title: E9.5 FVB/N erythroid cells-9

city: Richmond

first: Latasha

last: Redmond

state: Virginia

address: 401 College Street

department: Department of Human and Molecular Genetics

institute: Virginia Commonwealth University

description: Comparison between mouse embryonic day 9.5 (E9.5) wild-type and KLF2-/-   yolk sac microdissected erythroid precursors

hyb_protocol: Fifteen μg of labeled erythroid RNA was fragmented and 10 μg was hybridized to Affymetrix GeneChip Mouse Genome 430A 2.0 arrays for 18 hours (Affymetrix Inc.). The 8 microarrays were washed and stained with streptavidin–phycoerythrin as described (Redmond et al., Blood Cells Molecules and Diseases 2006, 37:27).

scan_protocol: Image analysis was performed on the E9.5 KLF2-/- erythroid  yolk sac data set using the GeneChip Operating System version 1.4 (GCOS1.1, Affymetrix Inc.). The image of the scanned array was stored as a DAT file using the Affymetrix software.

data_processing: Quality control parameters such as scaling factors used to normalize the chips, average background and noise were also analyzed.  The raw intensities for each probe set were stored in electronic formats by the GCOS software.  Scaling factors used to normalize the chips to a target value (TGT), and in this study, the TGT was set at 100. Probe set expression summaries were calculated with the Probe set expression summaries were calculated with the Robust Multi-average (RMA) algorithm (Irizarry et al., 2003). RMA expression summaries were obtained for wildtype (GSE10002) and KLF2-/- erythroid  GeneChips using the rma function in the affy package in R/Bioconductor. The Multi-Chip Significance score (S-score) method was used to compare the 4 different wildtype  and KLF2-/- GeneChips to determine significant changes in gene expression between these types of erythroid cells (Kennedy et al., 2006). S-score values were obtained using the SScore function in the sscore package in Bioconductor.  Probe sets with absolute values of the S-score greater or equal to 2.00 were considered to correspond to significant differences between the two types of samples.  P-values were calculated from S-score values and then used to obtain the q-values. The q-value, a quantifiable measure of the false discovery rate (FDR), was used to identify differentially expressed genes between the KLF2-/- and WT microarrays.  The FDR for a test is defined as the number of false positives among the total number of significant results.  For this study, a false discovery rate of 5% was used.

source_name: E9.5 FVB/N erythroid cells-9

label_protocol: Ten to 39 ng of erythroid RNA was used to generate double stranded cDNA with the T7-oligo (dT) primer according to the Affymetrix GeneChip Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA). Labeled cRNA yield and purity was determined as described (Redmond et al., 2006).

growth_protocol: Timed-pregnant FVB/N mice were anesthetized and sacrificed. E9.5 yolk sacs were dissected from the embryo and cryoprotected in PBS with 20% sucrose.

extract_protocol: Total RNA was isolated from wild type erythroid cells using reagents from the (ToTALLY RNA isolation kit; Ambion Inc., Austin, TX, USA) and quality assessment by capillary electrophoresis were performed as previously described (Redmond et al., Blood Cells Molecules and Diseases 2006, 37:27).

treatment_protocol: E9.5 yolk sacs tissues were rinsed once in 1:1 20% sucrose PBS:Optimal Cutting Temperature freezing media (OCT, Tissue-Tek), then OCT alone and frozen. Eight micron E9.5 sections were stained with the LCM frozen section staining kit (Molecular Devices, Mountain View, CA, USA) and used for laser capture dissection experiments. Using the PixCell II Laser Capture Microdissection System (Arcturus Bioscience), approximately 1 E9.5 yolk sac erythroid cell was collected for every 2 to 3 laser pulses.  Approximately 12 to 50 microscope slides, using 2 to 4 yolk sacs from 2 different litters were used per biological replicate.

tag: genotype

value: wild type FVB/N

tag: age

value: embryonic day 9.5


title: F9 teratocarcinoma cells after differentiation with retinoic acid/theophylline/cAMP. Replicate 2

status: Public on Mar 02 2011

type: RNA

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

country: USA

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v1 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: strain

tag: cell type

value: F9 teratocarcinoma

tag: disease state


title: F9 teratocarcinoma cells before differentiation. Replicate 3


title: E9.5 FVB/N erythroid cells-3

source_name: E9.5 FVB/N erythroid cells-3


title: E9.5 FVB/N erythroid cells-7

source_name: E9.5 FVB/N erythroid cells-7


title: E9.5 FVB/N erythroid cells-5

source_name: E9.5 FVB/N erythroid cells-5


title: KLF2-/- erythroid; KLF2KO-13

source_name: E9.5 KLF2-/- erythroid cells-13

label_protocol: Ten to 20 ng of KLF2-/- erythroid RNA  was used to generate double stranded cDNA with the T7-oligo (dT) primer according to the Affymetrix GeneChip Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA). Labeled cRNA yield and purity was determined as described (Redmond et al., 2006).

growth_protocol: Timed-pregnant KLF2-/- mice were anesthetized and sacrificed. E9.5 yolk sacs were dissected from the embryo and cryoprotected in PBS with 20% sucrose.

extract_protocol: Total RNA was isolated from KLF2-/-  erythroid  cells using reagents from the (ToTALLY RNA isolation kit; Ambion Inc., Austin, TX, USA) and quality assessment by capillary electrophoresis were performed as previously described (Redmond et al., Blood Cells Molecules and Diseases 2006, 37:27).

treatment_protocol: E9.5 yolk sacs tissues were rinsed once in 1:1 20% sucrose PBS:Optimal Cutting Temperature freezing media (OCT, Tissue-Tek), then OCT alone and frozen. A small portion of the embryo tail was used for PCR genotyping.  Eight micron KLF2-/- E9.5 sections were stained with the LCM frozen section staining kit (Molecular Devices, Mountain View, CA, USA) and used for laser capture dissection experiments. Using the PixCell II Laser Capture Microdissection System (Arcturus Bioscience), approximately 1 E9.5 yolk sac erythroid cell was collected for every 2 to 3 laser pulses. For the 4 erythroid KLF2-/- microarray samples, between 3,600 to 4,400 erythroid cells were collected from 30 to 80 microscope slides, using 2 to 4 yolk sacs from 2 different litters.


title: F9 teratocarcinoma cells before differentiation. Replicate 2


title: 3ng/mL BMP4 + FGF2 (3ng_103248)

status: Public on Mar 03 2011

type: mixed

city: madison

first: James

last: Thomson

state: Wisconsin

address: 425 Henry Mall

department: Regenerative Biology

institute: Mogridge Institute for Research

description: the second channel (genomic DNA) serve as common reference across the experiments

hyb_protocol: Array hybridization, wash were performed according to NimbleGen’s recommended protocol

scan_protocol: Arrays were scanned using a GenePix 4000B scanner and the PMT settings were followed by NimbleGen array manual

data_processing: 1. Image extraction:  NimbleScan provided by NimbleGen is used to extract signal data from image files  (*.TFF). Signal meansurements were saved in .pair files.  2. Normalization:  Signal intensities from RNA and gDNA samples are normalized with Robust Multiple-chip Analysis (RMA) algorithm (Irizarry et al., 2003) separately. A median-adjusted ratio is calculated for each gene by dividing its signal intensity from the RNA sample by the sum of the corresponding signal intensity from the gDNA sample and median signal intensity of all genes from the gDNA channel.

organism: Homo sapiens

source_name: Day 5 differentiated H1 cells with 3ng/mL BMP4 + FGF2 treatment

label_protocol: Amino Allyl labeling method

growth_protocol: H1 ES cells were maintained in defined TeSR1 medium on Matrigel plates.

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen) with on-column DNAse (Qiagen).

treatment_protocol: Cells were dissociated by TrpLE (Invitrogen) and plated into TeSR1 medium +BMP4 or TeSR1 medium -FGF2 +BMP4 to initiate differentiation. Different concentrations of BMP4 were used according to expreimental descriptions. Cells were collected at various time points during time course experiments.

tag: cell line

tag: passage

value: differentiated human embryonic stem cell

tag: treatment

value: 3ng/mL BMP4 + FGF2

molecule: genomic DNA

source_name: undifferentiated H1

value: undifferentiated H1


title: KLF2-/- erythroid; KLF2KO-14

source_name: E9.5 KLF2-/- erythroid cells-14


title: F9 teratocarcinoma cells before differentiation. Replicate 1


title: OCT4 immunoprecipitate

type: other

city: Providence

first: William

last: Fairbrother

state: RI

address: 70 Ship St

department: MCB

institute: Brown University

description:
MEGAshift protocol:
A complex pool of 60-mer oligonucleotides was synthesized as a custom oligonucletide microarray ('synthesized array') to contains the union of the intersection of ChIP-ChIP fragments of POU5F1 (Oct4), Nanog and Sox2 as found in Core Transcriptional Regulatory Circuitry In Humand Embryonic Stem Cell (Boyer et. Al, 2005). Each oligo was designed as a tiled genomic 30-mer flanked by the common sequence CCAGTAGATCTGCCA and ATGGAGTCCAGGTTG that were used as universal primers.
Oligo pool was liberated from the slide by boiling at 99C for 1 hour. Low cycle PCR was used to amplify the pool. The amplified oligonucleotide pool was then was incubated with embryonic stem cell extract to perform a binding assay.
A 'detection array' (Agilent_BrownUniversity/FairbrotherLab Human 2x105K OSN_Validation tiling array) complimentary to the 'synthesized array' is used to measure the degree to which each oligonucleotide is enriched in the bound fraction. The array returns binding measurements for each oligonucleotide, which can be used to define biologically relevant motifs and to create binding maps.

hyb_protocol: A 2 × 104 k Custom Agilent oligonucleotide detection microarray was designed complimentary to the oligonucleotide pool.  Microarrays were hybridized for 3 hours at 50C using an optimized Agilet gene expression hybridization kit and protocol.

scan_protocol: Microarrays were scanned at 5um using GenePix 400B scanner and analyzed using Feature Extraction Software from Agilent.

data_processing: We obtained the log10 ratio of normalized rProcessedSignal to normalized gProcessedSignal. Signal values were normalized by taking the ratio of each probe to the summed signal of probes on the array. Probes were omitted where Cy3 probes were not well above background.

molecule: other

source_name: [starting] oligo pool that tiles through genomic DNA representing 316 PluCR regions (i.e., regions of simulataneous in vivo Oct4, Sox2 and Nanog ChIP enrichement in human ES cells

label_protocol: RNA target were produced containing amino-allyl UTP using MEGAshortscript™ High-Yield Transcription kit (Ambion) after appending a T7 promoter to the oligonucleotides. Amino-Allyl UTP’s were then coupled to Cy3 and Cy5 dyes, through a labeling procedure. RNA was pelleted and resuspended in 1M NA2CO3, monoreactive dyes were added and reaction was allowed to continue for 1h at room temperature. 4M hydroxylamine was used to quench the reaction followed by phenol:chloroform and ethanol precipitation to remove remaining free nucleotides.

extract_protocol: DNA isolated from four different co-immunoprecipitation reactions (POU5F1(Oct4), POU2F1(Oct1), SOX2, NANOG) was  transcribed into RNA and used to produce targets for array analysis. Starting DNA pool was transcribe similarly.

tag: antibody

source_name: [co-immunoprecipitate] oligo pool that tiles through genomic DNA representing 316 PluCR regions (i.e., regions of simulataneous in vivo Oct4, Sox2 and Nanog ChIP enrichement in human ES cells

tag: antibody vendor

value: Santa Cruz Biotechnology, Inc.

tag: antibody lot#

tag: antibody catalog#


title: KLF2-/- erythroid; KLF2KO-11

source_name: E9.5 KLF2-/- erythroid cells-11


title: polyA_RNA_Tdp43_oligo_rep2

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

hyb_protocol: Hybridization cocktails containing ~5.5 ug of fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization was performed for 16 hours using the Fluidics 450 station.

scan_protocol: Arrays were scanned using the Affymetrix 3000 7G scanner and GeneChip Operating Software version 1.4 to produce .CEL intensity files. Even though the array was the mjay exon/splicing array, the scanner was set up for MoEx-1_0-st-v1.1sq parameters.

data_processing: Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.

