliter EB (10 mM Tris pH 8.5). Labeling efficiency was calculated by quantification with Nanodrop, obtaining between 50-80 pmol/microliter of Cy3 or Cy5 labeled probes. Labeled samples for the same array were combined, 1 microliter 1 microgram/microliter Human Cot DNA (Invitrogen) was added, and the labeled mix was desiccated by Speed-Vac centrifugation.

growth_protocol: TYML cells were routinely grown in MEM medium supplemented with 7% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100 microg/ml streptomycin.

extract_protocol:
RNeasy mini kit (QUIAGEN, cat.no. 74104)
Quality assesment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

treatment_protocol: TYML cells were plated in medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS (DCC/FBS), and 24 h later medium was replaced by fresh medium without serum. After 24 h in serum-free conditions, cells were treated with R5020 for 6 h at 37ºC.

tag: Human breast cancer cell line T47D-YV (PR-negative clonal derivative cell line of T47D) modified to contain one stably integrated copy of Luciferase reporter gene driven by the Mouse Mammary Tumor Virus promoter, named TYML. Infected with retroviral vector pRAV-Flag- PRB ERID, expressing GFP and progesterone receptor isoform B (PRB) with a deletion affecting ERID-I domain

value: residues 166-372.

source_name: Universal human reference RNA Stratagene® (cat.no.740000)

tag: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: IMR90_iPS

source_name: Induced pluripotent cells

tag: Cell line:IMR92

tag: Cell type:Induced pluripotent cells


title: IMR90.2

description:
This is a biological replicate of IMR90
Digital DNA methylation analysis of stem cell reprogramming by targeted bisulfite sequencing

source_name: Fibroblasts

tag: Cell line:IMR91

tag: Cell type:Fibroblasts


title: hFib2

tag: Cell line:hFib2


title: IMR90

tag: Cell line:IMR90


title: hFib2_iPS

tag: Cell line:hFib3


title: BJ

data_processing:
Reads were aligned to captured target sequences. CpG methylation levels were extracted from mapped reads. The resulting values are real numbers ranging from 0 to 1, which correspond to completely unmethylated and completely methylated.
Annotation track file (BED) and raw read file (seq) are attached. The full set of raw sequence data with quality information was not supplied.
Format of the attached BED file is as follows:
Column 1: chromosome
Column 2: chromosome_start of CpG
Column 3: chromosome_end of CpG
Column 4: methylation level [0-1]; 0=completely unmethylated, 1=completely methylated
Column 5: sequencing depth at the CpG site
Column 6: strand, ignored since the reads from both strands were combined
Column 7: chromosome_start, same as Column 2
Column 8: chromosome_end, same as Column 3
Column 9: pesudo color, red is methylated, and green is unmethylated

tag: Cell line:BJ


title: TYML-PRB ERID _EtOH_6h_ReplicateB_143

treatment_protocol: TYML cells were plated in medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS (DCC/FBS), and 24 h later medium was replaced by fresh medium without serum. After 24 h in serum-free conditions, cells were treated with ethanol for 6 h at 37ºC.


title: TYML-PRB ERID _EtOH_6h_ReplicateA_142


title: BJ_iPS12


title: TYML-PRB DBD _R5020_6h_ReplicateA_47

source_name: TYML-PRB DBD human breast cancer cell line

tag: Human breast cancer cell line T47D-YV (PR-negative clonal derivative cell line of T47D) modified to contain one stably integrated copy of Luciferase reporter gene driven by the Mouse Mammary Tumor Virus promoter, named TYML. Infected with retroviral vector pRAV-Flag- PRB DBD, expressing GFP and progesterone receptor isoform B (PRB) with a triple point mutation in DBD domain


title: TYML-PRB ERID _R5020_6h_ReplicateA_144


title: TYML-PRB DBD _EtOH_6h_ReplicateB_46

source_name: TYML-PRB DBD _EtOH_6h_ReplicateA


title: TYML-PRB DBD _R5020_6h_ReplicateB_48


title: TYML-PRB ERID _R5020_6h_ReplicateB_145


title: TYML-PRB E911A _R5020_6h_ReplicateB_60

source_name: TYML-PRB E911A human breast cancer cell line

tag: Human breast cancer cell line T47D-YV (PR-negative clonal derivative cell line of T47D) modified to contain one stably integrated copy of Luciferase reporter gene driven by the Mouse Mammary Tumor Virus promoter, named TYML. Infected with retroviral vector pRAV-Flag- PRB E911A, expressing GFP and progesterone receptor isoform B (PRB) with a single point mutation in AF2 domain


title: TYML-PRB DBD _EtOH_6h_ReplicateA_45


title: BW25113 w/t LB 37C planktonic cells OD=0.5 LB

description: RNA extracted from  planktonic cells of E. coli K-12 wild type at OD=0.5 in LB at 37ºC


title: TYML-PRB E911A _R5020_6h_ReplicateA_59


title: TYML-PRB E911A _EtOH_6h_ReplicateB_58


title: TYML-PRB E911A _EtOH_6h_ReplicateA_57


title: BJ_iPS11


title: TYML-PRB WT_R5020_6h_ReplicateA_55

source_name: TYML-PRB WT human breast cancer cell line

tag: Human breast cancer cell line T47D-YV (PR-negative clonal derivative cell line of T47D) modified to contain one stably integrated copy of Luciferase reporter gene driven by the Mouse Mammary Tumor Virus promoter, named TYML. Infected with retroviral vector pRAV-Flag- PRB WT, expressing GFP and wild-type progesterone receptor isoform B (PRB).


title: TYML-PRB WT_R5020_6h_ReplicateB_56


title: TYML-PRB WT_EtOH_6h_ReplicateA_53


title: TYML-PRB WT_EtOH_6h_ReplicateB_54


title: TYML_empty_R5020_6h_ReplicateB_72

source_name: TYML-empty human breast cancer cell line

tag: Human breast cancer cell line T47D-YV (PR-negative clonal derivative cell line of T47D) modified to contain one stably integrated copy of Luciferase reporter gene driven by the Mouse Mammary Tumor Virus promoter, named TYML. Infected with empty retroviral vector pRAV-Flag (Knuesel M et al., Mol.Cell Proteomics 2:1225-33), expressing GFP.


title: TYML_empty_R5020_6h_ReplicateA_71


title: CB: 835436

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

hyb_protocol: Agilent Mouse G4121B Microarrays (containing approximately 22,000 probes) were hybridized with 5 µg Cy5-labelled lung RNA and 5 µg Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays.  Arrays were incubated overnight at 60 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.

scan_protocol: Arrays were scanned using a ScanArray Express (Perkin-Elmer Life Sciences, Woodbridge, ON, Canada), and data were acquired with ImaGene 5.5 (BioDiscovery, CA, USA).

data_processing: The data were normalized by lowess curve (Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data:. Nucleic Acids Res. 2002; 30: e15.) using R 2.4.1 (R Development Core Team (2006). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.).  Data used to estimate foldchanges were adjusted for variation due to date of hybridization using the least square estimates.

source_name: Total RNA from a portion of mouse livers labeled with Cyanine-5 (red)

label_protocol: Individual 2.5 µg aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).

extract_protocol: RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON, Canada), and further purified using RNeasy Mini Kits (Qiagen Inc., Mississauga, ON, Canada).  RNA was quantified using the RiboGreen RNA Quantitation Reagent and Kit (Molecular Probes, Eugene, OR, USA), and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).

tag: Tissue

value: Whole liver

tag: Gender

value: Female

tag: Age

value: 12-13 weeks

tag: Strain

tag: Date of exposure

tag: Exposure

value: 20mg/m3 printex

tag: Time post exposure

value: 90 minutes

tag: Microarray ID

tag: Hybridization Block 1

source_name: universal mouse reference total RNA (Catalog #740100; Stratagene, La Jolla, CA, USA)

extract_protocol:
purchased from Stratagene
Unknown: Material was purchased as total RNA (universal mouse reference total RNA (Stratagene, CA, USA))

tag: Total RNA derived from 11 mouse cell lines

tag: MicroArray ID:835436


title: TYML_empty_EtOH_6h_ReplicateB_70

tag: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: CB: 446

tag: Hybridization Block 4

tag: MicroArray ID:446


title: CB: 445

tag: MicroArray ID:445


title: Air: 442

value: 90 minutes of air

tag: MicroArray ID:442


title: Air: 835433

tag: MicroArray ID:835433


title: DEP: 444

tag: Tissue

tag: MicroArray ID:444


title: CB: 58

tag: Gender

tag: Age

tag: Hybridization Block 3

tag: MicroArray ID:58


title: Air: 443

tag: Strain

tag: Date of exposure

tag: Exposure

tag: Time post exposure

tag: MicroArray ID:443


title: Air: 835432

tag: Microarray ID

tag: Hybridization Block 1

tag: Total RNA derived from 11 mouse cell lines

tag: MicroArray ID


title: DEP: 835434

tag: MicroArray ID:835434


title: PC-3 cells, passage 16-17, grown on Plastic, replicate 3

city: Oklahoma City

first: Hsueh-Kung

last: Lin

state: OK

address: Room 462, 800 Research Parkway

department: Urology

institute: University of Oklahoma Health Sciences Center

description: No other descriptions

hyb_protocol: Biotinylated cRNA was hybridized overnight to Illumina human Ref-8 version 3 BeadChips containing probes for a total of 24,526 transcripts.

