title: gsexp_FWAF_logphase_3

description: G. sulfureducens PCA were grown in standard FWAF medium, cells were harversted at log phase. This is the third biological replicate.


title: gsexp_gln_2

status: Public on Jun 28 2010

type: RNA

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

country: USA

institute: UCSD

description: G. sulfureducens PCA were grown in FWAF medium without NH3 but with Glutamine, cells were harversted at log phase. This is the second biological replicate.

hyb_protocol: Hybridization was performed by UCSD GeneChip Core, following Nimblegen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scan was performed with an Axon GenePix 4000B scanner by UCSD GeneChip Core, following Nimblegen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA without background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Geobacter sulfurreducens PCA

source_name: G. sulfureducens PCA, FWAF medium Glutamine as nitrogen source, log phase

label_protocol: Labeling was performed with an amino-allyl indirect labeling protocol followed by a Dnase I fragmentation step.

growth_protocol: G.sulfurreducens PCA strain was cultured in FWAF medium with glutamine as nitrogen source, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase

extract_protocol: Total RNA was extracted using the Trizol (Invitrogen)  and DNA was removed by DNase digestion. RNA quality and concentration was determined by analysis with an Thermo NanoDrop 1000.

tag: genotype

value: Wild type


title: e11.5_embryo_rep4 [exon version]

status: Public on Jun 29 2010

city: Montreal

first: Timothee

last: Revil

state: Quebec

address: 4060 Ste-Catherine W PT420

department: Human Genetics

country: Canada

institute: McGill University

hyb_protocol: 5 micrograms of biotinylated target was incubated with the GeneChip Human Exon 1.0 ST array (Affymetrix) at 45°C for 16–20 h. After hybridization, nonspecifically bound material was removed by washing and specifically bound target was detected using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing:
Affymetrix Power Tools and PLIER, on core PS and MPS only. For more info, refer to Revil, T. et al. 2010. BMC Genomics.
probe group file MoEx-1_0-st-v1.r2.pgf
meta-probeset file MoEx-1_0-st-v1.r2.dt1.mm8.core.mps

label: biotin

organism: Mus musculus

source_name: embryo, e11.5

label_protocol: cDNA was synthesized using the GeneChip Whole Transcript Sense Target Labeling and Control Reagents kit (Affymetrix) on 1 µg of total RNA treated with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen). This sense cDNA was then labeled using the GeneChip WT Terminal labeling kit (Affymetrix). All the protocols used were provided by the manufacturers.

growth_protocol: To generate embryos, C57BL/6J females were placed with C57BL/6J males overnight and checked for the presence of a vaginal plug in the morning. The day that a plug was detected was considered embryonic day (E) 0.5. All mouse breeding and manipulations were performed in accordance with the Canadian Council on Animal Research. Embryos were collected between E6.5 – E11.5 for RNA isolation.

extract_protocol: Total RNA was extracted using TriZOL (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Embryos for RNA isolation were stored in RNAlater (Ambion) prior to extraction.

tag: age

tag: tissue

value: embryo

tag: strain


title: ExvivoSpleen_VI14d_1

city: ADDLESTON

first: ELIHU

last: Aranday-Cortes

state: SURREY

address: Woodham Lane, New Haw

department: SEB 4

country: United Kingdom

institute: Central Veterinary Laboratories Agency-Weybridge

description: Vaccinated with BCG after 6 weeks and Infected with M. bovis after 14 days

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit. Briefly, 1.65 μg Cy3-labeled fragmented cDNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer (3.6M NaCl, 0.2M NaH2PO4, 0.02M EDTA pH 7.4) contaning 0.005% N-lauroylsarcosine for 1 min at room termperature followed by a second wash with preheated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 seconds.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System. The Agilent Feature Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences.

data_processing: For determination of differential gene expression FES derived output data files were further analyzed using GeneSpring GX 11 (Agilent). The default normalization for Agilent one-color data in the GeneSpring GX program is quantile normalization following Agilent’s guidelines. After normalization we decided to focus on those genes that reliably change their expression, then we filtered the microarrays following three conditions: 1) Filter by value. Genes that do not have normalized signal intensity values of more than -0.5 and 0.5 were disregarded. 2) Filter by flags. All the genes with flags values present in at least 100% of the values in any 1 out of the 6 conditions were considered. 3) Filter by percentile. All the genes with normalized signal intensity values between 25 and 100 in any 1 out of the 6 conditions were also considered. Finally, all the genes in coincidence between filtering by flags group and filtering by percentile group were kept for statistical analysis. After filtering, parametric test (analysis of variance) was applied to compare mean expression levels in each analysis. Data were considered significant when the Benjamini Hochberg false discovery rate (FDR) for the comparison under analysis was <0.05, and the significance level was <0.05. In order to focus on highly regulated genes, we also restricted the majority of the analysis to genes with changes in expression levels of at least 1.7-fold change in all the conditions.

source_name: Spleen

label_protocol: For the linear T7-based amplification step, 0.5 μg of each total RNA samples was used. To produce Cy3-labeled cDNA, the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit following the manufacturer’s protocol. Yields of cDNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer.

growth_protocol: Two groups of 20 mice each were immunised by a single intradermal injection of 2 x 105 CFU of M. bovis BCG (Vaccinated), or Hanks buffered salt solution (HBSS) (Unvaccinated). Six weeks later 5 mice from each group were euthanized for immunological analyses and the remaining mice from each group were challenged with approx 600 CFU M. bovis via the intranasal route. At days 3 and 14 post challenge five mice per group were euthanized and spleens and lungs harvested.

extract_protocol: RNA was isolated using standard RNA extraction protocols (Trizol). RNA samples were quality-checked via the Agilent 2100 Bioanalyzer platform

treatment_protocol: Five mice per group were sacrificed to evaluate the immune response of splenic lymphocytes. Spleen cells were prepared by passage through a 40μm cell strainer into DMEM supplemented with 10% (v/v) foetal calf serum (FCS) and antibiotics (100 U/ml penicillin and 100μg/ml streptomycin) (Gibco, UK) Following washing at 300 x g for 10 minutes cells were suspended at 5 x 10 to 6 /ml for assay. Lung cells were isolated by follow. Briefly, thoracic cavities were opened and gently inject sterile HBSS into right ventricle to perfuse lungs. Mince lungs were resuspended into digestion media DMEM supplemented plus 10 U/ml DNAse II (Sigma) and 150 U/ml collagenase type I (Gibco) and incubated for 1 hour at 37 ˚C and 200 rpm. After digestion lungs were prepared by passage through 100 μm cell strainer into DMEM. Following washing at 1600 rpm for 5 minutes, cells were poured into another tube through a 40 μm cell strainer, washed and used at 5 x 10 to 5.