source_name: Striatum

label_protocol: WT Terminal Labeling Kit, Affymetrix

extract_protocol: Trizol extraction of RNA and protein was performed according to the manufacturer’s instructions. In summary, tissues were homogenized in Trizol using a Polytron homogenizer (Company) for 15 sec. Homogenates were then incubated at room temperature for 5min. Chloroform was added to the homogenates (200 ul per 1 mL of Trizol) and tubes were shaken vigorously for 15 sec. After incubation at room temperature for 2-10 min, samples were centrifuged at 12,000 g for 15 min at 4oC. The RNA-containing aqueous phase was transferred to fresh tubes and after the addition of glycogen and isopropanol, RNA was precipitated at -20oC overnight. The next day, samples were centrifuged for 10 mins at maximum speed in a microcentrifuge at 4oC. RNA pellets were washed with 75% Ethanol twice, dried at room temperature and reconstituted in DEPC-treated water.

treatment_protocol: 8-10 week old female C57Bl/6 mice were anesthetized with 2.5-3% isofluorane, and a midline incision of approximately 1cm was made on their heads. Using stereotaxic guides, 3 mL of antisense oligonucleotide (ASO) solution targeting Tdp-43 or a control – corresponding to a total of 75 mg or 100 mg ASOs – or saline buffer was injected using a Hamilton syringe directly into their striatum. The incision was closed with sutures and the mice were allowed to recover in their cages. They were monitored for any adverse effects for the next two weeks until they were sacrificed. The striatum and adjacent cortex area were dissected, placed in separate tubes containing 1 mL Trizol (Invitrogen) and were frozen at -80oC until use.

value: 8-10 weeks

value: Tdp43 anti-sense oligo


title: polyA_RNA_Tdp43_oligo_rep3


title: polyA_RNA_Tdp43_oligo_rep1


title: KLF2-/- erythroid; KLF2KO-12

source_name: E9.5 KLF2-/- erythroid cells-12


title: Kidney 100% : Spleen 0% 2

source_name: Kidney 100% : Spleen 0%

tag: Sex

value: male

value: healthy


title: Kidney 100% : Spleen 0% 3


title: Kidney 100% : Spleen 0% 4


title: Kidney 100% : Spleen 0% 1


title: SOX2 immunoprecipitate


title: Kidney 75% : Spleen 25% 2

source_name: Kidney 75% : Spleen 25%


title: Kidney 75% : Spleen 25% 1


title: Kidney 50% : Spleen 50% 3

source_name: Kidney 50% : Spleen 50%


title: Kidney 50% : Spleen 50% 5


title: polyA_RNA_control_oligo_rep2

value: control anti-sense oligo


title: polyA_RNA_control_oligo_rep1


title: polyA_RNA_control_oligo_rep3


title: Kidney 50% : Spleen 50% 4


title: Kidney 50% : Spleen 50% 2


title: Kidney 50% : Spleen 50% 1


title: Kidney 25% : Spleen 75% 4

source_name: Kidney 25% : Spleen 75%


title: Kidney 25% : Spleen 75% 2


title: Kidney 0% : Spleen 100% 3

source_name: Kidney 0% : Spleen 100%


title: Kidney 0% : Spleen 100% 2


title: Kidney 75% : Spleen 25% 4


title: Kidney 0% : Spleen 100% 1


title: Kidney 25% : Spleen 75% 3


title: Kidney 0% : Spleen 100% 4


title: Kidney 25% : Spleen 75% 5


title: Kidney 25% : Spleen 75% 1


title: 90004: Human Prefrontal Cortical region (Brodmann Area 46), Schizophrenic, replicate #9.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v2 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

tag: duration of illness

value: 14 yrs

value: Schizophrenic

tag: tissue

value: brain (prefrontal cortical region)


title: 91017: Human Prefrontal Cortical region (Brodmann Area 46), Schizophrenic, replicate #6.

value: 12 yrs


title: 94120: Human Prefrontal Cortical region (Brodmann Area 46), Schizophrenic, replicate #10.

value: 15 yrs


title: 93086: Human Prefrontal Cortical region (Brodmann Area 46), Schizophrenic, replicate #12.

value: 17 yrs


title: 94127: Human Prefrontal Cortical region (Brodmann Area 46), Schizophrenic, replicate #11.


title: 95169: Human Prefrontal Cortical region (Brodmann Area 46), Schizophrenic, replicate #13.

value: female

value: 18 yrs


title: 98236: Human Prefrontal Cortical region (Brodmann Area 46), Schizophrenic, replicate #8.


title: 94123: Human Prefrontal Cortical region (Brodmann Area 46), Schizophrenic, replicate #7.


title: 95149: Human Prefrontal Cortical region (Brodmann Area 46), Control, replicate #13.


title: 96185: Human Prefrontal Cortical region (Brodmann Area 46), Schizophrenic, replicate #5.

value: 11 yrs


title: 94122: Human Prefrontal Cortical region (Brodmann Area 46), Schizophrenic, replicate #1.

value: 7 yrs


title: 93072: Human Prefrontal Cortical region (Brodmann Area 46), Schizophrenic, replicate #2.


title: 96175: Human Prefrontal Cortical region (Brodmann Area 46), Schizophrenic, replicate #4.


title: 95146: Human Prefrontal Cortical region (Brodmann Area 46), Control, replicate #11.


title: 94102: Human Prefrontal Cortical region (Brodmann Area 46), Control, replicate #12.


title: 98234: Human Prefrontal Cortical region (Brodmann Area 46), Control, replicate #4.


title: 93075: Human Prefrontal Cortical region (Brodmann Area 46), Control, replicate #5.


title: 93082: Human Prefrontal Cortical region (Brodmann Area 46), Control, replicate #10.


title: 94090: Human Prefrontal Cortical region (Brodmann Area 46), Control, replicate #9.


title: 95151: Human Prefrontal Cortical region (Brodmann Area 46), Control, replicate #7.


title: 95170: Human Prefrontal Cortical region (Brodmann Area 46), Schizophrenic, replicate #3.


title: 92033: Human Prefrontal Cortical region (Brodmann Area 46), Control, replicate #6.


title: 92032: Human Prefrontal Cortical region (Brodmann Area 46), Control, replicate #8.


title: Human lymphoma cell line Daudi

source_name: Human lymphoma cell line Daudi

value: unknown

value: Daudi

value: lymphoma


title: 96181: Human Prefrontal Cortical region (Brodmann Area 46), Control, replicate #2.


title: Human lymphoma cell line RL

source_name: Human lymphoma cell line RL

value: RL


title: 98231: Human Prefrontal Cortical region (Brodmann Area 46), Control, replicate #1.

value: male


title: 98231: Human Prefrontal Cortical region (Brodmann Area 46), Control, replicate #3.

value: healthy


title: Human myeloma cell line 8266

source_name: Human myeloma cell line 8266

value: myeloma


title: Human myeloma cell line U266

source_name: Human myeloma cell line U266


title: murine keratinocytes, wild-type murine keratinocytes, 24 hours. Replicate 3

tag: genotype/variation

value: wt

value: keratinocytes


title: murine keratinocytes, wild-type murine keratinocytes, 24 hours. Replicate 2


title: murine keratinocytes, wild-type murine keratinocytes, 24 hours. Replicate 1


title: murine keratinocytes, galectin-3 deficient murine keratinocytes, 12 hours. Replicate 2


title: murine keratinocytes, galectin-3 deficient murine keratinocytes, 12 hours. Replicate 3


title: murine keratinocytes, galectin-3 deficient murine keratinocytes, 12 hours. Replicate 1


title: murine keratinocytes, galectin-3 deficient murine keratinocytes, 24 hours. Replicate 3


title: murine keratinocytes, galectin-3 deficient murine keratinocytes, 24 hours. Replicate 1


title: murine keratinocytes, wild-type murine keratinocytes, 12 hours. Replicate 1


title: murine keratinocytes, wild-type murine keratinocytes, 12 hours. Replicate 2


title: murine keratinocytes, wild-type murine keratinocytes, 12 hours. Replicate 3


title: murine keratinocytes, wild-type murine keratinocytes, 6 hours. Replicate 3

source_name: wild-type murine keratinocytes, 6 hours


title: murine keratinocytes, wild-type murine keratinocytes, 6 hours. Replicate 2


title: murine keratinocytes, wild-type murine keratinocytes, 6 hours. Replicate 1


title: Kidney 75% : Spleen 25% 3


title: murine keratinocytes, galectin-3 deficient murine keratinocytes, 6 hours. Replicate 2

source_name: galextin-3 deficient murine keratinocytes, 6 hours


title: murine keratinocytes, galectin-3 deficient murine keratinocytes, 0 hours. Replicate 3


title: murine keratinocytes, galectin-3 deficient murine keratinocytes, 6 hours. Replicate 3


title: murine keratinocytes, galectin-3 deficient murine keratinocytes, 24 hours. Replicate 2


title: murine keratinocytes, wild-type murine keratinocytes, 0 hours. Replicate 3

source_name: wild-type murine keratinocytes, 0 hours


title: murine keratinocytes, wild-type murine keratinocytes, 0 hours. Replicate 2


title: murine keratinocytes, wild-type murine keratinocytes, 0 hours. Replicate 1


title: P19 mouse embryonal caricinoma cells with differentiation by retinoic acid. Replicate 3

tag: embryonic stage

value: differentiated embryonal caricinoma cells


title: P19 mouse embryonal caricinoma cells with differentiation by retinoic acid. Replicate 1


title: murine keratinocytes, galectin-3 deficient murine keratinocytes, 0 hours. Replicate 2


title: murine keratinocytes, galectin-3 deficient murine keratinocytes, 0 hours. Replicate 1


title: P19 mouse embryonal caricinoma cells without differentiation by retinoic acid. Replicate 3

value: undifferentiated embryonal caricinoma cells


title: P19 mouse embryonal caricinoma cells without differentiation by retinoic acid. Replicate 1


title: Mouse liver. Replicate 2

source_name: Mouse liver

tag: tissue or cell type

value: liver


title: P19 mouse embryonal caricinoma cells with differentiation by retinoic acid. Replicate 2


title: P19 mouse embryonal caricinoma cells without differentiation by retinoic acid. Replicate 2


title: Mouse embryoid body. Replicate 1

source_name: Mouse embryoid body

value: embryoid body


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line), treated with TNF. Replicate 2

value: bronchial mucosa


title: Mouse kidney. Replicate 3

source_name: Mouse kidney

value: kidney


title: Mouse embryoid body. Replicate 2


title: murine keratinocytes, galectin-3 deficient murine keratinocytes, 6 hours. Replicate 1


title: Mouse kidney. Replicate 1


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line), treated with IL-10 Replicate 1


title: Mouse liver. Replicate 3


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line), treated with IL-10 Replicate 3


title: Mouse liver. Replicate 1


title: Mouse kidney. Replicate 2


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line), treated with IL-8. Replicate 2


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line), treated with TNF. Replicate 3


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line), treated with TNF. Replicate 1


title: conjunctival cells patient 1

source_name: conjunctival cells

value: unkown

value: conjunctival


title: Mouse embryoid body. Replicate 3


title: Mouse embryonics stem cell. Replicate 2

source_name: Mouse embryonics stem cell

value: embryonics stem cell


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line), treated with IL-6. Replicate 1


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line), treated with IL-10 Replicate 2


title: Mouse embryonics stem cell. Replicate 1


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line), treated with IL-6. Replicate 2


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line), treated with IL-8. Replicate 3


title: Mouse embryonics stem cell. Replicate 3


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line), treated with IL-6. Replicate 3


title: WholeCell_MgProtoFeeding_180min_rep2

city: Freiburg

first: Bjoern

last: Voss

address: Schänzlestr. 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

hyb_protocol: Hybridization was done with 0.6 µg labeled cDNA per array according to the Agilent protocol for 8x15k single color microarrays at a temperature of 65˚C overnight.

scan_protocol: An Agilent G2565CA DNA microarray scanner was used to scan arrays at 5 μm resolution, Feature Extraction Software 9.5.3.1 was then used to process and analyse array images.

data_processing: The raw data was analyzed using GeneSpring GX 11.0 (Normalization: Shift to 75.0 percentile; Baseline Transformation: Median of all samples).

organism: Chlamydomonas reinhardtii

source_name: Whole cells

label_protocol: 0.5 µg of total RNA were reverse transcribed into cDNA, and Cy3 labeled using the Quick Amp Labeling Kit, one-color (Agilent 5190-0442)

growth_protocol: Strains were grown heterotrophically in Tris-Acetate-Phosphate (TAP) medium (Harris, 1989) on a rotary shaker at 23°C either in the dark or under continuous irradiation with white light (fluence rate 45 μEm-2s-1) provided by fluorescent tubes (Osram L36W/25).

extract_protocol: As described in von Gromoff et al., 1989, Mol Cell Biol 9: 3911-3918

treatment_protocol: For feeding experiments, a starter culture grown in the light with ~2 × 106 cells per ml was subdivided into 25 ml aliquots in 100 ml Erlenmeyer flasks and incubation continued in the dark for 16 h. At time 0, MgProto or hemin (final concentration 9 μM each) was added to the cultures in the dark and incubation in the dark was continued until harvest. Control cultures were treated the same way but did not receive the tetrapyrroles.