scan_protocol: Microarray chips were washed to high stringency and labeled with streptavidin -Cy3 (Amersham Biosciences, Piscataway, NJ) prior to scanning on an Illumina BeadArray Reader.

data_processing:
The data were first normalized based on normal distribution of low-level expressed genes using the previously described procedure (Dozmorov, Knowlton et al. 2004; Knowlton, Dozmorov et al. 2004).  Normalization was performed for each array by first plotting a frequency histogram of the raw expression data for all genes.  The histograms showed a right-skewed unimodal distribution curve with the mode around zero.  Normal distribution curve representing variability of the data around zero was then fitted around the mode, mirroring Gaussian profile of the left part of the histogram.  Two parameters [mean and standard deviation (SD)] were defined for this distribution; and the data were normalized to the SD of the noise after subtraction of the zero point.  The arrays were than adjusted to each other by robust linear regression (Hua, Balagurunathan et al. 2006; Gusnanto, Calza et al. 2007).Genes with expression value less than 3.0 were considered to be not expressed.  This is equivalent of setting a threshold at 3 SD above noise level, and each experiment accounted approximately 10,000 genes expressed below noise.
To identify differentially expressed genes between two experimental groups, we used associative analysis as described by Dozmorov et al. (Dozmorov and Centola 2003).  Briefly, in pooled microarray datasets, a reference group of genes expressed above background with low variability of expression identified by F-test was identified.  A t-test termed "associative t-test" was applied to test if a given gene belongs to or differs from this group.  The associative t-test is a standard t-test applied to the comparison of expression variability.  Due to a large number of genes that are differentially expressed between LNCaP and PC3 cells, a very stringent criterion was applied to identify genes with the most dramatic differences.  Only genes expressed below noise level in one group and greater than 50 SD above noise level in another group were selected for further analysis.  For genes that were expressed in both cell lines, genes that have greater than 10-fold differences in expression levels and expressed greater than 100 SD above noise level in at least in one cell line were also selected.  These genes can be considered to be “beacons” that point to pathways or gene networks that are altered.
Dozmorov, I. and M. Centola (2003). "An associative analysis of gene expression array data." Bioinformatics 19(2): 204-211.
Dozmorov, I., N. Knowlton, et al. (2004). "Statistical monitoring of weak spots for improvement of normalization and ratio estimates in microarrays." BMC Bioinformatics 5(1): 53.
Gusnanto, A., S. Calza, et al. (2007). "Identification of differentially expressed genes and false discovery rate in microarray studies." Curr Opin Lipidol 18(2): 187-93.
Hua, J., Y. Balagurunathan, et al. (2006). "Normalization benefits microarray-based classification." EURASIP J Bioinform Syst Biol: 43056.
Knowlton, N., I. M. Dozmorov, et al. (2004). "Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data." Bioinformatics 20(18): 3687-90.

source_name: PC-3 cells, passage 16-17, from ATCC

label_protocol: A total of 250 ng of total RNA from each passage and from each cell line was labeled using the Illumina Total Prep RNA Amplification Kit following manufacturer’s directions (Ambion, Austin. TX).  Briefly, cDNA was reverse transcribed from the total RNA after priming with T7-oligo-dT, and cRNA was synthesized in vitro from the T7 promoter with the incorporation of biotinylated UTP.

growth_protocol: PC-3 cells were maintained in phenol red-positive F-12 nutrient mixture (Invitrogen) containing 7% FBS and 100 units/ml penicillin-100 µg/ml streptomycin (25).  PC-3 cells were passaged twice a week.  PC-3 cells were used between passages 16 and 19.

extract_protocol: Total RNA was isolated from prostate LNCaP and PC-3 cells for probe preparation and microarray hybridization.  Briefly, 5x105 prostate cells were seeded in 60 mm tissue culture plates and cultured for 48 hours in their growth media.  Total RNA was isolated from 4 consecutive passages from each cell line using RNeasy® Mini total RNA isolation kit following the manufacturer’s recommendations (Qiagen, Valencia, CA).  The concentration of the isolated total RNA was determined with a Nanodrop scanning spectrophotometer, and then qualitatively assessed for their integrity using the ratio of 28:18s rRNA by a capillary gel electrophoresis system (Agilent 2100 Bioanalyzer, Agilent Technologies, Santa Clara CA).

treatment_protocol: No specific treatment

tag: PC-3 human prostate cancer cell line, passage 16-17


title: CB: 59

tag: Tissue

tag: MicroArray ID:59


title: DEP: 57

tag: Gender

tag: MicroArray ID:57


title: DEP: 835435

tag: Age

tag: MicroArray ID:835435


title: PC-3 cells, passage 16-17, grown on Plastic, replicate 4

description: No other descriptions


title: PC-3 cells, passage 16-17, grown on Plastic, replicate 2

description: No other descriptions


title: DEP: 55

tag: Strain

tag: Hybridization Block 2

tag: MicroArray ID:55


title: PC-3 cells, passage 16-17, grown on Plastic, replicate 1

description: No other descriptions


title: DEP: 56

tag: Date of exposure

tag: Exposure

tag: Time post exposure

tag: MicroArray ID:56


title: T47D_MTVL_R5020_6h_ReplicateB_76

source_name: T47D-MTVL human breast cancer cell line

growth_protocol: T47D-MTVL cells were routinely grown in RPMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100 microg/ml streptomycin.

treatment_protocol: T47D-MTVL cells were plated in medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS (DCC/FBS), and 24 h later medium was replaced by fresh medium without serum. After 24 h in serum-free conditions, cells were treated with R5020 for 6 h at 37ºC.

tag: Human breast cancer cell line T47D modified to contain one stably integrated copy of Luciferase reporter gene driven by the Mouse Mammary Tumor Virus promoter, named T47D-MTVL (Truss, M., J. Bartsch, A. Schelbert, R. J. Hache, and M. Beato. 1995). Hormone induces binding of receptors and transcription factors to a rearranged nucleosome on the MMTV promoter in vivo (EMBO J. 14:1737-1751).

tag: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: T47D_MTVL_R5020_6h_ReplicateA_75


title: TYML_empty_EtOH_6h_ReplicateA_69

tag: Human breast cancer cell line T47D-YV (PR-negative clonal derivative cell line of T47D) modified to contain one stably integrated copy of Luciferase reporter gene driven by the Mouse Mammary Tumor Virus promoter, named TYML. Infected with empty retroviral vector pRAV-Flag (Knuesel M et al., Mol.Cell Proteomics 2:1225-33), expressing GFP.


title: Air: 54

tag: Microarray ID

tag: Total RNA derived from 11 mouse cell lines

tag: MicroArray ID:54


title: LNCaP cells, passage 31-32, grown on Plastic, replicate 4

description: No other descriptions

source_name: LNCaP cells, passage 31-32, from ATCC

growth_protocol: LNCaP cells were routinely maintained in a complete growth medium consisting of phenol red-positive RPMI1640 (Invitrogen; Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS; Invitrogen) and 100 units/ml penicillin-100 µg/ml streptomycin (Invitrogen) (24).  LNCaP cells were passaged once a week, whereas PC-3 cells were passaged twice a week.  LNCaP cells were harvested between passages 31 and 34  for total RNA extraction

tag: LNCaP human prostate cancer cell line, passage 31-32


title: T47D_MTVL_EtOH_6h_ReplicateA_73

treatment_protocol: T47D-MTVL cells were plated in medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS (DCC/FBS), and 24 h later medium was replaced by fresh medium without serum. After 24 h in serum-free conditions, cells were treated with ethanol for 6 h at 37ºC.