value: BALB/c

value: Spleen

tag: cell type

value: lymphocytes

tag: treatment group


title: ExvivoSpleen_VU_4

description: Vaccinated with BCG after 6 weeks and Uninfected mice


title: gsexp_gln_3

description: G. sulfureducens PCA were grown in FWAF medium without NH3 but with Glutamine, cells were harversted at log phase. This is the third biological replicate.


title: e11.5_embryo_rep3 [exon version]


title: ExvivoSpleen_VU_5

description: Vaccinated with BCG after 6 weeks and Infected mice with M. bovis after 3 days


title: e9.5_embryo_rep1 [exon version]

source_name: embryo, e9.5


title: gsexp_asp_2

description: G. sulfureducens PCA were grown in FWAF medium without NH3 but with Aspartate, cells were harversted at log phase. This is the second biological replicate.

source_name: G. sulfureducens PCA, FWAF medium Aspartate as nitrogen source, log phase

growth_protocol: G.sulfurreducens PCA strain was cultured in FWAF medium with aspartate as nitrogen source, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase


title: gsexp_asp_3

description: G. sulfureducens PCA were grown in FWAF medium without NH3 but with Aspartate, cells were harversted at log phase. This is the third biological replicate.


title: e9.5_embryo_rep3 [exon version]


title: gsexp_asp_1

description: G. sulfureducens PCA were grown in FWAF medium without NH3 but with Aspartate, cells were harversted at log phase. This is the first biological replicate.


title: gsexp_FWAF_logphase_1

description: G. sulfureducens PCA were grown in standard FWAF medium, cells were harversted at log phase. This is the first biological replicate.

source_name: G. sulfureducens PCA, FWAF medium NH3 as nitrogen source, log phase

growth_protocol: G.sulfurreducens PCA strain was cultured in FWAF medium with ammonium chloride as nitrogen source, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase


title: Primary NK3-F-P3

type: genomic

city: London

first: Muy-Teck

last: Teh

state: England

address: Blizard Building, 4, Newark Street,

department: Centre for Clinical & Diagnostic Oral Sciences

institute: Queen Mary University of London

description: no additional information

hyb_protocol: Standard Affymetrix 10K XbaI protocol was used.

scan_protocol: Fluidics Station 400

data_processing: Affymetrix GCOS 1.4 and GTYPE 4.0

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cells were grown in EpiLife serum free keratinocyte medium in a humidified 5%CO2/95% air tissue culture incubator.

extract_protocol: Standard genomic DNA salt precipitation method was used to extract genomic DNA from cells.

treatment_protocol: Cells were either Mock-transduced (no virus) or transduced with EGFP control or EGFP-FOXM1B (EFOX).

value: skin

value: Primary skin keratinocytes

tag: cell passage

tag: genetic modification


title: e8.5_embryo_rep2 [exon version]

source_name: embryo, e8.5


title: N/TERT cell line-EGFP+UVB

description: no additional information

source_name: N/TERT-EGFP+UVB

label_protocol: Standard Affymetrix 10K XbaI protocol was used.

value: Immortal skin keratinocytes

value: N/TERT, EGFP control

tag: exposure

value: UVB


title: N/TERT cell line-EFOX+UVB

description: no additional information

source_name: N/TERT-EFOX+UVB

value: N/TERT, EGFP-FOXM1B


title: N/TERT cell line-Mock

description: no additional information

source_name: N/TERT-Mock


title: ExvivoSpleen_UI14d_4

description: Unvaccinated and Infected with M.bovis after 14 days


title: ExvivoSpleen_UI14d_3

value: Unvaccinated and Infected with M.bovis after 14 days


title: ExvivoSpleen_VU_1

value: Vaccinated with BCG after 6 weeks and Uninfected mice


title: ExvivoSpleen_VU_2


title: ExvivoSpleen_VU_3


title: Primary NK3-M-P3

description: no additional information


title: ExvivoSpleen_UI14d_5


title: e8.5_embryo_rep3 [exon version]


title: ExvivoSpleen_VI3d_1

value: Vaccinated with BCG after 6 weeks and Infected mice with M. bovis after 3 days


title: ExvivoSpleen_UI14d_1


title: ExvivoSpleen_UI3d_5


title: Primary NK3-G-P3

description: no additional information

value: EGFP control


title: ExvivoSpleen_UI3d_4

description: Unvaccinated and Infected with M.bovis after 3 days


title: ExvivoSpleen_UI14d_2


title: ExvivoSpleen_VI3d_3


title: e8.5_embryo_rep4 [exon version]


title: e8.5_embryo_rep5 [exon version]


title: e8.5_embryo_rep1 [exon version]


title: Primary NK3-M-P2

description: no additional information


title: Primary NK3-G-P2

description: no additional information


title: Primary NK3-M-P1

description: no additional information


title: Primary NK3-F-P1

description: no additional information


title: Primary NK3-G-P1

description: no additional information


title: Primary NK3-F-P2

description: no additional information


title: ExvivoSpleen_UI3d_3

value: Unvaccinated and Infected with M.bovis after 3 days


title: Primary NHEK3-EFOX

description: no additional information


title: Primary NHEK3-EGFP

description: no additional information


title: e9.5_embryo_rep4 [exon version]


title: ExvivoSpleen_UI3d_1


title: Primary NHEK2-EFOX

description: no additional information


title: ExvivoSpleen_UU_3

description: Unvaccinated and Uninfected

value: Unvaccinated and Uninfected


title: ExvivoSpleen_UU_5

description: Unvaccinated and Uninfected


title: Primary NHEK3-Mock

description: no additional information


title: ExvivoSpleen_UU_1

description: Unvaccinated and Uninfected


title: ExvivoSpleen_UU_4

description: Unvaccinated and Uninfected


title: Primary NHEK1-EGFP

description: no additional information


title: ExvivoLung_VI14d_5

source_name: Lung

value: Lung

value: Vaccinated with BCG after 6 weeks and Infected with M. bovis after 14 days


