title: PMK Lhx2 ChIP-chip

description: Lhx2 ChIP-chip from PMK

hyb_protocol: Standard NimbleGen protocol

scan_protocol: Arrays were scanned using NimblScan software (version 2.5.26)

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed. The supplementary GFF file contains the bi-weight mean adjusted log base 2 ratios in MM8 coordinates

source_name: Amplified input DNA

label_protocol: 3 µg ChIP and input DNA were directly labeled  with Cy5 and Cy3 respectivly using standartd Nimblegn protocol

growth_protocol: PMK were cultered until 80-90% confluency

extract_protocol: Primary mouse keratinocytes (P100) were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for 15 min on ice. The crosslinked chromatin was sheared to an average size of 300 bp using Sonifier 450D sonicator (Branson). The lysate was then centrifuged to remove cell debris, . The chromatin was diluted in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein G Dynabeads  (Invitrogen) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of Lhx2 antibody (Santa Cruz) or non-immune IgG at 4C. After incubation with protein G Dynabeads  (25 µl) for 1h at 4C, the immune complexes were washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 300 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/10 of the material used for ChIP) by phenol extraction and ethanol precipitation. ChIPed and input DNA were amplified with WGA2 kit (Sigma) per manufacturer's protocol

tag: cells

value: Primary mouse keratinocytes (P0.5)

tag: chip antibody

source_name: Amplified Lhx2 ChIP DNA

growth_protocol: Primary mouse keratinocytes (P0.5)

value: Goat anti-Lhx2 antibody (Santa Cruz)


title: cotyledon_TGR-1551_mock_1dpi_rep3

status: Public on Oct 03 2011

type: RNA

city: Espinardo

first: Daniel

last: Gonzalez-Ibeas

state: Murcia

address: Campus de Espinardo s/n

department: Biologia Estres y Patologia Vegetal

country: Spain

institute: CEBAS-CSIC

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Data were normalised using the normalisation algorithm RMA with the package oligo version 1.8.2 (Carvalho et al. 2007, Biostatistics 8 (2): 485-499) written in R (R Development Core Team, http://www.R-project.org).

molecule: total RNA

organism: Cucumis melo

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Germination of melon seeds was carried out in Petri dishes for 48 h at 25 ºC. After germination, seeds were sown in 0.5 L pots and kept in growth chambers (MLR-351H from Sanyo) with 16 h light/25 ºC and 8 h dark/18 ºC for about three weeks.

extract_protocol: Cotyledon samples were independently frozen in liquid N2 and stored at -80 ºC. RNA extracts were prepared from these samples using Tri-Reagent (Sigma Chemical Co., St. Louis, MO, USA) following the manufacturer´s instructions. To eliminate traces of genomic DNA, total RNA was incubated with DNAse I (New England Biolabs, London, UK) 10 min at 37 ºC. Then, reaction volume was adjusted to 100 µl and the aqueous phase extracted with phenol:chloroform:isoamilalcohol (125:24:1). Total RNA was precipitated with 10 % (v/v) NaCl 3M and 2.5 v of absolute ethanol by centrifugation (12.000 g, 20 min, 4º C).

treatment_protocol: The viral isolate used in this study was WMV-M116, kindly provided by Dr. Moriones (Estación Experimental “La Mayora”-CSIC, Málaga, Spain). Mechanical inoculations were carried out using standard procedures. Dehydrated viral inoculum was first revived by mechanical inoculation of squash fully-expanded cotyledons. Systemically infected squash leaves were harvested after 15 days post-inoculation (dpi) and used as inoculum source for melons. Squash leaves were ground in a sterile mortar in the presence of inoculation buffer (0.2 M phosphate buffer pH 8.0, 0.1 % v/v β-mercaptoethanol, 0.03 g/mL active charcoal) and, then, carborundum (0.037 mm diameter) dusted 7 days old melon cotyledons were rubbed with this infectious mixture. Control non-infected melon cotyledons were rubbed using only inoculation buffer (mock-inoculated controls).

tag: tissue

value: cotyledon

tag: genotype

tag: physiological condition

value: mock inoculated

tag: days post-inoculation


title: cotyledon_TGR-1551_WMVinfected_7dpi_rep3

value: WMV infected


title: cotyledon_TGR-1551_mock_3dpi_rep2


title: cotyledon_TGR-1551_mock_1dpi_rep1


title: 29486

type: genomic

city: Baltimore

first: NIKHIL

last: KUMAR

state: MD

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

country: USA

institute: University of Maryland, Baltimore

hyb_protocol: Slides were prehybridized in a 50 ml solution of 5X SSC, 0.1% SDS and 1% BSA for at least one hour at 42C, washed 10X in water and once in isopropanol, then dried by brief centrifugation. Labeled probes were re-suspended in hybridization buffer (50% formamide, 5X SSC, 0.1% SDS, 1 uL 0.1M DTT, 0.6 ug/uL salmon sperm DNA) and hybridized to the microarray slides in a 42C water bath for 16-20 h. Slides were washed twice in a low stringency buffer (2X SSC, 0.1% SDS) at 55C for 5 min, twice in a medium stringency buffer (0.1X SSC, 0.1% SDS) at room temperature for 5 min, twice in a high stringency buffer (0.1X SSC) at room temperature for 5 min, and finally in water for 2 min, and then dried by brief centrifugation.

scan_protocol: Scanned on GenePix 4000B.

data_processing: Iterative log-mean normalization and filtering using in-house scripts.

label: Cy3, Cy5

molecule: genomic DNA

organism: Streptococcus sp. 'group A'

source_name: Group A Streptococcus strain 29486

label_protocol: 4 ug aliquots of genomic DNAs were aminoallyl-labeled with random hexamers (Invitrogen), Klenow buffer (New England Biolabs), DNA Polymerase I Klenow Fragment (New England Biolabs), 5-(3-aminoallyl)-dUTP (Sigma) and 100mM dNTP set PCR grade (Invitrogen). The mixture was incubated overnight at 37C. Amine-modified DNA was purified using QIAquick PCR purification kit (Qiagen), followed by chemical labeling with Cy3- or Cy5-NHS-ester fluorescent dyes (GE Healthcare).

extract_protocol: Genomic DNA was isolated using the Invitrogen Easy DNA Kit, following manufacturer's instructions.

tag: strain

tag: sample type

value: query

source_name: Cy3, Cy5Group A Streptococcus strain Alab49

tag: type

value: reference


title: D997

source_name: Group A Streptococcus strain D997


title: cotyledon_TGR-1551_WMVinfected_3dpi_rep1


title: cotyledon_TGR-1551_WMVinfected_3dpi_rep3


title: SS1443

source_name: Group A Streptococcus strain SS1443


title: NS292

source_name: Group A Streptococcus strain NS292


title: cotyledon_TGR-1551_mock_1dpi_rep2


title: MGAS2111

source_name: Group A Streptococcus strain MGAS2111


title: SS1472

source_name: Group A Streptococcus strain SS1472


title: cotyledon_TGR-1551_WMVinfected_3dpi_rep2


title: CT95-169

source_name: Group A Streptococcus strain CT95-169


title: cotyledon_TGR-1551_mock_3dpi_rep1


title: cotyledon_TGR-1551_WMVinfected_1dpi_rep3


title: cotyledon_TGR-1551_WMVinfected_7dpi_rep1


title: cotyledon_TGR-1551_WMVinfected_1dpi_rep1


title: cotyledon_TGR-1551_WMVinfected_7dpi_rep2


title: MM466 untreated

city: Herston

first: Derek

middle: John

last: Nancarrow

state: Queensland

address: 300 Herston Road

department: Genetics & Population Health

country: Australia

institute: Queensland Institute of Medical Research

description:
1718911059_C
Cultured melanoma cell line established from metastatic melanoma mock for 3 days hours prior to mRNA extraction (reference)

data_processing: GenomeStudio software, version 2.0 (Illumina) was used to extract raw signal intensity data which was corrected for background and adjusted using Average normalization. Background is defined as the average signal intensity estimated from the negative control bead types. Outliers are removed using the median absolute deviation method. Sample intensities are then scaled by a factor equal to the ratio of average intensity of virtual sample to the average intensity of the  given sample such that the average signal of all samples becomes equal to the global average of all sample signals.

label: Biotin

organism: Homo sapiens

source_name: Melanoma cell line established from metastatic melanoma

label_protocol: Biotin labeled cRNA. Refer to the Illumina Gene Expression System Manual

growth_protocol: All cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum.

extract_protocol: RNeasy  Midi-kits  (Qiagen)  were used to extract total RNA from cells in log phase growth  according  to  the  manufacturer’s  instructions,  with  on-column  DNase  digestion  (Qiagen RNase-Free DNase Set). All RNA samples were run on an Agilent Bioanalyzer (Agilent, CA) using an  RNA  6000  Nano  LabChip  kit  to  check  for RNA  integrity,  purity  and  concentration.  Only samples with an RNA integrity number (RIN) of >8.0 were used for microarray analysis.

treatment_protocol: Cells  were  split  to  20%  conﬂuence  in  a  T25 ﬂask  (7%  for  MM96L)  24  hr  before  treatment. Cells  were  then  treated  for  3  days  with  5  l M 5AzadC  (Sigma)  from  100  m M 50%  acetic  acid dissolved  stock  or  were  mock  treated  with  the same volume of phosphate buffered saline (PBS)/50%  acetic  acid.  The  3-day  5AzadC  incubation was  followed  by  a  4-hr  incubation  with  300  nM TSA  (Sigma).

tag: cell line

tag: disease state

value: MM

tag: treatment

value: untreated

tag: matching cn sample id

tag: matching expn sample id

tag: matching meth sample id


title: D41 untreated

description:
1718911059_E
Cultured melanoma cell line established from metastatic melanoma mock for 3 days hours prior to mRNA extraction (reference)

hyb_protocol: Refer to the Illumina Gene Expression System Manual


title: cotyledon_TGR-1551_WMVinfected_1dpi_rep2


title: D633

source_name: Group A Streptococcus strain D633


title: leaf_Tendral_mock_15dpi_rep3

value: leaf

value: Tendral


title: 4426-S

source_name: Group A Streptococcus strain 4426-S


title: D41 5azadC

description:
1718911059_F
Cultured melanoma cell line established from metastatic melanoma treated with 5 µM of 5AzadC (Sigma) from 100 mM 50% acetic acid dissolved stock for 3 days hours prior to mRNA extraction

scan_protocol: Refer to the Illumina Gene Expression System Manual

value: 5azadC and TSA


title: SS1470

source_name: Group A Streptococcus strain SS1470


title: MM466 5azadC

description:
1718911059_D
Cultured melanoma cell line established from metastatic melanoma treated with 5 µM of 5AzadC (Sigma) from 100 mM 50% acetic acid dissolved stock for 3 days hours prior to mRNA extraction


title: MM415 untreated

description:
1718911059_A
Cultured melanoma cell line established from metastatic melanoma mock for 3 days hours prior to mRNA extraction (reference)


title: MM415 5azadC

description:
1718911059_B
Cultured melanoma cell line established from metastatic melanoma treated with 5 µM of 5AzadC (Sigma) from 100 mM 50% acetic acid dissolved stock for 3 days hours prior to mRNA extraction


title: leaf_Tendral_WMVinfected_15dpi_rep2


title: leaf_Tendral_mock_15dpi_rep2


title: MM386 5azadC

description:
1718911017_F
Cultured melanoma cell line established from metastatic melanoma treated with 5 µM of 5AzadC (Sigma) from 100 mM 50% acetic acid dissolved stock for 3 days hours prior to mRNA extraction