title: Air: 53

tag: Tissue

tag: Gender

tag: MicroArray ID:53


title: LNCaP cells, passage 31-32, grown on Plastic, replicate 3

description: No other descriptions


title: GENOMIC DNA CONTROL_46,X,der(X),t(X;14)(q21.1;q12.2) (CGH)

status: Public on Apr 26 2009

city: Leuven

first: Thierry

last: Voet

address: Herestraat 49

department: Department of Human Genetics

country: Belgium

institute: KULeuven

description: GENOMIC EBV_3

hyb_protocol: 1.75 µg of test and reference DNA were mixed with 50 µg of human Cot-1 DNA (Invitrogen) and precipitated by adding 2.5 volumes of 96% ethanol and 0.1 volume of sodium acetate (3M, pH5.2). The DNA pellet was resuspended in 15 µl hybridization buffer (50% formamide, 10% dextran sulfate, 0.1% Tween-20, 2xSSC and 10 mM Tris–HCl, pH 7.5) containing 200 µg yeast tRNA, denatured at 98°C for 15 minutes and hybridized to a BAC array (spotted area of 18 x 18 mm) over one night in a humid chamber at 37°C. This area was preblocked for 1 hour at 37°C with 16.6 µg human Cot-1 DNA and 0.1 mg salmon testes DNA (Sigma Aldrich) dissolved in 20 µl hybridization buffer. Arrays were washed in 1xPBS (pH8.0)/0,05% Tween20 for 10 minutes at room temperature, 2xSSC (pH7.0)/50% formamide for 30 minutes at 42°C, 1xPBS (pH8.0)/0,05% Tween20 for 10 minutes at room temperature and subsequently dried

scan_protocol: Slides were scanned at 532 and 635 nm using a GenePix 4000B scanner (Axon Instruments Inc., Foster City, CA). The scans were processed with GenePix Pro 6.0 software.

data_processing: Only spots with signal intensities at least 2-fold above the autosomal median background intensity were included in the analysis. Since all clones were present in duplicate, two log2-ratios of Cy5/Cy3-intensities were calculated per clone. Unmapped (n=150) and polymorphic clones (n=68) were masked out. As a preprocessing step, the ratios were loess normalised using the R package snapCGH;

source_name: EBV-lymphoblastoid cell line

label_protocol: Test and reference DNA were labeled for 2h by random primer labeling (BioPrime aCGH Genomic Labeling System; Invitrogen; Carlsbad, CA) using respectively Cy5- and Cy3-dCTPs (GE Healthcare). Labeled DNA was purified with the BioPrime Purification Module (Invitrogen; Carlsbad, CA).

extract_protocol: Single cells were transferred to a 200 µl PCR tube containing 1.5 µl alkaline lysis buffer (ALB; 200 mM KOH and 50 mM DTT) by mouth controlled pipetting using 75 µm stripper tips (MidAtlantic Diagnostics, Mount Laurel, USA). An aliquot from the last washing droplet was taken as a negative control per cell line. The samples were stored at -20°C for at least 30 min and were further incubated for 10 min at 65°C prior to the multiple displacement amplification (MDA) reaction. Single cell DNA was amplified following an MDA-approach with Genomi Phi V2 (GE Healthcare, Piscataway, NJ). The MDA products were purified and resuspended in 50 µl of elution buffer (High Pure PCR Product Purification Kit, Roche, Basel, Switzerland). All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer; Nanodrop Technologies, Rockland, DE). SC-amplifications yielding less than 2 µg DNA were not further used.

tag: EBV-lymphoblastoid cell line

source_name: Blood

tag: karyotype


title: LYMPHOBLASTOID CELL_47,XXX_replicate 2 (CGH)

description: LYMPHOBLASTOID CELL_12

source_name: single lymphoblastoid cell

treatment_protocol: Epstein-Barr virus (EBV)-transformed lymphoblastoids were washed three times in 500 µl phosphate-buffered saline and washed in droplets of Ca2+/Mg2+ free medium (PGD biopsy Medium, GlobalLife) and 0.01% (w/v) phenol red supplemented with 4 mg/ml BSA (Sigma-Aldrich, St Louis, MO) (dissociation medium).

tag: single cell from an Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line with karyotype 47,XXX


title: T47D_MTVL_EtOH_6h_ReplicateB_74


title: GENOMIC DNA CONTROL_47,XY,+21 (CGH)

description: GENOMIC EBV_4


title: LNCaP cells, passage 31-32, grown on Plastic, replicate 2

description: No other descriptions


title: LYMPHOBLASTOID CELL_47,XXX_replicate 7 (CGH)

description: LYMPHOBLASTOID CELL_17


title: LYMPHOBLASTOID CELL_47,XY,+21_replicate 4 (CGH)

description: LYMPHOBLASTOID CELL_19

tag: single cell from an Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line with karyotype 47,XY,+21


title: LYMPHOBLASTOID CELL_47,XXX_replicate 4 (CGH)

description: LYMPHOBLASTOID CELL_14


title: GENOMIC DNA CONTROL_46,XX,del(18)(p11.21->pter) (CGH)

description: GENOMIC EBV_1


title: Air: 50

tag: Age

tag: Strain

tag: Date of exposure

tag: Exposure

tag: Hybridization Block 3

tag: MicroArray ID:50


title: LYMPHOBLASTOID CELL_47,XY,+21_replicate 3 (CGH)

description: LYMPHOBLASTOID CELL_18


title: LYMPHOBLASTOID CELL_47,XXX_replicate 6 (CGH)

description: LYMPHOBLASTOID CELL_16


title: LYMPHOBLASTOID CELL_47,XXX_replicate 1 (CGH)

description: LYMPHOBLASTOID CELL_11


title: LYMPHOBLASTOID CELL_47,XXX_replicate 5 (CGH)

description: LYMPHOBLASTOID CELL_15


title: LYMPHOBLASTOID CELL_46,X,der(X),t(X;14)(q21.1;q12.2) (CGH)

description: LYMPHOBLASTOID CELL_9

tag: single cell from an Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line with karyotype 46,X,der(X),t(X;14)(q21.1;q12.2)


title: LYMPHOBLASTOID CELL_47,XY,+21_replicate 1 (CGH)

description: LYMPHOBLASTOID CELL_10


title: LYMPHOBLASTOID CELL_47,XY,+21_replicate 2 (CGH)

description: LYMPHOBLASTOID CELL_10BIS


title: CB: 48

tag: Time post exposure

tag: Microarray ID

tag: Hybridization Block 2

tag: Total RNA derived from 11 mouse cell lines

tag: MicroArray ID:48


title: LNCaP cells, passage 31-32, grown on Plastic, replicate 1

description: No other descriptions

tag: LNCaP human prostate cancer cell line, passage 31-32


title: Air: 49

tag: Tissue

tag: Gender

tag: MicroArray ID:49


title: CB: 835052

tag: Hybridization Block 1

tag: MicroArray ID:835052


title: DEP: 51

tag: Age

tag: Strain

tag: MicroArray ID:51


title: LYMPHOBLASTOID CELL_46,XY,der(20),t(18;20)(p11.21;p13) (CGH)

description: LYMPHOBLASTOID CELL_8

tag: single cell from an Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line with karyotype 46,XY,der(20),t(18;20)(p11.21;p13)

tag: karyotype


title: LYMPHOBLASTOID CELL_46,XX,del(4)(p16.1->pter)_replicate 3 (CGH)

description: LYMPHOBLASTOID CELL_7

tag: single cell from an Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line with karyotype 46,XX,del(4)(p16.1->pter)


title: LYMPHOBLASTOID CELL_46,XX,del(4)(p16.1->pter)_replicate 2 (CGH)

description: LYMPHOBLASTOID CELL_6


title: LYMPHOBLASTOID CELL_46,XX,del(18)(p11.21->pter)_replicate 4 (CGH)

description: LYMPHOBLASTOID CELL_4

tag: single cell from an Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line with karyotype 46,XX,del(18)(p11.21->pter)


title: LYMPHOBLASTOID CELL_46,XX,del(4)(p16.1->pter)_replicate 1 (CGH)

description: LYMPHOBLASTOID CELL_5


title: LYMPHOBLASTOID CELL_46,XX,del(18)(p11.21->pter)_replicate 2 (CGH)

description: LYMPHOBLASTOID CELL_2


title: CB: 47

tag: Date of exposure

tag: Exposure

tag: Time post exposure

tag: Microarray ID

tag: MicroArray ID:47


title: FERTILIZED OOCYTE_i (CGH)

description: FERTILIZED OOCYTE_9

source_name: fertilized oocyte

treatment_protocol: 17 fertilized oocytes survived the thawing procedure and were incubated in fresh cleavage medium (Cook IVF, Queensland, Australia) for maximum 2 hours. The zona pellucida (ZP) was removed by gently pipetting up and down in Acid Tyrod (AT; pH 2.4 Sigma-Aldrich, St Louis, MO). Immediately after the dissolution of the ZP, the fertilized oocytes were transferred into Ca2+/Mg2+ free medium (PGD biopsy Medium, GlobalLife) and 0.01% (w/v) phenol red supplemented with 4 mg/ml BSA (Sigma-Aldrich, St Louis, MO) (dissociation medium). After removal of the polar bodies by mouth controlled pipetting, the fertilized oocytes were washed in 3 droplets of the dissociation medium.

