title: 05LIU055


title: H3.T [Agilent-026595]

status: Public on Dec 01 2011

type: genomic

city: Baltimore

first: Wayne

last: Yu

state: MD

address: 417 N. Caroline St.

department: Cancer Center

country: USA

institute: Johns Hopkins University

description: H3 ChIP for SW480 cells treated with 2mM H2O2 for 30min at 37°C

hyb_protocol: 5 ug labeled material was mixed with blocking agent and hybridization buffer (Agilent Technologies) followed by denaturing at 95°C for 3 min and incubating at 37°C for 30 min. The mixtures were applied to microarrays in Agilent microarray hybridization chambers, and hybridizations were carried out for 40 hours at 65°C in a rotating oven (Robbins Scientific, Mountain View, CA) at 10 rpm.  Hybridized microarrays were washed and dried according to the Agilent CGH microarray wash protocol.

scan_protocol: Microarrays were scanned with Agilent G2565BA microarray scanner and data were extracted using Feature Extraction Software (Agilent Technologies) with recommended data extraction protocol for array CGH.

data_processing:
Bioconductor packages limma and Ringo were used for data processing. The median signals of non-control probes were selected and normalized using Tukey-biweight scaling procedure.
Normalized log2 ratio (Cy5/Cy3) representing ChIP/WCE (do not include control probes)

molecule: genomic DNA

organism: Homo sapiens

source_name: SW480 cells, 2mM H2O2, 30min

label_protocol: 2 ug of ligation-mediated PCR fragments was mixed with 2.5x random primer solution (Agilent Technologies) and incubated at 95°C for 5 minutes. Labeling reactions were performed using a BioPrime Array CGH Genomic Labeling Module (Invitrogen) and Cydine-5 or Cydine-3 dUTP (Perkin Elmer) at 37°C for 3 hours.  The labeled sample was purified, concentrated with affinity columns and buffers provided in the kit. Both nucleic acid and dye concentrations of purified material were determined by NanoDrop ND-1000

growth_protocol: SW480 cells were obtained from American Type Culture Collection and maintained at 37°C and 5% CO2 in McCoy's 5a, supplemented with 10% fetal bovine serum.

extract_protocol: ChIP-on-chip was performed as previously described (McGarvey et al., Cancer Res. 2008 Jul 15;68(14):5753-9.), following Agilent's instructions.

treatment_protocol: Cells were either untreated or treated with 2mM H2O2 for 30min at 37°C

tag: cell line

value: Human colorectal adenocarcinoma cell line SW480 (CCL-228)

tag: antibody

tag: fraction

value: Chromatin immunoprecipitated genomic DNA (ChIP)

value: Whole cell extract genomic DNA (WCE)


title: aCGH Tumor 1156

city: South San Francisco

first: Christiaan

middle: Nicolaas

last: Klijn

state: CA

address: 1 DNA Way

department: Bioinformatics and Computational Biology

country: Netherlands

institute: Genentech

description: aCGH analysis of Trp53-/-;Cdh1-/- murine mammary tumor

hyb_protocol: Hybridizations were carried out for 18 hr at 428C in the NimbleGen Service Laboratory. The arrays were washed using a NimbleGen Wash Buffer System (NimbleGen Systems, Inc.) and immediately dried down by centrifugation.

scan_protocol: Arrays were scanned at 5-lm resolution using the GenePix4000B scanner (Axon Instruments, Molecular Devices Corp., Sunnyvale, CA). Data were extracted from scanned images using NimbleScan 2.0 extraction software (NimbleGen Systems, Inc.), which allows for automated grid alignment, extraction, and generation of data files.

data_processing: Deletion and amplification breakpoints were determined by automated segmentation analysis of data sets as follows: each array data set was imported into R (www.r-project.org; Ihaka et al., 1996) for normalization. The normalize.qspline method from the affy Bioconductor package (www.bioconductor.org; Gentleman et al., 2004) was used to normalize the signal intensities of the test vs. reference.

organism: Mus musculus

source_name: DNA from Trp53-/-;Cdh1-/- murine mammary tumor

label_protocol: The labeling of genomic DNA samples for oligonucleotide microarray CGH analysis was performed using the method of Brennen et al., (2004) with modifications. Genomic DNA was randomly fragmented by sonication to a size range of 500–2,000 bp. For labeling, each DNA sample (1 lg) was denatured at 988C in the presence of 1 O.D. of 50-Cy3- or 50-Cy5-labeled random nonamer (TriLink Biotechnologies, SanDiego, CA) in 62.5 mM Tris-HCl, pH 7.5, 6.25 mM MgCl2, and 0.0875% b-mercaptoethanol. The denatured sample was chilled on ice, and then incubated with 100 units (exo-) Klenow fragment (NEB, Ipswich, MA) and dNTP mix (6 mM each in Tris, EDTA (TE), Invitrogen, Carlsbad, CA) for 2 hr at 378C. Reactions were terminated by addition of 0.5 M EDTA (pH 8.0); the end products were precipitated with isopropanol and resuspended in water. Fifty-fold amplification was typically achieved. The Cy-labeled test sample (Cy3) and reference sample (Cy5) were combined (15 lg each) and dried down by vacuum centrifugation. The reference sample was a pool of six male individuals (Promega, Madison, WI). The sample was rehydrated in 40 ll of NimbleGen Hybridization Buffer (NimbleGen Systems, Inc.), denatured at 958C for 5 min, and then cooled to 428C.

extract_protocol: Genomic DNA of tumor and spleen samples was extracted by the Qiagen Gentra Puregene Tissue kit according to the manufacturer’s specifications.

tag: strain

value: mixed background FVB/N and 129-OLA

tag: genotype

source_name: DNA from Trp53F/F;Cdh1F/F murine spleen


title: aCGH Tumor 1632


title: 01JOS065

city: Amsterdam

first: Rinske

last: Drost

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute

description:
aCGH data of KP mouse mammary tumor
GFF file column header descriptions:
CHROMOSOME: The chromosome or parent sequence on which the probe is located. This column can be different from the chromosome indicated by SEQ_ID and/or PROBE_ID.
CHR_POSITION: The genomic position of the probe on the chromosome. This column can be different than the probe position indicated in the POSITION column.
RAW_DATAPOINTS: Total number of features in the window.
POSITION_COUNT: Total number of genomic positions in the window.
RATIO_CORRECTED: The normalized log2 ratio of the experimental and reference signals (EXP_NORM - REF_NORM). This signal will be normalized and spatially corrected if these options were used.
WINDOW_SIZE: The size of the averaging window in base pairs

hyb_protocol: Samples were hybridized and washed according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

scan_protocol: Arrays were scanned with the MS 200 Microarray Scanner and the MS 200 Data Collection Software according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

data_processing:
Background correction and normalization was performed in the NimbleScan program according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).
Probe annotation and corrected log2 ratios were imported into the R programming language from the NimbleScan output.

source_name: DNA derived from KP mouse mammary tumor

label_protocol: Tumor and spleen samples were labeled with Nimblegen dual-color DNA labeling kit according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

extract_protocol: Genomic DNA of tumor and spleen samples was extracted by proteinase K lysis and organic extraction with phenol-chloroform.

tag: tissue

value: Mammary tumor

value: KP

source_name: DNA derived from KP mouse spleen

value: Spleen


title: 05LIU050


title: aCGH Tumor 211


title: H3.U [Agilent-026595]

description: H3 ChIP for untreated SW480 cells

source_name: SW480 cells


title: aCGH Tumor 1172


title: 01JOS080


title: 05LIU026


title: Cerebellum postnatal day 9 Nos2-/- III

type: RNA

city: Stanford

first: Daniel

last: Haag

state: Santa Clara

address: 265 Campus Drive

department: ISCBRM

institute: Stanford School of Medicine

hyb_protocol: Purified dye-labelled sample and reference cDNA were combined for two-color hybridizations with 140 µl UltraHyb buffer (Ambion) pre-warmed to 70 °C and agitated for 30–60 min at 60°C. Subsequently, the sample hybridization mix was heated to 70 °C for 10 minutes and then applied to pre-heated (60°C) microarrays mounted in a GeneTAC Hybridization Station (Genomic Solutions, Ann Arbor). Hybridization conditions were set to 42 °C for 23 hours with gentle agitation. Thereafter, the arrays were automatically washed at 36°C with (i) 0.5× SSC, 0.1% (w/v) SDS for 5 min; (ii) 0.05× SSC, 0.1% (w/v) SDS for 3 min; and (iii) 0.05× SSC for 2 min. Flow time was set to 40 s. Immediately after the final washing step, the arrays were unmounted, immersed in 0.05× SSC, 0.1% (w/v) Tween 20 and dried by centrifugation.

scan_protocol: Microarray read out was accomplished in a two-color Agilent Scanner G25505B with 5 µm resolution and automatically adjusting PMT voltages according to manufacturer’s specification. Recorded images were analyzed using GenePix Pro 6.0 software (Axon).

data_processing: Processing of raw data included filter application based on i) mean-to-median ratio in both color channels (< 3.0), ii) minimal signal intensity in at least one color channel (> 250), iii) signal-to-background ratio in at least one color channel (> 1.5) and iv) manual user flag for each feature. Subsequently, variance stabilization normalization (vsn) was applied and the gene-wise average signal values of color switch experiments were calculated. Annotation of oligonucleotide probes present on the gene expression array was retrieved by alignment to EnsEMBL database version 54.