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line), treated with IL-8. Replicate 1


title: WholeCell_MgProtoFeeding_120min_rep1


title: T cell; NZB/W F1 strain CD4 plus CD25 - Pre-activated  B

value: female

value: NZB/W F1

tag: age

value: 5 weeks


title: WholeCell_MgProtoFeeding_180min_rep1

tag: strain


title: T cell; NZB/W F1 strain CD4 plus CD25 - Pre-activated  C


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line) - Control Replicate 1

tag: cell type


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line) - Control Replicate 2


title: bronchial mucosa Calu-3 (Human Lung Cancer Cell Line) - Control Replicate 3


title: conjunctival cells patient 2

tag: disease state


title: conjunctival cells patient 3


title: T cell; NZB/W F1 strain CD4 plus CD25 plus Pre-activated C


title: T cell; NZB/W F1 strain CD4 plus CD25 - Pre-activated  A


title: WholeCell_MgProtoFeeding_120min_rep2


title: T cell; NZB/W F1 strain CD4 plus CD25- Freshly Isolated C

source_name: T cell; NZB/W F1 strain CD4 plus CD25- Freshly Isolated.


title: WholeCell_MgProtoFeeding_60min_rep2


title: WholeCell_MgProtoFeeding_60min_rep3


title: WholeCell_MgProtoFeeding_60min_rep4


title: T cell; NZB/W F1 strain CD4 plus CD25 plus Pre-activated A


title: T cell; NZB/W F1 strain CD4 plus CD25 plus Freshly Isolated B


title: T cell; NZB/W F1 strain CD4 plus CD25 plus Freshly Isolated A


title: WholeCell_MgProtoFeeding_0min_rep1


title: WholeCell_MgProtoFeeding_0min_rep2


title: WholeCell_HeminFeeding_180min_rep1


title: T cell; NZB/W F1 strain CD4 plus CD25 plus Freshly Isolated C


title: WholeCell_HeminFeeding_180min_rep2


title: T cell; MRL/Mp strain CD4 plus CD25 plus Pre-activated C

source_name: T cell; MRL/Mp strain CD4 plus CD25 plus Pre-activated.

value: MRL/Mp


title: T cell; NZB/W F1 strain CD4 plus CD25 plus Pre-activated B


title: T cell; MRL/Mp strain CD4 plus CD25 plus Pre-activated B


title: T cell; MRL/Mp strain CD4 plus CD25 plus Pre-activated A


title: T cell; NZB/W F1 strain CD4 plus CD25- Freshly Isolated B


title: WholeCell_MgProtoFeeding_60min_rep1


title: WholeCell_HeminFeeding_120min_rep4


title: T cell; NZB/W F1 strain CD4 plus CD25- Freshly Isolated A


title: T cell; MRL/Mp strain CD4 plus CD25 plus Freshly Isolated B

source_name: T cell; MRL/Mp strain CD4 plus CD25 plus Freshly Isolated.


title: T cell; MRL/Mp strain CD4 plus CD25 plus Freshly Isolated C


title: WholeCell_HeminFeeding_120min_rep1


title: WholeCell_HeminFeeding_60min_rep1


title: WholeCell_HeminFeeding_120min_rep2


title: WholeCell_HeminFeeding_0min_rep1


title: WholeCell_HeminFeeding_0min_rep2


title: WholeCell_HeminFeeding_60min_rep2


title: T cell; MRL/Mp strain CD4 plus CD25-Pre-activated A


title: T cell; MRL/Mp strain CD4 plus CD25- Freshly Isolated B

source_name: T cell; MRL/Mp strain CD4 plus CD25- Freshly Isolated.


title: T cell; MRL/Mp strain CD4 plus CD25- Freshly Isolated C


title: T cell; MRL/Mp strain CD4 plus CD25-Pre-activated C


title: T cell; MRL/Mp strain CD4 plus CD25-Pre-activated B


title: T cell; CBA/Ca strain CD4 plus CD25-Pre-activated C

value: CBA/Ca (haplotype-matched with the MRL/Mp; H-2k)


title: T cell; MRL/Mp strain CD4 plus CD25- Freshly Isolated A


title: T cell; MRL/Mp strain CD4 plus CD25 plus Freshly Isolated A


title: T cell; CBA/Ca strain CD4 plus CD25-Pre-activated B


title: T cell; CBA/Ca strain CD4 plus CD25-Pre-activated A


title: T cell; CBA/Ca strain CD4 plus CD25 plus Pre-activated C

source_name: T cell; CBA/Ca strain CD4 plus CD25 plus Pre-activated.


title: Root_24h_inoculated_rep3

city: Waurn Ponds

first: Jane

last: Allardyce

state: Victoria

address: Pigdons Road

country: Australia

institute: Deakin University

description: Z mays T24 inoc_3

hyb_protocol: Following QC checks, all samples were prepared for hybridisation to the maize Affymetrix GeneChip using a stain cocktail (Affymetrix GeneChip hybridisation, wash and stain kit, #900720). Total hybridisation volume of 300uL was prepared for each sample and 200uL was loaded onto each chip, each chip was then hybridised at 45°C for 16h in a hybridisation oven fixed with a rotating wheel at 60 rpm.

scan_protocol: Each GeneChip was washed and stained with streptavidin R-phycoerythrin (SAPE) using the prescribed fluidics script contained in the Affymetrix GeneChip Fluidics Station 450 (#00-0079), all chips were then scanned with the Affymetrix GeneChip Scanner 3000 7G. Scanner software then converted GeneChip signals into a .DAT file which was then used to generate .CEL files

data_processing: Raw data was processed using Partek® Genomics Suite™ software for gene expression data. All data was normalised using Robust Multi-Chip Average Software (RMA) as previously described (Irizarry et al. 2003). Differentially expressed genes were defined by a fold difference of >1.5 (log2) with a P value of <0.05

organism: Zea mays

source_name: Root, 24h, inoculated

label_protocol: A total of 7ug of purified RNA was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millenium Sciences, catalogue #900431) and labelling efficiency was confirmed by adding GeneChip eukaryotic poly-A RNA spikes to the reaction. The cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup Kit (Millenium Sciences #900371) and labelled by incorporating biotin into the resultant cRNA (Affymetrix IVT labelling kit, #900449).

growth_protocol: Z. mays seedlings were grown from seed for 10 days in a soil-less growth system as previously described (Gunning and Cahill 2008) and maintained in temperature controlled growth chambers under sodium lights (3 x 600 watt) with a 16h/8h photoperiod at 21°C at 200 µmol m-2 s-1.

extract_protocol: Total RNA was isolated and purified from all root tissue samples using the TRIzol® Plus RNA Purification System (Invitrogen, catalogue #12183-555) according to manufacturer's instructions for plant tissue, a minimum of 15ug of purified total RNA per sample was used for microarray analysis.

treatment_protocol: 10 day old seedlings were inoculated with 5 x 20 µL drops of P. cinnamomi spore suspension along the length of lateral roots (3 cm approx), control plants were mock inoculated with the equivalent volume of sdH2O.  All harvested root tissue within each treatment group, per time-point was pooled for all extractions, each technical replicate consisted of a total of 60 seedlings.

value: root

tag: infection

value: P. cinnamomi inoculation

tag: time

value: 24 hrs


title: WholeCell_Control_180min_rep1


title: WholeCell_Control_120min_rep3


title: WholeCell_Control_120min_rep4


title: T cell; CBA/Ca strain CD4 plus CD25 plus Pre-activated B


title: WholeCell_Control_180min_rep2


title: Root_6h_inoculated_rep3

description: Z mays T6 inoc_3

source_name: Root, 6h, inoculated

value: 6 hrs


title: T cell; CBA/Ca strain CD4 plus CD25 plus Pre-activated A


title: WholeCell_Control_120min_rep2


title: WholeCell_Control_120min_rep1


title: WholeCell_Control_60min_rep4


title: Root_6h_control_rep3

description: Z mays T6 con_3

source_name: Root, 6h, control

value: control


title: WholeCell_Control_60min_rep3


title: T cell; CBA/Ca strain CD4 plus CD25 plus Freshly Isolated A

source_name: T cell; CBA/Ca strain CD4 plus CD25 plus Freshly Isolated.


title: Root_24h_inoculated_rep2

description: Z mays T24 inoc_2


title: Root_6h_inoculated_rep2

description: Z mays T6 inoc_2


title: T cell; CBA/Ca strain CD4 plus CD25 plus Freshly Isolated B


title: Root_24h_control_rep3

description: Z mays T24 con_3

source_name: Root, 24h, control


title: T cell; CBA/Ca strain CD4 plus CD25 plus Freshly Isolated C


title: T cell; BALB/c strain CD4 plus CD25 plus Freshly Isolated C

source_name: T cell; BALB/c strain CD4 plus CD25 plus Freshly Isolated.

value: BALB/c


title: T cell; CBA/Ca strain CD4 plus CD25- Freshly Isolated A

source_name: T cell; CBA/Ca strain CD4 plus CD25- Freshly Isolated.


title: T cell; CBA/Ca strain CD4 plus CD25- Freshly Isolated B


title: T cell; CBA/Ca strain CD4 plus CD25- Freshly Isolated C


title: T cell; BALB/c strain CD4 plus CD25 plus Pre-activated A

source_name: T cell; BALB/c strain CD4 plus CD25 plus Pre-activated.


title: T cell; BALB/c strain CD4 plus CD25 plus Freshly Isolated B


title: Root_24h_control_rep2

description: Z mays T24 con_2


title: WholeCell_Control_60min_rep2


title: T cell; BALB/c strain CD4 plus CD25 plus Pre-activated C


title: T cell; BALB/c strain CD4 plus CD25 plus Freshly Isolated A


title: Kidney 0% : Spleen 100% 5

source_name: Kidney 0% : Spleen 100%

value: male

value: healthy


title: T cell; BALB/c strain CD4 plus CD25 plus Pre-activated B


title: WholeCell_Control_60min_rep1


title: Root_6h_control_rep2

description: Z mays T6 con_2


title: Root_24h_inoculated_rep1

description: Z mays T24 inoc_1


title: Root_6h_inoculated_rep1

description: Z mays T6 inoc_1


title: T cell; BALB/c strain CD4 plus CD25- Pre-activated B

source_name: T cell; BALB/c strain CD4 plus CD25- Pre-activated.


title: T cell; BALB/c strain CD4 plus CD25- Pre-activated C


title: WholeCell_HeatShock_45min_rep4

treatment_protocol: For heat shock, a 20 ml culture with ~4 × 106 cells per ml in a 100 ml Erlenmeyer flask was incubated at 42°C for 45 min in the light with shaking.


title: T cell; BALB/c strain CD4 plus CD25- Pre-activated A


title: T cell; BALB/c strain CD4 plus CD25- Freshly Isolated C

source_name: T cell; BALB/c strain CD4 plus CD25- Freshly Isolated.