title: MM386 untreated

description:
1718911017_E
Cultured melanoma cell line established from metastatic melanoma mock for 3 days hours prior to mRNA extraction (reference)


title: leaf_Tendral_WMVinfected_15dpi_rep1


title: leaf_Tendral_WMVinfected_15dpi_rep3


title: MM253 5azadC

description:
1718911017_D
Cultured melanoma cell line established from metastatic melanoma treated with 5 µM of 5AzadC (Sigma) from 100 mM 50% acetic acid dissolved stock for 3 days hours prior to mRNA extraction


title: MM329 untreated

description:
1718911017_A
Cultured melanoma cell line established from metastatic melanoma mock for 3 days hours prior to mRNA extraction (reference)


title: MM603 untreated

description:
1718911141_E
Cultured melanoma cell line established from metastatic melanoma mock for 3 days hours prior to mRNA extraction (reference)


title: MM329 5azadC

description:
1718911017_B
Cultured melanoma cell line established from metastatic melanoma treated with 5 µM of 5AzadC (Sigma) from 100 mM 50% acetic acid dissolved stock for 3 days hours prior to mRNA extraction


title: BV2 LLO+ infected, biological rep1

city: Liencres

first: carmen

last: alvarez-dominguez

state: Cantabria

address: Barrio de las Mazas, 17

department: Immunology Department-HUMV

institute: fundación marqués de valdecilla-IFIMAV

hyb_protocol: GeneChip Hybridization wash and stain kit

scan_protocol: GeneChip 3000 Scanner 3000 7G system; software: GeneChip Command Console (AGCC 3.0)

data_processing: RMA

label: biotin

organism: Mus musculus

source_name: BV2 cell line infected with LLO+

label_protocol: GeneChip 3’ IVT Express kit (Affymetrix) according to Affymetrix

extract_protocol: Total RNA was extracted from 5 x 10E6 cells using Qiagen kit (RNeasy total RNA isolation kit, QIAGEN, P/N 74104).

treatment_protocol: 5 x 10E6 cells per sample grown in 6-wells tissue culture plates after infection or not with 5 x 10E7 bacteria for 1hour and incubated in medium with antibiotics for 16 hours.

tag: cell type

value: microglia cells

tag: infected with

value: Listeria monocytogenes (LM) wild type (LLO+)


title: MM253 untreated

description:
1718911017_C
Cultured melanoma cell line established from metastatic melanoma mock for 3 days hours prior to mRNA extraction (reference)


title: BV2 1942 infected, biological rep2

source_name: BV2 cell line infected with 1942

value: Listeria monocytogenes (LM) deficient in ActA (1942)


title: leaf_TGR-1551_mock_15dpi_rep3


title: JA 5azadC

description:
1718911141_D
Cultured melanoma cell line established from metastatic melanoma treated with 5 µM of 5AzadC (Sigma) from 100 mM 50% acetic acid dissolved stock for 3 days hours prior to mRNA extraction

value: JA


title: BV2 1942 infected, biological rep1


title: MM603 5azadC

description:
1718911141_F
Cultured melanoma cell line established from metastatic melanoma treated with 5 µM of 5AzadC (Sigma) from 100 mM 50% acetic acid dissolved stock for 3 days hours prior to mRNA extraction


title: BV2 LLO- infected, biological rep2

source_name: BV2 cell line infected with LLO-

value: Listeria monocytogenes (LM) deficient in listeriolysin O (LLO-)


title: leaf_TGR-1551_mock_15dpi_rep2


title: CJM 5azadC

description:
1718911141_B
Cultured melanoma cell line established from metastatic melanoma treated with 5 µM of 5AzadC (Sigma) from 100 mM 50% acetic acid dissolved stock for 3 days hours prior to mRNA extraction

value: CJM


title: leaf_TGR-1551_mock_15dpi_rep1


title: BV2 LLO+ infected, biological rep2


title: BV2 LLO- infected, biological rep1


title: MM96L 5azadC

description:
1718911123_F
Cultured melanoma cell line established from metastatic melanoma treated with 5 µM of 5AzadC (Sigma) from 100 mM 50% acetic acid dissolved stock for 3 days hours prior to mRNA extraction


title: JA untreated

description:
1718911141_C
Cultured melanoma cell line established from metastatic melanoma mock for 3 days hours prior to mRNA extraction (reference)


title: MM96L untreated

description:
1718911123_E
Cultured melanoma cell line established from metastatic melanoma mock for 3 days hours prior to mRNA extraction (reference)


title: 6KGlaUNT

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

description: 6KGlaUNT: KG1a (the cell line is a suspended, hematopoietic progenitor cell) cells untreated, replicate #3.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v4 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 7G.

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

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: hematopoietic progenitor cell line KG1a

tag: treated w/ 4f-glcnac

value: No


title: leaf_TGR-1551_WMVinfected_15dpi_rep3


title: 5KGlaUNT

description: 5KGlaUNT: KG1a (the cell line is a suspended, hematopoietic progenitor cell) cells untreated, replicate #2.


title: CJM untreated

description:
1718911141_A
Cultured melanoma cell line established from metastatic melanoma mock for 3 days hours prior to mRNA extraction (reference)


title: A06 5azadC

description:
1718911123_D
Cultured melanoma cell line established from metastatic melanoma treated with 5 µM of 5AzadC (Sigma) from 100 mM 50% acetic acid dissolved stock for 3 days hours prior to mRNA extraction


title: A06 untreated

description:
1718911123_C
Cultured melanoma cell line established from metastatic melanoma mock for 3 days hours prior to mRNA extraction (reference)


title: BV2 non treated, biological rep2

source_name: BV2 cell line non-infected

value: non-infected control


title: D24 5azadC

description:
1718911123_B
Cultured melanoma cell line established from metastatic melanoma treated with 5 µM of 5AzadC (Sigma) from 100 mM 50% acetic acid dissolved stock for 3 days hours prior to mRNA extraction


title: 3KGla4F

description: 3KGla4F: KG1a (the cell line is a suspended, hematopoietic progenitor cell) cells KG1a treated for 48 hrs with 4F-GlcNAc [0.05 mM], a metabolic fluorosugar inhibitor of lactosamine chain synthesis, replicate #3.

source_name: KG1a (the cell line is a suspended, hematopoietic progenitor cell) cells treated KG1a treated for 48 hrs with 4F-GlcNAc [0.05 mM]

value: Yes


title: cotyledon_Tendral_mock_7dpi_rep3

value: cotyledon

value: mock inoculated


title: 2KGla4F

description: 2KGla4F: KG1a (the cell line is a suspended, hematopoietic progenitor cell) cells KG1a treated for 48 hrs with 4F-GlcNAc [0.05 mM], a metabolic fluorosugar inhibitor of lactosamine chain synthesis, replicate #2.


title: D24 untreated

description:
1718911123_A
Cultured melanoma cell line established from metastatic melanoma mock for 3 days hours prior to mRNA extraction (reference)

value: MM


title: 1KGla4F

description: 1KGla4F: KG1a (the cell line is a suspended, hematopoietic progenitor cell) cells treated KG1a treated for 48 hrs with 4F-GlcNAc [0.05 mM], a metabolic fluorosugar inhibitor of lactosamine chain synthesis, replicate #1.


title: 4KGlaUNT

description: 4KGlaUNT: KG1a (the cell line is a suspended, hematopoietic progenitor cell) cells untreated, replicate #1.


title: T. rubrum by human skin model_HSs12hr_rep_3

type: mixed

city: Beijing

first: Qi

last: Jin

address: East Street 6, Yizhuang

country: China

institute: Institute of Pathogen Biology

description:
T. rubrum cultured in a human skin suspension medium, and T. rubrum cultured in limited medium as control group were harvested at 1, 3, 6 and 12 hr. The samples total RNA and mRNA were isolated and reverse transcribed into cDNA and labeled with the fluorescent dye Cy5.
Also, reference genomic DNA (5 µg) isolated in the hyphal stage was labeled by Cy3. And then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner (Axon Instruments, Inc., CA).
Data processing Images were processed using GenePix 6.0 (Axon Instruments, Inc., CA)

hyb_protocol: Labeled cDNA and reference DNA were purified using the QIAquick PCR Purification kit (Qiagen), then mixed and resuspended in 10 µL of distilled water, mixed with 1.5 µL of 50x Denhardt's solution, 2.25 µL of 20x SSC, 1.125 µL of 500 μg/mL yeast tRNA, 0.375 µL of 1 M HEPES (pH 7.0), 0.375 µL of 10% SDS, 2 µL of poly(A) (5 mg/µL). The mixture was heated at 100ºC for 3 min.

data_processing: log2 ratio of medians defined as Ch1 divided by Ch2[(F635-B635)/(F532-BF532)]

molecule: polyA RNA

organism: Trichophyton rubrum

source_name: T. rubrum mRNA_induced by adding human skin sections into limited medium for 12 hour, labelled with Cy5

label_protocol: Test mRNA enriched from 50 µg of total RNA was reverse transcribed into cDNA and labeled with the fluorescent dye Cy5

extract_protocol: Extracted mRNA

tag: test

source_name: T. rubrum strain BMU01672 genomic DNA

extract_protocol: genomic DNA isolated in the hyphal stage

tag: reference

value: T. rubrum strain BMU01672 genomic DNA


title: T. rubrum by human skin model_HSs12hr_rep_2

scan_protocol: Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner (Axon Instruments, Inc., CA). Data processing Images were processed using GenePix 6.0 (Axon Instruments, Inc., CA)

value: T. rubrum mRNA_induced by adding human skin sections into limited medium for 12 hour

label_protocol: reference genomic DNA (5 µg) isolated in the hyphal stage was labeled by Cy3


title: leaf_TGR-1551_WMVinfected_15dpi_rep2

tag: tissue

value: leaf

tag: genotype

value: WMV infected


title: PBMC4F-1

description: PBMC4F-1: Untreated control, replicate #1.

source_name: T-cells; untreated control

value: T-cell


title: cotyledon_Tendral_mock_7dpi_rep2

value: Tendral

tag: physiological condition

tag: days post-inoculation


title: leaf_TGR-1551_WMVinfected_15dpi_rep1


title: T. rubrum by human skin model_HSs3hr_rep_3

source_name: T. rubrum mRNA_induced by adding human skin sections into limited medium for 3 hour, labelled with Cy5


title: T. rubrum by human skin model_HSs6hr_rep_2

source_name: T. rubrum mRNA_induced by adding human skin sections into limited medium for 6 hour, labelled with Cy5


title: T. rubrum by human skin model_HSs3hr_rep_2

value: T. rubrum mRNA_induced by adding human skin sections into limited medium for 3 hour


title: T. rubrum by human skin model_HSs12hr_rep_1


title: T. rubrum by human skin model_HSs3hr_rep_1


title: cotyledon_Tendral_mock_7dpi_rep1


title: T. rubrum by human skin model_HSs6hr_rep_1

value: T. rubrum mRNA_induced by adding human skin sections into limited medium for 6 hour


title: cotyledon_Tendral_mock_3dpi_rep3


title: cotyledon_Tendral_mock_3dpi_rep2


title: T. rubrum by human skin model_LM12hr_rep_2

source_name: T. rubrum mRNA_cultured in limited medium for 12hour, labelled with Cy5


title: T. rubrum by human skin model_HSs1hr_rep_2

source_name: T. rubrum mRNA_induced by adding human skin sections into limited medium for 1 hour, labelled with Cy5


title: cotyledon_Tendral_mock_3dpi_rep1


title: T. rubrum by human skin model_HSs1hr_rep_3

value: T. rubrum mRNA_induced by adding human skin sections into limited medium for 1 hour


title: T. rubrum by human skin model_LM12hr_rep_1

value: T. rubrum mRNA_cultured in limited medium for 12hour


title: PBMC4F-2

description: PBMC4F-2: Untreated control, replicate #2.