tag: thawed ICSI-oocyte in the pronuclear stage

tag: IVF/ICSI protocol

value: controlled ovarian hyperstimulation was performed using a “long protocol” as follows.  In the previous cycle an oral contraceptive pill was given for 25 days (Cilest®, Janssen-Cilag), followed by pituitary downregulation with bucerelin acetate (Suprefact®, Hoechst, Frankfurt, Germany; 600 µg daily) from day 21 onwards. Human menopausal gonadotropins or human recombinant gonadotrophins  (Humegon® or Puregon, Organon, Oss, The Netherlands; Gonal F, Merck Serono, Geneva, Switzerland) were started on the second day after the subsequent menstruation while ovulation was induced with 10000 IU HCG (Pregnyl®, Organon, Oss, The Netherlands) when at least 3 follicles with a diameter of at least 17 mm were observed at gynecological ultrasound. Ultrasound guided oocyte aspiration was performed 36 hours later. Luteal supplementation was given by vaginal progesterone (600 mg/day, Utrogestan®, Piette International, Drogenbos, Belgium). Subsequently, oocytes were fertilized using conventional IVF or ICSI with ejaculated sperm, checked for two pronuclei and subsequently frozen in liquid N2.

tag: Patient info

value: Frozen fertilized oocytes in the pronuclear stage from 4 couples of age ≤ 35 years were donated for research after informed consent. The type of infertility was primary in three couples (the indication for IVF was male factor for two couples and endometriosis for one couple) and secondary in the remaining couple (indication for IVF was male factor).


title: FERTILIZED OOCYTE_k (CGH)

description: FERTILIZED OOCYTE_11

tag: thawed IVF-oocyte in the pronuclear stage


title: FERTILIZED OOCYTE_j (CGH)

description: FERTILIZED OOCYTE_10


title: FERTILIZED OOCYTE_m (CGH)

description: FERTILIZED OOCYTE_13


title: LYMPHOBLASTOID CELL_46,XX,del(18)(p11.21->pter)_replicate 3 (CGH)

description: LYMPHOBLASTOID CELL_3


title: FERTILIZED OOCYTE_h (CGH)

description: FERTILIZED OOCYTE_8


title: FERTILIZED OOCYTE_n (CGH)

description: FERTILIZED OOCYTE_14


title: FERTILIZED OOCYTE_d (CGH)

description: FERTILIZED OOCYTE_4


title: FERTILIZED OOCYTE_f (CGH)

description: FERTILIZED OOCYTE_6


title: FERTILIZED OOCYTE_e (CGH)

description: FERTILIZED OOCYTE_5


title: LYMPHOBLASTOID CELL_46,XX,del(18)(p11.21->pter)_replicate 1 (CGH)

description: LYMPHOBLASTOID CELL_1


title: FERTILIZED OOCYTE_c (CGH)

description: FERTILIZED OOCYTE_3


title: BLASTOMERE-EMBRYO_23-cell_d (CGH)

source_name: blastomere

treatment_protocol: Embryos were incubated briefly in Acid Tyrod (AT; pH 2.4 Sigma-Aldrich, St Louis, MO) to remove the zona pellucida (ZP) by mouth controlled pipetting using Flexipet micromanipulation pipettes (130 µm, Cook, IVF Queensland, Australia). They were then transferred to Ca2+/Mg2+ free medium (PGD biopsy Medium, GlobalLife) and 0.01% (w/v) phenol red supplemented with 4 mg/ml BSA (Sigma-Aldrich, St Louis, MO) (dissociation medium) and gently pipetted to disaggregate the individual blastomeres. Single blastomeres were washed three times in the dissociation medium.

tag: single cell from a 3-day-old human IVF embryo

tag: IVF protocol

value: controlled ovarian hyperstimulation was performed using a “long protocol” as follows.  In the previous cycle an oral contraceptive pill was given for 25 days (Cilest®, Janssen-Cilag), followed by pituitary downregulation with bucerelin acetate (Suprefact®, Hoechst, Frankfurt, Germany; 600 µg daily) from day 21 onwards. Human menopausal gonadotropins or human recombinant gonadotrophins  (Humegon® or Puregon, Organon, Oss, The Netherlands; Gonal F, Merck Serono, Geneva, Switzerland) were started on the second day after the subsequent menstruation while ovulation was induced with 10000 IU HCG (Pregnyl®, Organon, Oss, The Netherlands) when at least 3 follicles with a diameter of at least 17 mm were observed at gynecological ultrasound. Ultrasound guided oocyte aspiration was performed 36 hours later. Luteal supplementation was given by vaginal progesterone (600 mg/day, Utrogestan®, Piette International, Drogenbos, Belgium). Subsequently, oocytes were fertilized using conventional IVF (n=8) or ICSI (n=1) with ejaculated sperm. Embryos were cultured in Global Medium (GlobalLife) and the morphology was daily assessed. Only genetically normal embryos of good morphology (with compaction or blastocyst formation) were transferred on day 4 or 5. Supernumerary genetically normal embryos of good morphology were frozen at day 4 or 5. Day 3 (evening) or day 4 (morning) embryos diagnosed with a microdeletion or with a normal sex but not suitable for transfer due to a familial genetic reason were used for this study if fulfilling all inclusion criteria (see patient info).

value: Couples entering the IVF-PGD-program for sex selection due to X-linked disorders or BRCA mutations or for familial microdeletion syndromes were asked to participate. Inclusion criteria were:(1) written informed consent from each couple, (2) maternal and paternal age ≤ 35 years, (3) normal karyotype for both partners, (4) a maternal body mass index of 18-30 kg/m², (5) initial normal semen parameters according to WHO regulation, (6) good quality embryos:2-5 blastomeres on day 2, 6-10 blastomeres on day 3, <20% fragmentation, equal sized blastomeres, (7) no recurrent miscarriages. The study was approved by the Ethical Committee of the University Hospital (registration number NCT00614367).


title: FERTILIZED OOCYTE_o (CGH)

description: FERTILIZED OOCYTE_15


title: FERTILIZED OOCYTE_b (CGH)

description: FERTILIZED OOCYTE_2


title: FERTILIZED OOCYTE_l (CGH)

description: FERTILIZED OOCYTE_12


title: GENOMIC DNA CONTROL_46,XY,der(20),t(18;20)(p11.21;p13) (CGH)

description: GENOMIC EBV_2

tag: EBV-lymphoblastoid cell line


title: BLASTOMERE-EMBRYO_23-cell_g (CGH)


title: FERTILIZED OOCYTE_a (CGH)

description: FERTILIZED OOCYTE_1


title: BLASTOMERE-EMBRYO_23-cell_i (CGH)


title: BLASTOMERE-EMBRYO_23-cell_h (CGH)


title: FERTILIZED OOCYTE_g (CGH)

description: FERTILIZED OOCYTE_7


title: BLASTOMERE-EMBRYO_23-cell_b (CGH)


title: BLASTOMERE-EMBRYO_23-cell_a (CGH)


title: BLASTOMERE-EMBRYO_22-cell_e (CGH)


title: BLASTOMERE-EMBRYO_22-cell_c (CGH)


title: BLASTOMERE-EMBRYO_23-cell_e (CGH)


title: BLASTOMERE-EMBRYO_22-cell_d (CGH)


title: BLASTOMERE-EMBRYO_22-cell_a (CGH)


title: BLASTOMERE-EMBRYO_22-cell_g (CGH)


title: BLASTOMERE-EMBRYO_23-cell_c (CGH)


title: BLASTOMERE-EMBRYO_21-cell_g (CGH)


title: BLASTOMERE-EMBRYO_21-cell_h (CGH)


title: BLASTOMERE-EMBRYO_21-cell_e (CGH)


title: BLASTOMERE-EMBRYO_21-cell_f (CGH)


title: BLASTOMERE-EMBRYO_20-cell_i (CGH)


title: BLASTOMERE-EMBRYO_22-cell_b (CGH)


title: BLASTOMERE-EMBRYO_22-cell_f (CGH)


title: BLASTOMERE-EMBRYO_20-cell_h (CGH)


title: BLASTOMERE-EMBRYO_20-cell_j (CGH)


title: BLASTOMERE-EMBRYO_20-cell_a (CGH)


title: BLASTOMERE-EMBRYO_21-cell_a (CGH)


title: BLASTOMERE-EMBRYO_21-cell_b (CGH)


title: BLASTOMERE-EMBRYO_21-cell_c (CGH)


title: BLASTOMERE-EMBRYO_20-cell_f (CGH)