molecule: total RNA

source_name: Cerebellum sample, Nos2-/-

label_protocol: For reverse transcription:  RNA/primer-mix: 2 µg total RNA, 500 ng (dT)-T7 primer, total volume 6 µl  * denature RNA/primer 4' at 70°C, chill on ice;  RT-mix: 2 µl M-MuLV RT buffer (Fermentas), 0.5 µl 10 mM dNTP-mix, 0.5 µl T4gp32, 0.5 µl RNase Inhibitor (Promega) , 0.5 µl reverse transcriptase (RevertAid, Fermentas), total volume 4 µl  * add ice cold RT-mix, mix well  * incubate 1h at 50°C with heated lid, inactivate 15' at 65°C, chill on ice;  For second strand synthesis:  SSS-mix: 15 µl 5x 2nd strand buffer (Invitrogen), 1.5 µl 10 mM dNTP-mix, 2.22 µl DNA Pol. I (9 U/µl) (Promega), 0.1 µl RNase H (10 U/µl) (Epicentre), 0.5 µl DNA Ligase (10 U/µl) (USB), 45.68 µl RNase-free water, total volume 65 µl  * add ice cold SSS-mix to RT reaction, mix well  * incubate 2h at 14-16°C in thermal cycler  * add 3.33 µl T4 DNA-Pol. (3 U/µl) (NEB) , mix by flicking  * incubate 15' at 14-16°C in thermal cycler, heat inactivate 10' at 70°C  * add 75 µl phenol/chlorof./isoamylalc. (pH 8), mix vigorously by pipetting  * transfer to prespun (30'' at 16000xg) PLG Heavy 0.5 ml (Eppendorf)  * spin 5' at 16000xg  * transfer aq. phase to prepared (resuspend, drain by gravity, 2' at 1000g) P-6 MicroSpin column (BioRad)  * spin 4' at 1000xg, recover eluate  * transfer eluate to 0.5 ml PCR tube  * add LPA, 3.5 µl 5 M NaCl, 220 µl 100% Ethanol, mix well  * precipitate 60' at -80°C over night  * spin tube 30' at 16000xg, 4°C, remove supernatant  * wash pellet with 500 µl 70% ethanol, spin tube 5' at 16000xg, remove supernatant  * resuspend dried cDNA-pellet in 10 µl water  For In Vitro transcription:  IVT-mix (Promega): 6 µl RNase free water, 8 µl 5x T7 Transcr. buffer, 3 µl each 100 mM ATP, GTP, CTP, UTP, 4 µl T7 Enzyme-mix, total volume 30 µl  * add IVT-mix to 10 µl cDNA, mix by pipetting  * incubate 12h at 37°C  For aRNA cleanup:  RLT / β-ME – mix: 3.5 µl β-mercapto-ethanol, 76.5 µl water, 350 µl RLT (Qiagen RNeasy), total volume 430 µl  * add RLT / β-ME-mix to IVT product (aRNA), mix well  * add 250 µl 100% ethanol, apply to RNeasy Mini column (Qiagen)  * spin 15 at 8000xg, discard flow-through, transfer column to new 2 ml tube  * wash with 500 µl RPE, spin 15 at 8000xg, discard flow-through  * add 30 µl RNase-free water onto membrane, spin 1' at 8000xg,repeat eluting step,  * precipitate aRNA with 1 µl LPA, 30 µl 7.5M ammonium-acetate and 227.5 µl 100% ethanol  * wash pellet with 500 µl 70% ethanol, spin tube 5' at 16000xg, remove supernatant  * resuspend in RNase-free water ( 200 µg/µl)  For 2nd Round RT:  RNA/primer-mix: 5 µl aRNA (1 µg), 1 µg N6-random-primer, total volume 6 µl  * RT-mix: 2 µl M-MuLV RT buffer (Fermentas), 0.5 µl 10 mM dNTP-mix, 0.5 µl T4gp32, 0.5 µl RNase Inhibitor (Promega) , 0.5 µl reverse transcriptase (RevertAid, Fermentas), total volume 4 µl  * denature RNA/primer-mix 5' at 70°C, snap cool on ice 2', hold 5' at room temperature, mix well  * incubate:  20' at 37°C  20' at 42°C  10' at 50°C  10' at 55°C  15' at 65°C  hold at 37°C  * add 1 µl RNase H-dilution (1:10 in 5x 2nd strand buffer, (Invitrogen))  * incubate 30' at 37°C, 2' at 95°C  For Klenow-labeling (per channel):  Klenow-mix (Invitrogen): 40 µl 2.5X Random Primer Solution, 10 µl 10X dNTP-(low dTTP)-mix*, 3 µl Cy-labeled dUTP (Cy3 or Cy5), 34 µl water, 2 µl Klenow fragment Exo- (40 U/µl), total volume 89 µl  * add to cDNA (11 µl), mix gently but thoroughly  * incubate 16h at 37°C  * add 450 µl TE to labeled cDNA, apply to Microcon YM-30 column (Millipore)  * spin 13’ at 16000xg, discard flow-through  * wash with 430 µl TE (measure dye incorporation on NanoDrop), add 18.75 µl blocking-mix (12.5 µl Cot-1 DNA (1 µg/µl), 2.5 µl poly-A RNA (5 µg/µl), 3.75 µl tRNA (10 µg/µl))  * spin 13’ at 16000xg, discard flow-through  * elute labeled cDNA by inverting column into new tube, spin 8’ at 16000xg  * 2 mM dATP, 2mM dCTP, 2mM dGTP, 0.5 mM dTTP

growth_protocol: Conservation breeding of the Nos2 knock-out mouse strains B6;129P2-Nos2tm1Lau/J and Ptch1 knockt-out mouse B6;129P2-Ptch1tm1Mps/J was conducted on wooden litter at 22±2 °C and 55±5 % relative humidity. Illumination was set to 320 Lux with a 12 hour day-night rhythm. Grain pellets (15 mm) and ozonized pH-adjusted (pH2.6-3.0) drinking water were available ad libitum. Accordingly, crossbreeding was performed under theses standard conditions.

extract_protocol: Total RNA of tissue samples was isolated by CsCl density gradient centrifugation

value: Cerebellum

tag: genetic background

value: C57BL/6 129P2 mixed

tag: age

value: postnatal day 9

source_name: Universal Mouse Reference RNA (Stratagene)

tag: sample type


title: Cerebellum 6 weeks after birth Nos2-/- 1

value: 6 weeks after birth

value: Universal Mouse Reference RNA (Stratagene)


title: DNMT3B.T [Agilent-026595]

description: DNMT3B ChIP for SW480 cells treated with 2mM H2O2 for 30min at 37°C

value: DNMT3B:Custom-made Antibody


title: 05LIU028


title: Cerebellum postnatal day 9 Nos2-/- II


title: aCGH Tumor 1134


title: TSA 0.3 uM 5

city: Bethesda

first: Robert

middle: Scott

last: Hudson

address: National Cancer Institute Room Blgd.37/3044

department: NCI

institute: NIH

hyb_protocol: The chips were hybridized on Tecan HS 4800 hybridization station. Chips were pre-hybridized at 25C for 30 min in the buffer of 6x SSPE/ 30% formamide/ 1x Denhardt's solution. The chips were further hybridized with labeled target in 6x SSPE/ 30% formamide at 25C for 18 hr. Hybridization, post-hybridization washing in 0.75x TNT (Tris, sodium, Tween 20) (see PNAS) at 37C for 40 mins. The chips were stained by streptavidin-alexa647 (1:500) dilution in TNT for 30 mins. Post-staining washing in 1x TNT FOR 40 min. Rinse with water and spin dry.

scan_protocol: Arrays were scanned on the GenePix scanner and analyzed using the GenePix Pro software package.

data_processing: Raw gpr data files were MAS.5 median-based normalization and filtered for probes with low intensities (<10), minimum fold-change (i.e., less than 20% of expression data values with at least a 1.5-fold change in either direction from the gene’s median value) and >50% missing data were excluded. Class comparisons between treatments were carried out using randomized block univariate t-tests across independent experiments.

label: Biotin

source_name: Prostate cancer LNCaP cells

label_protocol: Refer to Liu et al (PNAS 101: 9740-9744 (2004)). 5 ug of total RNA was labeled in reverse transcription at 37C for 90 mins by using biotin-labeled rand-octomer oligo primer. The RT reaction mix was further denatured by using 0.5 N NaOH / 1 mM EDTA at 65C for 15 mins and neutralized by 1 M Tris HCl pH 7.6. Biotin signal was detected with an Alexa 647-Streptavidin conjugate.

growth_protocol: LNCaP cells were plated at 1x10^6 cells per 10 cm2 for 48 hours post treatment

extract_protocol: Total RNA was isolated with TRIZOL reagent according to the manufacturer protocol

treatment_protocol: Cells were treated with dimethylsulfoxide (DMSO) as a control and 5-AzaC (5 microM), and/or TSA (0.3 microM). For combined treatments, TSA was added after 12 hr of pre-treatment with 5-AzaC or control. After 36 hr, all cell treatments were harvested for RNA extraction. DMSO, 5-AzaC and TSA n=5; TSA/5-AzaC n=4 independent experiments.