title: Primary NHEK1-Mock

description: no additional information


title: Primary NHEK1-EFOX

description: no additional information


title: ExvivoSpleen_UI3d_2

value: BALB/c


title: ExvivoSpleen_UU_2

description: Unvaccinated and Uninfected

value: Spleen


title: ExvivoLung_VI14d_4


title: Primary NHEK2-Mock

description: no additional information


title: Primary NHEK2-EGFP

description: no additional information


title: ExvivoLung_VI14d_2


title: ExvivoLung_VI14d_3


title: ExvivoLung_VI3d_5


title: ExvivoLung_VI3d_1


title: ExvivoLung_VU_5


title: ExvivoLung_VI3d_3


title: ExvivoLung_VI3d_2


title: ExvivoLung_VI14d_1


title: ExvivoLung_VU_3


title: SinglePositive4+_2_nonamplified

city: Wageningen

first: Dick

middle: de

last: de Ridder

address: Droevendaalsesteeg 1

department: Plant Sciences

country: Netherlands

institute: Wageningen University

hyb_protocol: Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640

scan_protocol: GeneChip® Scanner 3000 ; GCOSv1

data_processing: Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.

source_name: thymic cells, purified using high-speed cell sorting

label_protocol: ENZO kit followed by Qiagen RNeasy “clean-up” spin columns

extract_protocol: Qiagen RNAesy plus shredder

tag: development stage

value: single positive 4+

tag: tissue (organ)

value: thymus

tag: double amplification

value: no


title: SinglePositive4+_1_nonamplified


title: DoublePositive2_2_nonamplified

value: double positive 2


title: ExvivoLung_VU_2


title: SinglePositive8+_2_nonamplified

value: single positive 8+


title: ExvivoLung_VU_4


title: SinglePositive8+_1_nonamplified


title: DoublePositive2_1_nonamplified


title: DoublePositive1_1_nonamplified

value: double positive 1


title: DoubleNegative3_2_nonamplified

value: double negative 3 (pre-T)


title: ImmatureSinglePositive_2_nonamplified

value: immature single positive


title: ExvivoLung_VU_1

value: Vaccinated with BCG after 6 weeks and Uninfected mice


title: ExvivoLung_UI14d_3

value: Unvaccinated and Infected with M.bovis after 14 days


title: ExvivoLung_UI14d_5


title: DoublePositive1_2_nonamplified


title: ImmatureSinglePositive_1_nonamplified


title: DoubleNegative3_1_nonamplified


title: ExvivoLung_UI14d_2


title: ExvivoLung_UI14d_1


title: DoubleNegative12_2_nonamplified

value: double negative 1+2 (pro-T)


title: ExvivoLung_UI3d_5

value: Unvaccinated and Infected with M.bovis after 3 days


title: ExvivoLung_UI14d_4


title: DoubleNegative12_2_amplified

label_protocol: Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II

value: yes


title: DoubleNegative12_1_nonamplified


title: DoubleNegative12_1_amplified


title: StemCellLike_2_amplified

value: stem-cell like


title: ExvivoLung_UI3d_4

value: Lung


title: SAHA-rep2

city: Boston

first: Benjamin

middle: L

last: Ebert

state: MA

address: Harvard Medical School

institute: Dana-Farber Cancer Institute

description: Primary human erythroid progenitor cells treated with 0.5uM SAHA replicate 2

hyb_protocol: Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.

scan_protocol: Scans were performed on Affymetrix scanners.

data_processing: Raw expression values were normalized using Robust Multiarray Averaging (RMA).

label_protocol: First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.

growth_protocol: Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex).  Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol.  Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec).  Erythroid differentiation was induced in vitro in two steps.(1)  For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3),  40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo).  After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.

extract_protocol: RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).

treatment_protocol: Primary erythroid cells were left untreated or treated with 0.5uM SAHA.

tag: treatment

value: 0.5uM SAHA


title: Untreated-rep1

description: Primary human erythroid progenitor cells replicate 1

value: Untreated


title: HDAC2_H6-rep3

description: Primary human erythroid progenitor cells expressing HDAC2 H6 shRNA biological replicate 3

treatment_protocol: Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.

tag: construct

value: HDAC2 H6 shRNA


title: ExvivoLung_UI3d_3

value: BALB/c


title: ExvivoLung_UI3d_2

description: Unvaccinated and Uninfected

value: Unvaccinated and Uninfected


title: ExvivoLung_UU_4

description: Unvaccinated and Uninfected


title: CordBlood_2_amplified

source_name: cord blood, purified using high-speed cell sorting

value: cord blood


title: HDAC2_H6-rep1

description: Primary human erythroid progenitor cells expressing HDAC2 H6 shRNA biological replicate 1


title: HDAC2_H6-rep2

description: Primary human erythroid progenitor cells expressing HDAC2 H6 shRNA biological replicate 2


title: RpoN_N2_logphase_2

description: ChIP-chip G.sulfurreducens, RpoN, FWAF, N2 as nitrogen source

data_processing: IP/mock-IP ratio computation and enriched region identification as implemented in the NimbleScan software package, version 2.4.27 (www.nimblegen.com).

source_name: G.sulfurreducens RpoN ChIP DNA N2 Logphase 2

label_protocol: Labeling was performed following Nimblegen standard operating protocol. See www.nimblegen.com.

growth_protocol: G.sulfurreducens PCA strain was cultured in FWAF medium with N2 as nitrogen source, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase

extract_protocol: Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min. The cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug/mL RNaseA, protease inhibitor cocktail (Sigma) and 1 kU Ready-LyseTM lysozyme (Epicentre). The cells were incubated at room temperature for 30 min and then treated with 0.5 mL of 2XIP buffer with the protease inhibitor cocktail. The lysate was then sonicated four times for 20 sec each in an ice bath to fragment the chromatin complexes using Misonix sonicator 3000 (output level = 2.5). The range of the DNA size resulting from the sonication procedure was 300 – 1000 bp. 6 uL of mouse antibody (NT63, Neoclone) was used to immunoprecipitate the chromatin complex of RNA polymerase subunit (rpoB) and DNA. For the control (mock-IP), 2 ug of normal mouse IgG (Upstate) was added into the cell extract. IP DNAs were purified with QIAquick PCR Purification Kit (Qiagen) then amplified PCR.