title: PBMCUNT-1

description: PBMCUNT-1: Treated with 4F-GlcNAc , replicate #1.

source_name: T-cells; treated with 4F-GlcNAc


title: T. rubrum by human skin model_HSs1hr_rep_1


title: PBMCUNT-2

description: PBMCUNT-2: Treated with 4F-GlcNAc , replicate #2.


title: PBMCUNT-3

description: PBMCUNT-3: Treated with 4F-GlcNAc , replicate #3.


title: T. rubrum by human skin model_LM12hr_rep_3


title: T. rubrum by human skin model_LM6hr_rep_2

source_name: T. rubrum mRNA_cultured in limited medium for 6hour, labelled with Cy5


title: T. rubrum by human skin model_LM6hr_rep_3

value: T. rubrum mRNA_cultured in limited medium for 6hour


title: cotyledon_Tendral_mock_1dpi_rep3


title: PBMC4F-3

description: PBMC4F-3: Untreated control, replicate #3.

value: No


title: T. rubrum by human skin model_LM3hr_rep_3

source_name: T. rubrum mRNA_cultured in limited medium for 3hour, labelled with Cy5


title: T. rubrum by human skin model_LM3hr_rep_2

value: T. rubrum mRNA_cultured in limited medium for 3hour


title: Ovarian Cancer - Sample M4171

city: Tampa

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

institute: Moffitt Cancer Center

description: Advanced-stage serous epithelial ovarian cancer resected at the time of primary surgery from patient who would receive platinum-based therapy.

hyb_protocol: Affymetrix standard protocol

scan_protocol: GeneChip scanner 3000,1.5 micrometer resolution

data_processing: MAS5.0 was used to process the data and chips were scaled to a trimmed mean of 500.

source_name: advanced-stage serous epithelial OVCAs

label_protocol: Affymetrix standard amplification protocol

extract_protocol: Qiagen RNeasy Mini kit

tag: overall survival in days

tag: vital status

value: Dead

tag: cisplatin response (complete response or incomplete response)

value: CR

tag: debulking

value: S

tag: grade


title: T. rubrum by human skin model_LM6hr_rep_1


title: cotyledon_Tendral_mock_1dpi_rep2

value: cotyledon

value: mock inoculated


title: Ovarian Cancer - Sample M897


title: T. rubrum by human skin model_LM1hr_rep_2

source_name: T. rubrum mRNA_cultured in limited medium for 1 hour, labelled with Cy5

value: T. rubrum strain BMU01672 genomic DNA


title: leaf_Tendral_mock_15dpi_rep1

value: leaf


title: 60xHC-2: 60X Hydrocortisone, replicate #2.

source_name: Human tissue engineered self assembled dermal equivalents cultured in 60X Hydrocortisone

tag: tissue type

value: engineered tissue


title: 60xHC: 60X Hydrocortisone, replicate #1.


title: T. rubrum by human skin model_0hr_rep_3

source_name: T. rubrum mRNA_induced in different culture conditions, labelled with Cy5

value: T. rubrum cultured in a human skin suspension medium, in limited medium.


title: 60xHC-3: 60X Hydrocortisone, replicate #3.


title: T. rubrum by human skin model_LM1hr_rep_3

value: T. rubrum mRNA_cultured in limited medium for 1 hour


title: 500xHC: 500X Hydrocortisone, replicate #1.

source_name: Human tissue engineered self assembled dermal equivalents cultured in 500X Hydrocortisone


title: T. rubrum by human skin model_LM1hr_rep_1

value: T. rubrum mRNA_cultuted in limited medium for 1 hour


title: Ovarian Cancer - Sample M3705

value: IR

value: O


title: T. rubrum by human skin model_0hr_rep_1


title: 500xHC-2: 500X Hydrocortisone, replicate #2.


title: 251729810112_slide9-array4_Cy5

city: Ames

first: Susan

middle: J

last: Lamont

state: IA

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

hyb_protocol: Blocking agent, fragment buffer and hybridization buffer were added to 825ng of Cy3 and 825ng Cy5 labeled cRNA.  Samples were applied to a gasket slide and hybridized to the microarray slide.  After hybridization, slides were washed in wash buffer then a stabilization agent

scan_protocol: Slides scanned using GenePix 4100A scanner Images quantified using GenePix Pro v6.0

data_processing: Probes with an average Signal to Noise ratio of less than 3 over all slides were excluded from further study, where SNR is (Median Foreground - Median Background) / Standard Deviation of Background.  Median background was subtracted from median foreground, LOWESS normalization was done using R program

organism: Gallus gallus

source_name: Chicken spleen non-vaccinated, challenged, day 5, mild

label_protocol: 400ng of total RNA was primed by adding T7 Promoter primer and incubating at 65C for 10 minutes.  RNA was reverse-transcribed into cDNA by using RT enzyme and dNTP mix, incubating at 40C for 2 hours followed by 65C for 15 minutes.  cDNA was transcribed into cRNA which was labeled with either Cy3 or Cy5 dye, then purified using RNeasy kit.

extract_protocol: Total RNA extracted using MagMax-96 for microarrays

treatment_protocol: Male broilers chicks were vaccinated/non-vaccinated at 2 weeks of age and challenged/non-challenged at 4 weeks of age.  Necropsies took place 1 and 5 days post-challenge, at which time tissues were taken and lesion scores assessed.

tag: Sex

value: male

value: spleen

tag: vaccine status

value: Non-vaccinated

tag: challenge status

value: Challenged

tag: day

value: Day 5

tag: pathology

value: Mild


title: 251729810112_slide9-array3_Cy3

source_name: Chicken spleen non-vaccinated, non-challenged, day 1

value: Non-challenged

value: Day 1


title: Ovarian Cancer - Sample M2241

value: Dead


title: 251729810112_slide9-array2_Cy3


title: 500xHC-3: 500X Hydrocortisone, replicate #3.


title: 251729810112_slide9-array1_Cy5

source_name: Chicken spleen non-vaccinated, challenged, day 1, mild


title: Ovarian Cancer - Sample D2775

value: Alive

value: CR


title: Ovarian Cancer - Sample M1777

value: S


title: Ovarian Cancer - Sample D2791


title: T. rubrum by human skin model_LM3hr_rep_1

tag: test

value: T. rubrum mRNA_cultured in limited medium for 3hour

source_name: T. rubrum strain BMU01672 genomic DNA

value: T. rubrum strain BMU01672 genomic DNA


title: Ovarian Cancer - Sample M3035


title: 251729810112_slide9-array1_Cy3


title: 251729810112_slide9-array4_Cy3


title: 251729810112_slide9-array2_Cy5

source_name: Chicken spleen vaccinated, non-challenged, day 1

value: Vaccinated


title: 251729810112_slide9-array3_Cy5

source_name: Chicken spleen vaccinated, challenged, day 5


title: 251729810111_slide8-array3_Cy3


title: 251729810111_slide8-array3_Cy5

source_name: Chicken spleen non-vaccinated, non-challenged, day 5


title: T. rubrum by human skin model_0hr_rep_2

value: T. rubrum cultured in a human skin suspension medium, in limited medium.

tag: reference


title: Ovarian Cancer - Sample D2734

value: O


title: 500nMRA-2: 500nM Retinoic Acid, replicate #2.

source_name: Human tissue engineered self assembled dermal equivalents cultured in 500nM Retinoic Acid

value: engineered tissue


title: 500nMRA: 500nM Retinoic Acid, replicate #1.


title: 500nMRA-3: 500nM Retinoic Acid, replicate #3.


title: Ovarian Cancer - Sample D2736


title: D3FeP6-2: Fetal construct, 22 weeks gestation cells, replicate #2.

value: fetal construct


title: 251729810111_slide8-array1_Cy5

source_name: Chicken spleen non-vaccinated, challenged, day 5, severe

value: male

tag: tissue

value: spleen

value: Non-vaccinated

value: Severe


title: Ovarian Cancer - Sample D2732


title: D3FeP6-1: Fetal construct, 22 weeks gestation cells, replicate #1.


title: 251729810111_slide8-array2_Cy5

source_name: Chicken spleen vaccinated, challenged, day 1

value: Challenged


title: 251729810111_slide8-array4_Cy3

value: Non-challenged

value: Day 1


title: Normal-3: Base construct to which all constructs should be compared, replicate #3.

source_name: Control base construct to which all constructs should be compared

value: base construct


title: 251729810111_slide8-array2_Cy3


title: D3FeP6-3: Fetal construct, 22 weeks gestation cells, replicate #3.


title: T. rubrum by human skin model_HSs6hr_rep_3

source_name: T. rubrum mRNA_induced by adding human skin sections into limited medium for 6 hour, labelled with Cy5


title: Ovarian Cancer - Sample D2651

source_name: advanced-stage serous epithelial OVCAs

value: Dead

value: IR


title: 251729810110_slide7-array3_Cy5


title: Normal-2: Base construct to which all constructs should be compared, replicate #2.


title: Ovarian Cancer - Sample D2679

value: CR


title: 251729810110_slide7-array4_Cy5

source_name: Chicken spleen vaccinated, non-challenged, day 5

value: Day 5


title: BV2 non treated, biological rep1

source_name: BV2 cell line non-infected

tag: cell line

tag: cell type

value: microglia cells

tag: infected with

value: non-infected control


title: 251729810110_slide7-array2_Cy5


title: 251729810110_slide7-array3_Cy3

source_name: Chicken spleen non-vaccinated, challenged, day 1, severe


title: 251729810111_slide8-array1_Cy3


title: Normal-1: Base construct to which all constructs should be compared, replicate #1.


title: 251729810110_slide7-array4_Cy3


title: 251729810110_slide7-array2_Cy3


title: 251729810110_slide7-array1_Cy3

value: Vaccinated


title: BSA1

description: BSA1: NT2N neurons grown on poly-Lysine, replicate #1.

source_name: NT2N neurons grown on poly-Lysine

value: NT2N neuron


title: 251729810109_slide6-array3_Cy5


title: Ovarian Cancer - Sample D2578

tag: overall survival in days

value: Alive

value: O


title: 251729810109_slide6-array4_Cy5

value: male

value: spleen


title: 251729810109_slide6-array3_Cy3


title: BSA2

description: BSA2: NT2N neurons grown on poly-Lysine, replicate #2.


title: Ovarian Cancer - Sample D2711

tag: vital status


title: Ovarian Cancer - Sample D2612

tag: cisplatin response (complete response or incomplete response)


title: Ovarian Cancer - Sample D2528

tag: debulking


title: BSA3

description: BSA3: NT2N neurons grown on poly-Lysine, replicate #3.