tag: treatment

value: TSA 0.3 uM

tag: experiment

value: LNCaP


title: aCGH Tumor 1136


title: Cerebellum postnatal day 9 Nos2-/- I


title: Cerebellum 6 weeks after birth Nos2-/- 2


title: 05LIU025


title: DNMT1.U [Agilent-026595]

description: DNMT1 ChIP for untreated SW480 cells


title: Cerebellum 1 year after birth Ptch1+/- Nos2-/- 268

source_name: Cerebellum sample, Ptch1+/- Nos2-/-

value: 1 year of age


title: DNMT3B.U [Agilent-026595]

description: DNMT3B ChIP for untreated SW480 cells


title: 10RDR449

description:
aCGH data of KB1P mouse mammary tumor
GFF file column header descriptions:
CHROMOSOME: The chromosome or parent sequence on which the probe is located. This column can be different from the chromosome indicated by SEQ_ID and/or PROBE_ID.
CHR_POSITION: The genomic position of the probe on the chromosome. This column can be different than the probe position indicated in the POSITION column.
RAW_DATAPOINTS: Total number of features in the window.
POSITION_COUNT: Total number of genomic positions in the window.
RATIO_CORRECTED: The normalized log2 ratio of the experimental and reference signals (EXP_NORM - REF_NORM). This signal will be normalized and spatially corrected if these options were used.
WINDOW_SIZE: The size of the averaging window in base pairs

source_name: DNA derived from KB1P mouse mammary tumor

source_name: DNA derived from KB1P mouse spleen


title: Cerebellum 1 year after birth Ptch1+/- Nos2-/- 319


title: 10RDR539


title: DNMT1.T [Agilent-026595]

description: DNMT1 ChIP for SW480 cells treated with 2mM H2O2 for 30min at 37°C


title: 5-AzaC 5uM 5

value: 5-AzaC 5uM


title: 10RDR428


title: Cerebellum 1 year after birth Ptch1+/- Nos2-/- 110


title: 09RDR418


title: aCGH Tumor 1128


title: gamma.H2AX.T [Agilent-026595]

description: gamma-HA2X ChIP for SW480 cells treated with 2mM H2O2 for 30min at 37°C

value: Human colorectal adenocarcinoma cell line SW480 (CCL-228)


title: aCGH Tumor 1144


title: 5-AzaC 5uM TSA 0.3 uM 4

value: 5-AzaC 5uM TSA 0.3 uM


title: Cerebellum 6 weeks after birth Ptch1+/- Nos2-/- 671


title: DMSO 5

value: DMSO


title: gamma.H2AX.U [Agilent-026595]

description: gamma-HA2X ChIP for untreated SW480 cells

value: Chromatin immunoprecipitated genomic DNA (ChIP)

value: Whole cell extract genomic DNA (WCE)


title: SIRT1.U [Agilent-026595]

description: SIRT1 ChIP for untreated SW480 cells


title: TSA 0.3 uM 4


title: 5-AzaC 5uM 4


title: Cerebellum 6 weeks after birth Ptch1+/- Nos2-/- 1723


title: Cerebellum 6 weeks after birth Ptch1+/- Nos2-/- 645


title: aCGH Tumor 1124

value: mixed background FVB/N and 129-OLA


title: DMSO 4


title: aCGH Tumor 1047


title: 09RDR148

value: Mammary tumor

value: Spleen


title: Met1

city: Gaithersburg

first: Peter

last: Johansson

state: Maryland

address: 8717 Grovemont Circle

department: Pediatric Oncology Branch

institute: National Cancer Institute

hyb_protocol: nimblegen standard protocol

scan_protocol: nimblegen standard protocol

data_processing: Nimblegen data were normalized by Nimblegen. The Cy3 and Cy5 signal intensities are normalized to one another using qspline normalization. Qspline normalization is a simple and robust non-linear method of normalization for two-color experiments that has been shown to perform comparably to loess normalization.

source_name: Metastatic Neuroblastoma Tumor

label_protocol: nimblegen standard protocol

extract_protocol: Triozole

value: Metastasis in Bonemarrow

tag: Stage

source_name: Human Reference DNA

tag: reference

value: Human Male Genomic DNA, Promega Cat # G147A


title: aCGH Tumor 1020


title: aCGH Tumor 1024


title: PT

source_name: Primary Tumor

value: Primary Neuroblastoma Tumor


title: 09RDR413


title: 09RDR217


title: 5-AzaC 5uM TSA 0.3 uM 3


title: aCGH Tumor 1015


title: TSA 0.3 uM 3


title: SIRT1.T [Agilent-026595]

description: SIRT1 ChIP for SW480 cells treated with 2mM H2O2 for 30min at 37°C


title: 09RDR015


title: Cerebellum postnatal day 9 Ptch1+/- Nos2-/- II

value: Cerebellum

value: C57BL/6 129P2 mixed

value: postnatal day 9

value: Universal Mouse Reference RNA (Stratagene)


title: Cerebellum postnatal day 9 Ptch1+/- Nos2-/- III


title: 09RDR188


title: 09RDR187


title: 5-AzaC 5uM 3

value: LNCaP


title: Cerebellum postnatal day 9 Ptch1+/- Nos2-/- I


title: 5-AzaC 5uM TSA 0.3 uM 2


title: Cerebellum 1 year after birth Ptch1+/- 131

source_name: Cerebellum sample, Ptch1+/-

value: 1 year of age


title: aCGH Tumor 1007


title: DMSO 3


title: Cerebellum 1 year after birth Ptch1+/- 126


title: 09RDR009


title: TSA 0.3 uM 2

value: TSA 0.3 uM


title: Cerebellum 6 weeks after birth Ptch1+/- 378

value: 6 weeks after birth


title: 09RDR052


title: aCGH Tumor 1013


title: aCGH Tumor 1005


title: Cerebellum 1 year after birth Ptch1+/- 127


title: 09RDR042


title: aCGH Tumor 1010


title: 5-AzaC 5uM 2

value: 5-AzaC 5uM


title: Cerebellum 6 weeks after birth Ptch1+/- 407


title: 09RDR047


title: 09RDR043


title: aCGH Tumor 620


title: DMSO 2

value: DMSO


title: 5-AzaC 5uM TSA 0.3 uM 1

value: 5-AzaC 5uM TSA 0.3 uM


title: 09RDR067


title: aCGH Tumor 1001

value: mixed background FVB/N and 129-OLA


title: aCGH Tumor 507


title: Cerebellum 6 weeks after birth Ptch1+/- 432


title: aCGH Tumor 511


title: aCGH Tumor 256


title: 5-AzaC 5uM 1


title: TSA 0.3 uM 1


title: Cerebellum postnatal day 9 Ptch1+/- I


title: aCGH Tumor 236


title: Cerebellum postnatal day 9 Ptch1+/- III


title: 09RDR084

value: Mammary tumor


title: DMSO 1


title: aCGH Tumor 545


title: Cerebellum postnatal day 9 Ptch1+/- II


title: 09RDR092

value: Spleen


title: 10RDR080

description:
aCGH data of KB1C61GP mouse mammary tumor
GFF file column header descriptions:
CHROMOSOME: The chromosome or parent sequence on which the probe is located. This column can be different from the chromosome indicated by SEQ_ID and/or PROBE_ID.
CHR_POSITION: The genomic position of the probe on the chromosome. This column can be different than the probe position indicated in the POSITION column.
RAW_DATAPOINTS: Total number of features in the window.
POSITION_COUNT: Total number of genomic positions in the window.
RATIO_CORRECTED: The normalized log2 ratio of the experimental and reference signals (EXP_NORM - REF_NORM). This signal will be normalized and spatially corrected if these options were used.
WINDOW_SIZE: The size of the averaging window in base pairs

source_name: DNA derived from KB1C61GP mouse mammary tumor

source_name: DNA derived from KB1C61GP mouse spleen


title: Cerebellum 1 year after birth wildtype 83

source_name: Cerebellum sample, wildtype

value: wild type


title: 10RDR026


title: CIRM1_4°C_9days_rep2

city: Fermoy

first: Marion

last: Dalmasso

address: Moorepark

department: Food Safety

country: Ireland

institute: Teagasc

description:
9DB
Gene expression after 9 days at 4°C

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of  25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction,  25µl of  2x Hi-RPM hybridization buffer (Agilent) was added to the fragmentation mixture and hybridized to Agilent  specific  8x15K microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and for 1 minute with 37°C GE Wash buffer 2 (Agilent),  and terminal 1 min at room temperature with Acetonetril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner  (G2565CA) using one color scan setting for  8x15K array slides (Scan Area 61x21.6 mm, Scan resolution 5µM, Dye channel  is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters ( GE1_105_Dec08 and Grid: array specific) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Propionibacterium freudenreichii subsp. shermanii

source_name: strain CIRM1, 4°C, 9 days, repetition 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from (50-100 ng) RNA using the  Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Bacteria were grown in YEL broth under air atmosphere without agitation. Cultures were incubated at 30°C until they reached an OD650 of about 2. Then, cultures were incubated for a further 9 days at 4°C. Lactate was added after 24 h of incubation at 4°C in order to prevent carbon starvation.