title: Mutant A

source_name: olfactory neurons from b3GNT2 KO

value: unknown

tag: genotype

value: b3GNT2 KO


title: Wild Type C

source_name: olfactory neurons WT

value: wild type


title: WholeCell_HeatShock_45min_rep3

source_name: Whole cells


title: Mutant B


title: T cell; BALB/c strain CD4 plus CD25- Freshly Isolated.  A


title: WholeCell_Control_0min_rep1


title: Wild Type B


title: Mutant C


title: Wild Type A


title: T cell; BALB/c strain CD4 plus CD25- Freshly Isolated B


title: Root_6h_control_rep1

description: Z mays T6 con_1


title: WholeCell_HeatShock_45min_rep2


title: WholeCell_Control_45min_rep4


title: PV2: Neonatal Ventricle, replicate #2

source_name: Mouse Neonatal Ventricle

value: 3 days


title: normal placenta 8-3-2 and 2

city: hsinchu

first: wei-chung

last: cheng

address: adqwerqr ew

country: Taiwan

institute: NTHU

description: Placental specimens were obtained from the same region of placentas immediately after delivery. This study was approved by the Institutional Review Board of Chang Gung Memorial Hospital (IRB#96-0630B). The tissues were snap frozen in liquid nitrogen and stored at -80°C.

hyb_protocol: Two-step hybridizations were performed. During the first hybridization, cDNA products was pipetted onto the array. Then, the array was incubated in the hybridization chamber in a water bath at 65℃ for 16 to 20 hours for the probe/target hybridization. At the second hybridization, the 3DNA dendrimer was pipetted onto the array and the array was submerged in a 65℃ water bath for only 2 to 3 hours for capture primer – 3DNA dendrimer hybridization. After hybridization, array was washed with SSC and SDS mixed buffer suggested by manufacturer’s instruction of 3DNA array 50 kit.

scan_protocol: Microarrays were scanned by using GenePix 4100A (Axon, Foster City, CA) and images were taken at a resolution of 5μm. GenePix Pro 5.1 software was used to analyze image data.

data_processing: Spots were first selected by (1) excluding spots defined as flag or absent (2) keeping only channels with signal - background / SD of background greater than 2 (3) keeping spot diameter greater 75μm (4) eliminating spots with intensity CV greater than 100 in ether channel. The log ratio of the last spots were calculated and normalized by pin-wised LOWESS fit normalization.

source_name: normal placenta of sample 8-3-2

label_protocol: Each RNA sample was labeled by an indirect method using the 3DNA Array 50 Kit (Genisphere, USA). Briefly, 20 μg total RNA was used to perform reverse transcription reaction with SuperScript Ⅱ RNase H- reverse transcriptase and specific primers (Invitrogen life technologies, USA). Then all synthesized tagged cDNA targets were purified by Microcon YM-30 column (Millipore, USA).

extract_protocol: Total RNA was isolated by using Trizol reagent (Life Technologies, Rockville, MD).Total RNA was quantified by UV absorption at 260 nm, and RNA quality was examined by Agilent 2100 bioanalyzer (Agilent technologies, USA).

value: placenta

tag: physiological state

value: normal

tag: sample #

source_name: normal placenta of sample 2

tag: sample#


title: WholeCell_HeatShock_45min_rep1


title: WholeCell_Control_45min_rep3


title: PV3: Neonatal Ventricle, replicate #3


title: Root_24h_control_rep1

description: Z mays T24 con_1


title: AV3: Adult Ventricle, replicate #3

source_name: Mouse Adult Ventricle

value: 12 days


title: AV1: Adult Ventricle, replicate #1


title: PA2: Neonatal Atria, replicate #2

source_name: Mouse Neonatal Atria


title: WholeCell_Control_45min_rep1


title: PV1: Neonatal Ventricle, replicate #1


title: normal placenta 8-3-1 and 2

source_name: normal placenta of sample 8-3-1


title: PA3: Neonatal Atria, replicate #3:


title: normal placenta 8-2 and 8-3-1

source_name: normal placenta of sample 8-2


title: AA2: Adult Atria, replicate #2

source_name: Mouse Adult Atria


title: normal placenta 8-2 and 8-3-2


title: WholeCell_Control_45min_rep2


title: PA1: Neonatal Atria, replicate #1


title: normal placenta 9 and 8-3-2

source_name: normal placenta of sample 9


title: normal placenta 8-1 and 8-2

source_name: normal placenta of sample 8-1


title: AA3: Adult Atria, replicate #3


title: WholeCell_HeminFeeding_120min_rep3


title: AV2: Adult Ventricle, replicate #2


title: Mouse brain, striatum; Wild type, Post Symptomatic 16 weeks. Replicate 2


title: Mock control rep1 [genex]

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: HL-1 cells infected with adenovirus expressing control siRNA.

hyb_protocol: Affymetrix standard protocol was used.

scan_protocol: GeneChips were scanned using GeneArray Scanner 3000.

data_processing: The data were analyzed with Affymetrix Power Tools version 1.10 using Affymetrix default analysis settings of PLIER algorithm and quantile normalization method.

source_name: HL-1 cells

label_protocol: Affymetrix standard protocol was used.

growth_protocol: HL-1 cells were cultured as described by Claycomb, and split 1:3 every 3-4 days until full confluence.

extract_protocol: Trizol then Rneasy

treatment_protocol: HL-1 cells were infected with adenovirus expressing control siRNA or Gata4 and Mef2a-Gata4 and siRNA for 72 hrs before RNA extraction and Dnase I treatment followed by Mouse Gene expression ST 1.0 arrays.

tag: cell line

value: HL-1 cardiac muscle cell line

tag: protocol


title: Mouse brain, striatum; Wild type, Post Symptomatic 16 weeks. Replicate 3

tag: Sex


title: Mouse brain, striatum; Wild Type, Pre-Symtomatic 6 weeks. Replicate 2


title: Mouse brain, striatum; Wild Type, Pre-Symtomatic 6 weeks. Replicate 1


title: AA1: Adult Atria, replicate #1


title: normal placenta 8-3-1 and 1

tag: tissue

source_name: normal placenta of sample 1


title: normal placenta 8-1 and 8-3-1


title: Mouse brain, striatum; Wild Type, Pre-Symtomatic 6 weeks. Replicate 3


title: normal placenta 6 and 8-1

source_name: normal placenta of sample 6


title: Mouse brain, striatum; Wild type, Post Symptomatic 16 weeks. Replicate 1


title: normal placenta 7 and 8-2

source_name: normal placenta of sample 7


title: normal placenta 9 and 1


title: Mock control rep2 [genex]


title: Mock control rep3 [genex]


title: Gata4 kd rep3 [genex]

description: HL-1 cells infected with adenovirus expressing Gata4 siRNA.

value: Gata4 knockdown


title: Gata4 kd rep2 [genex]


title: Gata4 Mef2a kd rep1 [genex]

description: HL-1 cells infected with adenovirus expressing Gata4 & Mef2a siRNA.

value: Gata4 & Mef2a knockdown


title: normal placenta 7 and 9


title: normal placenta 5 and 8-1

source_name: normal placenta of sample 5


title: normal placenta 6 and 9


title: Gata4 Mef2a kd rep3 [genex]


title: Gata4 kd rep1 [genex]


title: Gata4 Mef2a kd rep2 [genex]


title: normal placenta 5 and 7


title: p53wildtype_spleen_amsacrine_rep1

city: Dunedin

first: Aaron

last: Jeffs

address: PO Box 56

country: New Zealand

institute: University of Otago

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalised by using the lumi R package with BRB ArrayTools

label_protocol: Biotinylated cRNA was prepared by using an Illumina TotalPrep RNA Amplification Kit according to the manufacturer’s instructions (Ambion)

growth_protocol: Pooled single-cell suspensions were prepared from spleens of four 5-6-week-old mice of the following genotypes: wild type; ∆122p53; and p53-/-.  Cells (2x10^6 cells/mL) were cultured in DMEM supplemented with 20% foetal calf serum, L-glutamine (2 mM), and antibiotics, and grown at 37C, 5% CO2.

extract_protocol: Total RNA was extracted by using Tri reagent according to the manufacturer's instructions

treatment_protocol: Cells were treated with 1µg/mL of amsacrine or carrier control (30% ethanol) for 5 hours at 37C, 5% CO2. For irradiation experiments, cells were left untreated or irradiated with a pulse of 4Gy of gamma-irradiation.

value: 5-6 weeks

tag: genotype/variation

value: Wild type

value: spleen


title: p53wildtype_spleen_control_rep1

description: replicate 1


title: Uns_Late-E

city: Oxford

first: Alison

middle: T

last: Merryweather-Clarke

address: John Radcliffe Hospital, Headley Way, Headington

country: United Kingdom

institute: NHSBT Oxford

description: RNA was pooled from 4 samples of unsorted cells from erythroblast cultures at the Late-E stage.

hyb_protocol: Biotinylated cRNA was hybridized to GeneChip Human Genome U133_Plus_2.0 arrays (Affymetrix) following the manufacturer’s recommendations. Briefly, hybridisation was for 16 hours at 45 degrees C, rotating at 60rpm.

scan_protocol: Genechips were scanned using an Affymetrix GeneChip scanner following washing on a Fluidics Station 450.

data_processing: Cell intensity calculation and scaling was performed using GeneChip Operating Software (GCOS) (Affymetrix) and data analysed by the Robust Multiarray Average (RMA) method of Irrizarry using the Bioconductor suite of packages in R (www.bioconductor.org).

source_name: Unsorted PBMC-derived cells present after culture in EPO for 12-15 days

label_protocol: For each of the four stages of erythroid precursors included in the study, three RNA pools were prepared from non-overlapping sets of four different RNA preparations mixed in equal proportions. One RNA pool of four RNA preparations from unsorted cells harvested at each of the four different stages of culture was also prepared for comparison. Biotinylated fragmented cRNA was synthesized from 100ng of pooled RNA using the 2-Cycle cDNA Synthesis and the 2-Cycle Target Labelling and Control Reagent kits (Affymetrix, Santa Clara, CA), and hybridized to GeneChip Human Genome U133_Plus_2.0 arrays (Affymetrix) following the manufacturer’s recommendations.

growth_protocol: Human primary differentiating erythroblasts derived from peripheral blood buffy coat (NHSBT, Bristol, UK) were obtained with informed consent in accordance with the declaration of Helsinki. Erythroblasts were cultured using a two-phase liquid culture system as previously described. In brief, PBMCs were obtained from peripheral blood buffy coat by Ficoll-Hypaque density-gradient centrifugation and seeded at 2.5 x 106 cells/ml in MEM with 10% FCS, 1 µg/ml cyclosporin A, and 10% conditioned medium from the 5637 bladder carcinoma cell line. The cells were cultured for 6–7 d (phase I), and the non-adherent cells were washed and re-seeded in fresh medium with 30% FCS, 1% deionized BSA, 1 U/ml of human recombinant erythropoietin (EPO), 10-5 M β-mercaptoethanol, 10-6 mol/l dexamethasone, 0.3 mg/ml holotransferrin (ICN Biochemicals), and 10 ng/ml of human stem cell factor (phase II). Maturation of erythroblasts was monitored by May Grünwald-Giemsa stained cytospin preparations using light microscopy. Cells were harvested following phase II culture in the presence of EPO for four, five-six, eight-eleven or thirteen-fifteen days to obtain populations of CFU-Es, Pro-Es, Int-Es, or Late-Es, respectively.

extract_protocol: Following confirmation of purity of the sorted erythroblast population by examining cell morphology on cytospins, total RNA was extracted using Trizol (Invitrogen, Paisley, UK) in accordance with the manufacturer’s instructions with an additional phenol-chloroform step. RNA integrity was evaluated using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Cells were stained and sorted using anti–CD36-PE (BD Biosciences; used for CFU-Es, Pro-Es and Int-Es), anti–CD71-FITC (DakoCytomation), anti–CD235a-APC (BD Biosciences; used for CFU-Es, Pro-Es and Int-Es), and anti–CD235a-RPE (DakoCytomation; used for Late-Es).

tag: stage

value: Late-E

tag: facs-sorted using cell surface markers cd36, cd71, cd235a?

value: No


title: p53null_spleen_irradiated_rep1

description: replicate 1

tag: age

value: p53 null


title: Uns_Int-E

description: RNA was pooled from 4 samples of unsorted cells from erythroblast cultures at the Int-E stage.