title: BLASTOMERE-EMBRYO_19-cell_f (CGH)


title: BLASTOMERE-EMBRYO_20-cell_g (CGH)


title: BLASTOMERE-EMBRYO_20-cell_d (CGH)


title: BLASTOMERE-EMBRYO_20-cell_c (CGH)


title: BLASTOMERE-EMBRYO_20-cell_e (CGH)


title: BLASTOMERE-EMBRYO_19-cell_d (CGH)


title: BLASTOMERE-EMBRYO_19-cell_e (CGH)


title: BLASTOMERE-EMBRYO_19-cell_b (CGH)


title: BLASTOMERE-EMBRYO_19-cell_c (CGH)


title: BLASTOMERE-EMBRYO_19-cell_a (CGH)


title: BLASTOMERE-EMBRYO_18-cell_a (CGH)

tag: single cell from a 3-day-old human ICSI embryo

tag: ICSI protocol


title: BLASTOMERE-EMBRYO_18-cell_e (CGH)

tag: karyotype


title: BLASTOMERE-EMBRYO_18-cell_b (CGH)


title: BLASTOMERE-EMBRYO_18-cell_d (CGH)


title: BLASTOMERE-EMBRYO_18-cell_f (CGH)


title: BLASTOMERE-EMBRYO_17-cell_d (CGH)


title: BLASTOMERE-EMBRYO_18-cell_c (CGH)


title: BLASTOMERE-EMBRYO_17-cell_c (CGH)


title: BLASTOMERE-EMBRYO_16-cell_g (CGH)


title: BLASTOMERE-EMBRYO_17-cell_a (CGH)


title: BLASTOMERE-EMBRYO_16-cell_e (CGH)


title: BLASTOMERE-EMBRYO_16-cell_f (CGH)


title: BLASTOMERE-EMBRYO_16-cell_h (CGH)


title: BLASTOMERE-EMBRYO_18-cell_i (CGH)


title: BLASTOMERE-EMBRYO_16-cell_d (CGH)


title: BLASTOMERE-EMBRYO_17-cell_b (CGH)


title: LYMPHOBLASTOID CELL_47,XXX_replicate 3 (CGH)

description: LYMPHOBLASTOID CELL_13

tag: single cell from an Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line with karyotype 47,XXX


title: BLASTOMERE-EMBRYO_16-cell_c (CGH)


title: BLASTOMERE-EMBRYO_15-cell_e (CGH)


title: BLASTOMERE-EMBRYO_15-cell_d (CGH)


title: BLASTOMERE-EMBRYO_16-cell_b (CGH)


title: BLASTOMERE-EMBRYO_16-cell_a (CGH)


title: BLASTOMERE-EMBRYO_15-cell_c (CGH)


title: BLASTOMERE-EMBRYO_15-cell_a (CGH)


title: BLASTOMERE-EMBRYO_14-cell_e (CGH)


title: BLASTOMERE-EMBRYO_14-cell_c (CGH)


title: BLASTOMERE-EMBRYO_14-cell_d (CGH)


title: BLASTOMERE-EMBRYO_14-cell_a (CGH)


title: BLASTOMERE-EMBRYO_13-cell_f (CGH)


title: BLASTOMERE-EMBRYO_13-cell_e (CGH)


title: BLASTOMERE-EMBRYO_13-cell_g (CGH)


title: BLASTOMERE-EMBRYO_13-cell_c (CGH)


title: BLASTOMERE-EMBRYO_13-cell_b (CGH)


title: BLASTOMERE-EMBRYO_13-cell_a (CGH)


title: LYMPHOBLASTOID CELL_46,XX,del(18)(p11.21->pter)_replicate 2 (SNP)

description: LYMPHOBLASTOID CELL_2

hyb_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual

data_processing: GeneChip Human Mapping 250K NspI technology (Affymetrix, SNP annotation 2008/01/04) was used for independent copy number determination as well as for SNP-typing and LOH-screening. Experiments were performed according to manufacturer’s instructions using 250 ng of SC amplified DNA. For SNP-copy number analysis, probe intensities were quantile normalized per cell type and compared by the ‘Copy Number Analysis Tool’ (CNAT4.0.1) to a publicly available reference pool of 41 female HapMap genomic DNA samples that were hybridized on the same platform. All user-tunable CNAT4.0.1 parameters were optimized for the detection of the known chromosome imbalances of the lymphoblastoids. Log2-ratios were Gaussian smoothed using a 16 Mb window and interpreted by a five-state Hidden Markov model with prior probabilities set equal for all five states. Standard deviation settings were 0.11 for hidden-states 0, 1, 3 and 4, while 0.08 for hidden-state 2. Transition decay was set at 4000 Mb. Outliers were allowed to be readjusted. For SNP-typing, probe intensities were analyzed by the ‘GeneChip Genotyping Analysis Software (GTYPE) version 4.1’ using the dynamic model with a stringency (P=0.12) tuned for LOH detection in hemizygous regions. Subsequently, LOH was determined using ‘Copy Number Analyzer for Genechip (CNAG) version 2.0’ by application of a likelihood threshold of 100 for blastomeres and 50 for lymphoblastoids.

treatment_protocol: Treatment protocol: Epstein-Barr virus (EBV)-transformed lymphoblastoids were washed three times in 500 µl phosphate-buffered saline and washed in droplets of Ca2+/Mg2+ free medium (PGD biopsy Medium, GlobalLife) and 0.01% (w/v) phenol red supplemented with 4 mg/ml BSA (Sigma-Aldrich, St Louis, MO) (dissociation medium).

tag: single lymphoblastoid cell of the EBV-cell line with karyotype


title: BLASTOMERE-EMBRYO_12-cell_g (CGH)

tag: single cell from a 4-day-old human ICSI embryo


title: GENOMIC DNA CONTROL_46,XX,del(18)(p11.21->pter) (SNP)

description: GENOMIC EBV_1

scan_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual

source_name: EBV lymphoblastoid cell line

tag: Epstein Barr virus (EBV) transformed lymphoblastoid cells


title: LYMPHOBLASTOID CELL_46,XY,der(20),t(18;20)(p11.21;p13) (SNP)

description: LYMPHOBLASTOID CELL_8

label_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual


title: LYMPHOBLASTOID CELL_46,XX,del(18)(p11.21->pter)_replicate 3 (SNP)

description: LYMPHOBLASTOID CELL_3


title: BLASTOMERE-EMBRYO_23-cell_e (SNP)

treatment_protocol: Treatment protocol: Embryos were incubated briefly in Acid Tyrod (AT; pH 2.4 Sigma-Aldrich, St Louis, MO) to remove the zona pellucida (ZP) by mouth controlled pipetting using Flexipet micromanipulation pipettes (130 µm, Cook, IVF Queensland, Australia). They were then transferred to Ca2+/Mg2+ free medium (PGD biopsy Medium, GlobalLife) and 0.01% (w/v) phenol red supplemented with 4 mg/ml BSA (Sigma-Aldrich, St Louis, MO) (dissociation medium) and gently pipetted to disaggregate the individual blastomeres. Single blastomeres were washed three times in the dissociation medium.


title: BLASTOMERE-EMBRYO_12-cell_e (CGH)


title: GENOMIC DNA CONTROL_46,X,der(X),t(X;14)(q21.1;q12.2) (SNP)

description: GENOMIC EBV_3


title: LYMPHOBLASTOID CELL_46,X,der(X),t(X;14)(q21.1;q12.2) (SNP)

description: LYMPHOBLASTOID CELL_9


title: FERTILIZED OOCYTE_n (SNP)

description: FERTILIZED OOCYTE_14

treatment_protocol: Treatment protocol: 17 fertilized oocytes survived the thawing procedure and were incubated in fresh cleavage medium (Cook IVF, Queensland, Australia) for maximum 2 hours. The zona pellucida (ZP) was removed by gently pipetting up and down in Acid Tyrod (AT; pH 2.4 Sigma-Aldrich, St Louis, MO). Immediately after the dissolution of the ZP, the fertilized oocytes were transferred into Ca2+/Mg2+ free medium (PGD biopsy Medium, GlobalLife) and 0.01% (w/v) phenol red supplemented with 4 mg/ml BSA (Sigma-Aldrich, St Louis, MO) (dissociation medium). After removal of the polar bodies by mouth controlled pipetting, the fertilized oocytes were washed in 3 droplets of the dissociation medium.