extract_protocol: Cells were harvested (8000 × g, 10 min, ambient temperature or 4°C regarding the sampling time). Cell pellets were suspended in 100 µl of TE buffer 1x (Qiagen, Courtaboeuf, France) containing lysozyme (20 mg/ml), and incubated for 15 min at 24 °C before RLT buffer (from the Qiagen RNeasy minikit) addition at a ratio of 35/10 (vol/vol). 50 mg of zirconium beads and 100 µl of sodium dodecyl sulfate (SDS, 20%) were then added and cells were disrupted for 2 × 90 seconds at 30 Hz by using a Retsch MM301 high-speed mixer mill (Grosseron, France). RNA was extracted according to the instructions of the RNeasy kit. Then DNase treatments of the RNA samples were performed using a DNA-free kit (Ambion, Texas, USA) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: CIRM-BIA1 (CIP103027)


title: Cerebellum 1 year after birth wildtype 86


title: CIRM1_4°C_9days_rep3

description:
9DC
Gene expression after 9 days at 4°C

source_name: strain CIRM1, 4°C, 9 days, repetition 3


title: Cerebellum 1 year after birth wildtype 79


title: 10RDR025


title: 09RDR414


title: aCGH Tumor 221

source_name: DNA from Trp53-/-;Cdh1-/- murine mammary tumor

source_name: DNA from Trp53F/F;Cdh1F/F murine spleen


title: aCGH Tumor 228


title: 09RDR314


title: aCGH Tumor 505


title: Cerebellum 6 weeks after birth wildtype 629


title: Cerebellum 6 weeks after birth wildtype 429


title: Cerebellum postnatal day 9 wildtype III


title: CIRM1_4°C_6days_rep3

description:
6DC
Gene expression after 6 days at 4°C

source_name: strain CIRM1, 4°C, 6 days, repetition 3


title: Cerebellum 6 weeks after birth wildtype 634

source_name: Universal Mouse Reference RNA (Stratagene)


title: 09RDR219


title: 09RDR367


title: CIRM1_4°C_6days_rep1

description:
6DA
Gene expression after 6 days at 4°C

source_name: strain CIRM1, 4°C, 6 days, repetition 1


title: aCGH Tumor 577


title: aCGH Tumor 191


title: 09RDR210


title: CIRM1_4°C_6days_rep2

description:
6DB
Gene expression after 6 days at 4°C

source_name: strain CIRM1, 4°C, 6 days, repetition 2


title: CIRM1_4°C_9days_rep1

description:
9DA
Gene expression after 9 days at 4°C

source_name: strain CIRM1, 4°C, 9 days, repetition 1


title: aCGH Tumor 266


title: Cerebellum postnatal day 9 wildtype II


title: CIRM1_4°C_3days_rep3

description:
3DC
Gene expression after 3 days at 4°C

source_name: strain CIRM1, 4°C, 3 days, repetition 3


title: Cerebellum postnatal day 9 wildtype I


title: Medulloblastoma Ptch1+/- Nos2-/- 17

source_name: Medulloblastoma sample, Ptch1+/- Nos2-/-

value: Medulloblastoma


title: CIRM1_30°C_40h_rep3

description:
40HC
Gene expression at the end of exponential growth at 30°C

source_name: strain CIRM1, 30°C, 40h, repetition 3


title: CIRM1_4°C_3days_rep1

description:
3DA
Gene expression after 3 days at 4°C

source_name: strain CIRM1, 4°C, 3 days, repetition 1


title: 09RDR154


title: 09RDR198-1


title: aCGH Tumor 64


title: Medulloblastoma Ptch1+/- Nos2-/- 457


title: 09RDR191


title: 09RDR181


title: Medulloblastoma Ptch1+/- Nos2-/- 626


title: aCGH Tumor 284


title: Medulloblastoma Ptch1+/- Nos2-/- 164


title: CIRM1_30°C_40h_rep1

description:
40HA
Gene expression at the end of exponential growth at 30°C

source_name: strain CIRM1, 30°C, 40h, repetition 1


title: CIRM1_4°C_3days_rep2

description:
3DB
Gene expression after 3 days at 4°C

source_name: strain CIRM1, 4°C, 3 days, repetition 2


title: Medulloblastoma Ptch1+/- Nos2-/- 180


title: aCGH Tumor 125


title: aCGH Tumor 81


title: 09RDR164

source_name: DNA derived from KB1C61GP mouse mammary tumor

source_name: DNA derived from KB1C61GP mouse spleen


title: CIRM1_30°C_40h_rep2

description:
40HB
Gene expression at the end of exponential growth at 30°C

source_name: strain CIRM1, 30°C, 40h, repetition 2


title: CIRM1_30°C_20h_rep3

description:
20HC
Gene expression during exponential growth at 30°C

source_name: strain CIRM1, 30°C, 20h, repetition 3


title: 09RDR173


title: 09RDR165


title: aCGH Tumor 60

source_name: DNA from Trp53-/-;Cdh1-/- murine mammary tumor


title: Medulloblastoma Ptch1+/- Nos2-/- 321


title: CIRM1_30°C_20h_rep2

description:
20HB
Gene expression during exponential growth at 30°C

source_name: strain CIRM1, 30°C, 20h, repetition 2


title: Third larval stage worms (L3) from hpl-2(tm1489) strain, biological replicate 2

status: Public on Nov 30 2011

city: Bern

last: Meister

address: Baltzerstrasse 4

department: Institute of Cell Biology

country: Switzerland

institute: University of Bern

description: Gene expression data from hpl-2(tm1489) third larval stage (L3)

hyb_protocol: 7ug fragmented and labeled cDNA were hybridized to GeneChip C. elegans Tiling 1.0R Arrays for 16h followed by washing with the fluidics protocol FS450_0001 on a Affymetrix washing station.

scan_protocol: Scanning was performed with Affymetix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader.

data_processing: Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probesets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction. The R code is available upon request. The CDF package is available as a Series Supplementary file [Ce25b_MR_v02.CDF]. RMA normalized expression values created with R/Bioconductor package affy using the attached CDF file [RMA_normalized_data.txt available as a Series Supplementary file]

organism: Caenorhabditis elegans

source_name: C. elegans third larval stage worms,hpl-2(tm1489) strain

label_protocol: 300ng total RNA were amplified with the GeneChip Whole Transcript Amplified Double-Stranded Target Assay (Affymetrix) according to the manufacturer's instructions; 7ug of sense cDNA fragmented and labeled with the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: Wild-type and mutant strains were grown on NG Agar plates.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Following trizol extraction, RNA was further purified using RNAEasy column (Qiagen) according to manufacturer's protocol

treatment_protocol: All strains were grown at 20 degrees. Embryos were recovered by bleaching of gravid adults. Synchronized cultures of L3 stage worms were obtained by bleaching and L1 starving. Staging was carried out according to vulval and somatic gonad development (28 to 29 hours).

tag: strain/genotyp


title: Third larval stage worms (L3) from wild-type strain, biological replicate 3

description: Gene expression data from N2 wild-type third larval stage (L3)

source_name: C. elegans third larval stage worms,wild-type N2 (Bristol) strain

value: N2 (WT)


title: Third larval stage worms (L3) from hpl-2(tm1489) strain, biological replicate 1


title: aCGH Tumor 259

source_name: DNA from Trp53F/F;Cdh1F/F murine spleen


title: aCGH Tumor 62


title: Third larval stage worms (L3) from wild-type strain, biological replicate 1


title: aCGH Tumor 347


title: Third larval stage worms (L3) from wild-type strain, biological replicate 2


title: Medulloblastoma Ptch1+/- 758

source_name: Medulloblastoma sample, Ptch1+/-

value: C57BL/6 129P2 mixed

source_name: Universal Mouse Reference RNA (Stratagene)


title: Medulloblastoma Ptch1+/- 223


title: Mixed-stage embryos from hpl-2(tm1489) strain, biological replicate 2

description: Gene expression data from hpl-2(tm1489) mixed-stage embryos

source_name: C. elegans embryos, mixed stage, hpl-2(tm1489) strain

value: Embryos


title: Third larval stage worms (L3) from hpl-2(tm1489) strain, biological replicate 3


title: CIRM1_30°C_20h_rep1bis

description:
20HAbis
Gene expression during exponential growth at 30°C

source_name: strain CIRM1, 30°C, 20h, (technical) repetition 1


title: Mixed-stage embryos from hpl-2(tm1489) strain, biological replicate 3


title: Medulloblastoma Ptch1+/- 679

value: Universal Mouse Reference RNA (Stratagene)


title: CIRM1_30°C_20h_rep1

description:
20HA
Gene expression during exponential growth at 30°C

source_name: strain CIRM1, 30°C, 20h, repetition 1


title: aCGH Tumor 257

description: aCGH analysis of Trp53-/-;Cdh1-/- murine mammary tumor


title: 09RDR142


title: aCGH Tumor 261


title: Mixed-stage embryos from hpl-2(tm1489) strain, biological replicate 1


title: 09RDR048


title: aCGH Tumor 263


title: aCGH Tumor 59


title: 09RDR066


title: Mixed-stage embryos from wild-type strain, biological replicate 2

description: Gene expression data from N2 wild-type mixed stage embryos

source_name: C. elegans embryos, mixed stage, wild-type N2 (Bristol) strain


title: 09RDR056-2


title: Mixed-stage embryos from wild-type strain, biological replicate 1


title: Mixed-stage embryos from wild-type strain, biological replicate 3


title: aCGH Tumor 295


title: 14178733 - Ader7 30nM 6h R2 vs Ader7 0nM 6h R2

status: Public on Nov 01 2011

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Does DspA/E repress defenses at the transcriptionnal level? What defenses are triggered directly in response to the perception of DspA/E?

hyb_protocol: Ader7 0nM 6h R2 Cy5 / Ader7 30nM 6h R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: DspA (Ader7) 0nM 6h R2

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seedling - Media=MS (1/5) Saccharose 1% Temperature=25°C  Light=16h

extract_protocol: Ader7 0nM 6h R2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:DMSO - compound based treatment - compound addition,dmso:time 6hour . Plantlets are immersed for 10 minutes in 30nM estradiol solution or 0nM estradiol solution (to obtain the 0nM estradiol solution, we add a volume of DMSO equal to the estradiol volume added to obtain the 30nM estradiol solution). The solution is removed, plantlets are put in growth chamber for 6h and then harvested.