source_name: Unsorted PBMC-derived cells present after culture in EPO for 8-11 days

value: Int-E


title: Mouse brain, striatum; Huntington Disease, Pre-Symptomatic 6 weeks. Replicate 1

value: unknown

tag: strain

value: pre-symptomatic for Huntington's disease


title: Mouse brain, striatum; Huntington Disease, Pre-Symptomatic 6 weeks. Replicate 2


title: Mouse brain, striatum; Huntington Disease, Pre-Symptomatic 6 weeks. Replicate 3


title: normal placenta 3 and 6

source_name: normal placenta of sample 3


title: normal placenta 8-3-2 and 3

source_name: normal placenta of sample 8-3-2


title: normal placenta 4 and 7

source_name: normal placenta of sample 4


title: normal placenta 4 and 6


title: normal placenta 3 and 5


title: Mouse brain, striatum; Huntington Disease Post Symptomatic 16 weeks. Replicate 2

value: symptomatic for Huntington's disease


title: Mouse brain, striatum; Huntington Disease Post Symptomatic 16 weeks. Replicate 3


title: Uns_Pro-E

description: RNA was pooled from 4 samples of unsorted cells from erythroblast cultures at the Pro-E stage.

source_name: Unsorted PBMC-derived cells present after culture in EPO for 6 days

tag: cell type

value: Pro-E


title: normal placenta 1 and 3

value: placenta


title: p53null_spleen_control_rep2

description: replicate 2


title: WholeCell_Control_0min_rep2

source_name: Whole cells


title: Uns_CFU-E

description: RNA was pooled from 4 samples of unsorted cells from erythroblast cultures at the CFU-E stage.

source_name: Unsorted PBMC-derived cells present after culture in EPO for 4 days

value: CFU-E


title: Late-E_3

description: RNA was pooled from 4 samples of Late-E stage PBMC-derived sorted erythroblasts.

value: Yes


title: normal placenta 2 and 4

source_name: normal placenta of sample 2

value: normal


title: Mouse brain, striatum; Huntington Disease Post Symptomatic 16 weeks. Replicate 1

tag: disease state


title: Late-E_2

value: Late-E stage PBMC-derived sorted erythroblasts


title: Late-E_1


title: p53delta122_spleen_control_rep1

description: replicate 1

value: p53 delta 122


title: Int-E_3

description: RNA was pooled from 4 samples of Int-E stage PBMC-derived sorted erythroblasts.

source_name: Intermediate stage PBMC-derived sorted erythroblasts


title: p53null_spleen_control_rep1

description: replicate 1

value: 5-6 weeks


title: Int-E_1

value: Int-E stage PBMC-derived sorted erythroblasts


title: normal placenta 2 and 5


title: p53delta122_spleen_amsacrine_rep1

description: replicate 1

value: spleen


title: p53null_spleen_amsacrine_rep1

description: replicate 1


title: normal placenta 1 and 4


title: Pro-E_3

description: RNA was pooled from 4 samples of Pro-E stage PBMC-derived sorted erythroblasts.

source_name: Pro-erythroblast stage PBMC-derived sorted erythroblasts


title: Int-E_2


title: Yeast in small-scale lab fermentiation vial, day10, biological rep2

city: Stellenbosch

first: Debra

last: Rossouw

state: Western Cape

address: Cnr Neethling and Victoria rd

department: Institute for Wine Biotechnology

country: South Africa

institute: University of Stellenbosch

hyb_protocol: Following fragmentation, 5 ug of labelled fragmented amplified RNA was hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The GeneChips were scanned using the Affymetrix GeneChip® 3000 Scanner 7G. AGCC is used for image acquisition.

data_processing: The cell intensity data was analyzed in Affymetrix Expression Console using the RMA algorithm. The RMA workflow is quantile normalisation with general background correction.

organism: Saccharomyces cerevisiae Vin13

source_name: Yeast VIN13 from small-scale Chardonnay fermentation

label_protocol: Following second strand cDNA synthesis (starting material 100ng of total RNA), biotinylated cRNA was prepared in accordance with the Affymetrix 3' Expression protocol .  The expected profile of amplified RNA should be in the range of 250 -5500nt with most of the amplified RNA appearing in the 600-12--nt range. 7.5ug of amplified RNA is required for hybridisation to an array.

growth_protocol: Yeast were inoculated at an OD600 of 0.1 in Chardonnay wine must in microaerobic fermentation vials (80ml volume) and large commercial fermentation tanks (300L).  Fermentation was carried out at 20 degrees celsius.

extract_protocol: RNA was extracted as described using a modified hot-phenol method as described by Abbott et al (2007).

treatment_protocol: Cells were harvested by brief centrifugation and washed prior to extraction.

tag: fermentor scale

value: Small

tag: time point

tag: replicate


title: CFU-E_3

description: RNA was pooled from 4 samples of CFU-E stage PBMC-derived sorted erythroblasts.


title: Pro-E_2

value: Pro-E stage PBMC-derived sorted erythroblasts


title: Yeast in small-scale lab fermentiation vial, day10, biological rep3


title: Yeast in industrial fermentation tank, day10, biological rep1

source_name: Yeast VIN13 from commercial-scale Chardonnay fermentation

value: Large


title: Yeast in industrial fermentation tank, day10, biological rep3


title: Pro-E_1


title: Yeast in small-scale lab fermentiation vial, day10, biological rep1


title: CFU-E_1

source_name: CFU-E stage PBMC-derived sorted erythroblasts


title: Yeast in small-scale lab fermentiation vial, day5, biological rep1


title: CFU-E_2

value: CFU-E stage PBMC-derived sorted erythroblasts


title: Yeast in small-scale lab fermentiation vial, day5, biological rep3


title: Yeast in small-scale lab fermentiation vial, day5, biological rep2


title: Yeast in industrial fermentation tank, day10, biological rep2


title: Yeast in industrial fermentation tank, day5, biological rep3


title: PBS 4

city: Evanston

first: Jingjing

last: Kipp

state: IL

address: 2205 Tech Dr.

institute: Northwestern University

description: Biological replicate 4 of 4, granulosa cells in primary cultures were collected from a pool of 14-20 ovaries from days 21-23 old immature mice

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 1.2.0). It was vst transformed and quantile normalized.

source_name: Total RNA from primary cultured mouse granulosa cells

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: agent

value: PBS 4

value: granulosa cells in primary cultures


title: Activin 4

value: Activin 4


title: Activin+Follistatin 4

value: Activin+Follistatin 4


title: Yeast in industrial fermentation tank, day5, biological rep1


title: Control Anopheles gambiae Sua5B cells, replicate 2

city: Baltimore

first: Grant

last: Hughes

state: MD

address: 615 N Wolfe St

department: Bloomberg School of Public Health

institute: Johns Hopkins

description: Control gene expression data

hyb_protocol: Fragmented, biotinylated cRNA was hybridized to Plasmodium/Anoptheles GeneChips for 16hours at 45oC and 60rpm.  Affymetrix recommended signal amplifcation protocol for washing/staining of Eukaryotic targets was performed in a FS450 automated fluidics station.

scan_protocol: GeneChips were scanned in an Affymetrix GCS3000 scanner with autoloader.

data_processing: The data were analyzed with Partek Genomics Suite software, version 6.4. GC-RMA algorithm defaults were used for background correction (GC-RMA), normalization (Quantile), and summarization (median polish) of probesets

organism: Anopheles gambiae

source_name: Anopheles gambiae Sua5B cells

label_protocol: 5 ug total RNA was processed according to the Affymetrix recommended protocol for Eukaryotic samples, Affymetrix technical manual, revison 5.

growth_protocol: Anopheles gambiae Sua5B cells were cultured in Scnhieder's medium at room tempreture.

extract_protocol: Homogenization and lysis of cells with Lysing Matrix D (Qbiogene) in Trizol LS (Invitrogen) with FastPrep120 (Qbiogene) instrument. Purification with Qiagen RNeasy Mini kit. All performed according to the manufacturers' instructions.

treatment_protocol: Either wAlbB or wRi were transferred into Sua5B cells then passaged for over 30 generations before microarray analysis.

tag: infection

value: No infection


title: Yeast in small-scale lab fermentiation vial, day2, biological rep3


title: Control Anopheles gambiae Sua5B cells, replicate 1

description: Control gene expression data


title: Activin+Follistatin 3

description: Biological replicate 3 of 4, granulosa cells in primary cultures were collected from a pool of 14-20 ovaries from days 21-23 old immature mice

value: Activin+Follistatin 3


title: Activin 3

value: Activin 3


title: Activin+Follistatin 2

description: Biological replicate 2 of 4, granulosa cells in primary cultures were collected from a pool of 14-20 ovaries from days 21-23 old immature mice

value: Activin+Follistatin 2


title: Yeast in industrial fermentation tank, day5, biological rep2


title: Yeast in small-scale lab fermentiation vial, day2, biological rep2


title: 32 ug/ml ODN 1826 TLR9

city: Bethesda

first: O M Zack

last: Howard

address: 6701 Rockledge Dr.

department: DBIB

institute: NIH/CSR

description: qPCR using SABiosciences

hyb_protocol: As directed by SA Biosciences

scan_protocol: ABI Prism 7900HT Detector Software Version 2.1

data_processing: RT² Profiler PCR Array Data Analysis software

label: Sybr Green/ROX

source_name: 32 ug/ml ODN 1826 (InvivoGen) TLR9

label_protocol: RNA was reverse-transcribed into cDNA using RT2first strand kit (SA Biosciences)

growth_protocol: DRG from 13 day old NIH Swiss embryos were harvested, disrupted with trypsin and plated onto 4 well culture slides precoated with collagen type1 and poly-L-lysineneurobasal medium supplemented with 10% heat-inactivated horse serum (nuclease containing), 2% B-27 supplement, 3μg/ml glucose, 0.5 μg/ml mitotic inhibitor and 100 ng/ml nerve growth factor (NGF) for 4 days

extract_protocol: RT² qPCR-Grade™ RNA isolation kit (SA Biosciences) as directed

treatment_protocol: On day 5 -  ODN 1826 32 μg/ml, (InvivoGen) was added to the cultures for 16 hours

tag: genetic background

value: NIH Swiss

tag: treatment

value: 32 ug/ml ODN 1826 (InvivoGen)

value: 13 d embryo

value: dorsal root ganglion neurons


title: 3 ug/ml gardiquimod TLR7

description: qPCR using SABiosciences

source_name: 3 ug/ml gardiquimod TLR7

treatment_protocol: On day 5 -  3 ug/ml gardiquimod (InvivoGen) was added to the cultures for 16 hours

value: 3 ug/ml gardiquimod (InvivoGen)


title: Yeast in small-scale lab fermentiation vial, day2, biological rep1

value: Small


title: untreated control

description: qPCR using SABiosciences

source_name: untreated control

value: untreated control


title: Activin 2

value: Activin 2


title: Sua5B cells infected with Wolbachia strain wRi from Drosophila simulans, replicate 2

description: wRI strain Wolbachia infection gene expression data


title: Sua5B cells infected with Wolbachia strain wRi from Drosophila simulans, replicate 3


title: 25 ug/ml CpG TLR3

description: qPCR using SABiosciences

source_name: 25 ug/ml CpG TLR3

treatment_protocol: On day 5 25 ug/ml CpG (InvivoGen) was added to the cultures for 16 hours

value: 25 ug CpG ODN (InvivoGen)


title: PBS 2

value: PBS 2


title: Control Anopheles gambiae Sua5B cells, replicate 3

description: Control gene expression data


title: Sua5B cells infected with Wolbachia strain wRi from Drosophila simulans, replicate 1


title: Activin 1

description: Biological replicate 1 of 4, granulosa cells in primary cultures were collected from a pool of 14-20 ovaries from days 21-23 old immature mice

value: Activin 1

value: granulosa cells in primary cultures


title: Activin+Follistatin 1

value: Activin+Follistatin 1


title: PBS 1

value: PBS 1


title: Yeast in industrial fermentation tank, day2, biological rep2

value: Large


title: PBS 3

value: PBS 3


title: Yeast in industrial fermentation tank, day2, biological rep1


title: Sua5B cells infected with Wolbachia strain wAlbB from Aedes albopictus AS23 cells, replicate 2

description: wAlbB strain Wolbachia infection gene expression data


title: Yeast in industrial fermentation tank, day2, biological rep3


title: Sua5B cells infected with Wolbachia strain wAlbB from Aedes albopictus AS23 cells, replicate 3


title: tumor tissue from gastric cancer patient 76

status: Public on Mar 01 2011

city: Athens

first: Juan

last: Cui

address: 120 Green Street

department: Biochemistry and Molecular Biology

institute: University of Georgia

hyb_protocol: The labeled samples were mixed with hybridization cocktail and hybridized to the microarray at 45°C, 60 rpm, and incubated for 17 h. After hybridization, the array was washed and stained on the GeneChip® Fluidics Station 450, using the appropriate fluidics script.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
The raw probe intensities was normalized using the quartile normalization approach, and the PLIER method. was utilized to summarize the probe signal to both the exon- and gene-level expressions
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.mps

source_name: gastric cancer tissue

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Samples dissected from 80 gastric cancer patients

extract_protocol: All samples were snap-frozen and stored in liquid nitrogen within 20 min after resection. A total of 15μg RNA was extracted from each tissue sample using Trizol (Invitrogen) followed by purification using the RNeasy Mini kit (QIAGEN) according to the manufacture’s recommendation. Ratios of A260/A280 >1.9 and 28S/18S rRNA of 2 were used, ensuring that the RNA samples were highly purified and not degraded.