title: LYMPHOBLASTOID CELL_47,XY,+21 (SNP)

description: LYMPHOBLASTOID CELL_10


title: FERTILIZED OOCYTE_l (SNP)

description: FERTILIZED OOCYTE_12


title: LYMPHOBLASTOID CELL_46,XX,del(18)(p11.21->pter)_replicate 4 (SNP)

description: LYMPHOBLASTOID CELL_4


title: LYMPHOBLASTOID CELL_46,XX,del(18)(p11.21->pter)_replicate 1 (SNP)

description: LYMPHOBLASTOID CELL_1


title: FERTILIZED OOCYTE_k (SNP)

description: FERTILIZED OOCYTE_11


title: FERTILIZED OOCYTE_f (SNP)

description: FERTILIZED OOCYTE_6


title: FERTILIZED OOCYTE_m (SNP)

description: FERTILIZED OOCYTE_13


title: BLASTOMERE-EMBRYO_12-cell_f (CGH)


title: GENOMIC DNA CONTROL_47,XY,+21 (SNP)

description: GENOMIC EBV_4


title: BLASTOMERE-EMBRYO_23-cell_c (SNP)


title: GENOMIC DNA CONTROL_46,XY,der(20),t(18;20)(p11.21;p13) (SNP)

description: GENOMIC EBV_2


title: FERTILIZED OOCYTE_j (SNP)

description: FERTILIZED OOCYTE_10


title: BLASTOMERE-EMBRYO_12-cell_c (CGH)


title: FERTILIZED OOCYTE_h (SNP)

description: FERTILIZED OOCYTE_8


title: BLASTOMERE-EMBRYO_12-cell_b (CGH)


title: BLASTOMERE-EMBRYO_21-cell_e (SNP)


title: BLASTOMERE-EMBRYO_12-cell_d (CGH)


title: BLASTOMERE-EMBRYO_11-cell_f (CGH)


title: BLASTOMERE-EMBRYO_11-cell_e (CGH)


title: BLASTOMERE-EMBRYO_11-cell_d (CGH)


title: BLASTOMERE-EMBRYO_21-cell_h (SNP)


title: BLASTOMERE-EMBRYO_21-cell_c (SNP)


title: FERTILIZED OOCYTE_a (SNP)

description: FERTILIZED OOCYTE_1


title: BLASTOMERE-EMBRYO_23-cell_b (SNP)


title: BLASTOMERE-EMBRYO_10-cell_i (CGH)

tag: single cell from a 4-day-old human IVF embryo


title: BLASTOMERE-EMBRYO_11-cell_a (CGH)


title: BLASTOMERE-EMBRYO_21-cell_b (SNP)


title: BLASTOMERE-EMBRYO_10-cell_h (CGH)


title: BLASTOMERE-EMBRYO_22-cell_c (SNP)


title: BLASTOMERE-EMBRYO_21-cell_a (SNP)


title: BLASTOMERE-EMBRYO_12-cell_a (CGH)


title: BLASTOMERE-EMBRYO_10-cell_e (CGH)


title: BLASTOMERE-EMBRYO_20-cell_h (SNP)


title: BLASTOMERE-EMBRYO_10-cell_f (CGH)


title: BLASTOMERE-EMBRYO_11-cell_g (CGH)


title: BLASTOMERE-EMBRYO_11-cell_b (CGH)


title: BLASTOMERE-EMBRYO_10-cell_d (CGH)


title: BLASTOMERE-EMBRYO_10-cell_g (CGH)


title: BLASTOMERE-EMBRYO_10-cell_c (CGH)


title: BLASTOMERE-EMBRYO_10-cell_a (CGH)


title: BLASTOMERE-EMBRYO_20-cell_i (SNP)


title: BLASTOMERE-EMBRYO_9-cell_h (CGH)


title: BLASTOMERE-EMBRYO_9-cell_g (CGH)


title: BLASTOMERE-EMBRYO_9-cell_j (CGH)


title: BLASTOMERE-EMBRYO_20-cell_e (SNP)


title: BLASTOMERE-EMBRYO_11-cell_c (CGH)


title: BLASTOMERE-EMBRYO_9-cell_f (CGH)


title: BLASTOMERE-EMBRYO_20-cell_c (SNP)


title: BLASTOMERE-EMBRYO_9-cell_d (CGH)


title: BLASTOMERE-EMBRYO_20-cell_f (SNP)


title: BLASTOMERE-EMBRYO_9-cell_c (CGH)


title: BLASTOMERE-EMBRYO_20-cell_a (SNP)


title: BLASTOMERE-EMBRYO_9-cell_b (CGH)


title: BLASTOMERE-EMBRYO_20-cell_d (SNP)


title: BLASTOMERE-EMBRYO_8-cell_g (CGH)


title: BLASTOMERE-EMBRYO_9-cell_e (CGH)


title: BLASTOMERE-EMBRYO_19-cell_f (SNP)


title: BLASTOMERE-EMBRYO_8-cell_f (CGH)


title: BLASTOMERE-EMBRYO_19-cell_e (SNP)


title: BLASTOMERE-EMBRYO_19-cell_c (SNP)


title: BLASTOMERE-EMBRYO_8-cell_e (CGH)


title: BLASTOMERE-EMBRYO_8-cell_d (CGH)


title: BLASTOMERE-EMBRYO_19-cell_d (SNP)


title: BLASTOMERE-EMBRYO_19-cell_b (SNP)


title: BLASTOMERE-EMBRYO_18-cell_c (SNP)


title: BLASTOMERE-EMBRYO_8-cell_b (CGH)


title: BLASTOMERE-EMBRYO_17-cell_b (SNP)


title: BLASTOMERE-EMBRYO_18-cell_f (SNP)


title: BLASTOMERE-EMBRYO_19-cell_a (SNP)


title: BLASTOMERE-EMBRYO_18-cell_d (SNP)


title: BLASTOMERE-EMBRYO_8-cell_a (CGH)


title: BLASTOMERE-EMBRYO_20-cell_g (SNP)


title: BLASTOMERE-EMBRYO_7-cell_e (CGH)


title: BLASTOMERE-EMBRYO_18-cell_e (SNP)


title: BLASTOMERE-EMBRYO_7-cell_b (CGH)


title: BLASTOMERE-EMBRYO_7-cell_f (CGH)


title: BLASTOMERE-EMBRYO_18-cell_i (SNP)


title: BLASTOMERE-EMBRYO_17-cell_a (SNP)


title: BLASTOMERE-EMBRYO_18-cell_b (SNP)


title: BLASTOMERE-EMBRYO_6-cell_e (CGH)


title: BLASTOMERE-EMBRYO_6-cell_i (CGH)


title: BLASTOMERE-EMBRYO_18-cell_a (SNP)


title: BLASTOMERE-EMBRYO_17-cell_c (SNP)


title: BLASTOMERE-EMBRYO_7-cell_a (CGH)


title: BLASTOMERE-EMBRYO_6-cell_d (CGH)


title: BLASTOMERE-EMBRYO_17-cell_d (SNP)


title: BLASTOMERE-EMBRYO_16-cell_a (SNP)


title: BLASTOMERE-EMBRYO_16-cell_h (SNP)


title: BLASTOMERE-EMBRYO_6-cell_c (CGH)


title: BLASTOMERE-EMBRYO_15-cell_e (SNP)


title: BLASTOMERE-EMBRYO_15-cell_a (SNP)


title: BLASTOMERE-EMBRYO_6-cell_b (CGH)


title: BLASTOMERE-EMBRYO_6-cell_a (CGH)


title: BLASTOMERE-EMBRYO_16-cell_f (SNP)


title: BLASTOMERE-EMBRYO_5-cell_e (CGH)


title: BLASTOMERE-EMBRYO_14-cell_d (SNP)


title: BLASTOMERE-EMBRYO_5-cell_c (CGH)


title: BLASTOMERE-EMBRYO_14-cell_c (SNP)


title: BLASTOMERE-EMBRYO_5-cell_b (CGH)


title: BLASTOMERE-EMBRYO_5-cell_a (CGH)


title: BLASTOMERE-EMBRYO_14-cell_a (SNP)


title: BLASTOMERE-EMBRYO_13-cell_a (SNP)


title: BLASTOMERE-EMBRYO_4-cell_e (CGH)


title: BLASTOMERE-EMBRYO_4-cell_d (CGH)


title: BLASTOMERE-EMBRYO_15-cell_d (SNP)


title: BLASTOMERE-EMBRYO_5-cell_d (CGH)


title: BLASTOMERE-EMBRYO_13-cell_c (SNP)


title: BLASTOMERE-EMBRYO_5-cell_f (CGH)


title: BLASTOMERE-EMBRYO_10-cell_h (SNP)


title: BLASTOMERE-EMBRYO_4-cell_c (CGH)


title: BLASTOMERE-EMBRYO_4-cell_b (CGH)


title: BLASTOMERE-EMBRYO_12-cell_c (SNP)


title: BLASTOMERE-EMBRYO_7-cell_d (CGH)