treatment_protocol: Cross-linked and sonicated chromatin complex of RpoN and DNA was immunoprecipitated by rabbit serum containing RpoN antibody.

value: Wild type

tag: chip antibody

value: RpoN antibody

source_name: G.sulfurreducens RpoN ChIP DNA N2 Logphase Mock 2

treatment_protocol: Cross-linked and sonicated chromatin complex of RpoN and DNA was immunoprecipitated by normal rabbit IgG for the control.


title: SAHA-rep1

description: Primary human erythroid progenitor cells treated with 0.5uM SAHA replicate 1


title: ExvivoLung_UU_5

description: Unvaccinated and Uninfected


title: ExvivoLung_UU_2

description: Unvaccinated and Uninfected


title: HDAC2_B10-rep3

description: Primary human erythroid progenitor cells expressing HDAC2 B10 shRNA biological replicate 3

value: HDAC2 B10 shRNA


title: CordBlood_1_amplified


title: RpoN_FCA_logphase_3

description: ChIP-chip G.sulfurreducens, RpoN, FCA, NH3 as nitrogen source

source_name: G.sulfurreducens RpoN ChIP DNA FCA Logphase 3

growth_protocol: G.sulfurreducens PCA strain was cultured in FCA medium with ammonium chloride as nitrogen source, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase

source_name: G.sulfurreducens RpoN ChIP DNA FCA Logphase Mock 3


title: RpoN_FWAF_logphase_5

description: ChIP-chip G.sulfurreducens, RpoN, FWAF, NH3 as nitrogen source

source_name: G.sulfurreducens RpoN ChIP DNA FWAF Logphase 5

source_name: G.sulfurreducens RpoN ChIP DNA FWAF Logphase Mock 5


title: HDAC2_B10-rep2

description: Primary human erythroid progenitor cells expressing HDAC2 B10 shRNA biological replicate 2


title: SAHA-rep3

description: Primary human erythroid progenitor cells treated with 0.5uM SAHA replicate 3


title: RpoN_N2_logphase_3

source_name: G.sulfurreducens RpoN ChIP DNA N2 Logphase 3

source_name: G.sulfurreducens RpoN ChIP DNA N2 Logphase Mock 3


title: HDAC1_G10-rep3

description: Primary human erythroid progenitor cells expressing HDAC1 G10 shRNA biological replicate 3

value: HDAC1 G10 shRNA


title: HDAC2_B10-rep1

description: Primary human erythroid progenitor cells expressing HDAC2 B10 shRNA biological replicate 1


title: ExvivoLung_UU_1

description: Unvaccinated and Uninfected


title: Untreated-rep2

description: Primary human erythroid progenitor cells replicate 2


title: NK57_treated-2uM-3day-rep1

description: Primary human erythroid progenitor cells treated with 2uM NK57 for 3 days, rep. 1

treatment_protocol: Primary erythroid cells were left untreated or treated with 2uM NK57 for 3 days.

value: NK57 2uM for 3 days


title: Untreated-rep3

description: Primary human erythroid progenitor cells replicate 3


title: RpoN_N2_logphase_1

source_name: G.sulfurreducens RpoN ChIP DNA N2 Logphase 1

source_name: G.sulfurreducens RpoN ChIP DNA N2 Logphase Mock 1


title: RpoN_FCA_logphase_1

source_name: G.sulfurreducens RpoN ChIP DNA FCA Logphase 1

source_name: G.sulfurreducens RpoN ChIP DNA FCA Logphase Mock 1


title: NK57_treated-2uM-3day-rep2

description: Primary human erythroid progenitor cells treated with 2uM NK57 for 3 days, rep. 2


title: HDAC1_G10-rep2

description: Primary human erythroid progenitor cells expressing HDAC1 G10 shRNA biological replicate 2


title: RpoN_FWAF_logphase_4

source_name: G.sulfurreducens RpoN ChIP DNA FWAF Logphase 4

source_name: G.sulfurreducens RpoN ChIP DNA FWAF Logphase Mock 4


title: RpoN_FWAF_logphase_3

source_name: G.sulfurreducens RpoN ChIP DNA FWAF Logphase 3

source_name: G.sulfurreducens RpoN ChIP DNA FWAF Logphase Mock 3


title: Untreated-3day-rep2b

description: Primary human erythroid progenitor cells after 3 days, rep. 2b

value: Untreated 3 days


title: Hif 2alpha Knockdown replicate 7

city: Philadelphia

first: Dhruv

middle: K

last: Pant

state: PA

address: 421 Curie Blvd.

institute: University of Pennsylvania

hyb_protocol: Dye-coupled cDNA was hybridized to MOE430A microarray gene chips (Affymetrix)

scan_protocol: Arrays were scanned using the Hewlett-Packard GeneArray Scanner

data_processing: GCRMA (the gcrma package in Bioconductor)

label: Biotin

source_name: Hif 2alpha knockdown mice

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

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

value: a mixed 129 SvJ/C57Bl6 genetic background

tag: genotype/variation

value: Hif2alpha deficient


title: Luciferase-rep3

description: Primary human erythroid progenitor cells expressing a luciferase control shRNA biological replicate 3

value: Luciferase Control shRNA


title: HDAC1_A3-rep1

description: Primary human erythroid progenitor cells expressing HDAC1 A3 shRNA biological replicate 1

value: HDAC1 A3 shRNA


title: RpoN_FCA_logphase_2

source_name: G.sulfurreducens RpoN ChIP DNA FCA Logphase 2

source_name: G.sulfurreducens RpoN ChIP DNA FCA Logphase Mock 2


title: HDAC1_G10-rep1

description: Primary human erythroid progenitor cells expressing HDAC1 G10 shRNA biological replicate 1