title: Ovarian Cancer - Sample D2622

value: S

tag: grade


title: 251729810110_slide7-array1_Cy5

value: Non-vaccinated


title: 251729810109_slide6-array2_Cy5

value: Non-challenged


title: 251729810109_slide6-array2_Cy3

source_name: Chicken spleen non-vaccinated, challenged, day 5, mild

value: Challenged

value: Mild


title: Ovarian Cancer - Sample D2457

value: Dead


title: Ovarian Cancer - Sample D2443

value: IR


title: 251729810109_slide6-array1_Cy5

source_name: Chicken spleen non-vaccinated, non-challenged, day 1

value: Day 1


title: 251729810108_slide5-array4_Cy5


title: 251729810109_slide6-array4_Cy3

value: Day 5


title: L1ECD1

description: L1ECD1: NT2N neurons grown on poly-Lysine plus cell adhesion molecule L1, replicate #1.


title: 251729810108_slide5-array3_Cy5


title: Ovarian Cancer - Sample D2287


title: 251729810108_slide5-array4_Cy3


title: 251729810108_slide5-array3_Cy3

source_name: Chicken spleen non-vaccinated, challenged, day 1, mild


title: L1ECD2

description: L1ECD2: NT2N neurons grown on poly-Lysine plus cell adhesion molecule L1, replicate #2.


title: Ovarian Cancer - Sample D2251


title: 251729810109_slide6-array1_Cy3


title: 251729810108_slide5-array2_Cy5


title: 251729810111_slide8-array4_Cy5

value: Severe


title: L1Ig1-41

description: L1Ig1.41: NT2N neurons grown on poly-Lysine plus truncated from of cell adhesion molecule L1 (L1/Ig1-4), replicate #1.


title: L1ECD3

description: L1ECD3: NT2N neurons grown on poly-Lysine plus cell adhesion molecule L1, replicate #3.


title: 251729810108_slide5-array2_Cy3


title: 251729810108_slide5-array1_Cy5


title: Ovarian Cancer - Sample D2247

value: CR


title: 251729810108_slide5-array1_Cy3


title: Ovarian Cancer - Sample D2171


title: L1Ig1-42

description: L1Ig1.42: NT2N neurons grown on poly-Lysine plus truncated from of cell adhesion molecule L1 (L1/Ig1-4), replicate #2.


title: L1Ig1-43

description: L1Ig1.43: NT2N neurons grown on poly-Lysine plus truncated from of cell adhesion molecule L1 (L1/Ig1-4), replicate #3.


title: 251729810107_slide4-array4_Cy5

value: Vaccinated


title: Ovarian Cancer - Sample D2159


title: 251729810107_slide4-array3_Cy3


title: 251729810107_slide4-array2_Cy5


title: L1Ig5-62

description: L1Ig5.62: NT2N neurons grown on poly-Lysine plus truncated form of cell adhesion molecule L1 (L1/Ig5-6), replicate #2.

source_name: NT2N neurons grown on poly-Lysine plus truncated form of cell adhesion molecule L1 (L1/Ig5-6).

value: NT2N neuron


title: L1Ig5-61

description: L1Ig5.61: NT2N neurons grown on poly-Lysine plus truncated form of cell adhesion molecule L1 (L1/Ig5-6), replicate #1.


title: 251729810107_slide4-array4_Cy3


title: 251729810107_slide4-array3_Cy5


title: Ovarian Cancer - Sample D2147


title: 251729810107_slide4-array2_Cy3


title: 251729810107_slide4-array1_Cy5


title: 251729810107_slide4-array1_Cy3


title: Ovarian Cancer - Sample D1462


title: NT2-1

description: NT2.1: Non-differentiated teratocarcinoma cells, replicate #1.

value: NT2 non-differentiated teratocarcinoma


title: L1Ig5-63

description: L1Ig5.63: NT2N neurons grown on poly-Lysine plus truncated form of cell adhesion molecule L1 (L1/Ig5-6), replicate #3.


title: Ovarian Cancer - Sample D1858


title: 251729810106_slide3-array4_Cy3


title: NT2-2

description: NT2.2: Non-differentiated teratocarcinoma cells, replicate #2.


title: 251729810106_slide3-array3_Cy5


title: NT2-3

description: NT2.3: Non-differentiated teratocarcinoma cells, replicate #3.


title: 251729810106_slide3-array3_Cy3


title: 251729810106_slide3-array4_Cy5


title: 251729810106_slide3-array2_Cy5


title: NT2N1

description: NT2N1: Human NT2N neurons that are differentiated in vitro with retinoic acid and cultured in the presence of mitosis inhibitors (neurons grown on poly-Lysine plus Matrigel), replicate #1.


title: 251729810106_slide3-array2_Cy3


title: 251729810106_slide3-array1_Cy5


title: NT2N2

description: NT2N2: Human NT2N neurons that are differentiated in vitro with retinoic acid and cultured in the presence of mitosis inhibitors (neurons grown on poly-Lysine plus Matrigel), replicate #2.


title: Olfactory bulbs 2 copies biological 3 technical 2

city: Cold Spring Harbor

first: Guy

last: Horev

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: Mus Musculus Olfactory Dosage 2

hyb_protocol: The arrays were hybridized and washed using the FS450 fluidics station (Affymetrix)

scan_protocol: scanned using the GCS300 7G GeneChip Scanner (Affymetrix)

data_processing: Data was extracted using Expression Console (Affymetrix) with the RMA sketch workflow for gene level analysis

source_name: Olfactory Dosage 2

label_protocol: The samples were amplified and converted to cDNA using the Whole Transcript Expression kit (Ambion), fragmented and labeled using the Whole Transcript Sense Target Labeling Assay (Affymetrix)

tag: mouse id

tag: brain region

value: Olfactory

tag: strain

tag: gender


title: 251729810053_slide2-array4_Cy3

tag: Sex

value: male

tag: vaccine status

tag: challenge status

tag: day


title: 251729810053_slide2-array3_Cy5

tag: tissue

value: spleen

tag: pathology


title: 251729810053_slide2-array4_Cy5


title: Cortex 2 copies biological 3 technical 2

description: Mus Musculus Cortex Dosage 2

source_name: Cortex Dosage 2

value: Cortex


title: 251729810106_slide3-array1_Cy3

source_name: Chicken spleen vaccinated, non-challenged, day 1


title: Cerebellum 2 copies biological 3 technical 2

description: Mus Musculus Cerebellum Dosage 2

source_name: Cerebellum Dosage 2

value: Cerebellum


title: NT2N3

description: NT2N3: Human NT2N neurons that are differentiated in vitro with retinoic acid and cultured in the presence of mitosis inhibitors (neurons grown on poly-Lysine plus Matrigel), replicate #3.

tag: cell type


title: 251729810053_slide2-array3_Cy3

value: Non-challenged


title: Cerebellum 2 copies biological 3 technical 1

description: Mus Musculus Cerebellum Dosage 2


title: 251729810053_slide2-array2_Cy5

value: Non-vaccinated


title: 251729810053_slide2-array2_Cy3

value: Challenged

value: Mild


title: Brain Stem 2 copies biological 3 technical 1

description: Mus Musculus Brain Stem Dosage 2

source_name: Brain Stem Dosage 2

value: Brain Stem


title: 251729810053_slide2-array1_Cy5

value: Day 1


title: Cortex 2 copies biological 3 technical 1

description: Mus Musculus Cortex Dosage 2


title: G1-B: 5mM glucose for 24 hours, replicate #2.

source_name: Podocytes cultured in 5mM glucose for 24 hours

value: podocyte

tag: culture conditions

value: 5mM Glucose


title: Olfactory bulbs 3 copies biological 3 technical 1

description: Mus Musculus Olfactory Dosage 3

source_name: Olfactory Dosage 3

value: dp/+


title: G1-A: 5mM glucose for 24 hours, replicate #1.


title: G1-C: 5mM glucose for 24 hours, replicate #3.


title: 251729810053_slide2-array1_Cy3

value: Day 5


title: 251729810052_slide1-array4_Cy5


title: G2-A: 15mM glucose for 24 hours, replicate #1.

source_name: Podocytes cultured in 15mM glucose for 24 hours

value: 15nM Glucose


title: G2-B: 15mM glucose for 24 hours, replicate #2.


title: 251729810052_slide1-array4_Cy3

source_name: Chicken spleen vaccinated, challenged, day 5

value: Vaccinated


title: 251729810052_slide1-array3_Cy5


title: Cerebellum 3 copies biological 3 technical 1

description: Mus Musculus Cerebellum Dosage 3

source_name: Cerebellum Dosage 3


title: 251729810052_slide1-array3_Cy3

source_name: Chicken spleen vaccinated, challenged, day 1


title: 251729810052_slide1-array2_Cy5


title: G2-C: 15mM glucose for 24 hours, replicate #3.


title: GSC-A: Glucose free media for 24 hours, replicate #1.

source_name: Podocytes cultured in glucose free media for 24 hours

value: Glucose free


title: GSC-B: Glucose free media for 24 hours, replicate #2.


title: Cerebellum 1 copy biological 2 technical 1

description: Mus Musculus Cerebellum Dosage 1

source_name: Cerebellum Dosage 1

value: df/+

value: male


title: GSC-C: Glucose free media for 24 hours, replicate #3.


title: 251729810052_slide1-array1_Cy5

value: spleen


title: Brain Stem 3 copies biological 3 technical 1

description: Mus Musculus Brain Stem Dosage 3

source_name: Brain Stem Dosage 3


title: Cortex 1 copy biological 2 technical 1

description: Mus Musculus Cortex Dosage 1

source_name: Cortex Dosage 1

value: Cortex


title: 251729810052_slide1-array2_Cy3

source_name: Chicken spleen non-vaccinated, challenged, day 1, severe

value: Severe


title: Olfactory bulbs 1 copy biological 2 technical 1

description: Mus Musculus Olfactory Dosage 1

source_name: Olfactory Dosage 1

value: Olfactory


title: H13C hESC cultured in mesenchymal stem cells-conditioned media

city: Oviedo

first: Agustin

middle: F

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

institute: Oviedo University-HUCA

description:
H13C-MSC
healthy sample

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

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

data_processing: BeadStudio software v3.2

source_name: human embryonic stem cell

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by Phenol/Chloroform extraction of DNA followed by ethanol precipitation

value: human embryonic stem cell

tag: cell line

tag: growth condition


title: I1-A: 50nM insulin 15 minutes incubation after 20 hours serum and insulin starvation, replicate #1.

source_name: Podocytes cultured in 50nM insulin 15 minutes incubation after 20 hours serum and insulin starvation

value: 50nM Insuline after starved


title: Olfactory bulbs 2 copies biological 2 technical 1

description: Mus Musculus Olfactory Dosage 2

source_name: Olfactory Dosage 2


title: SHEF2 hESC cultured in human foreskin fibroblast-conditioned media

description:
SHEF2-HFF
healthy sample


title: Brain Stem 1 copy biological 2 technical 1

description: Mus Musculus Brain Stem Dosage 1

source_name: Brain Stem Dosage 1

value: Brain Stem


title: T8_5.3.6

description: T8 cells after 3 treatment/recovery cycles of 3ug/ml of cisplatin followed by 3 treatment/recovery cycles of 5ug/ml of cisplatin (Schedule C)

data_processing: The images were analyzed for defects and normalized using RMA

source_name: T8 ovarian cancer cells

growth_protocol: These cell lines were grown in RPMI-1640 supplemented with 10% fetal bovine serum, 1% sodium pyruvate, and 1% nonessential amino acids.