value: Columbia mutant (ader7)

tag: dev. stage (boyes et al. plant cell 2001)

source_name: DspA (Ader7) 30nM 6h R2

extract_protocol: Ader7 30nM 6h R2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:oestradiol - compound based treatment - compound addition,oestradiol:quantity 30nM time 6hour . Plantlets are immersed for 10 minutes in 30nM estradiol solution or 0nM estradiol solution (to obtain the 0nM estradiol solution, we add a volume of DMSO equal to the estradiol volume added to obtain the 30nM estradiol solution). The solution is removed, plantlets are put in growth chamber for 6h and then harvested.


title: STZ-injected, FK-treated, 3 week

city: Tsukuba-shi, Ibaraki

first: Shunji

last: Yamazaki

address: 21, Miyukigaoka

country: Japan

institute: Astellas Phama Inc.

description:
3w_STZ_FR
Gene expression data from DRG in STZ rat with FK treatment at 3 week.

hyb_protocol: Hybridization, washing, staining, and scanning of Affymetrix probe arrays were performed as described in the standard Affymetrix protocol for GeneChip Rat Expression Array 230A (Affymetrix, Santa Clara, CA, USA) using 10 ug fragmented RNA.

scan_protocol: Scanning was performed using Affymetrix protocols provided by the manufacturer.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

organism: Rattus norvegicus

source_name: DRG 3 week

label_protocol: Labeling was performed using Affymetrix protocols provided by the manufacturer.

extract_protocol: RNAlater reagent (Qiagen, Hilden, Germany) was used according to the manufacturer's instructions. Ganglia from each rat were homogenized using Qiazol reagent (Qiagen, Hilden, Germany) and total RNA was extracted from each sample individually using an RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

value: Sprague-Dawley (SD)

value: Dorsal root ganglia from L4 to L6 in rats

tag: stz injection

value: YES

value: FK

tag: sampling time after initiation of treatment

value: 3 week


title: 14178734 - Ader13-1-2 0nM 6h R2 vs Ader13-1-2 30nM 6h R2

hyb_protocol: Ader13-1-2 30nM 6h R2 Cy5 / Ader13-1-2 0nM 6h R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: GFP::DspA (Ader13-1-2) 30nM 6h R2

extract_protocol: Ader13-1-2 30nM 6h R2:10ug. (Qiagen_RNeasy.pdf)

value: Columbia mutant (ader13-1-2)

source_name: GFP::DspA (Ader13-1-2) 0nM 6h R2

extract_protocol: Ader13-1-2 0nM 6h R2:10ug. (Qiagen_RNeasy.pdf)


title: Normal vehicle-treated, 1 week

description:
1w_Norm_Veh
Gene expression data from DRG in normal rat at 1 week.

source_name: DRG 1 week

value: NO

value: Vehicle

value: 1 week


title: 14162426 - Ader7 0nM 6h R2 vs Ader7 30nM 6h R2

hyb_protocol: Ader7 30nM 6h R2 Cy5 / Ader7 0nM 6h R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: STZ-injected, vehicle-treated, 1 week

description:
1w_STZ_Veh
Gene expression data from DRG in STZ rat at 1 week.


title: Normal vehicle-treated, 2 week

description:
2w_Norm_Veh
Gene expression data from DRG in normal rat at 2 week.

source_name: DRG 2 week

value: 2 week


title: STZ-injected, vehicle-treated, 2 week

description:
2w_STZ_Veh
Gene expression data from DRG in STZ rat at 2 week.


title: 14162423 - Ader13-1-2 30nM 6h R1 vs Ader13-1-2 0nM 6h R1

hyb_protocol: Ader13-1-2 0nM 6h R1 Cy5 / Ader13-1-2 30nM 6h R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: GFP::DspA (Ader13-1-2) 0nM 6h R1

extract_protocol: Ader13-1-2 0nM 6h R1:10ug. (Qiagen_RNeasy.pdf)

source_name: GFP::DspA (Ader13-1-2) 30nM 6h R1

extract_protocol: Ader13-1-2 30nM 6h R1:10ug. (Qiagen_RNeasy.pdf)


title: 14162425 - Ader13-1-2 0nM 6h R1 vs Ader7 0nM 6h R1

hyb_protocol: Ader7 0nM 6h R1 Cy5 / Ader13-1-2 0nM 6h R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: DspA (Ader7) 0nM 6h R1

extract_protocol: Ader7 0nM 6h R1:10ug. (Qiagen_RNeasy.pdf)


title: 14178737 - Ader13-1-2 30nM 6h R2 vs Ader13-1-2 0nM 6h R2

hyb_protocol: Ader13-1-2 0nM 6h R2 Cy5 / Ader13-1-2 30nM 6h R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 09RDR208

description:
aCGH data of KB1C61GP mouse mammary tumor
GFF file column header descriptions:
CHROMOSOME: The chromosome or parent sequence on which the probe is located. This column can be different from the chromosome indicated by SEQ_ID and/or PROBE_ID.
CHR_POSITION: The genomic position of the probe on the chromosome. This column can be different than the probe position indicated in the POSITION column.
RAW_DATAPOINTS: Total number of features in the window.
POSITION_COUNT: Total number of genomic positions in the window.
RATIO_CORRECTED: The normalized log2 ratio of the experimental and reference signals (EXP_NORM - REF_NORM). This signal will be normalized and spatially corrected if these options were used.
WINDOW_SIZE: The size of the averaging window in base pairs

source_name: DNA derived from KB1C61GP mouse mammary tumor

value: Mammary tumor

source_name: DNA derived from KB1C61GP mouse spleen

value: Spleen


title: STZ-injected, vehicle-treated, 3 week

description:
3w_STZ_Veh
Gene expression data from DRG in STZ rat at 3 week.


title: 14162422 - Ader13-1-2 0nM 6h R1 vs Ader13-1-2 30nM 6h R1

hyb_protocol: Ader13-1-2 30nM 6h R1 Cy5 / Ader13-1-2 0nM 6h R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Normal vehicle-treated, 3 week

description:
3w_Norm_Veh
Gene expression data from DRG in normal rat at 3 week.


title: STZ-injected, FK-treated, 2 week

description:
2w_STZ_FR
Gene expression data from DRG in STZ rat with FK treatment at 2 week.


title: 14162424 - Ader7 0nM 6h R1 vs Ader13-1-2 0nM 6h R1

hyb_protocol: Ader13-1-2 0nM 6h R1 Cy5 / Ader7 0nM 6h R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: STZ-injected, FK-treated, 1 week

description:
1w_STZ_FR
Gene expression data from DRG in STZ rat with FK treatment at 1 week.


title: aCGH Tumor 119

source_name: DNA from Trp53-/-;Cdh1-/- murine mammary tumor

value: mixed background FVB/N and 129-OLA

source_name: DNA from Trp53F/F;Cdh1F/F murine spleen


title: aCGH Tumor 353


title: aCGH Tumor 117


title: 14162407 - Ader7 30nM 6h R2 vs Ader13-1-2 30nM 6h R2

hyb_protocol: Ader13-1-2 30nM 6h R2 Cy5 / Ader7 30nM 6h R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14162411 - Ader7 30nM 6h R1 vs Ader13-1-2 30nM 6h R1

hyb_protocol: Ader13-1-2 30nM 6h R1 Cy5 / Ader7 30nM 6h R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: DspA (Ader7) 30nM 6h R1

extract_protocol: Ader7 30nM 6h R1:10ug. (Qiagen_RNeasy.pdf)


title: 14162409 - Ader7 0nM 6h R1 vs Ader7 30nM 6h R1

hyb_protocol: Ader7 30nM 6h R1 Cy5 / Ader7 0nM 6h R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14162408 - Ader13-1-2 30nM 6h R2 vs Ader7 30nM 6h R2

hyb_protocol: Ader7 30nM 6h R2 Cy5 / Ader13-1-2 30nM 6h R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178728 - Ader13-1-2 0nM 6h R2 vs Ader7 0nM 6h R2

hyb_protocol: Ader7 0nM 6h R2 Cy5 / Ader13-1-2 0nM 6h R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14162410 - Ader7 30nM 6h R1 vs Ader7 0nM 6h R1

hyb_protocol: Ader7 0nM 6h R1 Cy5 / Ader7 30nM 6h R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14162419 - Ader7 0nM 6h R2 vs Ader13-1-2 0nM 6h R2

hyb_protocol: Ader13-1-2 0nM 6h R2 Cy5 / Ader7 0nM 6h R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14162413 - Ader13-1-2 30nM 6h R1 vs Ader7 30nM 6h R1

hyb_protocol: Ader7 30nM 6h R1 Cy5 / Ader13-1-2 30nM 6h R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PAXgene 12 months frozen; donor 1

status: Public on Jul 22 2011

city: Bonn

first: Joachim

middle: L

last: Schultze

address: Carl-Troll-Str. 31

department: LIMES Institute

country: Germany

institute: University of Bonn

description: replicate 12 months

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: peripheral blood stabilized with PAXgene RNA tube, 12 months frozen

label_protocol: Biotinylated cRNA were prepared with the Illumina© TotalPrep™ RNA Amplification Kit (Applied Biosystems, Darmstadt, Germany).

extract_protocol: Total RNA from whole blood samples was prepared with the PAXgene Blood RNA Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction including an optional DNase digestion step. Quality control was performed with denaturing gel electrophoresis and UV measurement.