title: Untreated-3day-rep3a

description: Primary human erythroid progenitor cells after 3 days, rep. 3


title: Untreated-6hour-rep2

description: Primary human erythroid progenitor cells after 6 hours, rep. 2

value: Untreated 6 hours


title: Untreated-3day-rep1b

description: Primary human erythroid progenitor cells after 3 days, rep. 1b


title: Hif 2alpha Knockdown replicate 5


title: Untreated-3day-rep3b

description: Primary human erythroid progenitor cells after 3 days, rep. 3b


title: Untreated-3day-rep1a

description: Primary human erythroid progenitor cells after 3 days, rep. 1


title: Hif 2alpha Knockdown replicate 6


title: Luciferase-rep2

description: Primary human erythroid progenitor cells expressing a luciferase control shRNA biological replicate 2


title: Untreated-6hour-rep1

description: Primary human erythroid progenitor cells after 6 hours, rep. 1


title: Hif 2alpha Knockdown replicate 4


title: HDAC1_A3-rep3

description: Primary human erythroid progenitor cells expressing HDAC1 A3 shRNA biological replicate 3


title: StemCellLike_1_amplified

source_name: thymic cells, purified using high-speed cell sorting

value: stem-cell like

value: thymus

value: yes


title: Luciferase-rep1

description: Primary human erythroid progenitor cells expressing a luciferase control shRNA biological replicate 1


title: Hif 2alpha Knockdown replicate 2


title: Hif 2alpha Knockdown replicate 3


title: Control replicate 6

source_name: Control mice

value: control


title: Yeast_rapamycin_30min_rep2

city: Los Angeles

first: Mariam

last: Aghajan

address: 650 Charles E. Young Drive South, CHS 23-231

institute: UCLA

description: growth in YPD media, 100 nM rapamycin

hyb_protocol: Hybridization of labeled cRNA probes to Affymetrix GeneChip Yeast Genome 2.0 arrays (www.affymetrix.com) was done according to manufacturer’s specifications.

scan_protocol: The arrays were scanned using Affymetrix GeneChip Scanner 3000 and raw data generated using the GeneChip Operating System GCOSv1.4.

data_processing: Gene expression data were normalized in dChip (www.dchip.org). Model-based expression indices (MBEIs) were calculated and log2 transformed. We have only shown the data pertaining to the Saccharomyces cerevisiae probes and had deleted the data pertaining to Saccharomyces pombe since that data is irrelevant to our study, which only uses S. cerevisiae. We do show ALL Saccharomyces cerevisiae probe data.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae, Rapa-treated

label_protocol: Biotin-labeled cRNA probes were generated from total RNA using the One-Cycle Target Labeling Assay (Affymetrix).

growth_protocol: Yeast cells were grown to mid-log phase (0.5–2 x 107 cells/ml) at 30°C, 300 rpm, in YPD medium before treatment with small molecules for 30 min.

extract_protocol: Total RNA was isolated using the RiboPure™-Yeast kit (Ambion) and RNA quality was checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Following 30 min small molecule treatment, cells were harvested and flash frozen in liquid nitrogen.


title: Hif 2alpha Knockdown replicate 1


title: Control replicate 7


title: Yeast_rapamycin_30min_rep1

description: growth in YPD media, 100 nM rapamycin


title: Control replicate 5


title: Yeast_SMER5_30min_rep1

description: growth in YPD media, 20 μM SMER5

source_name: S. cerevisiae, SMER5-treated


title: Yeast_SMER4_30min_rep1

description: growth in YPD media, 20 μM SMER4

source_name: S. cerevisiae, SMER4-treated


title: Yeast_SMER1_30min_rep1

description: growth in YPD media, 20 μM SMER1

source_name: S. cerevisiae, SMER1-treated


title: Yeast_SMER1_30min_rep2

description: growth in YPD media, 20 μM SMER1


title: Yeast_SMER2_30min_rep1

description: growth in YPD media, 20 μM SMER2

source_name: S. cerevisiae, SMER2-treated


title: Control replicate 2


title: Control replicate 4


title: Yeast_SMER3_30min_rep1

description: growth in YPD media, 20 μM SMER3

source_name: S. cerevisiae, SMER3-treated


title: Control replicate 1


title: Yeast_SMER1+Rapa_30min_rep1

description: growth in YPD media, 20 μM SMER1, 100 nM rapamycin

source_name: S. cerevisiae, SMER1+Rapa-treated


title: 3T12-8hpi-CHX-Rep3

city: St. Louis

first: Steven

last: Johnson

state: MO

address: 660 S. Euclid

department: Department of Pathology and Immunology

institute: Washington University-School of Medicine

hyb_protocol: The paired and balanced cDNAs are suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and water to a total volume of 110ul.  This hybridization solution is applied to custom Agilent 4x44K microarrays.  Hybridization is carried out at 65C for 20 hours. Washing procedures are carried out according to Agilent gene expression protocols.

scan_protocol: Slides are scanned on a Molecular Devices 4000B scanner to detect Alexa Fluor 555 and Alexa Fluor 647 fluorescence.  Gridding and analysis of images is performed using Genepix v6.1 (Molecular Devices).

data_processing: Local background signal was subtracted from all probe fluorescence signals. Probe signals from mock and γHV68-infected samples were normalized to each other by spike-in RNA ratios.  The normalized mock-infected probe signals were subtracted from the respective γHV68 infected samples.  Quantile normalization was performed between replicates.  Average spike-in RNA fluorescence signal was used to normalize between cycloheximide and cidofovir-treated infected cells with untreated infected cells.

organism: Murid gammaherpesvirus 4

source_name: gHV68-infected 3T12 cells 8hpi + cyclohexamide

label_protocol: First strand cDNA is generated by random-primed reverse transcription utilizing the Superscript Plus Indirect labeling system (Invitrogen).  For cDNA synthesis, 1ul of concentrated random primer (RP Primer; Genisphere) is added to 20ug of total RNA and the solution is incubated at 70C for 5 minutes then cooled on ice for 1 minute.  To each sample are added RNase inhibitor (RNaseOUT; Invitrogen) (1ul), 5X first strand buffer (6ul), dNTP mix (dATP, dCTP, dGTP, dTTP, one aminoallyl-modified nucleotide, and one aminohexyl-modified nucleotide) (1.5ul), 0.1M DTT (1.5ul), and Superscript III RNase H- Reverse Transcriptase (2ul).  Reverse transcription is carried out at 55C for 3 hours.  The reaction is terminated by adding 1N NaOH (15ul) and incubation at 70C for 10 minutes then neutralized with 1N HCL (15ul).  First-strand cDNA is purified with Zymo Research Clean and Concentrator 25 clean-up columns according to manufacturer’s instructions. First-strand cDNA is dried down in a speed vac at medium heat until the volume is reduced to 3ul.  Alexa Fluor 555 and 647 reactive dyes are prepared for coupling reaction by adding DMSO (2ul) directly to each dye pack.  2X coupling buffer (5ul) and either DMSO resuspended Alexa Fluor 555 or Alexa Fluor 647 reactive dye (2ul) are then added to each appropriate cDNA sample.  Sample/dyes are then incubated at room temperature in the dark for 2 hours.  Coupling reactions are then quenched with 3M sodium acetate (20ul).  Fluorescently labeled cDNAs are purified with Zymo Research Clean and Concentrator 25 clean-up columns according to manufacturer’s instructions.  The cDNAs are quantitated via NanoDrop to confirm recovery.  Samples are then paired and balanced by mass.