tag: gender

value: F

tag: Stage

value: II

tag: grade

value: gastric cancer tissue


title: tumor tissue from gastric cancer patient 77

value: IV

tag: tissue


title: tumor tissue from gastric cancer patient 75

value: M

value: IIIB


title: tumor tissue from gastric cancer patient 78

value: III


title: tumor tissue from gastric cancer patient 68


title: control from gastric cancer patient 78

source_name: normal tissue

value: normal gastric tissue


title: tumor tissue from gastric cancer patient 69

value: unknown


title: control from gastric cancer patient 79


title: control from gastric cancer patient 80


title: tumor tissue from gastric cancer patient 79


title: control from gastric cancer patient 69


title: tumor tissue from gastric cancer patient 72


title: Sua5B cells infected with Wolbachia strain wAlbB from Aedes albopictus AS23 cells, replicate 1


title: tumor tissue from gastric cancer patient 71


title: tumor tissue from gastric cancer patient 73


title: tumor tissue from gastric cancer patient 74


title: control from gastric cancer patient 74


title: control from gastric cancer patient 71


title: control from gastric cancer patient 77


title: tumor tissue from gastric cancer patient 67

value: IIIA


title: tumor tissue from gastric cancer patient 80


title: tumor tissue from gastric cancer patient 70


title: control from gastric cancer patient 70


title: control from gastric cancer patient 75


title: control from gastric cancer patient 76


title: control from gastric cancer patient 72


title: control from gastric cancer patient 73


title: control from gastric cancer patient 67


title: control from gastric cancer patient 66


title: control from gastric cancer patient 68


title: tumor tissue from gastric cancer patient 65


title: control from gastric cancer patient 60


title: control from gastric cancer patient 62


title: control from gastric cancer patient 63


title: tumor tissue from gastric cancer patient 62


title: tumor tissue from gastric cancer patient 58


title: tumor tissue from gastric cancer patient 63


title: control from gastric cancer patient 59


title: tumor tissue from gastric cancer patient 59


title: tumor tissue from gastric cancer patient 60


title: tumor tissue from gastric cancer patient 64


title: control from gastric cancer patient 58


title: tumor tissue from gastric cancer patient 53


title: control from gastric cancer patient 61


title: tumor tissue from gastric cancer patient 55


title: control from gastric cancer patient 57


title: tumor tissue from gastric cancer patient 57


title: tumor tissue from gastric cancer patient 54


title: control from gastric cancer patient 56


title: tumor tissue from gastric cancer patient 61


title: control from gastric cancer patient 64


title: tumor tissue from gastric cancer patient 56


title: control from gastric cancer patient 53


title: control from gastric cancer patient 65


title: tumor tissue from gastric cancer patient 52


title: control from gastric cancer patient 52


title: control from gastric cancer patient 54


title: tumor tissue from gastric cancer patient 51


title: tumor tissue from gastric cancer patient 50


title: tumor tissue from gastric cancer patient 66


title: control from gastric cancer patient 45


title: control from gastric cancer patient 41

value: IB


title: control from gastric cancer patient 48


title: 6-12_mm_disc_48hpi_rep3

city: Cape Town

first: Joseph

middle: Mary Kusasira

last: Mulema

address: Private Bag, Rondebosch

department: Molecular and Cell Biology

institute: University of Cape Town

hyb_protocol: Microarray slides were prepared based on Manufacturers instructions (Galbraith Laboratory, Arizona, USA) Labeled probes were concetrated, quantified and mixed in equal concentrations of labeled cDNA. Hybridization solution ( 20 μL of 20X SSC, 12 μL of 10% (v/v) BSA, 8 μL of SDS) was added and the volume made to 200 μL with Milli-Q water. The labeled probe was denatured by placing in boiling water for 2 min and transferred immediately to ice. The microarray slide was placed on a 65 oC heating block (label-side-up); the labeled probe was applied and covered with a coverslip avoiding trapping any air bubbles. The slide was incubated in a sealed chamber in a 55 oC water bath for 8-12 hrs. Slides were washed in 2X SSC, 0.5% (v/v) SDS for 5 min at 55 oC followed by 0.5X SSC for 5 min and 0.05X SSC for 5 min at room temperature.

scan_protocol: Slided were scanned on a GenePix scanner 4200A (Axon Instruments, Union City, CA). Images were analyzed with Genepix (Version 5.1) (Axon Instruments, Union City, CA) to generate fluorescent and background intensity values for each spot in both the Cy3 (green) and Cy5 (red) channels.

data_processing:
Print-tip LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.
Following normalization, IDs replicated within each slide were merged based on average

organism: Arabidopsis thaliana

source_name: 6-12-mm B. cinera-infected arabidopsis leaf disc harvested after 48hr

label_protocol:
25 µg of total RNA were reversed transcribed at 46°C overnight for in the presence of 200 U SuperScript II RTase (Invitrogen), 10 mM aminoallyl-dUTP, 15 mM dTTP and 25 mM each of dATP, dCTP, dGTP.
Synthesized cDNA was prurified using the RNeasy mini columns (Qiagen, Valencia, CA) based on manufacturer’s instructions and its concentration determined with a NanoDrop.
Purified cDNA was dried under vacuum and resuspended in 0.1 M NaHCO3 and labeled with 5 µL of cyanine 3 (Cy3) and cyanine 5 (Cy5) (Amersham Pharmacia, UK) for 1 hr in the dark mixing every 15 min.
cDNA from control and infected disks was labled with Cy3 and Cy5 in the first two replicates respectively while cDNA for the last replicate was labeled with Cy5 (control) and Cy3 (infected) (dye-swap)

growth_protocol: Arabidopsis thalaina plants (Col-0 ecotype) were grown in a mixture of soil composed of peat plugs and vermiculite (1:1 ratio) in a controlled environment room at 22°C under fluorescent light (80-100 μmol photon/sec/m2) with a 16 hr light and 8 hr dark cycle.

extract_protocol: Total RNA extracted from control and test leaf disks for the two distances (0-6 mm and 6-12 mm) using Phenol-Lithium chloride method

treatment_protocol:
Four-week Arabidopsis thaliana leaves were detached and inoculated in the middle with one 10 ul Botrytis cinerea (Pepper isolate) spore suspension adjusted to a concentration of 500,000 spores/ml prepared in half strength commercial grape juice.
Control leaves were inoculated with half-stregnth commercial grape juice with no spores.
Leaf discs were harvested using a 6-mm cock borer from the edge of the lesion (0-6 mm (close)) and edge of the first disk (6-12 mm (away))

tag: ecotype

value: leaves

source_name: 6-12-mm contol arabidopsis leaf disc harvested after 48hr


title: control from gastric cancer patient 46


title: tumor tissue from gastric cancer patient 42


title: 6-12_mm_disc_48hpi_rep2


title: 6-12_mm_disc_48hpi_rep1


title: control from gastric cancer patient 44


title: 0-6_mm_disc_48hpi_rep3

source_name: 0-6-mm B. cinera-infected arabidopsis leaf disc harvested after 48hr

source_name: 0-6-mm contol arabidopsis leaf disc harvested after 48hr


title: tumor tissue from gastric cancer patient 43


title: control from gastric cancer patient 47


title: control from gastric cancer patient 42


title: control from gastric cancer patient 43


title: control from gastric cancer patient 40


title: tumor tissue from gastric cancer patient 48


title: control from gastric cancer patient 50


title: tumor tissue from gastric cancer patient 45


title: control from gastric cancer patient 49


title: tumor tissue from gastric cancer patient 44


title: control from gastric cancer patient 51


title: tumor tissue from gastric cancer patient 49


title: tumor tissue from gastric cancer patient 47


title: tumor tissue from gastric cancer patient 40


title: control from gastric cancer patient 55


title: tumor tissue from gastric cancer patient 41


title: 0-6_mm_disc_48hpi_rep1


title: 0-6_mm_disc_48hpi_rep2


title: LCL14-6_rep1

city: Philadelphia

first: Minal

last: Caliskan

state: PA

address: 415 Curie Blvd., Room 540

department: Genetics

institute: University of Pennsylvania

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with lumi package in R.

label: Biotin

source_name: Lymphoblastoid cell line_Individual 6-6

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

extract_protocol: QIAGEN Rnaeasy Plus Mini Kit.