tag: gender

value: m

value: 41.2 years

value: peripheral blood

tag: tissue source

value: healthy subject

tag: donor #

tag: collection vessel

value: PAXgene tube

tag: protocol

value: frozen

tag: time

value: 12 months


title: PAXgene 6 weeks frozen; donor 2

description: replicate 6 weeks

source_name: peripheral blood stabilized with PAXgene RNA tube, 6 weeks frozen

value: 34.86 years

tag: tissue

value: 6 weeks


title: PAXgene 6 months frozen; donor 3

description: replicate 6 months

source_name: peripheral blood stabilized with PAXgene RNA tube, 6 months frozen

value: w

tag: age

value: 42.35 years

value: 6 months


title: PAXgene 6 months frozen; donor 2

description: replicate 6 months


title: PAXgene 12 months frozen; donor 2

description: replicate 12 months


title: PAXgene 6 weeks frozen; donor 4

description: replicate 6 weeks

value: 27.31 years


title: PAXgene 6 weeks frozen; donor 3

description: replicate 6 weeks


title: PAXgene 12 months frozen; donor 5

description: replicate 12 months

value: 34.2 years


title: PAXgene 6 months frozen; donor 6

description: replicate 6 months

value: 30.78 years


title: PAXgene 6 months frozen; donor 5

description: replicate 6 months


title: PAXgene 6 months frozen; donor 4

description: replicate 6 months


title: PAXgene 12 months frozen; donor 4

description: replicate 12 months


title: PAXgene 6 weeks frozen; donor 6

description: replicate 6 weeks


title: y_tr_2_Rep1

status: Public on Oct 07 2011

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

description:
Gene expression in root tips of soybean.
KS7

hyb_protocol: Hybridization of the GeneChips was carried out  following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO.  The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA.  The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip.  Hybridization was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours.  Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type.  The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20.  The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE).  The GeneChips were washed in non-stringent wash buffer.  A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above).  Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.

scan_protocol: Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).

data_processing:
ArrayAssist Enterprise (Agilent, CA).
Note: The raw data (.CEL) file can be read and processed using Affymetrix software but not with Bioconductor.

organism: Glycine max

source_name: One centimeter long tap root tip of soybean genotype Young, Al, 2hr

label_protocol: The labeling of the RNA was done as per the manufacturer's instructions (Affymetrix, Santa Clara, CA).  Briefly, two microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions.  The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA.  The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen).  The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions.  The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.

growth_protocol: Plants were grown in hydroponic conditions in growth chamber at 28oC /16 hours light and 20oC/8 hours dark cycle.

extract_protocol: Total RNA was extracted using Qiagen plant RNeasy extraction kit according to manufacturer's protocol.

treatment_protocol: 10 µM Al  (treated) or 0 µM Al (control).

tag: genotype

value: Young

value: root

tag: aluminum sensitivity

value: sensitive

value: aluminum

tag: treatment time


title: PAXgene 12 months frozen; donor 3

description: replicate 12 months

value: peripheral blood


title: PAXgene 6 months frozen; donor 1

description: replicate 6 months

value: m

value: 41.2 years

value: healthy subject


title: PAXgene 6 weeks frozen; donor 1

description: replicate 6 weeks

value: PAXgene tube

value: frozen


title: CLL_Peripheral_Blood_GED013 HGU133A

status: Public on Oct 14 2011

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner

data_processing: Normalization was performed using the Robust Multichip Average (RMA) method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set summarization. The 44 HG-U133 A, B chips and the 107 HG-U133 Plus 2.0 chips were normalized separately by the Robust Multichip Average (RMA) method as described by Irizarry et al 2003. Only the 44754 probe sets present on A, B chips and the 2.0 chips were included in the analysis. Some probe sets on the A, B chips tend to have lower mean signal levels and higher standard deviations than the corresponding probe sets on the Plus 2.0 chips. To eliminate this batch effect resulting from the different chip designs, we performed a second normalization using an empirical Bayesian method. This data was used in the statistical analysis. Finally we separated the normalized data for publication in GEO again. This separated normalized data is provided in the VALUE column.

source_name: peripheral_blood_mononuclear cells

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

extract_protocol: Mononuclear cells from peripheral blood (PB) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany). cDNA preparation and  in vitro transcription were performed according to standard Affymetrix protocols.

treatment_protocol: Peripheral blood mononuclear cells from patients with chronic lymphocytic leukaemia (CLL)

tag: life status (censoring day)

tag: overall survival (days)

tag: treatment status (censoring day)

tag: time to treatment (days)

tag: cell type

value: peripheral blood mononuclear cell

tag: disease state

value: Chronic lymphocytic leukemia


title: PAXgene 6 weeks frozen; donor 5

description: replicate 6 weeks

tag: gender

value: w

value: 6 weeks


title: PAXgene 24h room temperature; donor 6

description: replicate 24h

source_name: peripheral blood stabilized with PAXgene RNA tube,  24h room temperature

tag: tissue source

value: room temperature


title: PAXgene 12 months frozen; donor 6

description: replicate 12 months

tag: donor #

value: 12 months


title: PAXgene 24h room temperature; donor 3

description: replicate 24h

value: 42.35 years

tag: collection vessel


title: PAXgene 24h room temperature; donor 5

description: replicate 24h

value: 34.2 years

tag: protocol


title: PAXgene 24h room temperature; donor 2

description: replicate 24h

value: 34.86 years

tag: time


title: PAXgene 24h room temperature; donor 4

description: replicate 24h

value: 27.31 years

tag: tissue


title: PAXgene 24h room temperature; donor 1

description: replicate 24h

tag: age


title: long-term frozen PBMC_49

description: replicate 1; 21 - 30 months cryopreservation

source_name: long-term frozen peripheral blood mononuclear cells

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy MiniElute Cleanup Kit  in accordance with the prescribed protocol provided with the kit. Quality control was performed with denaturing gel electrophoresis and UV measurement.

value: PBMC

tag: cell source

value: melanoma patient

value: cryopreservation

value: 21-30 months


title: long-term frozen PBMC_50

value: m


title: long-term frozen PBMC_48


title: long-term frozen PBMC_52


title: long-term frozen PBMC_51


title: long-term frozen PBMC_53


title: long-term frozen PBMC_47


title: p_tr_48_Rep2

status: Public on Oct 05 2011

description: gene expression in tap root tip of soybean seedlings in control and under aluminum stress

data_processing:
ArrayAssist Enterprise (Agilent, CA)
Note: The raw data (.CEL) file can be read and processed using Affymetrix software but not with Bioconductor.

source_name: One centimeter long  tap root tip of soybean genotype PI 416937 treated with Al

label_protocol: The labeling of the RNA was done as per the manufacturers instructions (Affymetrix, Santa Clara, CA).  Briefly, Two microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions.  The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA.  The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen).  The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions.  The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.

growth_protocol: Plants were grown in hydroponic in growth chamber at 28oC /16 hours light and 20oC/8 hours dark cycle

extract_protocol: Total RNA was extracted using Qiagen plant RNeasy extraction kit according to manufucturer's protocol

treatment_protocol: 10 µM Al  (treated) or 0 µM Al (control)