extract_protocol: Trizol Total RNA extraction, Turbo DNAse, final P/C/I extraction

tag: sample type

tag: cell line


title: 3T12-8hpi-CHX-Rep1

value: gHV68-infected 3T12 cells 8hpi + cyclohexamide


title: Yeast_SMER1+Rapa_30min_rep2


title: Yeast_DMSO_30min_rep3

description: growth in YPD media

source_name: S. cerevisiae, DMSO-treated


title: 3T12-8hpi-Rep2

source_name: gHV68-infected 3T12 cells 8hpi

value: gHV68-infected 3T12 cells 8hpi


title: 3T12-8hpi-CHX-Rep2


title: Control replicate 3


title: 3T12-8hpi-Rep3


title: 3T12-18hpi-CID-Rep1

source_name: gHV68-infected 3T12 cells 18hpi + cidofovir


title: 3T12-8hpi-Rep1


title: 3T12-18hpi-CID-Rep3

value: gHV68-infected 3T12 cells 18hpi + cidofovir


title: 3T12-18hpi-Rep2

source_name: gHV68-infected 3T12 cells 18hpi

value: gHV68-infected 3T12 cells 18hpi


title: Yeast_DMSO_30min_rep2

description: growth in YPD media


title: 3T12-18hpi-Rep3


title: Yeast_DMSO_30min_rep1

description: growth in YPD media


title: S35_sarcoma

status: Public on Jun 27 2010

city: Bordeaux

first: fred

last: chibon

address: 229 cours de l'argonne

department: Pathology

country: France

institute: Institut Bergonie

hyb_protocol: Samples were then analyzed on Human Genome U133 Plus 2.0 array (Affymetrix®), according to the manufacturer’s procedures.

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

data_processing: All microarray data were simultaneously normalized using the GCRMA algorithm.

source_name: Internal trunk

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

extract_protocol: Total RNA were extracted from frozen tumor samples with TRIzol reagent (Life Technologies, Inc.) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures. RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: RNA was extracted from frozen tissue of the untreated primary tumor.