extract_protocol: Ambion RNAqueous MICRO kit

treatment_protocol: Cells were subject to sequential treatment with increasing doses of cis-diammine-dichloroplatinum (cisplatin, CIS), using three dosing schedules resulting in a total of 144 treatment/expansion cycles. Treatment schedules A, B and C included three treatments with 1, 2 and 3μg/ml CIS respectively, followed by three treatments with 3, 4 and 5μg/ml, respectively. Each CIS-treatment was followed by a cell recovery/expansion phase.

value: C

value: 5 ug/ml

tag: treatment/expansion cycle number within schedule


title: SHEF2 hESC cultured in mesenchymal stem cells-conditioned media

description:
SHEF2-MSC
healthy sample


title: T8_3.3.6

description: T8 cells after 3 treatment/recovery cycles of 1ug/ml of cisplatin followed by 3 treatment/recovery cycles of 3ug/ml of cisplatin (Schedule A)

value: A

value: 3 ug/ml


title: T8_4.3.6

description: T8 cells after 3 treatment/recovery cycles of 2ug/ml of cisplatin followed by 3 treatment/recovery cycles of 4ug/ml of cisplatin (Schedule B)

value: B

value: 4 ug/ml


title: 251729810052_slide1-array1_Cy3

source_name: Chicken spleen non-vaccinated, non-challenged, day 5

value: Non-vaccinated

value: Non-challenged

value: Day 5


title: Cortex 2 copies biological 2 technical 1

description: Mus Musculus Cortex Dosage 2

source_name: Cortex Dosage 2

value: male


title: Brain Stem 2 copies biological 2 technical 1

description: Mus Musculus Brain Stem Dosage 2

source_name: Brain Stem Dosage 2


title: H9 hESC cultured in human foreskin fibroblast-conditioned media

description:
H9-HFF
healthy sample


title: H9 hESC cultured in mesenchymal stem cells-conditioned media

description:
H9-MSC
healthy sample


title: I1-B: 50nM insulin 15 minutes incubation after 20 hours serum and insulin starvation, replicate #2.

value: podocyte


title: T8_2.3.3

description: T8 cells after three treatment/recovery cycles with 2ug/ml of cisplatin (Schedule B)

value: 2 ug/ml


title: I1-C: 50nM insulin 15 minutes incubation after 20 hours serum and insulin starvation, replicate #3.


title: T8_3.3.3

description: T8 cells after three treatment/recovery cycles with 3ug/ml of cisplatin (Schedule C)


title: H13C hESC cultured in human foreskin fibroblast-conditioned media

description:
H13C-HFF
healthy sample


title: Cerebellum 2 copies biological 2 technical 1

description: Mus Musculus Cerebellum Dosage 2

source_name: Cerebellum Dosage 2

value: Cerebellum


title: Olfactory bulbs 2 copies biological 1 technical 1

description: Mus Musculus Olfactory Dosage 2

value: Olfactory


title: I3-C: 100nM insulin 15 minutes incubation after 20 hours serum and insulin starvation, replicate #3.

source_name: Podocytes cultured in 100nM insulin 15 minutes incubation after 20 hours serum and insulin starvation.

value: 100nM Insulin after starved


title: OVCAR5_3.3.6

description: OVCAR5 cells after 3 treatment/recovery cycles of 1ug/ml of cisplatin followed by 3 treatment/recovery cycles of 3ug/ml of cisplatin (Schedule A)

source_name: OVCAR5 ovarian cancer cells


title: OVCAR5_4.3.6

description: OVCAR5 cells after 3 treatment/recovery cycles of 2ug/ml of cisplatin followed by 3 treatment/recovery cycles of 4ug/ml of cisplatin (Schedule B)


title: Olfactory bulbs 2 copies biological 1 technical 2

description: Mus Musculus Olfactory Dosage 2


title: OVCAR5_3.3.3

description: OVCAR5 cells after three treatment/recovery cycles with 3ug/ml of cisplatin (Schedule C)


title: T8

description: Baseline expression of T8 cell line

value: Untreated

value: 0 ug/ml


title: OVCAR5_5.3.6

description: OVCAR5 cells after 3 treatment/recovery cycles of 3ug/ml of cisplatin followed by 3 treatment/recovery cycles of 5ug/ml of cisplatin (Schedule C)

value: C


title: I3-B: 100nM insulin 15 minutes incubation after 20 hours serum and insulin starvation, replicate #2.


title: I3-A: 100nM insulin 15 minutes incubation after 20 hours serum and insulin starvation, replicate #1.


title: T8_1.3.3

description: T8 cells after three treatment/recovery cycles with 1ug/ml of cisplatin (Schedule A)

value: 1 ug/ml


title: I2-C: 75nM insulin 15 minutes incubation after 20 hours serum and insulin starvation, replicate #3.

source_name: Podocytes cultured in 75nM insulin 15 minutes incubation after 20 hours serum and insulin starvation

value: 75nM Insulin after starved


title: I2-B: 75nM insulin 15 minutes incubation after 20 hours serum and insulin starvation, replicate #2.


title: I2-A: 75nM insulin 15 minutes incubation after 20 hours serum and insulin starvation, replicate #1.


title: OV2008_3.3.6

description: OV2008 cells after 3 treatment/recovery cycles of 1ug/ml of cisplatin followed by 3 treatment/recovery cycles of 3ug/ml of cisplatin (Schedule A)

source_name: OV2008 ovarian cancer cells

value: A

value: 3 ug/ml


title: Cerebellum 2 copies biological 1 technical 1

description: Mus Musculus Cerebellum Dosage 2


title: NC-E: Normal culture conditions (RPMI-1640, 10%FBS, 1xITS supplement), replicate #5.

source_name: Podocytes in normal culture conditions (RPMI-1640, 10%FBS, 1xITS supplement)

value: Normal


title: Cerebellum 3 copies biological 2 technical 1

description: Mus Musculus Cerebellum Dosage 3

source_name: Cerebellum Dosage 3

value: dp/+


title: OV2008_3.3.3

description: OV2008 cells after three treatment/recovery cycles with 3ug/ml of cisplatin (Schedule C)


title: Cortex 2 copies biological 1 technical 1

description: Mus Musculus Cortex Dosage 2

value: Cortex


title: OV2008_5.3.6

description: OV2008 cells after 3 treatment/recovery cycles of 3ug/ml of cisplatin followed by 3 treatment/recovery cycles of 5ug/ml of cisplatin (Schedule C)

value: 5 ug/ml


title: NC-D: Normal culture conditions (RPMI-1640, 10%FBS, 1xITS supplement), replicate #4.


title: OV2008_4.3.6

description: OV2008 cells after 3 treatment/recovery cycles of 2ug/ml of cisplatin followed by 3 treatment/recovery cycles of 4ug/ml of cisplatin (Schedule B)

value: B

value: 4 ug/ml


title: Brain Stem 3 copies biological 2 technical 1

description: Mus Musculus Brain Stem Dosage 3

source_name: Brain Stem Dosage 3

value: Brain Stem

value: male


title: OVCAR5_2.3.3

description: OVCAR5 cells after three treatment/recovery cycles with 2ug/ml of cisplatin (Schedule B)

value: 2 ug/ml


title: OV2008_2.3.3

description: OV2008 cells after three treatment/recovery cycles with 2ug/ml of cisplatin (Schedule B)


title: Olfactory bulbs 3 copies biological 2 technical 1

description: Mus Musculus Olfactory Dosage 3

source_name: Olfactory Dosage 3

value: Olfactory


title: Cortex 3 copies biological 2 technical 1

description: Mus Musculus Cortex Dosage 3

source_name: Cortex Dosage 3


title: OV2008

description: Baseline expression of OV2008 cell line

value: Untreated


title: OVCAR5

description: Baseline expression of OVCAR5 cell line

value: 0 ug/ml


title: IGROV1_5.3.6

description: IGROV1 cells after 3 treatment/recovery cycles of 3ug/ml of cisplatin followed by 3 treatment/recovery cycles of 5ug/ml of cisplatin (Schedule C)

source_name: IGROV1 ovarian cancer cells

value: C


title: Olfactory bulbs 3 copies biological 1 technical 1

description: Mus Musculus Olfactory Dosage 3


title: OVCAR5_1.3.3

description: OVCAR5 cells after three treatment/recovery cycles with 1ug/ml of cisplatin (Schedule A)

value: 1 ug/ml


title: OV2008_1.3.3

description: OV2008 cells after three treatment/recovery cycles with 1ug/ml of cisplatin (Schedule A)


title: IGROV1_3.3.3

description: IGROV1 cells after three treatment/recovery cycles with 3ug/ml of cisplatin (Schedule C)


title: IGROV1_3.3.6

description: IGROV1 cells after 3 treatment/recovery cycles of 1ug/ml of cisplatin followed by 3 treatment/recovery cycles of 3ug/ml of cisplatin (Schedule A)


title: Cortex 3 copies biological 1 technical 1

description: Mus Musculus Cortex Dosage 3


title: IGROV1_4.3.6

description: IGROV1 cells after 3 treatment/recovery cycles of 2ug/ml of cisplatin followed by 3 treatment/recovery cycles of 4ug/ml of cisplatin (Schedule B)


title: IGROV1_1.3.3

description: IGROV1 cells after three treatment/recovery cycles with 1ug/ml of cisplatin (Schedule A)


title: I4-B: 200 nM insulin 15 min incubation after 20 hours serum and insulin starvation, replicate #2.

source_name: Human podocyte cell line; 200 nM insulin 15 min incubation after 20 hours serum and insulin starvation

value: podocyte

value: 200nm Insulin after starved


title: I4-C: 200 nM insulin 15 min incubation after 20 hours serum and insulin starvation, replicate #3.


title: IGROV1_2.3.3

description: IGROV1 cells after three treatment/recovery cycles with 2ug/ml of cisplatin (Schedule B)


title: Cerebellum 3 copies biological 1 technical 2

description: Mus Musculus Cerebellum Dosage 3

value: Cerebellum


title: I4-A: 200 nM insulin 15 min incubation after 20 hours serum and insulin starvation, replicate #1.


title: G3-B: 25mM glucose for 24h, replicate #2.

source_name: Human podocyte cell line: 25mM glucose for 24 hours

value: 25mM glucose 24hrs


title: G3-A: 25mM glucose for 24h, replicate #1.


title: Cerebellum 3 copies biological 1 technical 1

description: Mus Musculus Cerebellum Dosage 3

value: dp/+


title: IGROV1

description: Baseline expression of IGROV1 cell line


title: C13_1.3.3

description: C13 cells after three treatment/recovery cycles with 1ug/ml of cisplatin (Schedule A)

source_name: C13 ovarian cancer cells

value: A


title: C13_3.3.6

description: C13 cells after 3 treatment/recovery cycles of 1ug/ml of cisplatin followed by 3 treatment/recovery cycles of 3ug/ml of cisplatin (Schedule A)

value: 3 ug/ml


title: G3-C: 25mM glucose for 24h, replicate #3.


title: ISC-A: Insulin test starved control: 20 hour serum and insulin starvation, replicate #1.