title: BLASTOMERE-EMBRYO_11-cell_d (SNP)


title: BLASTOMERE-EMBRYO_12-cell_b (SNP)


title: BLASTOMERE-EMBRYO_4-cell_a (CGH)


title: BLASTOMERE-EMBRYO_3-cell_e (CGH)


title: BLASTOMERE-EMBRYO_10-cell_f (SNP)


title: BLASTOMERE-EMBRYO_3-cell_d (CGH)


title: BLASTOMERE-EMBRYO_3-cell_c (CGH)


title: BLASTOMERE-EMBRYO_3-cell_f (CGH)


title: BLASTOMERE-EMBRYO_13-cell_g (SNP)


title: BLASTOMERE-EMBRYO_14-cell_e (SNP)


title: BLASTOMERE-EMBRYO_10-cell_i (SNP)


title: BLASTOMERE-EMBRYO_11-cell_g (SNP)


title: BLASTOMERE-EMBRYO_3-cell_b (CGH)


title: BLASTOMERE-EMBRYO_3-cell_a (CGH)


title: BLASTOMERE-EMBRYO_9-cell_f (SNP)


title: BLASTOMERE-EMBRYO_10-cell_g (SNP)


title: BLASTOMERE-EMBRYO_10-cell_e (SNP)


title: BLASTOMERE-EMBRYO_2-cell_f (CGH)


title: BLASTOMERE-EMBRYO_9-cell_j (SNP)


title: BLASTOMERE-EMBRYO_2-cell_d (CGH)


title: BLASTOMERE-EMBRYO_10-cell_a (SNP)


title: BLASTOMERE-EMBRYO_2-cell_c (CGH)


title: BLASTOMERE-EMBRYO_9-cell_g (SNP)


title: BLASTOMERE-EMBRYO_10-cell_d (SNP)


title: BLASTOMERE-EMBRYO_10-cell_c (SNP)


title: BLASTOMERE-EMBRYO_8-cell_e (SNP)


title: BLASTOMERE-EMBRYO_1-cell_f (CGH)


title: BLASTOMERE-EMBRYO_9-cell_d (SNP)


title: BLASTOMERE-EMBRYO_9-cell_e (SNP)


title: BLASTOMERE-EMBRYO_1-cell_c (CGH)


title: BLASTOMERE-EMBRYO_1-cell_e (CGH)


title: BLASTOMERE-EMBRYO_1-cell_d (CGH)


title: BLASTOMERE-EMBRYO_9-cell_c (SNP)


title: BLASTOMERE-EMBRYO_2-cell_b (CGH)

hyb_protocol: 1.75 µg of labeled single cell amplified DNA and reference DNA were mixed with 50 µg of human Cot-1 DNA (Invitrogen) and precipitated by adding 2.5 volumes of 96% ethanol and 0.1 volume of sodium acetate (3M, pH5.2). The DNA pellet was resuspended in 15 µl hybridization buffer (50% formamide, 10% dextran sulfate, 0.1% Tween-20, 2xSSC and 10 mM Tris–HCl, pH 7.5) containing 200 µg yeast tRNA, denatured at 98°C for 15 minutes and hybridized to a BAC array (spotted area of 18 x 18 mm) over one night in a humid chamber at 37°C. This area was preblocked for 1 hour at 37°C with 16.6 µg human Cot-1 DNA and 0.1 mg salmon testes DNA (Sigma Aldrich) dissolved in 20 µl hybridization buffer. Arrays were washed in 1xPBS (pH8.0)/0,05% Tween20 for 10 minutes at room temperature, 2xSSC (pH7.0)/50% formamide for 30 minutes at 42°C, 1xPBS (pH8.0)/0,05% Tween20 for 10 minutes at room temperature and subsequently dried

label_protocol: Single cell (SC) amplified DNA and reference DNA were labeled for 2h by random primer labeling (BioPrime aCGH Genomic Labeling System; Invitrogen; Carlsbad, CA) using respectively Cy5- and Cy3-dCTPs (GE Healthcare). Labeled DNA was purified with the BioPrime Purification Module (Invitrogen; Carlsbad, CA).


title: BLASTOMERE-EMBRYO_1-cell_b (CGH)


title: BLASTOMERE-EMBRYO_2-cell_a (CGH)


title: BLASTOMERE-EMBRYO_1-cell_a (CGH)


title: BLASTOMERE-EMBRYO_7-cell_e (SNP)


title: L4G1_N3I5_R3

status: Public on Apr 25 2009

city: Le Rheu

first: Denis

last: TAGU

department: UMR 1099 BiO3P

institute: INRA Rennes

hyb_protocol: Hybridizations were performed with a Discovery XT System Hybridization Robot using the ChipMap 80 kit (Ventana Medical Systems, Tucson, AZ, USA) at INRA–SCRIBE transcriptomic facilities (IFR 140 GFAS, Rennes). Prehybridization was performed at 42°C for 1h in a 0.5% BSA, 2X SSC and 0.2% SDS prehybridization buffer. Target labelled cDNAs were mixed before hybridizations at 42°C for 6h (protocol no. 2, ALC-D60/10-H48/8, Ventana) in a ChypHybe80 (Ventana Medical Systems, Tucson, AZ, USA) hybridization buffer. Hybridized slides were washed manually with a RiboWash solution (2 times) and a 0.1X SSC solution (1 time). The 3 washes were performed at room temperature for 2 minutes.

scan_protocol: Fluorescent images of the microarrays were generated with a Genepix 4000B scanner and Genepix Pro analysis software v5.0 (Axon Instruments, Molecular Devices Co., Sunnyvale, CA, USA).

data_processing: Raw data were normalized by the MADSCAN software. After subtraction of the fluorescence background, a rank-invariant method and a spatial normalisation were performed before a scaling of the variance within each slide and between all the slides at the same rank. The normalized values were log-transformed and used to perform statistical analysis by Significance Analysis of Microarray (SAM). To detect genes significantly regulated, the same delta-value was applied for the 4 analyzes, which resulted in a maximum False Discovery Rate (FDR) of 6.5%.

organism: Acyrthosiphon pisum

source_name: Heads of L4G1 pea aphid reared under 16h photoperiod

label_protocol: 1.5 µg of aRNA were labelled and purified using the ChipShot Indirect Labelling and Clean-Up System (Promega, Madison, WI, USA). Labelling was performed with the CyDye (Cy3/Cy5) Reactive (Amersham Biosciences-GE, Faifield, CT, USA).

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 16 h of light (“Short night” or SN) that maintained parthenogenesis. To initiate the experiment clonal third instar larvae (L3) were placed under SN photoperiod. This corresponds to generation G0. They reached adulthood 4 days later and when they began to lay their offspring, 1 L1 per WA was conserved. When these L1 reached L4 stage , a batch of 25 L4-G1 aphids was collected and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of asexual forms in SN 2 genrrations later.

extract_protocol: RNAs were extracted from heads (after their dissection under liquid nitrogen) using SV Total RNA Isolation kit (Promega, Madison, WI, USA). RNAs were amplified by using MessageAmp aRNA kit (Ambion, Austin, TX, USA), starting with 1 µg of total RNA. RNAs were checked with a Bioanalyzer 2100 (Agilent Tech. Inc., Palo Alto, CA, USA), and quantified with a Nanodrop (Agilent).

treatment_protocol: Short night reared pea aphids

tag: strain

value: YR2 (red holocyclic clone)

tag: tissue

value: head

tag: gender

value: parthenogenetic female

tag: treatment

value: 16 days of 16h photoperiod

tag: developmental stage

value: instar stage L4

tag: generation

tag: reproductive mode

value: female producing parthenogenetic females

source_name: Heads of L4G1 pea aphid reared under 12h photoperiod

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 12 h of light (“Long-Night” or LN) that induced sexual forms after two generations. To initiate the experiment clonal third instar larvae (L3) were placed at LN photoperiod. This corresponds to generation G0. L3-G0 aphids reached adulthood 4 days later and when they began to lay their offspring, 1 L1 per WA was conserved. When these L1 reached L4 stage , a batch of 25 L4-G1 aphids was collected and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of sexual forms in LN.

extract_protocol: RNAs were extracted from heads using SV Total RNA Isolation kit (Promega, Madison, WI, USA). RNAs were amplified by using MessageAmp aRNA kit (Ambion, Austin, TX, USA), starting with 1 µg of total RNA. RNAs were checked with a Bioanalyzer 2100 (Agilent Tech. Inc., Palo Alto, CA, USA), and quantified with a Nanodrop (Agilent).

treatment_protocol: Long Night reared pea aphids

value: 16 days of 12h photoperiod

value: female producing sexual individuals


title: XBP1 KO MEF_adipogenesis_d0

city: Ithaca

first: Ling

last: Qi

state: NY

address: 307 Biotech Bldg, Cornell Univ

department: Division of Nutritional Sciences

institute: Cornell University

hyb_protocol: Hybridized by Phalanx Biotech Group.