value: Internal trunk sarcoma

tag: diagnosis

value: DDLPS


title: 3T12-18hpi-CID-Rep2


title: S1_sarcoma

tag: tissue


title: S58_sarcoma

source_name: Trunk wall

value: Trunk wall sarcoma

value: US


title: S13_sarcoma


title: S5_sarcoma

source_name: Extremities

value: Extremities sarcoma

value: LEIOMYOSARCOME


title: 3T12-18hpi-Rep1


title: S29_sarcoma


title: S18_sarcoma


title: S56_sarcoma


title: S27_sarcoma


title: S25_sarcoma


title: S24_sarcoma


title: S2_sarcoma

value: LIPOS PLEOMORPHE


title: S44_sarcoma


title: S45_sarcoma


title: S51_sarcoma


title: S43_sarcoma


title: S28_sarcoma


title: S11_sarcoma


title: S15_sarcoma


title: S38_sarcoma


title: S42_sarcoma


title: S23_sarcoma


title: S50_sarcoma


title: S26_sarcoma


title: S108_sarcoma


title: S125_sarcoma


title: S107_sarcoma


title: S146_sarcoma


title: S128_sarcoma


title: S126_sarcoma


title: S142_sarcoma


title: S145_sarcoma


title: S144_sarcoma


title: S143_sarcoma


title: S113_sarcoma


title: S54_sarcoma


title: S149_sarcoma


title: S138_sarcoma


title: S150_sarcoma


title: S130_sarcoma


title: S135_sarcoma


title: S147_sarcoma


title: S148_sarcoma


title: S129_sarcoma


title: S131_sarcoma


title: S112_sarcoma


title: S132_sarcoma


title: S133_sarcoma


title: S139_sarcoma


title: S134_sarcoma


title: S141_sarcoma


title: S122_sarcoma


title: S120_sarcoma


title: S137_sarcoma


title: S140_sarcoma


title: S118_sarcoma


title: S14_sarcoma


title: S121_sarcoma


title: S57_sarcoma


title: S63_sarcoma


title: S114_sarcoma


title: S119_sarcoma


title: S115_sarcoma


title: S124_sarcoma


title: S53_sarcoma


title: S116_sarcoma


title: S88_sarcoma


title: S60_sarcoma


title: S59_sarcoma


title: S117_sarcoma


title: S10_sarcoma


title: S123_sarcoma


title: S61_sarcoma


title: S62_sarcoma


title: S160_sarcoma


title: S47_sarcoma


title: S40_sarcoma


title: S173_sarcoma


title: S177_sarcoma


title: S9_sarcoma


title: S156_sarcoma


title: S162_sarcoma


title: S180_sarcoma


title: S163_sarcoma


title: S158_sarcoma


title: S164_sarcoma


title: S151_sarcoma


title: S111_sarcoma


title: S161_sarcoma


title: S179_sarcoma


title: S171_sarcoma


title: S46_sarcoma


title: S182_sarcoma


title: S153_sarcoma


title: S159_sarcoma


title: S174_sarcoma


title: S183_sarcoma


title: S99_sarcoma


title: S96_sarcoma


title: S95_sarcoma


title: S93_sarcoma


title: S152_sarcoma


title: S100_sarcoma


title: S105_sarcoma


title: S94_sarcoma


title: S102_sarcoma


title: S104_sarcoma


title: S74_sarcoma


title: S76_sarcoma


title: S92_sarcoma


title: S67_sarcoma


title: S73_sarcoma


title: S80_sarcoma


title: S103_sarcoma


title: S31_sarcoma


title: S68_sarcoma


title: S71_sarcoma


title: S65_sarcoma


title: S87_sarcoma


title: S72_sarcoma


title: S77_sarcoma


title: S83_sarcoma

source_name: Head and Neck

value: Head and Neck sarcoma


title: S81_sarcoma


title: S82_sarcoma


title: S85_sarcoma


title: S39_sarcoma


title: S70_sarcoma


title: S37_sarcoma


title: S66_sarcoma


title: S75_sarcoma


title: S69_sarcoma


title: S19_sarcoma


title: S84_sarcoma


title: S98_sarcoma


title: S78_sarcoma


title: S109_sarcoma


title: S106_sarcoma


title: S89_sarcoma


title: S97_sarcoma


title: S79_sarcoma


title: S22_sarcoma


title: S33_sarcoma


title: S8_sarcoma


title: S36_sarcoma


title: S52_sarcoma


title: S32_sarcoma


title: S181_sarcoma


title: S12_sarcoma


title: S7_sarcoma


title: S90_sarcoma


title: S34_sarcoma


title: S20_sarcoma


title: S175_sarcoma


title: S17_sarcoma


title: S41_sarcoma


title: S176_sarcoma


title: S21_sarcoma


title: S55_sarcoma


title: S30_sarcoma


title: S86_sarcoma


title: S178_sarcoma


title: S91_sarcoma


title: S6_sarcoma


title: TuMV infected 1

city: Brisbane

first: Shazia

last: Iram

state: Queensland

address: John Hines building # 62

department: School of Biological Sciences

country: Australia

institute: University of Queensland

hyb_protocol: In situ hybridization protocol. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry. LC Sciences catalogue No. MA1038

scan_protocol: Axon GenePix 4000B Microarray Scanner was used. LC Sciences Catalogue No. MA1038

data_processing: Lowess Global normalization, replicate spots averaged

organism: Arabidopsis thaliana

source_name: Two weeks inoculated

label_protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.

growth_protocol: Arabidopsis thaliana plants grown for four weeks in soil.

extract_protocol: Triazol method was used for RNA extraction as per manufacturer protocol.

treatment_protocol: Four weeks old plants inoculated with sap from TuMV infected plants and mock inoculated.

tag: ecotype

tag: infection

value: TuMV

value: whole plant


title: Mock control 2

value: uninfected


title: TuMV infected 2


title: S172_sarcoma


title: Mock control 1


title: S169_sarcoma


title: S4_sarcoma


title: S168_sarcoma


title: S165_sarcoma


title: S154_sarcoma


title: S166_sarcoma

source_name: nd

value: nd sarcoma


title: Liver, mouse injected ip. with saline 1

status: Public on Jun 26 2010

city: Rotterdam

first: Patric

last: Delhanty

address: Dr Molewaterplein 50

department: Internal Medicine

institute: Erasmus MC

description: Gene expression data from liver

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G, enabled for high-resolution scanning.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Array intensities and calls were collected using R, and quantile normalization was used on one time present calls. An intensity threshold of 30 was then applied to generate datasets for analysis.

source_name: GHSR KO mouse (12 weeks)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix one cycle protocol using 5 ug of total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The RNA was then further purified over a Qiagen Rneasy column. RNA was checked for integrity using an Agilent BioAnalyzer and the RNA 6000 Nano Labchip (RIN>=8).

tag: strain

value: GHSR KO mouse (C57bl/6)

value: Liver


title: Muscle, mouse injected ip. with UAG 1

description: Gene expression data from skeletal muscle

value: Skeletal muscle (M. vastus lateralis)


title: Liver, mouse injected ip. with saline 2

description: Gene expression data from liver


title: S155_sarcoma


title: S170_sarcoma


title: S3_sarcoma


title: Hypothlamus, inhaled (R)-(-)-linalool and exposed restraint stress for 2h #2

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

description: Group SO

hyb_protocol: Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

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.

organism: Rattus norvegicus

source_name: Hypothlamus

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy Lipid Tissue mini kit (Qiagen, Valencia, CA, USA).

value: Wistar

tag: gender

value: male

tag: age

value: 7-8 weeks

value: Hypothlamus


title: Hypothlamus, inhaled (R)-(-)-linalool and exposed restraint stress for 2h #4

description: Group SO


title: S167_sarcoma

value: Internal trunk sarcoma

value: DDLPS


title: Hypothlamus, inhaled (R)-(-)-linalool and exposed restraint stress for 2h #3

description: Group SO


title: Hypothlamus, inhaled (R)-(-)-linalool and exposed restraint stress for 2h #1

description: Group SO


title: Liver, mouse injected ip. with UAG 2

description: Gene expression data from liver


title: S157_sarcoma

value: Extremities sarcoma


title: Muscle, mouse injected ip. with UAG 2


title: SG231, Vacant vehicle stably expressing

city: Pittsburgh

first: Yoshiaki

last: Mizuguchi

address: 200 Lothrop st

institute: UPMC

description:
Gene expression data from Vacant vehicle stably expressing SG231
090224_Demetris_SG231D_hu133.2_Signal

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Microarray Suite 5.0 was used to generate results from GeneChip expression arrays. One set of quantitative algorithms compute Signal and Signal Log Ratio (log2) directly from the hybridization intensities of probes.

source_name: Vacant vehicle stably expressing SG231

label_protocol: Standard Affymetrix protocol

growth_protocol: Human HuCCT-1 cells and SG231 cells were cultured at 37 degree with 5% CO2. The culture medium were RPMI 1640 and DMEM, respectively, which were supplemented with 10% FCS. In addition, SPRR2a stable cells are maintained with Zeocin.

extract_protocol: We used Trizol (Invitrogen) for tRNA extraction.