source_name: Human podocyte cell line: Insulin test starved control

value: Insulin Starved


title: C13_5.3.6

description: C13 cells after 3 treatment/recovery cycles of 3ug/ml of cisplatin followed by 3 treatment/recovery cycles of 5ug/ml of cisplatin (Schedule C)

value: 5 ug/ml


title: C13_2.3.3

description: C13 cells after three treatment/recovery cycles with 2ug/ml of cisplatin (Schedule B)

value: B


title: C13

description: Baseline expression of C13 cell line


title: Olfactory bulbs 1 copy biological 1 technical 1

description: Mus Musculus Olfactory Dosage 1

source_name: Olfactory Dosage 1

value: df/+

value: male


title: Cortex 1 copy biological 1 technical 2

description: Mus Musculus Cortex Dosage 1

source_name: Cortex Dosage 1

value: Cortex


title: A2780S_5.3.6

description: A2780S cells after 3 treatment/recovery cycles of 3ug/ml of cisplatin followed by 3 treatment/recovery cycles of 5ug/ml of cisplatin (Schedule C)

source_name: A2780S ovarian cancer cells


title: C13_4.3.6

description: C13 cells after 3 treatment/recovery cycles of 2ug/ml of cisplatin followed by 3 treatment/recovery cycles of 4ug/ml of cisplatin (Schedule B)

value: 4 ug/ml


title: ISC-C: Insulin test starved control: 20 hour serum and insulin starvation, replicate #3.


title: C13_3.3.3

description: C13 cells after three treatment/recovery cycles with 3ug/ml of cisplatin (Schedule C)


title: Cortex 1 copy biological 1 technical 1

description: Mus Musculus Cortex Dosage 1


title: ISC-B: Insulin test starved control: 20 hour serum and insulin starvation, replicate #2.


title: A2780S_3.3.6

description: A2780S cells after 3 treatment/recovery cycles of 1ug/ml of cisplatin followed by 3 treatment/recovery cycles of 3ug/ml of cisplatin (Schedule A)


title: Brain Stem 3 copies biological 1 technical 1

description: Mus Musculus Brain Stem Dosage 3

value: Brain Stem


title: Cerebellum 1 copy biological 1 technical 1

description: Mus Musculus Cerebellum Dosage 1

source_name: Cerebellum Dosage 1


title: A2780S_2.3.3

description: A2780S cells after three treatment/recovery cycles with 2ug/ml of cisplatin (Schedule B)

value: 2 ug/ml


title: NC-A: Normal culture conditions: RPM-1640, 10% FBS, 1*ITS supplement, replicate #1.

source_name: Human podocyte cell line; Normal culture conditions

value: Normal


title: A2780S_4.3.6

description: A2780S cells after 3 treatment/recovery cycles of 2ug/ml of cisplatin followed by 3 treatment/recovery cycles of 4ug/ml of cisplatin (Schedule B)


title: NC-B: Normal culture conditions: RPM-1640, 10% FBS, 1*ITS supplement, replicate #2.

value: podocyte


title: A2780CP_5.3.6

description: A2780CP cells after 3 treatment/recovery cycles of 3ug/ml of cisplatin followed by 3 treatment/recovery cycles of 5ug/ml of cisplatin (Schedule C)

source_name: A2780CP ovarian cancer cells

value: C


title: A2780S_1.3.3

description: A2780S cells after three treatment/recovery cycles with 1ug/ml of cisplatin (Schedule A)

value: 1 ug/ml


title: A2780CP_4.3.6

description: A2780CP cells after 3 treatment/recovery cycles of 2ug/ml of cisplatin followed by 3 treatment/recovery cycles of 4ug/ml of cisplatin (Schedule B)


title: Brain Stem 1 copy biological 1 technical 1

description: Mus Musculus Brain Stem Dosage 1

source_name: Brain Stem Dosage 1


title: SHAM: Dermal fibroblasts, Sham replicate #1.

source_name: Dermal fibroblasts, Sham replicate #1.

value: dermal fibroblasts

tag: uvb treated

value: No

tag: il-α treated

tag: disease state


title: Cerebellum 1 copy biological 1 technical 2

description: Mus Musculus Cerebellum Dosage 1

tag: mouse id

tag: brain region

value: Cerebellum


title: SHAMIL: Dermal fibroblasts, Sham-IL replicate #1.

value: Yes


title: Brain Stem 2 copies biological 1 technical 1

description: Mus Musculus Brain Stem Dosage 2

source_name: Brain Stem Dosage 2

tag: strain

tag: gender


title: A2780S

description: Baseline expression of A2780S cell line

value: Untreated

value: 0 ug/ml


title: A2780S_3.3.3

description: A2780S cells after three treatment/recovery cycles with 3ug/ml of cisplatin (Schedule C)

value: 3 ug/ml


title: NC-C: Normal culture conditions: RPM-1640, 10% FBS, 1*ITS supplement, replicate #3.


title: A2780CP

description: Baseline expression of A2780CP cell line


title: A2780CP_2.3.3

description: A2780CP cells after three treatment/recovery cycles with 2ug/ml of cisplatin (Schedule B)

value: B


title: A2780CP_3.3.6

description: A2780CP cells after 3 treatment/recovery cycles of 1ug/ml of cisplatin followed by 3 treatment/recovery cycles of 3ug/ml of cisplatin (Schedule A)

value: A


title: A2780CP_1.3.3

description: A2780CP cells after three treatment/recovery cycles with 1ug/ml of cisplatin (Schedule A)


title: UVB30MJ: Dermal fibroblasts, UVB-30MJ replicate #1.


title: UVBIL: Dermal fibroblasts, UVB-IL replicate #1.

source_name: Dermal fibroblasts, UVB-IL replicate #1


title: EpiSC-derived-Oligos_passage11

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

description:
Gene expression of passage 11 EpiSC-derived OPCs differentiated to oligodendrocytes
Oligos_p11

hyb_protocol: Labeled cRNA (10 ug) was hybridized for 17 hours at 45 degrees C on Affmetrix Mouse Gene 1.0 ST arrays, washed, and stained in the Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using Affymetrix Scanner 3000 7G

data_processing: Cel files were generated with the Affymetrix GeneChip Command Console 2.0 and the data were normalized with the RMA method using the default settings in Expression Console Software (Affymetrix)

source_name: EpiSC-derived oligodendrocytes, p11

label_protocol: Biotinylated cRNA was prepared from 150ng of total RNA using the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer's instructions

growth_protocol: EpiSCs were grown in Knockout DMEM +20% KSR, +10ng/ml FGF2.

extract_protocol: Total RNA prepared using the RNeasy Plus Kit (Qiagen) according to the manufacturer’s protocol

treatment_protocol: EpiSCs were differentiated to to patterned neural rosettes with SB431542, Dorsomorphin, Noggin, RA, and SHH over 5 days.  Rosettes were dissociated to generate OPC cultures which were grown in N2B27 +FGF2, PDGF-AA, and SHH.  OPCs were differentiated to oligodendrocytes by addition of thyroid hormone and removal of FGF2 and PDGF-AA.

tag: developmental stage/cell type

value: oligodendrocytes

tag: passage


title: A2780CP_3.3.3

description: A2780CP cells after three treatment/recovery cycles with 3ug/ml of cisplatin (Schedule C)


title: A2008_4.3.6

description: A2008 cells after 3 treatment/recovery cycles of 2ug/ml of cisplatin followed by 3 treatment/recovery cycles of 4ug/ml of cisplatin (Schedule B)

source_name: A2008 ovarian cancer cells

value: 4 ug/ml


title: A2008_5.3.6

description: A2008 cells after 3 treatment/recovery cycles of 3ug/ml of cisplatin followed by 3 treatment/recovery cycles of 5ug/ml of cisplatin (Schedule C)

value: 5 ug/ml


title: EpiSC-derived-OPCs_passage3

description:
Gene expression of passage 3 oligodendrocyte progenitor cells (OPCs) differentiated from EpiSC-derived rosettes
OPCs_p3

source_name: EpiSC-derived OPCs, passage 3

value: oligodendrocyte progenitor cells


title: EpiSC_undifferentiated

description:
Gene expression of epiblast stem cells (EpiSCs)
EpiSCs

source_name: EpiSCs

value: epiblast


title: EpiSC-derived-OPCs_passage11

description:
Gene expression of passage 11 oligodendrocyte progenitor cells (OPCs) differentiated from EpiSC-derived rosettes
OPCs_p11

source_name: EpiSC-derived OPCs, passage 11


title: EpiSC-derived-Oligos_passage3

description:
Gene expression of passage 3 EpiSC-derived OPCs differentiated to oligodendrocytes
Oligos_p3

source_name: EpiSC-derived oligodendrocytes, p3


title: EpiSC-derived-rosettes_day5

description:
Gene expression of EpiSCs differentiated to patterned neural rosettes for 5 days
Rosettes

source_name: EpiSC-derived rosettes, day 5

value: ventral neural tube


title: A2008_3.3.3

description: A2008 cells after three treatment/recovery cycles with 3ug/ml of cisplatin (Schedule C)

value: C


title: A2008_3.3.6

description: A2008 cells after 3 treatment/recovery cycles of 1ug/ml of cisplatin followed by 3 treatment/recovery cycles of 3ug/ml of cisplatin (Schedule A)


title: A2008_1.3.3

description: A2008 cells after three treatment/recovery cycles with 1ug/ml of cisplatin (Schedule A)

value: 1 ug/ml


title: A2008_2.3.3

description: A2008 cells after three treatment/recovery cycles with 2ug/ml of cisplatin (Schedule B)

value: 2 ug/ml


title: colon_heme_repl9

status: Public on Oct 02 2011

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description:
A108_C18_HEME_MCOLON
Colon from heme-fed mouse after 2 weeks of heme diet (40en%fat and 0.5 umol/g heme added).

hyb_protocol: Hybridization of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA (v2.22.0) in Bioconductor, applying the empirical Bayes (EB) model for background estimation.

source_name: colon, 2 weeks of heme diet (40en%fat and 0.5 umol/g heme added)

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).

extract_protocol:
Colons were taken out of the mice and mesenteric fat was removed. Colons were cut open longitudinally, washed in PBS and scraped. RNA was isolated from scrapings. All mice were individually analyzed by microarray.

Total RNA was prepared from mouse colon scrapings using TRIzol reagent, and total RNA was purified using Qiagen RNeasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Male control and heme-fed mice were maintained on a high fat-low calcium diet (high fat and low calcium diet with or high fat and low calcium diet without heme) for 2 weeks. After 2 weeks diet intervention, all mice were sacrificed.

value: male

tag: age

value: 11 weeks

value: colon

tag: treatment

value: high fat and low calcium diet with heme

tag: treatment duration

value: 14 days


title: A2008

description: Baseline expression of A2008 cell line

value: Untreated

value: 0 ug/ml


title: colon_control_repl3

description:
A108_C09_CTR_MCOLON
Colon from control mouse after 2 weeks of control diet (40en% fat).

source_name: colon, 2 weeks of control diet (40en% fat)

tag: tissue

value: high fat and low calcium diet without heme


title: colon_control_repl2

description:
A108_C03_CTR_MCOLON
Colon from control mouse after 2 weeks of control diet (40en% fat).


title: colon_heme_repl6

description:
A108_C12_HEME_MCOLON
Colon from heme-fed mouse after 2 weeks of heme diet (40en%fat and 0.5 umol/g heme added).


title: colon_heme_repl3

description:
A108_C06_HEME_MCOLON
Colon from heme-fed mouse after 2 weeks of heme diet (40en%fat and 0.5 umol/g heme added).


title: colon_control_repl6

description:
A108_C15_CTR_MCOLON
Colon from control mouse after 2 weeks of control diet (40en% fat).


title: colon_heme_repl5

description:
A108_C10_HEME_MCOLON
Colon from heme-fed mouse after 2 weeks of heme diet (40en%fat and 0.5 umol/g heme added).


title: colon_heme_crypt_pool

description:
A139_04_CRYPT_HEME
Pool of colon crypt cells from 3 mice after 2 weeks of heme diet (40en% fat diet, with 0.5 umol/g heme added).