scan_protocol: Scanned by Phalanx Biotech Group.

data_processing: Data are normalized using Quantile normalization by Phalanx Biotech Group.

source_name: XBP1 KO MEF, adipogenesis, at d0

label_protocol: Labeled by Phalanx using 1 ug of total RNA after amplification.

extract_protocol: Total RNAs were extracted using QIAGEN Rneasy Plus Mini kit following the manufacture's manual.

treatment_protocol: Cells were differentiated as 3T3-L1 with the following modifications: when the cells became confluent (d0), they were treated with 0.25 mM IBMX, 5 µM DXM, 10 µg/ml insulin and 5 µM troglitazone for the first 72 h. Subsequently, cells were maintained in 1 µg/ml insulin and 5 µM troglitazone (EMD Calbiochem) to induce terminal differentiation.

tag: cell line

value: Xbp1 knockout mouse embryonic fibroblast cells

value: adipogenesis

tag: stage


title: L4G1_N5I3_R3


title: BLASTOMERE-EMBRYO_9-cell_b (SNP)

tag: IVF protocol

tag: Patient info


title: L4G1_N5I3_R2


title: BLASTOMERE-EMBRYO_6-cell_e (SNP)


title: BLASTOMERE-EMBRYO_7-cell_f (SNP)


title: BLASTOMERE-EMBRYO_8-cell_d (SNP)


title: BLASTOMERE-EMBRYO_8-cell_a (SNP)


title: BLASTOMERE-EMBRYO_6-cell_a (SNP)


title: L4G1_N5I3_R1


title: L4G1_N3I5_R1


title: L4G1_N3I5_R2


title: BLASTOMERE-EMBRYO_7-cell_a (SNP)


title: L2G1_N3I5_R2

source_name: Heads of L2G1 pea aphid reared under 16h photoperiod

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 16 h of light (“Short night” or SN) that maintained parthenogenesis. To initiate the experiment clonal third instar larvae (L3) were placed under SN photoperiod. This corresponds to generation G0. They reached adulthood 4 days later and when they began to lay their offspring, 1 L1 per WA was conserved. When these L1 reached L2 stage , a batch of 25 L2-G1 aphids was collected and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of asexual forms in SN 2 genrrations later.

value: 12 days of 16h photoperiod

value: instar stage L2

source_name: Heads of L2G1 pea aphid reared under 12h photoperiod

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 12 h of light (“Long-Night” or LN) that induced sexual forms after two generations. To initiate the experiment clonal third instar larvae (L3) were placed at LN photoperiod. This corresponds to generation G0. L3-G0 aphids reached adulthood 4 days later and when they began to lay their offspring, 1 L1 per WA was conserved. When these L1 reached L2 stage , a batch of 25 L2-G1 aphids was collected and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of sexual forms in LN.

value: 12 days of 12h photoperiod


title: L2G1_N5I3_R3


title: BLASTOMERE-EMBRYO_6-cell_c (SNP)


title: L2G1_N5I3_R1


title: BLASTOMERE-EMBRYO_5-cell_a (SNP)

tag: ICSI protocol


title: XBP1 KO MEF_adipogenesis_d3

scan_protocol: Scanned by halanx Biotech Group.

source_name: XBP1 KO MEF, adipogenesis, at d3


title: WAG0_N5I3_R3

source_name: Heads of WAG0 pea aphid reared under 16h photoperiod

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 16 h of light (“Short night” or SN) that maintained parthenogenesis. To initiate the experiment clonal third instar larvae (L3) were placed under SN photoperiod. This corresponds to generation G0. They reached adulthood 4 days later and a batch of 25 WA-G0 aphids was collected and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of asexual forms in SN 2 generations later.

value: 4 days of 16h photoperiod

value: wingless adult stage

source_name: Heads of WAG0 pea aphid reared under 12h photoperiod

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 12 h of light (“Long-Night” or LN) that induced sexual forms after two generations. To initiate the experiment clonal third instar larvae (L3) were placed at LN photoperiod. This corresponds to generation G0. L3-G0 aphids reached adulthood 4 days later.  A batch of 25 WA-G0 aphids was collected in the middle of the photophase and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of sexual forms in LN.

value: 4 days of 12h photoperiod


title: BLASTOMERE-EMBRYO_8-cell_g (SNP)

value: controlled ovarian hyperstimulation was performed using a “long protocol” as follows.  In the previous cycle an oral contraceptive pill was given for 25 days (Cilest®, Janssen-Cilag), followed by pituitary downregulation with bucerelin acetate (Suprefact®, Hoechst, Frankfurt, Germany; 600 µg daily) from day 21 onwards. Human menopausal gonadotropins or human recombinant gonadotrophins  (Humegon® or Puregon, Organon, Oss, The Netherlands; Gonal F, Merck Serono, Geneva, Switzerland) were started on the second day after the subsequent menstruation while ovulation was induced with 10000 IU HCG (Pregnyl®, Organon, Oss, The Netherlands) when at least 3 follicles with a diameter of at least 17 mm were observed at gynecological ultrasound. Ultrasound guided oocyte aspiration was performed 36 hours later. Luteal supplementation was given by vaginal progesterone (600 mg/day, Utrogestan®, Piette International, Drogenbos, Belgium). Subsequently, oocytes were fertilized using conventional IVF (n=8) or ICSI (n=1) with ejaculated sperm. Embryos were cultured in Global Medium (GlobalLife) and the morphology was daily assessed. Only genetically normal embryos of good morphology (with compaction or blastocyst formation) were transferred on day 4 or 5. Supernumerary genetically normal embryos of good morphology were frozen at day 4 or 5. Day 3 (evening) or day 4 (morning) embryos diagnosed with a microdeletion or with a normal sex but not suitable for transfer due to a familial genetic reason were used for this study if fulfilling all inclusion criteria (see patient info).

value: Couples entering the IVF-PGD-program for sex selection due to X-linked disorders or BRCA mutations or for familial microdeletion syndromes were asked to participate. Inclusion criteria were:(1) written informed consent from each couple, (2) maternal and paternal age ≤ 35 years, (3) normal karyotype for both partners, (4) a maternal body mass index of 18-30 kg/m², (5) initial normal semen parameters according to WHO regulation, (6) good quality embryos:2-5 blastomeres on day 2, 6-10 blastomeres on day 3, <20% fragmentation, equal sized blastomeres, (7) no recurrent miscarriages. The study was approved by the Ethical Committee of the University Hospital (registration number NCT00614367).


title: BLASTOMERE-EMBRYO_6-cell_i (SNP)


title: L2G1_N5I3_R2

value: YR2 (red holocyclic clone)

value: head


title: WAG0_N3I5_R1

value: parthenogenetic female


title: WAG0_N3I5_R3


title: BLASTOMERE-EMBRYO_3-cell_d (SNP)

tag: single cell from a 3-day-old human IVF embryo


title: WAG0_N5I3_R2


title: L2G1_N3I5_R3


title: L2G1_N3I5_R1


title: BLASTOMERE-EMBRYO_1-cell_d (SNP)


title: BLASTOMERE-EMBRYO_1-cell_a (SNP)


title: L4G0_N5I3_R3

source_name: Heads of L4G0 pea aphid reared under 16h photoperiod

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 16 h of light (“Short night” or SN) that maintained parthenogenesis. To initiate the experiment clonal third instar larvae (L3) were placed under SN photoperiod. This corresponds to generation G0. They reached L4-G0 stage 2 days later and a batch of 25 L4-G0 aphids was collected in the middle of the photophase and immedialtely frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of asexual forms in SN 2 generations later.

value: 2 days of 16h photoperiod

value: instar stage L4

source_name: Heads of L4G0 pea aphid reared under 12h photoperiod

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 12 h of light (“Long-Night” or LN) that induced sexual forms after two generations. To initiate the experiment clonal third instar larvae (L3) were placed at LN photoperiod. This corresponds to generation G0. L3-G0 aphids reached L4-G0 stage A batch of 25 L4-G0 aphids was collected in the middle of the photophase and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of sexual forms in LN.

value: 2 days of 12h photoperiod


title: L4G0_N3I5_R3

value: female producing parthenogenetic females

value: female producing sexual individuals


title: L4G0_N3I5_R2


title: BLASTOMERE-EMBRYO_6-cell_d (SNP)


title: L4G0_N5I3_R1


title: L4G0_N5I3_R2


title: BLASTOMERE-EMBRYO_1-cell_e (SNP)


title: BLASTOMERE-EMBRYO_1-cell_f (SNP)