value: root

tag: stress

value: aluminum


title: long-term frozen PBMC_46


title: long-term frozen PBMC_44

description: replicate 2; 31 - 40 months cryopreservation

value: 31-40 months


title: long-term frozen PBMC_43


title: long-term frozen PBMC_45


title: long-term frozen PBMC_41


title: long-term frozen PBMC_38


title: long-term frozen PBMC_40


title: long-term frozen PBMC_42


title: long-term frozen PBMC_37


title: long-term frozen PBMC_36


title: long-term frozen PBMC_35


title: long-term frozen PBMC_34


title: long-term frozen PBMC_32


title: long-term frozen PBMC_31


title: long-term frozen PBMC_30


title: long-term frozen PBMC_26

description: replicate 3; 41 -50 months cryopreservation

value: 41-50 months


title: long-term frozen PBMC_25

value: w


title: long-term frozen PBMC_23


title: long-term frozen PBMC_39


title: long-term frozen PBMC_28


title: long-term frozen PBMC_22


title: long-term frozen PBMC_24


title: long-term frozen PBMC_29


title: long-term frozen PBMC_21


title: long-term frozen PBMC_17

description: replicate 4; 51 -60 months cryopreservation

value: 51-60 months


title: long-term frozen PBMC_27


title: long-term frozen PBMC_12


title: long-term frozen PBMC_13


title: long-term frozen PBMC_9


title: long-term frozen PBMC_6


title: long-term frozen PBMC_16


title: long-term frozen PBMC_10


title: long-term frozen PBMC_15


title: long-term frozen PBMC_14


title: long-term frozen PBMC_20


title: long-term frozen PBMC_18


title: long-term frozen PBMC_11


title: long-term frozen PBMC_19


title: long-term frozen PBMC_5


title: long-term frozen PBMC_8


title: long-term frozen PBMC_2


title: long-term frozen PBMC_3


title: long-term frozen PBMC_4


title: long-term frozen PBMC_7


title: long-term frozen PBMC_1


title: frozen PBMC_22

description: replicate frozen

source_name: frozen peripheral blood mononuclear cells

value: 64 years

value: healthy subject

value: frozen


title: frozen PBMC_20

description: replicate frozen

value: 39 years


title: frozen PBMC_21

description: replicate frozen

value: 41 years


title: frozen PBMC_23

description: replicate frozen

value: 40 years


title: fresh PBMC_12

description: replicate fresh

source_name: fresh peripheral blood mononuclear cells

value: PBMC

value: fresh


title: frozen PBMC_17

description: replicate frozen

value: 63 years


title: frozen PBMC_16

description: replicate frozen

value: 38 years


title: frozen PBMC_18

description: replicate frozen

value: 54 years


title: fresh PBMC_7

description: replicate fresh


title: frozen PBMC_19

description: replicate frozen

value: 28 years


title: fresh PBMC_11

description: replicate fresh


title: fresh PBMC_6

description: replicate fresh


title: frozen PBMC_13

description: replicate frozen

value: 50 years


title: frozen PBMC_15

description: replicate frozen

value: 53 years


title: fresh PBMC_10

description: replicate fresh


title: frozen PBMC_14

description: replicate frozen

value: 49 years


title: frozen PBMC_24

description: replicate frozen

value: 43 years


title: fresh PBMC_5

description: replicate fresh


title: fresh PBMC_4

description: replicate fresh


title: fresh PBMC_3

description: replicate fresh


title: Brassica rapa_Leaf_BraIRRI267_Low P_Rep_2

status: Public on Jun 29 2011

city: Crawley

first: John

last: Hammond

state: WA

address: 35 Stirling Highway

department: School of Plant Biology

country: Australia

institute: University of Western Australia

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Brassica 95k Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then air dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 2x105k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 018073_D_F_20071106) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. gProcessedSignal values within arrays were normalized to the 50th percentile. Normalized signal values for individual probes were standardized to the median signal value for the probe across all arrays.

organism: Brassica rapa

source_name: Leaf tissue from RIL BraIRRI267, Low P

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

growth_protocol: Plants were grown from seed in individual pots (9cm x 9cm x 8cm; Desch Plantpak B.V., Waalwijk, NL) containing a moistened peat-based compost, under controlled-environment conditions. The potting mix consisted of 25% sand and 75% (v/v) compost (Shamrock medium grade sphagnum peat, Scotts UK, Bromford, UK). Unfertilised, the potting mix had an Olsen extractable P (Olsen et al., 1954) of 8 mg L-1.  The compost contained the following nutrients in sufficient amounts to prevent deficiencies as follows: NH4NO3 (0.4 g L-1), KNO3 (0.75 g L-1), ground limestone 2.25 g L-1, magnesium limestone 2.25 g L-1, and a fritted trace elements mixture containing B, Cu, Fe, Mn, Mo and Zn (WM255, Fargro Ltd, Littlehampton, UK) at 0.4 g L-1. Potting mixes were made in bulk using a paddle mixer (Model 156, St Moritz, Spalding, UK). The CE was a walk-in high specification growth room (Weiss-Gallenkamp, Loughborough, UK), set to a 16 h photoperiod using metal halide lamps, giving a photon flux density between 400 and 700 nm (PAR) of 250 µmol photons m-2 s-1 at plant height. The day/night settings for temperature and relative humidity were 18/15ºC and 76/71%.

extract_protocol: All plants were harvested 21 days after sowing. For each line at each treatment, fully-expanded leaves from 3 plants (6-leaf stage, not flowering) were sampled, snap-frozen in liquid nitrogen, freeze-dried, ground, and stored at -80°C. RNA was extracted from leaf samples using a modified TRIzol extraction method (Hammond et al., 2006). Extracted total RNA was purified using the ‘RNA Cleanup’ protocol for RNeasy columns with on-column DNase digestion to remove residual genomic DNA (Qiagen, Crawley, UK). Samples of total RNA were checked for integrity and quality using an Agilent Bioanalyser (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Two [P]ext treatments of 9 mg L-1 (low) or 30 mg L-1 (optimal) Olsen extractable P were produced by incorporating 0.075 g and 0.45 g of sieved (mesh 500 µm) single superphosphate (SSP, 7% P) per litre of compost, and used to induce a growth response based on previous studies with Brassica (Broadley et al., 2008, 2010; Hammond et al., 2009; White et al., 2010).

value: leaf

tag: ril

tag: treatment

value: Low P


title: fresh PBMC_9

description: replicate fresh

value: healthy subject


title: Brassica rapa_Leaf_BraIRRI267_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI267, Optimal P

value: Optimal P


title: fresh PBMC_8

description: replicate fresh


title: Preglaucoma control rep8 (OHN)

status: Public on Apr 15 2011

city: Mount Desert

first: Gareth

middle: Rhys

last: Howell

address: 600 Main Street

institute: The Jackson Laboratory

description: ONH L126910

hyb_protocol: Hybridization and post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: The arrays were scanned with a GeneChipTM  Scanner 3000 laser confocal slide scanner

data_processing: The images were quantified using GeneChipTM Operating Software (GCOS) v1.2.  Probe level data were imported into the R statistical software environment (http://www.r-project.org) and expression values for each probe set on the array were summarized using the Robust MultiChip Average (RMA) method with quantile normalization in the R/affy package

source_name: ONH preglaucoma

label_protocol: Biotin-labeled cDNA was synthesized separately from 20ng of each total RNA sample per the manufacturer’s protocols (Ovation™ Biotin System (NuGEN, San Carlos, CA). 2.5 μg of each biotin-labeled and fragmented cDNA sample was then hybridized onto Mouse Genome 430 v2.0 GeneChip™ arrays (Affymetrix, Santa Clara, CA).

growth_protocol: All mice were housed in a 14 h light to 10 h dark cycle

extract_protocol: For tissue harvesting, mice were anesthetized and the left eye was dissected free, and the cornea and lens removed. The optic nerve was cut close to the back of the eye. The optic nerve head was excised using a sharpened 1mm glass capillary centered over the optic nerve and immediately placed in RNAlater® (Qiagen). A small portion of central retina as well as a small portion of choroid and sclera are included in this tissue. This tissue is substantially enriched for the glial lamina. The retina (containing no optic nerve head) was then dissected free from the back of the eye and placed in a separate vial containing RNAlater (Ambion, Austin TX) and stored at 4oC until required. The process was repeated for the right eye. Dissection of each eye was completed in ≤5 minutes (10 minutes per mouse)

tag: phenotype

value: preglaucoma

value: female

tag: strain

value: optic nerve head

value: 4.5 months


title: Preglaucoma control rep10 (OHN)

description: ONH R126914


title: fresh PBMC_2

description: replicate fresh

value: PBMC

value: fresh


title: Preglaucoma control rep9 (OHN)

description: ONH L126913


title: fresh PBMC_1

description: replicate fresh


title: Control expression array-4

status: Public on Apr 13 2011

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

description:
mice were treated with tamoxifen for 5 consecutive days (1mg/day) and the jejunal epithelium was harvested 4 days after completion of the timecourse.  RNA was extracted using the Trizol method and prepared for arrays using manufacturer's instructions (Affymetrix).
Affymetrix mouse 4302 microarray

hyb_protocol: according to manufacturer's instructions (Affymetrix)

data_processing: Microarray expression: RMA (bioconductor) with custom CDF (Mouse4302_Mm_REFSEQ) for background elimination and normalization. Limma for detection of differentially expressed genes between controls and Cdx2 KO or Cdx2-Cdx1 D KO.

source_name: jejunum epithelium

value: C57BL/6-129 mixed

tag: genotype/variation

value: littermate controls

value: jejunum epithelium


title: Preglaucoma control rep7 (OHN)

description: ONH R126909


title: Preglaucoma control rep4 (OHN)

description: ONH R126901


title: iPSST5 endoderm day 5-rep3

status: Public on Mar 31 2011

city: New York

first: steve

last: shen

state: NY

address: 545 First Ave

department: Biochemistry

institute: New York University

description: Gene expression data from ES cells, iPS cells and Mouse Embryos

hyb_protocol: Affymetrix GeneChip® Mouse Gene 1.0 ST arrays

scan_protocol: affy scanner

data_processing: data in this table were processed with RMA method at different batches, ES/iPS experiment consisting of samples GSM668576 to GSM668593 is the first batch, and ES/Embryos experiment consisting of samples GSM668564 to GSM668575 is the second batch.

source_name: Day 5 differentiated iPS cells (clone ST5); sorted ckit+/Sox2dim

label_protocol: Affy labeling kit

extract_protocol: Total RNA was isolated from three biological replicates corresponding to different cell and tissue types using miRNeasy Mini Kit (Qiagen,217004) according to the manufacturer’s protocol.