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.14.0).

source_name: pool of colon crypt cells, 2 weeks of heme diet (40en% fat diet, with 0.5 umol/g heme added)

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction.A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

extract_protocol:
Colons were taken out of the mice and mesenteric fat was removed. Colons were cut open longitudinally and washed in PBS, and a Swiss roll was made and immediately snap frozen. Laser capture microdissection was applied to isolate either surface or crypt cells. RNA was isolated from the surface and crypt cells of 4 control mice and 3 heme-fed mice. Samples were pooled into 4 groups: control surface (n=4), control crypt (n=4), heme surface (n=3), and heme crypt (n=3). Pools were analyzed by microarray.

RNA was isolated from LCM caps by using the PicoPure RNA isolation Kit (Arcturus). RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Male control and heme-fed mice were maintained on a high fat-low calcium diet (with or without heme) for 2 weeks. After 2 weeks diet intervention, all mice were sacrificed.

tag: cell type

value: crypt cells

tag: number of mice


title: colon_control_repl4

description:
A108_C11_CTR_MCOLON
Colon from control mouse after 2 weeks of control diet (40en% fat).


title: colon_heme_repl2

description:
A108_C04_HEME_MCOLON
Colon from heme-fed mouse after 2 weeks of heme diet (40en%fat and 0.5 umol/g heme added).


title: colon_heme_repl8

description:
A108_C16_HEME_MCOLON
Colon from heme-fed mouse after 2 weeks of heme diet (40en%fat and 0.5 umol/g heme added).


title: colon_control_repl5

description:
A108_C13_CTR_MCOLON
Colon from control mouse after 2 weeks of control diet (40en% fat).


title: colon_heme_repl1

description:
A108_C02_HEME_MCOLON
Colon from heme-fed mouse after 2 weeks of heme diet (40en%fat and 0.5 umol/g heme added).


title: colon_heme_repl7

description:
A108_C14_HEME_MCOLON
Colon from heme-fed mouse after 2 weeks of heme diet (40en%fat and 0.5 umol/g heme added).


title: colon_control_repl1

description:
A108_C01_CTR_MCOLON
Colon from control mouse after 2 weeks of control diet (40en% fat).


title: colon_control_repl7

description:
A108_C17_CTR_MCOLON
Colon from control mouse after 2 weeks of control diet (40en% fat).


title: colon_control_crypt_pool

description:
A139_02_CRYPT_CTR
Pool of colon crypt cells from 4 mice after 2 weeks of control diet (40en% fat).

source_name: pool of colon crypt cells, 2 weeks of control diet (40en% fat)


title: colon_heme_repl4

description:
A108_C08_HEME_MCOLON
Colon from heme-fed mouse after 2 weeks of heme diet (40en%fat and 0.5 umol/g heme added).


title: colon_heme_surface_pool

description:
A139_03_SURF_HEME
Pool of colon surface cells from 3 mice after 2 weeks of heme diet (40en% fat diet, with 0.5 umol/g heme added).

source_name: pool of colon surface cells, 2 weeks of heme diet (40en% fat diet, with 0.5 umol/g heme added)

value: surface cells


title: steady-state sulfate limitation biological rep 2 of 3

status: Public on Oct 01 2011

city: Athens

first: Shalabh

last: Sharma

state: GA

address: Department of Marine Science

department: Marine Science

institute: UGA

description: Biological replicate 2 of 3 of the sulfate limitation sample

hyb_protocol: Labeled mRNA samples were hybridized to custom microarray slides manufactured by Combimatrix (Mukilteo, WA, USA) and imaged according to the procedures described in the manufacturer's protocol. Hybridized slides were stripped according to Combimatrix's protocol and re-used up to three times.

scan_protocol: Axon Genpix GenPix 4000B microarray scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) at 5 µm resolution.

data_processing: The procedures were modified from Burgmann et al., 2007 (Environmental Microbiology 9: 2742-2755). Each gene was represented by up to two probes and each probe was spotted up to three times on the array (Burgmann et al., 2007). Each hybridized spot was manually examined in GenePix Pro 6.0 Software (Molecular Devices, Sunnyvale, CA) for quality. The fluorescence value for each hybridized spot was subtracted from the five closest empty spots on the array (F635-B635; PRE_VALUE). Spots were flagged as bad with Acuity 4.0 (Molecular Devices) when they were unevenly hybridized (determined manually by checking the hybridization circularity), when the detected fluorescence minus the background fluorescence was less than two standard deviations of the background fluorescence (F635-B635 <2 SD(B635)), or when the signal to noise ratio (SNR635) was <3. Probes were removed when the flagged spots were present in >25% of arrays. For the remaining probes with good hybridization signal, those  targeting 5S rRNA, 16S rRNA, 23S rRNA, mismatch probes, and manufacturer's control probes were removed. These processing steps resulted in 5145 probes across 14 arrays (three biological replicates from glucose, ammonium, phosphate, and sulfate limitations and one technical replicate each for the ammonium and sulfate limitations) whose fluorescence values (PRE_VALUE) were used for global normalization (VALUE).

label: AlexaFluor dye 647 (red emission)

organism: Ruegeria pomeroyi DSS-3

source_name: Steady-state cells limited with 25 µM sulfate

label_protocol: This protocol was described by Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755. Amplified mRNA was labeled with AlexaFluor 647 dye (Invitrogen, Carlsbad, CA, USA) according to manufacturer's recommended procedures. Amplified and labeled mRNA was purified with the MEGAclear kit (Applied Biosystems/Ambion, Austin, TX, USA) and concentrated by ethanol precipitation.

growth_protocol: Ruegeria pomeroyi strain DSS-3 was grown in 320 ml custom-made chemostats with a culture volume of 200 ml. Steady-state biomass was limited by sulfur (sulfate, 25 µM) whereas other non-limiting macronutrients were provided in excess. The culture medium was buffered with 10 mM 1,3-bis(tris(hydroxymethyl)methylamino)propane. Vitamins and trace metals were added to the culture medium. The feed medium was added to each chemostat culture at a constant rate, and spent medium and cells were removed at the same rate. During the incubation, cell cultures were mixed by constant stirring. Growth temperature was maintained at 30 degree celsius using a circulating water bath. Salinity was constant at 25. Oxygen was bubbled into the culture at a flow rate of 2 ml per minute through an aquarium air pump, controlled by a flow meter. The pH ranged from 6.6 to 7.0 during all growth regimes. Cell cultures were considered to be at steady-state when the change in OD600 was less than or equal to 10% between two successive measurements.

extract_protocol: Total RNA from steady-state cell culture was purified using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s procedures. DNA was removed by TURBO DNase treatment (Applied Biosystems/Ambion, Austin, TX, USA). Ribosomal RNA was removed with MicrobeExpress (Applied Biosystems/Ambion) according to manufacturer's recommendations. Purified mRNA was amplified with MessageAmp II-Bacteria Kit (Applied Biosystems/Ambion) with procedures as described in manufacturer's manual.

tag: cell growth conditions

value: Chemostat culture with sulfate (25 µM) limitation


title: colon_control_surface_pool

description:
A139_01_SURF_CTR
Pool of colon surface cells from 4 mice after 2 weeks of control diet (40en% fat).

source_name: pool of colon surface cells, 2 weeks of control diet (40en% fat)


title: steady-state sulfate limitation biological rep 3 of 3

description: Biological replicate 3 of 3 of the sulfate limitation sample


title: TGFb-3

city: Birmingham

first: Rosa

last: Serra

state: AL

address: 1918 University Blvd. 660 MCLM

department: Cell Biology

institute: University of Alabama at Birmingham

hyb_protocol: The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).

scan_protocol: Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).

data_processing: The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used.

organism: Bos taurus

source_name: Chondrocytes in micromass, TGFb treated

label_protocol: Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions. After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed. Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.

growth_protocol: Bovine articular chondrocyte micromass cultures were set up according to the methods of Chen et al., BBRC 1993; Luyten et al., ECR 1994.

extract_protocol: RNA was extracted from the cells in culture using the standard Trizol method. RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.

treatment_protocol: After overnight culture, cells were treated with vehicle or with 5ng/ml of TGFß1 (R&D Systems) for 8 hours.

value: articular chondrocyte micromass

tag: treatment group

value: TGFb treated


title: TGFb-2


title: Untreated-1

source_name: Chondrocytes in micromass, untreated


title: steady-state sulfate limitation tech rep 2 of 2 from the biological rep 1 of 3

description: Technical replicate 2 of 2 from biological replicate 1 of 3 of the sulfate limitation sample


title: TGFb-1


title: Untreated-2


title: Untreated-3


title: steady-state sulfate limitation tech rep 1 of 2 from the biological rep 1 of 3

description: Technical replicate 1 of 2 from biological replicate 1 of 3 of the sulfate limitation sample


title: steady-state glucose limitation biological rep 2 of 3

description: Biological replicate 2 of 3 of the glucose limitation sample

source_name: Steady-state cells limited with 1 mM glucose

growth_protocol: Ruegeria pomeroyi strain DSS-3 was grown in 320 ml custom-made chemostats with a culture volume of 200 ml. Steady-state biomass was limited by carbon (glucose, 1 mM) whereas other non-limiting macronutrients were provided in excess. The culture medium was buffered with 10 mM 1,3-bis(tris(hydroxymethyl)methylamino)propane. Vitamins and trace metals were added to the culture medium. The feed medium was added to each chemostat culture at a constant rate, and spent medium and cells were removed at the same rate. During the incubation, cell cultures were mixed by constant stirring. Growth temperature was maintained at 30 degree celsius using a circulating water bath. Salinity was constant at 25. Oxygen was bubbled into the culture at a flow rate of 2 ml per minute through an aquarium air pump, controlled by a flow meter. The pH ranged from 6.6 to 7.0 during all growth regimes. Cell cultures were considered to be at steady-state when the change in OD600 was less than or equal to 10% between two successive measurements.

value: Chemostat culture with glucose (1 mM) limitation


title: Mafosfamide

city: Ludwigshafen

first: Kamran

last: Harati

address: Ludwig-Guttmanstrasse 13

department: Department of Hand and Plastic Surgery, Burn Centre

country: Germany

institute: BG University Hospital Ludwigshafen

description: mRNA expression

hyb_protocol: Samples were hybridized using Agilent 10x blocking agent and 25x fragmentation buffer, and 2xGEx hybridization buffer according to the manufacturer's instructions  for 17 hours at 65C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B ) using standard setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 014850_D_F_20100430 ) to obtain background subtracted and spatially detrended Processed Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: 100 ng of total RNA were labeled using the QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, using T7 priming and MMLV-RT to generate cDNA. cRNA is then prepared using T7 RNA Polymerase according to the manufacturer's instructions, and labeled with cyanine-3-CTP (Cy3)

growth_protocol: Human fibrosarcoma cells, HT1080, were maintained in modified Eagle's medium (MEM) and NEAA (non-essential amino acids) + 10% FBS (foetal bovine serum) supplemented with 1% penicillin (100 U/ml) and streptomycin (100 μg/ ml), 1% sodium pyruvate and 1% L-glutamine. The cells were cultured in a humidified atmosphere with 5% CO2 at 37°C .

extract_protocol: Total RNA was extracted by a standard protocol.