value: EBV-transformed lymphoblastoid cell line

value: male

tag: individual


title: LCL10-8_rep2

source_name: Lymphoblastoid cell line_Individual 5-6


title: T-2_rep1

source_name: T cell_Individual 1

value: T cell


title: LCL9-4_rep1

source_name: Lymphoblastoid cell line_Individual 4-3

value: female


title: LCL10-5_rep2

source_name: Lymphoblastoid cell line_Individual 5-4


title: T-9_rep2

source_name: T cell_Individual 4


title: LCL5-3_rep2

source_name: Lymphoblastoid cell line_Individual 2-3


title: B-10_rep1

source_name: B cell_Individual 5

value: B cell


title: T-6_rep1

source_name: T cell_Individual 3


title: LCL9-3_rep1

source_name: Lymphoblastoid cell line_Individual 4-2


title: LCL10-4_rep1

source_name: Lymphoblastoid cell line_Individual 5-3


title: LCL9-8_rep2

source_name: Lymphoblastoid cell line_Individual 4-6


title: LCL6-3_rep1

source_name: Lymphoblastoid cell line_Individual 3-2


title: LCL2-2_rep1

source_name: Lymphoblastoid cell line_Individual 1-1


title: LCL14-2_rep2

source_name: Lymphoblastoid cell line_Individual 6-2


title: LCL14-4_rep1

source_name: Lymphoblastoid cell line_Individual 6-4


title: LCL6-6_rep2

source_name: Lymphoblastoid cell line_Individual 3-5


title: LCL10-2_rep1

source_name: Lymphoblastoid cell line_Individual 5-2


title: LCL6-4_rep2

source_name: Lymphoblastoid cell line_Individual 3-3


title: LCL9-3_rep2


title: LCL5-4_rep2

source_name: Lymphoblastoid cell line_Individual 2-4


title: LCL2-6_rep2

source_name: Lymphoblastoid cell line_Individual 1-5


title: LCL2-3_rep2

source_name: Lymphoblastoid cell line_Individual 1-2


title: LCL6-1_rep1

source_name: Lymphoblastoid cell line_Individual 3-1


title: LCL6-1_rep2


title: B-5_rep1

source_name: B cell_Individual 2


title: LCL5-4_rep1


title: LCL5-5_rep1

source_name: Lymphoblastoid cell line_Individual 2-5


title: LCL9-7_rep1

source_name: Lymphoblastoid cell line_Individual 4-5


title: LCL14-3_rep1

source_name: Lymphoblastoid cell line_Individual 6-3


title: T-10_rep2

source_name: T cell_Individual 5


title: T-2_rep2

source_name: T cell_Individual 1


title: LCL14-5_rep1

source_name: Lymphoblastoid cell line_Individual 6-5


title: LCL10-5_rep1

source_name: Lymphoblastoid cell line_Individual 5-4


title: LCL9-1_rep2

source_name: Lymphoblastoid cell line_Individual 4-1


title: B-2_rep1

source_name: B cell_Individual 1


title: B-14_rep2

source_name: B cell_Individual 6


title: LCL2-4_rep2

source_name: Lymphoblastoid cell line_Individual 1-3


title: LCL6-5_rep2

source_name: Lymphoblastoid cell line_Individual 3-4


title: LCL14-1_rep2

source_name: Lymphoblastoid cell line_Individual 6-1


title: LCL10-1_rep1

source_name: Lymphoblastoid cell line_Individual 5-1


title: LCL6-4_rep1

source_name: Lymphoblastoid cell line_Individual 3-3


title: LCL5-6_rep2

source_name: Lymphoblastoid cell line_Individual 2-6


title: T-6_rep2

source_name: T cell_Individual 3


title: LCL14-1_rep1


title: T-5_rep1

source_name: T cell_Individual 2


title: LCL5-3_rep1

source_name: Lymphoblastoid cell line_Individual 2-3


title: B-10_rep2

source_name: B cell_Individual 5


title: LCL2-8_rep2

source_name: Lymphoblastoid cell line_Individual 1-6


title: LCL9-4_rep2

source_name: Lymphoblastoid cell line_Individual 4-3


title: LCL2-4_rep1


title: LCL10-4_rep2

source_name: Lymphoblastoid cell line_Individual 5-3


title: LCL10-2_rep2

source_name: Lymphoblastoid cell line_Individual 5-2


title: tumor tissue from gastric cancer patient 46

source_name: gastric cancer tissue

tag: age


title: B-2_rep2

source_name: B cell_Individual 1


title: LCL2-8_rep1


title: LCL2-2_rep2

source_name: Lymphoblastoid cell line_Individual 1-1


title: B-9_rep1

source_name: B cell_Individual 4


title: LCL9-6_rep1

source_name: Lymphoblastoid cell line_Individual 4-4


title: LCL10-7_rep1

source_name: Lymphoblastoid cell line_Individual 5-5


title: LCL14-2_rep1

source_name: Lymphoblastoid cell line_Individual 6-2


title: LCL6-6_rep1

source_name: Lymphoblastoid cell line_Individual 3-5


title: LCL2-5_rep2

source_name: Lymphoblastoid cell line_Individual 1-4


title: LCL6-3_rep2

source_name: Lymphoblastoid cell line_Individual 3-2


title: B-9_rep2


title: LCL14-5_rep2

source_name: Lymphoblastoid cell line_Individual 6-5


title: T-14_rep2

source_name: T cell_Individual 6


title: LCL14-3_rep2

source_name: Lymphoblastoid cell line_Individual 6-3


title: LCL2-5_rep1


title: LCL5-2_rep2

source_name: Lymphoblastoid cell line_Individual 2-2


title: LCL9-6_rep2


title: B-5_rep2

source_name: B cell_Individual 2


title: LCL6-5_rep1

source_name: Lymphoblastoid cell line_Individual 3-4


title: LCL10-8_rep1

source_name: Lymphoblastoid cell line_Individual 5-6


title: T-9_rep1

source_name: T cell_Individual 4


title: LCL5-1_rep1

source_name: Lymphoblastoid cell line_Individual 2-1


title: T-14_rep1


title: LCL2-6_rep1

source_name: Lymphoblastoid cell line_Individual 1-5


title: LCL5-1_rep2


title: LCL10-7_rep2


title: LCL9-8_rep1

source_name: Lymphoblastoid cell line_Individual 4-6


title: B-6_rep1

source_name: B cell_Individual 3


title: B-14_rep1

source_name: B cell_Individual 6


title: LCL14-4_rep2

source_name: Lymphoblastoid cell line_Individual 6-4


title: B-6_rep2


title: LCL6-7_rep1

source_name: Lymphoblastoid cell line_Individual 3-6


title: LCL14-6_rep2

source_name: Lymphoblastoid cell line_Individual 6-6


title: LCL6-7_rep2


title: LCL5-6_rep1

source_name: Lymphoblastoid cell line_Individual 2-6


title: LCL2-3_rep1

source_name: Lymphoblastoid cell line_Individual 1-2


title: Myoblast TSA treated

first: Roy

middle: M

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description: Mb TSA

data_processing: The data were normalised using quantile normalisation in GeneSpringGX11

source_name: HSMM Cells

label_protocol: Biotinylated cRNA were prepared with the Ambion Retic Lysate IVT™ kit

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: myoblast

value: TSA

tag: sample type

value: primary cell line


title: Myotubes TSA treated

description: Mt TSA

tag: cell type

value: myotube


title: Myoblast Ctr

description: Mb Ctr

value: control


title: Myotubes Ctr

description: Mt Ctr


title: T-10_rep1

source_name: T cell_Individual 5


title: In vitro exp 1 LNCaP 50µM ABR-215050 24h

city: Lund

first: Johan

last: Vallon-Christersson

address: Lund University

department: Department of Oncology, Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: Prior to hybridization, arrays were UV-cross-linked at 500 mJ/cm2 and pretreated using the Universal Microarray Hybridization Kit (Corning) according to manufacturers' instructions. Slides were hybridized using Corning Pronto Plus system 6 (Corning) on a MAUI®Hybridization System.

scan_protocol: Arrays were washed using Universal Microarray Hybridization Kit (Corning) according to manufacturers' instructions and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for treated sample were stored as channel 1 (ch1) whereas quantified intensities for control sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots that were flagged during image-analysis or had a background corrected intensity value >64999 signal units were removed and regarded as missing values. Spots with a background corrected intensity value <1 signal units were set to value 1. Spots from dye-swap hybridization were merged using geometric mean of ratios requiring presence in both replicates. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Normalization was performed by applying Lowess on M values stratified into 8 separate groups defined spatially by pin-tip (8 neighboring pin-tips per group).

source_name: Experimental samples after 24h treatment.

label_protocol: Fluorescently labeled cDNA targets for hybridization were prepared according to manufacturers' instructions using the Corning Pronto Plus system 6 (Corning).

growth_protocol: LNCaP cells were seeded at a cell density of 1-106 cells per 5 ml culture medium (RPMI-10% FCS) 25 ml cell culture flasks the day before treatment started.

extract_protocol: The total RNA was isolated by extracting the Trizol® (Invitrogen) samples with chloroform followed by separation and purification using a modified protocol for the RNeasy RNA extraction Kit (Qiagen). 1 µl RNAse inhibitor mix was added per 50 µl total RNA before treatment with DNAse for 20 min (DNA-free™; Ambion, Austin TX). The RNA concentration and purity was quality controlled by analysis with a Bioanalyser.

treatment_protocol: Cell cultures were exposed to ± 50µM ABR-215050 for 24h at 37°C. After 24h the cell culture medium was removed and the adherent cells were washed with 10 ml cold PBS before 1 ml Trizol® (Invitrogen) was added. After homogenization the Trizol  was transferred into 2 ml Eppendorf tubes and frozen at  -70°C.

tag: cell line

value: LNCaP

source_name: Control samples no treatment.


title: In vitro exp 2 LNCaP 50µM ABR-215050 24h


title: LCL5-5_rep2

source_name: Lymphoblastoid cell line_Individual 2-5


title: T-5_rep2

source_name: T cell_Individual 2


title: control from gastric cancer patient 39

source_name: normal tissue

value: M

value: III


title: tumor tissue from gastric cancer patient 37

source_name: gastric cancer tissue

value: gastric cancer tissue


title: tumor tissue from gastric cancer patient 39


title: LCL10-1_rep2

source_name: Lymphoblastoid cell line_Individual 5-1


title: LCL5-2_rep1

source_name: Lymphoblastoid cell line_Individual 2-2


title: control from gastric cancer patient 37

value: normal gastric tissue


title: LCL9-1_rep1

source_name: Lymphoblastoid cell line_Individual 4-1


title: LCL9-7_rep2

source_name: Lymphoblastoid cell line_Individual 4-5


title: control from gastric cancer patient 38


title: In vitro exp 4 LNCaP 50µM ABR-215050 24h


title: In vitro exp 3 LNCaP 50µM ABR-215050 24h


title: tumor tissue from gastric cancer patient 36

value: IB


title: control from gastric cancer patient 34

value: IIIA

value: unknown


title: tumor tissue from gastric cancer patient 34


title: control from gastric cancer patient 33

value: F


title: tumor tissue from gastric cancer patient 33


title: control from gastric cancer patient 30


title: control from gastric cancer patient 36


title: tumor tissue from gastric cancer patient 32

value: II


title: control from gastric cancer patient 29


title: control from gastric cancer patient 31


title: tumor tissue from gastric cancer patient 29


title: control from gastric cancer patient 35

value: IV


title: tumor tissue from gastric cancer patient 31


title: tumor tissue from gastric cancer patient 30


title: control from gastric cancer patient 32


title: control from gastric cancer patient 24


title: control from gastric cancer patient 27


title: tumor tissue from gastric cancer patient 35


title: tumor tissue from gastric cancer patient 24


title: tumor tissue from gastric cancer patient 26


title: control from gastric cancer patient 26


title: tumor tissue from gastric cancer patient 28


title: control from gastric cancer patient 25


title: tumor tissue from gastric cancer patient 25


title: tumor tissue from gastric cancer patient 27


title: control from gastric cancer patient 23


title: control from gastric cancer patient 18


title: control from gastric cancer patient 22


title: tumor tissue from gastric cancer patient 22


title: control from gastric cancer patient 20


title: tumor tissue from gastric cancer patient 21


title: tumor tissue from gastric cancer patient 23


title: control from gastric cancer patient 21


title: control from gastric cancer patient 19


title: control from gastric cancer patient 28


title: tumor tissue from gastric cancer patient 20


title: tumor tissue from gastric cancer patient 38


title: tumor tissue from gastric cancer patient 19


title: tumor tissue from gastric cancer patient 17


title: control from gastric cancer patient 17


title: control from gastric cancer patient 13

value: IIIB


title: tumor tissue from gastric cancer patient 16


title: control from gastric cancer patient 12


title: tumor tissue from gastric cancer patient 15


title: control from gastric cancer patient 14


title: tumor tissue from gastric cancer patient 11


title: control from gastric cancer patient 11


title: control from gastric cancer patient 9


title: control from gastric cancer patient 15


title: tumor tissue from gastric cancer patient 12


title: tumor tissue from gastric cancer patient 13


title: tumor tissue from gastric cancer patient 10


title: control from gastric cancer patient 8


title: tumor tissue from gastric cancer patient 18


title: control from gastric cancer patient 10


title: tumor tissue from gastric cancer patient 14


title: tumor tissue from gastric cancer patient 9


title: tumor tissue from gastric cancer patient 7


title: tumor tissue from gastric cancer patient 8


title: tumor tissue from gastric cancer patient 4


title: tumor tissue from gastric cancer patient 6


title: control from gastric cancer patient 3


title: control from gastric cancer patient 16


title: control from gastric cancer patient 5


title: control from gastric cancer patient 6


title: control from gastric cancer patient 2


title: tumor tissue from gastric cancer patient 1


title: tumor tissue from gastric cancer patient 2


title: tumor tissue from gastric cancer patient 3


title: tumor tissue from gastric cancer patient 5


title: control from gastric cancer patient 1


title: control from gastric cancer patient 4


title: control from gastric cancer patient 7


title: T186 [aCGH]

type: genomic

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

hyb_protocol: see Agilent CGH 244k standard protocols

scan_protocol: see Agilent CGH 244k standard protocols

data_processing: Agilent Feature Extraction Software (v 10.7.1.1) was used for background subtraction and LOWESS normalization. Segmentation value obtain by CBS (DNAcopy, R package, v 1.16.0) of the normalized log2 ratio Cy5/Cy3.

source_name: Human primary breast tumor sample T186

label_protocol: Standard protocol with BioPrime« Array CGH Genomic Labeling System (ref:18095-011)

extract_protocol: Guanidinium isothiocyanate and centrifugation over a cesium chloride gradient.

value: positive

source_name: A pool of 13 normal male DNA.