value: iPS cells


title: iPSST5 endoderm day 5-rep2


title: iPSST8 undifferentiated-rep2

source_name: Day 0 undifferentiated iPS cells (clone ST8); sorted Sox2bright


title: Preglaucoma control rep1 (OHN)

description: ONH L104298


title: long-term frozen PBMC_33

value: w

tag: cell type

value: melanoma patient

value: cryopreservation

value: 31-40 months


title: Preglaucoma control rep5 (OHN)

description: ONH L126904


title: ES undifferentiated-rep3

source_name: Day 0 undifferentiated ES cells; sorted Sox2bright

value: ES cells


title: Preglaucoma control rep2 (OHN)

description: ONH R104298


title: Preglaucoma control rep6 (OHN)

description: ONH R126904


title: iPSST8 undifferentiated-rep1


title: Preglaucoma control rep3 (OHN)

description: ONH L126901


title: iPSST5 undifferentiated-rep3

source_name: Day 0 undifferentiated iPS cells (clone ST5); sorted Sox2bright


title: ES endoderm day 5-rep3

source_name: Day 5 differentiated ES cells; sorted ckit+/Sox2dim


title: iPSST5 undifferentiated-rep1


title: iPSST5 endoderm day 5-rep1


title: ES endoderm day 5-rep1


title: ES undifferentiated-rep1


title: iPSST8 endoderm day 5-rep3

source_name: Day 5 differentiated iPS cells (clone ST8); sorted ckit+/Sox2dim


title: iPSST5 undifferentiated-rep2


title: iPSST8 undifferentiated-rep3


title: ES endoderm day 5-rep2


title: E8.25 embryo foregut endoderm-amplified rep3

source_name: mouse E8.25 embryo foregut endoderm; sorted ENDM1+/Epcam+/SSlo

label_protocol: EncoreT  Biotin Module (Nugen)

extract_protocol: Total RNA was isolated from three biological replicates corresponding to different cell and tissue types using RNeasy Micro Kit (Qiagen, 74004) according to the manufacturer’s protocol, and the WT-OvationTM Pico RNA amplification system (Nugen) was used to amplify the RNA

value: embryos

value: Swiss webster


title: iPSST8 endoderm day 5-rep1


title: E8.25 embryo foregut endoderm-amplified rep1


title: E8.25 embryo foregut endoderm-amplified rep2


title: ES undifferentiated-amplified rep3

extract_protocol: Total RNA was isolated from three biological replicates corresponding to different cell and tissue types using miRNeasy Mini Kit (Qiagen,217004) according to the manufacturer’s protocol, and the WT-OvationTM Pico RNA amplification system (Nugen) was used to amplify the RNA


title: E8.25 embryo ENDM1 neg- amplified rep3

source_name: sorted mouse E8.25 embryos; comparator population; sorted Epcam+/ENDM1neg.


title: iPSST8 endoderm day 5-rep2


title: ES undifferentiated-amplified rep2


title: ES endoderm day 5-amplified rep2


title: ES undifferentiated-amplified rep1


title: ES endoderm day 5-amplified rep3


title: E8.25 embryo ENDM1 neg- amplified rep1


title: ES undifferentiated-rep2


title: ES endoderm day 5-amplified rep1


title: M7 114D-2

status: Public on Jan 06 2011

city: Giessen

first: Hamid

last: Hossain

address: Frankfurter Str. 107

department: University of Giessen

institute: Institute for Medical Microbiology

hyb_protocol: Portions of 20 µg cRNA were subjected to fragmentation in the presence of Mg2+. Subsequently 10 µg fragmented cRNA (target) was loaded onto CodeLink Mouse Whole Genome Microarray glass slides containing 36.227 probe sets (Applied microarrays, Tempe AZ, USA) and hybridised for 18 h in a Minitron shaker incubator (Infors AG, Bottmingen, Germany) at 37Co/300rpm (n = 2 arrays per sample). Washing and dyeing with Cy-5 coupled streptavidin was done according to the original protocol for CodeLink arrays (Applied microarrays, Tempe AZ, USA)

scan_protocol: Arrays were scanned using a GenePix 4000 B scanner and GenePix Pro 4.0 Software (Axon Instruments, Arlington, USA)

data_processing: Spot signals of CodeLink bioarrays were quantified using CodeLink System Software consisting of Batch Submission (V2.2.27) and Expression Analysis (V2.2.25) (GE Healthcare) as outlined in the user's manual. CodeLink Expression Software 1.21 generated background corrected raw as well as median centered intra-slide normalized data. The intra-slide normalized data were used for further analysis. These data were checked for quality control. Qutlier values were discarded. Missing values were imputed using sequential K-nearest neighbour (SKNN) imputation. Resulting data were quantile normalized and logged to base 2. Differentially regulated genes between KO and WT mice were identified using a novel two-class rank statistics (Rank products, RP). For each gene, a false discovery rate (FDR) < 0.05 was defined as the significance level.

source_name: testicular tissue

label_protocol: 1 µg total RNA were used in cDNA synthesis reaction with a poly-A binding primer containing the T7-polymerase promoter. Resulting cDNA was transcribed into cRNA in one round amplification in the presence of 11-Bio-UTP. Double stranded cDNA and biotin labelled cRNA were purified using the mini columns included in the kit.

growth_protocol: Breeding strategy, genotyping and confirmation of Cx43-gene loss by b-gal immunohistochemistry (IHC) of WT and homozygous SCCx43KO-/- mice were realized as described previously [Brehm et al. Am J Pathol, 2007. 171 (1):19-31]. For all experiments, eight day old mice were used, except for immunofluorescence (IF) where fifteen day old mice were utilised, since DMRT7 protein is known to be first detectable from day 13.5 onwards

extract_protocol: To carry out Microarray analysis, one testis of three mice of each genotype was used. Total RNA was prepared from dissected testis tissues using RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions

treatment_protocol: Mice were anesthetized and sacrificed by intraperitoneal injection of an overdose cocktail of ketamine hydrochloride (Medistar, Holzwickede, Germany) and xylazine (Serumwerk Bernburg, Bernburg, Germany). The body and testis weights were defined. Both testes were removed immediately. One testis was snap-frozen in liquid nitrogen and then stored at -80°C until RNA extraction, the other was placed in Bouin´s solution over night for IHC and hematoxylin and eosin staining (H&E), followed by paraffin embedding. For IF the second testis was placed in formalin for two hours before paraffin embedding.

value: wildtype


title: M8 114E-1

value: Knock-out (SCCx43KO-/-)


title: Cdx2 knockout expression array-3

status: Public on Nov 17 2010

description: Cdx2 knockout gene expression profiling

hyb_protocol: standary Affy protocols

scan_protocol: standary Affy protocols

data_processing: Microarray expression: RMA (bioconductor) with custom CDF (Mouse4302_Mm_REFSEQ) for background elimination and normalization. Limma for detection of differentially expressed genes between controls and CDX2 KO.

label_protocol: standary Affy protocols

extract_protocol: RNA was extracted using the Trizol method and prepared for arrays using manufacturer's instructions (Affymetrix).

treatment_protocol: mice were treated with tamoxifen for 5 consecutive days (1mg/day) and the jejunal epithelium was harvested 4 days after completion of the timecourse.

value: outbred hybrid of BL6/129

value: Cdx2 knockout


title: M8 114E-2


title: E8.25 embryo ENDM1 neg- amplified rep2


title: Control expression array-3

description: control gene expression profiling


title: Control expression array-1

description: control gene expression profiling


title: Cdx2 knockout expression array-1

description: Cdx2 knockout gene expression profiling


title: Cdx2 knockout expression array-2

description: Cdx2 knockout gene expression profiling


title: Control expression array-2

description: control gene expression profiling


title: RNA_DNAref1 Genomic DNA

status: Public on Dec 09 2010

city: Cambridge

first: Tsute

state: MA

address: 245 First Street

department: Microbiology

institute: The Forsyth Institute

hyb_protocol: Hybridization was performed on microarray slides covered with a HybriWell chamber (Grace Bio-Labs, Bend, OR, USA). Prehybridization was carried out for 90 min at 42°C in a 400 μl solution containing 343 μl Long Oligo hybridization buffer [94 mM Tris/HCl pH 7.0, 9.4 mM EDTA, 29.15% formamide, 5.83X SSC, 0.12% SDS], 0.5 mg/ml BSA, and 0.1 mg/ml salmon sperm DNA (Applied Biosystems/Ambion) . The slide was spin-dried at low-speed for 2 min, and a new HybriWell chamber was sealed onto the slide. For each microarray 3 μg of labeled genomic DNA was denatured at 65°C for 5 min in a final volume of 300 μl hybridization solution containing 257 μl Long Oligo hybridization buffer, 3 μl Alignment Oligo (NimbleGen), and 0.7 mg/ml salmon sperm DNA. Denatured DNA was then loaded in the chamber and hybridization was carried out at 42°C for 16 hours with 10 rpm rotation in an oven (Labnet, Edison, NJ, USA). The slide was washed according to NimbleGen’s protocol (NimbleGen Arrays User’s Guide Gene Expression Analysis).

scan_protocol: After washing and drying, the microarray slides were immediately scanned in a GenePix 4000B Scanner (Axon Instruments, Union City, CA, USA) using the provided GenePix Pro 6.1 software. NimbleScan v2.5 software was then used for spot features extraction from the scanned images.

data_processing: This is one of the 2 genomic DNA reference microarrays for the direct RNA-labeling method. They were used in the normalization as described in the Data Processing of other samples in this series.

organism: Porphyromonas gingivalis

source_name: Laboratory culture on BAPHK blood plate

label_protocol: Genomic DNA was fragmented with DNase I (Applied Biosystems/Ambion) to 100-200 nucleotides in size and then labeled either with Label IT Reagent (Mirus Bio, Madison, WI, USA).

extract_protocol: Genomic DNA for DNA reference microarray hybridization was extracted with the MasterPure DNA Purification Kit (Epicentre) and RNA was removed using the RNase A supplied in the kit.

tag: media

value: BAPHK

tag: labeled molecule

value: genomic DNA


title: RNA_DNAref2 Genomic DNA


title: cDNA_DNAref2 Genomic DNA

data_processing: This is one of the 3 genomic DNA reference microarrays used in the normalization as described in the Data Processing of other samples in this series.

label_protocol: Genomic DNA was fragmented with DNase I (Applied Biosystems/Ambion) to 100-200 nucleotides in size and then labeled either with biotin 3’end-labeling.


title: cDNA_DNAref1 Genomic DNA


title: cDNA_DNAref3 Genomic DNA


title: M7 114D-1

value: Wild Type