treatment_protocol: For every drug experiment, 80 µl of 3.125 × 10^6 cells/ml were placed in 6-well plates containing the medium. After 24 hours, the medium was replaced and the drugs were added to each well. The cultivated human fibrosarcoma cells were incubated with doxorubicin (0.25 µg/ml), mafosfamide (1.5 µg/ml) and trabectedin (4 µg/ml) either alone or in combination with TRD (250 μmol/l) and/or TRAIL (50 ng/ml) for 6 hours.

tag: cell line

value: fibrosarcoma cells


title: Infested plant, biological rep2

city: Pontevedra

first: Victor

middle: M

last: Rodriguez

address: Apartado 28

department: Plant Genetics and Breeding

institute: Mision Biologica de Galicia (CSIC)

description: Gene expression data from maize plants challenged with S. nonagrioides

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Fluorescence signaling was scanned using a GeneChip® 3000 scanner

data_processing: Data analysis was performed using the Robust Multichip Average (RMA) tool included in the Affymetrix Expression Console software

organism: Zea mays

source_name: Maize genotype EP39 after S. nonagrioides feeding

label_protocol: Two hundred and fifty ng of total RNA were labeled with the GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA) following manufacturer’s instructions

growth_protocol: Four genetically unrelated maize inbred lines (EP39, EP42, CM151 and PB130) were grown in the greenhouse under controlled conditions

extract_protocol: Individual sample tissues were ground in liquid nitrogen and the RNA from four biological replicates of each genotype and treatment was extracted using the RiboPureTM kit (Ambion, Foster City, CA)

treatment_protocol: Infestation was carried out at VT (tasseling) developmental stage with a mass of approximately 40 eggs of S. nonagrioides laid on the sheath of the main ear. Fifteen days after infestation tissue samples were collected and conserved at -80ºC

value: Stem internode below the ear

tag: genotype


title: Mafosfamide and TRD and TRAIL

description: mRNA expression


title: Doxorubicin and TRD and TRAIL

description: mRNA expression


title: Infested plant, biological rep3

source_name: Maize genotype EP42 after S. nonagrioides feeding


title: Mafosfamide and TRAIL

description: mRNA expression


title: Control plant, biological rep2

source_name: Maize genotype EP39 in resting conditions


title: Control plant, biological rep3

source_name: Maize genotype EP42 in resting conditions


title: steady-state glucose limitation biological rep 3 of 3

description: Biological replicate 3 of 3 of the glucose limitation sample


title: steady-state glucose limitation biological rep 1 of 3

description: Biological replicate 1 of 3 of the glucose limitation sample


title: Mafosfamide and TRD

description: mRNA expression


title: Control plant, biological rep4

source_name: Maize genotype PB130 in resting conditions


title: Control plant, biological rep1

source_name: Maize genotype CM151 in resting conditions


title: Infested plant, biological rep4

source_name: Maize genotype PB130 after S. nonagrioides feeding


title: Doxorubicin and TRAIL

description: mRNA expression


title: Infested plant, biological rep1

source_name: Maize genotype CM151 after S. nonagrioides feeding


title: Trabectedin and TRD and TRAIL

description: mRNA expression


title: Doxorubicin

description: mRNA expression


title: Trabectedin and TRAIL

description: mRNA expression


title: Trabectedin and TRD

description: mRNA expression


title: Trabectedin

description: mRNA expression


title: Hdhq111 brain_rep5

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

hyb_protocol: The hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization, slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying, slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2.  Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner, and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA).  Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio-based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation.

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA, individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from the OD260/280 measurement, and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

value: HdhQ111/+ heterozygote

value: 18 weeks

value: brain

tag: sample type

value: individual

source_name: WT RNA pool, brain

label_protocol:
For labeling, 20 µg of total RNA was reverse transcribed and indirectly labeled with Cy3 or Cy5 fluorescent dye according to the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from four control animals) labeled with the second dye.

HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

value: wildtype

value: RNA pool

tag: mouse ids


title: Hdhq111 brain_rep7

label_protocol:
For labeling, 20 µg of total RNA was reverse transcribed and indirectly labeled with Cy3 or Cy5 fluorescent dye according to the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from four control animals) labeled with the second dye.

HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray

value: male

tag: mouse id


title: Hdhq111 brain_rep8

tag: strain


title: Hdhq111 liver_rep8

tag: gender

value: liver

source_name: WT RNA pool, liver


title: Hdhq111 liver_rep7


title: Hdhq111 liver_rep6


title: Hdhq111 liver_rep1


title: Hdhq111 liver_rep3


title: Hdhq111 brain_rep1


title: Hdhq111 liver_rep2


title: Hdhq111 brain_rep3


title: Hdhq111 brain_rep2


title: Hdhq111 liver_rep5


title: Doxorubicin and TRD

description: mRNA expression


title: Hdhq111 liver_rep4


title: Control

description: mRNA expression


title: Hdhq111 brain_rep4


title: MEF_DKO3

city: Rotterdam

first: Eugin

last: Destici

address: Dr. Molewaterplein 50

department: Genetics

institute: Erasmus MC

description: The MEFs were isolated from embryos in a near-C57BL/6J background (>7 backcrosses from BL6/129 mice).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse 430 2.0 arrays using the Affymetrix hybridization Oven 640.

scan_protocol: GeneChips were scanned using the Affymetrix hybridization Oven 640.

data_processing: Initial data extraction and normalization within each array were performed using GCOS software (Affymetrix) using standard settings. Data were log2 transformed and normalized between arrays by means of the quantile normalization method in R. Probe sets that were called ABSENT in all arrays were excluded from the analysis.

source_name: primary MEF, Cry DKO

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

growth_protocol: DMEM/F10 medium+10% FCS, 3% O2-incubator, asynchronous proliferation.

treatment_protocol: None.

tag: background strain

value: mouse embryonic fibroblast (MEF)


title: MEF_DKO2


title: MEF_DKO4


title: MEF_WT3

source_name: primary MEF, WT

value: wild-type


title: MEF_WT4


title: Hdhq111 brain_rep6


title: MEF_DKO1


title: MEF_WT1


title: P59, biol rep1

city: Irvine

first: William

last: Gordon

address: 839 Health sciences way

department: Medicine

institute: University of CA Irvine

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array

scan_protocol: Standard Affymetrix protocol.

data_processing: The data was analyzed with Affymetrix Gene Expression Console software using RMA

source_name: Dorsal Skin Postnatal day 59

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug total RNA

extract_protocol: RNA was extracted using Invitrogen's Trizol reagent and cleaned over Invitrogen RNA purification columns

treatment_protocol: Dorsal skin wash shaved, removed, and placed into RNA Later after mice were sacrificed

tag: Sex

value: Male


title: P59, biol rep2


title: P54, biol rep2

source_name: Dorsal Skin Postnatal day 54


title: T-ALL Cell Line T4100 (Y6)

city: San Francisco

first: Ashley

middle: Flynn

last: Ward

address: 505 Parnassus Ave, M649

institute: UCSF

hyb_protocol: Following fragmentation, 12.5 microgram of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Hematopoietic tissue cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix).

growth_protocol: Cell lines were created from the spleens of diseased animals by culturing cells in lymphocyte media (DMEM H-21, 20% FBS, 10mM HEPES, 1x NEAA, 1x NaPyruvate, 1x glutamate, 1x penn/strep, 50uM BME, 10ng/ml IL-2 and 10ng/ml IL-7).  RNA was extracted from these cell lines.

extract_protocol: Trizol

value: Balb/c

value: T-ALL

tag: input kras mutations


title: T-ALL Cell Line F1006 (Y1)


title: MEF_WT2

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


title: T-ALL Cell Line T1000 (E2)


title: T-ALL Cell Line F1007 (Y2)


title: T-ALL Cell Line T2006 (Y3)


title: 393P, MKK4shRNA B

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description:
393P cells with MKK4 knockdown (393P-shZ), sample 2 of 3.
H0022317

hyb_protocol: Following fragmentation, cRNA was hybridized on Mouse430 2.0 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10% of intensity values.

source_name: 393P lung cancer cell line, MKK4 knockdown

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

growth_protocol: Cell lines from p53R172H∆g/+ K-rasLA1/+ mice were derived from tumor tissues removed at autopsy. The tissues were minced, placed in culture, and passed serially in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), which yielded mass populations of tumor cells derived from primary lung tumors (393P).

extract_protocol: Total RNA was isolated by the Ambion kit. RNA quality and quantity were evaluated on a NanoDrop spectrophotometer and the Agilent 2100 Bioanalyzer.

treatment_protocol: Vectors expressing mouse MKK4 shRNA were purchased from OriGene. Cells were transfected using Lipofectamine-PlusTM (Invitrogen).

value: lung tumor

tag: vector

value: MKK4 shRNA


title: T-ALL Cell Line T3104 (Y5)


title: 393P, MKK4shRNA C

description:
393P cells with MKK4 knockdown (393P-shZ), sample 3 of 3.
H0022318


title: T-ALL Cell Line F1002 (E1)

description: Acquired Kras T50I Mutation


title: T-ALL Cell Line T4203 (E4)

description: Acquired PTEN loss Mutation


title: 393P, MKK4shRNA A

description:
393P cells with MKK4 knockdown (393P-shZ), sample 1 of 3.
H0022316


title: T-ALL Cell Line T3006 (Y4)

description: Acquired Kras 69RN70 Mutation


title: P54, biol rep1


title: Noto-GFP_negative_sort_rep1

city: Madison

first: Owen

middle: James

last: Tamplin

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

description: replicate 1: posterior regions dissected and pooled from 23 embryos

hyb_protocol: Samples were hybridized to Affymetrix MOE430v2 arrays using the manufacturer's protocols

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Data was analyzed using GCOS software v1.4

source_name: GFP negative cells sorted from the posterior of E8.5 mouse embryos

label_protocol: Total RNA was amplified and labeled using the AFFYMETRIX GeneChip® Two-Cycle Target Labeling Kit

growth_protocol: Litters of heterozygous Noto-GFP embryos (mixed 129S3;ICR background) were collected at embryonic day (E) 8.5 (median somite number 6; ~25-50 embryos per experiment)

extract_protocol: Small-scale RNA extraction was performed using Trizol or Trizol LS as per the manufacturer's instructions. Sigma GeneElute linear polyacrylamide was used as carrier

treatment_protocol: The region posterior to the SI-SII somite boundary was dissected, pooled, and dissociated using 1% trypsin in PBS. Noto-GFP+ cells were sorted from Noto-GFP- cells and both populations were collected (~2600-6600 cells per experiment)

tag: STRAIN

tag: GENDER

value: MIXED


title: T-ALL Cell Line T2002 (E3)

description: Acquired Kras T50I Mutation

tag: cell type


title: 393P, control A

description:
393P cells with control vector (393P-scr), sample 1 of 3.
H0022313

source_name: 393P lung cancer cell line, control

value: control


title: Noto-GFP_negative_sort_rep2

description: replicate 2: posterior regions dissected and pooled from 39 embryos


title: Noto-GFP_negative_sort_rep3

description: replicate 3: posterior regions dissected and pooled from 52 embryos


title: 393P, control B

description:
393P cells with control vector (393P-scr), sample 2 of 3.
H0022314


title: 393P, control C

description:
393P cells with control vector (393P-scr), sample 3 of 3.
H0022315


title: Noto-GFP_positive_sort_rep3

description: replicate 3: posterior regions dissected and pooled from 52 embryos; ~6600 Noto-GFP positive cells sorted

source_name: Noto-GFP positive cells sorted from the posterior of E8.5 mouse embryos