tag: reference

value: A pool of 13 normal male DNA


title: T188 [aCGH]

source_name: Human primary breast tumor sample T188

value: negative


title: T187 [aCGH]

source_name: Human primary breast tumor sample T187


title: T189 [aCGH]

source_name: Human primary breast tumor sample T189


title: T178 [aCGH]

source_name: Human primary breast tumor sample T178


title: T184 [aCGH]

source_name: Human primary breast tumor sample T184


title: T168 [aCGH]

source_name: Human primary breast tumor sample T168


title: T182 [aCGH]

source_name: Human primary breast tumor sample T182


title: T193 [aCGH]

source_name: Human primary breast tumor sample T193


title: T195 [aCGH]

source_name: Human primary breast tumor sample T195


title: T172 [aCGH]

source_name: Human primary breast tumor sample T172


title: T191 [aCGH]

source_name: Human primary breast tumor sample T191


title: T196 [aCGH]

source_name: Human primary breast tumor sample T196


title: T171 [aCGH]

source_name: Human primary breast tumor sample T171


title: T197 [aCGH]

source_name: Human primary breast tumor sample T197


title: T173 [aCGH]

source_name: Human primary breast tumor sample T173


title: T164 [aCGH]

source_name: Human primary breast tumor sample T164


title: T181 [aCGH]

source_name: Human primary breast tumor sample T181

source_name: A pool of 13 normal male DNA.


title: T167 [aCGH]

source_name: Human primary breast tumor sample T167


title: T176 [aCGH]

source_name: Human primary breast tumor sample T176


title: T170 [aCGH]

source_name: Human primary breast tumor sample T170


title: T165 [aCGH]

source_name: Human primary breast tumor sample T165


title: T166 [aCGH]

source_name: Human primary breast tumor sample T166


title: T174 [aCGH]

source_name: Human primary breast tumor sample T174


title: T163 [aCGH]

source_name: Human primary breast tumor sample T163


title: T179 [aCGH]

source_name: Human primary breast tumor sample T179


title: T175 [aCGH]

source_name: Human primary breast tumor sample T175


title: T192 [aCGH]

source_name: Human primary breast tumor sample T192


title: T162 [aCGH]

source_name: Human primary breast tumor sample T162


title: T160 [aCGH]

source_name: Human primary breast tumor sample T160


title: T177 [aCGH]

source_name: Human primary breast tumor sample T177


title: T158 [aCGH]

source_name: Human primary breast tumor sample T158


title: T156 [aCGH]

source_name: Human primary breast tumor sample T156


title: T151 [aCGH]

source_name: Human primary breast tumor sample T151


title: T161 [aCGH]

source_name: Human primary breast tumor sample T161

source_name: A pool of 13 normal male DNA.


title: T155 [aCGH]

source_name: Human primary breast tumor sample T155


title: T154 [aCGH]

source_name: Human primary breast tumor sample T154


title: T159 [aCGH]

source_name: Human primary breast tumor sample T159


title: T153 [aCGH]

source_name: Human primary breast tumor sample T153


title: T143 [aCGH]

source_name: Human primary breast tumor sample T143


title: T150 [aCGH]

source_name: Human primary breast tumor sample T150


title: T137 [aCGH]

source_name: Human primary breast tumor sample T137


title: T148 [aCGH]

source_name: Human primary breast tumor sample T148


title: T147 [aCGH]

source_name: Human primary breast tumor sample T147


title: T146 [aCGH]

source_name: Human primary breast tumor sample T146


title: T140 [aCGH]

source_name: Human primary breast tumor sample T140


title: T135 [aCGH]

source_name: Human primary breast tumor sample T135


title: T138 [aCGH]

source_name: Human primary breast tumor sample T138


title: T134 [aCGH]

source_name: Human primary breast tumor sample T134


title: T152 [aCGH]

source_name: Human primary breast tumor sample T152


title: T142 [aCGH]

source_name: Human primary breast tumor sample T142


title: T139 [aCGH]

source_name: Human primary breast tumor sample T139

source_name: A pool of 13 normal male DNA.


title: T136 [aCGH]

source_name: Human primary breast tumor sample T136


title: T128 [aCGH]

source_name: Human primary breast tumor sample T128


title: T169 [aCGH]

source_name: Human primary breast tumor sample T169


title: T130 [aCGH]

source_name: Human primary breast tumor sample T130


title: T133 [aCGH]

source_name: Human primary breast tumor sample T133


title: T141 [aCGH]

source_name: Human primary breast tumor sample T141


title: T132 [aCGH]

source_name: Human primary breast tumor sample T132


title: T126 [aCGH]

source_name: Human primary breast tumor sample T126


title: T125 [aCGH]

source_name: Human primary breast tumor sample T125


title: T157 [aCGH]

source_name: Human primary breast tumor sample T157


title: T144 [aCGH]

source_name: Human primary breast tumor sample T144


title: T119 [aCGH]

source_name: Human primary breast tumor sample T119


title: T149 [aCGH]

source_name: Human primary breast tumor sample T149


title: T123 [aCGH]

source_name: Human primary breast tumor sample T123


title: T121 [aCGH]

source_name: Human primary breast tumor sample T121


title: T122 [aCGH]

source_name: Human primary breast tumor sample T122


title: T124 [aCGH]

source_name: Human primary breast tumor sample T124

source_name: A pool of 13 normal male DNA.


title: T118 [aCGH]

source_name: Human primary breast tumor sample T118


title: T105 [aCGH]

source_name: Human primary breast tumor sample T105


title: T110 [aCGH]

source_name: Human primary breast tumor sample T110


title: T127 [aCGH]

source_name: Human primary breast tumor sample T127


title: T114 [aCGH]

source_name: Human primary breast tumor sample T114


title: T117 [aCGH]

source_name: Human primary breast tumor sample T117


title: T108 [aCGH]

source_name: Human primary breast tumor sample T108


title: T99 [aCGH]

source_name: Human primary breast tumor sample T99


title: T103 [aCGH]

source_name: Human primary breast tumor sample T103


title: T106 [aCGH]

source_name: Human primary breast tumor sample T106


title: T96 [aCGH]

source_name: Human primary breast tumor sample T96


title: T92 [aCGH]

source_name: Human primary breast tumor sample T92


title: T111 [aCGH]

source_name: Human primary breast tumor sample T111


title: T116 [aCGH]

source_name: Human primary breast tumor sample T116


title: T97 [aCGH]

source_name: Human primary breast tumor sample T97


title: T89 [aCGH]

source_name: Human primary breast tumor sample T89


title: T102 [aCGH]

source_name: Human primary breast tumor sample T102

source_name: A pool of 13 normal male DNA.


title: T112 [aCGH]

source_name: Human primary breast tumor sample T112


title: T113 [aCGH]

source_name: Human primary breast tumor sample T113


title: T115 [aCGH]

source_name: Human primary breast tumor sample T115


title: T104 [aCGH]

source_name: Human primary breast tumor sample T104


title: T95 [aCGH]

source_name: Human primary breast tumor sample T95


title: T91 [aCGH]

source_name: Human primary breast tumor sample T91


title: T107 [aCGH]

source_name: Human primary breast tumor sample T107


title: T87 [aCGH]

source_name: Human primary breast tumor sample T87


title: T93 [aCGH]

source_name: Human primary breast tumor sample T93


title: T109 [aCGH]

source_name: Human primary breast tumor sample T109


title: T86 [aCGH]

source_name: Human primary breast tumor sample T86


title: T84 [aCGH]

source_name: Human primary breast tumor sample T84


title: T83 [aCGH]

source_name: Human primary breast tumor sample T83


title: T78 [aCGH]

source_name: Human primary breast tumor sample T78


title: T80 [aCGH]

source_name: Human primary breast tumor sample T80


title: T73 [aCGH]

source_name: Human primary breast tumor sample T73


title: T77 [aCGH]

source_name: Human primary breast tumor sample T77

source_name: A pool of 13 normal male DNA.


title: T88 [aCGH]

source_name: Human primary breast tumor sample T88


title: T90 [aCGH]

source_name: Human primary breast tumor sample T90


title: T76 [aCGH]

source_name: Human primary breast tumor sample T76


title: T69 [aCGH]

source_name: Human primary breast tumor sample T69


title: T71 [aCGH]

source_name: Human primary breast tumor sample T71


title: T74 [aCGH]

source_name: Human primary breast tumor sample T74


title: T72 [aCGH]

source_name: Human primary breast tumor sample T72


title: T85 [aCGH]

source_name: Human primary breast tumor sample T85


title: T68 [aCGH]

source_name: Human primary breast tumor sample T68


title: T79 [aCGH]

source_name: Human primary breast tumor sample T79


title: T82 [aCGH]

source_name: Human primary breast tumor sample T82


title: T59 [aCGH]

source_name: Human primary breast tumor sample T59


title: T62 [aCGH]

source_name: Human primary breast tumor sample T62


title: T60 [aCGH]

source_name: Human primary breast tumor sample T60


title: T61 [aCGH]

source_name: Human primary breast tumor sample T61


title: T56 [aCGH]

source_name: Human primary breast tumor sample T56


title: T64 [aCGH]

source_name: Human primary breast tumor sample T64

source_name: A pool of 13 normal male DNA.


title: T51 [aCGH]

source_name: Human primary breast tumor sample T51


title: T49 [aCGH]

source_name: Human primary breast tumor sample T49


title: T50 [aCGH]

source_name: Human primary breast tumor sample T50


title: T52 [aCGH]

source_name: Human primary breast tumor sample T52


title: T65 [aCGH]

source_name: Human primary breast tumor sample T65


title: T48 [aCGH]

source_name: Human primary breast tumor sample T48


title: T46 [aCGH]

source_name: Human primary breast tumor sample T46


title: T63 [aCGH]

source_name: Human primary breast tumor sample T63


title: T45 [aCGH]

source_name: Human primary breast tumor sample T45


title: T67 [aCGH]

source_name: Human primary breast tumor sample T67


title: T42 [aCGH]

source_name: Human primary breast tumor sample T42


title: T47 [aCGH]

source_name: Human primary breast tumor sample T47


title: T38 [aCGH]

source_name: Human primary breast tumor sample T38


title: T40 [aCGH]

source_name: Human primary breast tumor sample T40


title: T58 [aCGH]

source_name: Human primary breast tumor sample T58


title: T41 [aCGH]

source_name: Human primary breast tumor sample T41


title: T43 [aCGH]

source_name: Human primary breast tumor sample T43

source_name: A pool of 13 normal male DNA.


title: T32 [aCGH]

source_name: Human primary breast tumor sample T32


title: T39 [aCGH]

source_name: Human primary breast tumor sample T39


title: T28 [aCGH]

source_name: Human primary breast tumor sample T28


title: T24 [aCGH]

source_name: Human primary breast tumor sample T24


title: T17 [aCGH]

source_name: Human primary breast tumor sample T17


title: T21 [aCGH]

source_name: Human primary breast tumor sample T21


title: T22 [aCGH]

source_name: Human primary breast tumor sample T22


title: T29 [aCGH]

source_name: Human primary breast tumor sample T29


title: T13 [aCGH]

source_name: Human primary breast tumor sample T13


title: T18 [aCGH]

source_name: Human primary breast tumor sample T18


title: T23 [aCGH]

source_name: Human primary breast tumor sample T23


title: T33 [aCGH]

source_name: Human primary breast tumor sample T33


title: T25 [aCGH]

source_name: Human primary breast tumor sample T25


title: T30 [aCGH]

source_name: Human primary breast tumor sample T30


title: T14 [aCGH]

source_name: Human primary breast tumor sample T14


title: T34 [aCGH]

source_name: Human primary breast tumor sample T34


title: T27 [aCGH]

source_name: Human primary breast tumor sample T27

source_name: A pool of 13 normal male DNA.


title: T37 [aCGH]

source_name: Human primary breast tumor sample T37


title: T31 [aCGH]

source_name: Human primary breast tumor sample T31


title: T15 [aCGH]

source_name: Human primary breast tumor sample T15


title: Cancerous prostate

city: New Haven

first: Yong

last: Zhu

address: 60 collage street

institute: Yale Medical School

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software

label: C-Bio and A-DNP

source_name: FFPE section 2

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from formalin-fixed paraffin-embedded sectiions using Qiagen DNeasy Kit according to standard instructions

value: Male

value: FFPE section

tag: disease state

value: cancer

value: prostate cancer tumor


title: Normal prostate

source_name: FFPE section 1

value: normal

value: normal prostate


title: T36 [aCGH]

source_name: Human primary breast tumor sample T36


title: T16 [aCGH]

source_name: Human primary breast tumor sample T16


title: T7 [aCGH]

source_name: Human primary breast tumor sample T7


title: T8 [aCGH]

source_name: Human primary breast tumor sample T8


title: T10 [aCGH]

source_name: Human primary breast tumor sample T10