value: Cholangiocarcinoma


title: SG231, SPRR2a stably expressing

description:
Gene expression data from SPRR2a stably expressing SG231
090224_Demetris_SG231CL7_hu133.2_Signal

source_name: SPRR2a stably expressing SG231


title: Liver, mouse injected ip. with UAG 1

description: Gene expression data from liver


title: HuCCT-1, Vacant vehicle stably expressing

description:
Gene expression data from Vacant vehicle stably expressing HuCCT-1
090224_Demetris_HUCCTDU9_hu133.2_Signal


title: Hypothlamus, inhaled (R)-(-)-linalool for 2h #4

description: Group O


title: Hypothlamus, inhaled (R)-(-)-linalool for 2h #1

description: Group O


title: Type I hTERT-immortalized hMECs

city: Omaha

first: Gautam

last: Malhotra

state: NE

address: 985805 Nebraska Medical Center

institute: UNMC

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 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 100.

source_name: human mammary epithelial cells (TERT immortalized), K5+K19-

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT Express protocol from 200 ng total RNA.

growth_protocol: Normal human mammary epithelial cells (hMECs) were isolated from Reduction Mammoplasty. hTERT-immortalized hMEC stem/progenitor and myoepithelial cells were grown in DFCI-1 and MEGM medium.

treatment_protocol: No treatment. Logarithmically growing cells were collected for RNA extraction.

value: female

value: breast

tag: cell type

value: hTERT-immortalized K5+K19- mammary epithelial cells


title: Hypothlamus, exposed restraint stress for 2h #4

description: Group S


title: Muscle, mouse injected ip. with saline 2


title: Type II hTERT-immortalized hMECs

source_name: human mammary epithelial cells (TERT immortalized), K5+K19+

value: hTERT-immortalized K5+K19+ mammary epithelial cells


title: Hypothlamus, inhaled (R)-(-)-linalool for 2h #3

description: Group O


title: Hypothlamus, exposed restraint stress for 2h #2

description: Group S


title: Hypothlamus, Control #3

description: Group C


title: Muscle, mouse injected ip. with saline 1


title: Hypothlamus, inhaled (R)-(-)-linalool for 2h #2

description: Group O


title: White adipose, mouse injected ip. with UAG 1

description: Gene expression data from white adipose

value: Gonadal white adipose tissue


title: Myoepithelial cells

source_name: myoepithelial cells differentiated from human mammary epithelial cells (TERT immortalized) K5+K19-

value: myoepithelial cells differentiated from hTERT-immortalized K5+K19- mammary epithelial cells


title: White adipose, mouse injected ip. with saline 2

description: Gene expression data from white adipose

value: GHSR KO mouse (C57bl/6)


title: White adipose, mouse injected ip. with UAG 2

description: Gene expression data from white adipose


title: Hypothlamus, exposed restraint stress for 2h #3

description: Group S


title: Hypothlamus, exposed restraint stress for 2h #1

description: Group S


title: Hypothlamus, Control #4

description: Group C


title: Hypothlamus, Control #2

description: Group C


title: HuCCT-1, SPRR2a stably expressing

description:
Gene expression data from SPRR2a stably expressing HuCCT-1
090224_Demetris_HUCCTCL1_hu133.2_Signal

source_name: SPRR2a stably expressing HuCCT-1


title: Hypothlamus, Control #1

description: Group C


title: White adipose, mouse injected ip. with saline 1

description: Gene expression data from white adipose


title: Cord blood CD4+_Act+IL-4_6h_rep3

status: Public on Jun 25 2010

city: Turku

first: Henna

last: Kallionpää

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

description: biological replicate 3

hyb_protocol: 15 ug of biotinylated and fragmented cRNA was hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays overnight (16-18 hours) at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with AutoLoader.

data_processing: The PM probe intensities were quantile-normalized using the R/Bioconductor package affy and log2-transformed. To identify consistent changes across the biological replicates, the probe-level expression change averaging procedure (PECA) was applied (Elo et al., Nucleic Acids Res 33:e193, 2005). The benefit of this approach is that is that the reliability of estimation can be improved by considering the distribution of probe-level expression changes instead of a single probeset-level value. Specifically, linear modeling with moderated F- and t-statistics was first applied to the probe-level time series data using the R/Bioconductor package limma and the obtained probe-level estimates were then summarized into probeset-level values using the Tukey biweight average. The probe-level estimates are contained in the sample (57) data tables. Since the PECA-estimation requires always at least two samples to be compared, the probeset-level data is represented as a supplemental file on the Series record and contains the PECA-estimates for the signal log-ratios between each non-Thp sample (54) and the corresponding Th cell precursor-samples (0h timepoint).

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 6h

label_protocol: Amplification used 100 ng of total RNA using the Affymetrix Two-Cycle cDNA Synthesis Kit (P/N 900432), and cDNA/cRNA synthesis reactions and sample cleanup steps were performed according to Affymetrix´s GeneChip Expression Analysis Technical Manual.

growth_protocol: Umbilical cord blood was collected from healthy neonates born in Turku University Hospital, Hospital District of Southwest Finland. Mononuclear cells were isolated with Ficoll-Paque (Amersham Biosciences) gradient centrifugation, and CD4+ cell population was purified using magnetic beads (Dynal CD4 Positive Isolation Kit, Invitrogen) according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen) according to manufacturer's instructions. In-column DNase (RNase-Free Dnase Set, Qiagen) treatment was performed for 15 minutes. RNA was eluted in dH2O.

treatment_protocol: Cells were activated on 24-well plates, 4x106 cells/1ml Yssel´s medium, through the T cell receptor (plate bound antiCD3 500 ng/well, and soluble antiCD28 500 ng/ml, Immunotech, France), and to half of the samples IL-4 (10ng/ml, R&D Systems) and anti IL-12 (10µg/ml, R&D Systems) were added to induce Th2 polarization. At 48h timepoint IL-2 (17ng/ml, R&D Systems) was added to the culture medium. Cells were harvested at 0.5, 1, 2, 4, 6, 12, 24, 48 and 72 h. Naive cells without any treatment were collected as 0h controls for every replicate.

value: cord blood

value: CD4+ T cells


title: Cord blood CD4+_Act_4h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated, 4h


title: Cord blood CD4+_Act+IL-4_4h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 4h


title: Cord blood CD4+_Act_2h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated, 2h


title: Cord blood CD4+_Act+IL-4_2h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 2h


title: Cord blood CD4+_Act_0.5h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated, 0.5h


title: Cord blood CD4+_Act_6h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated, 6h


title: Cord blood CD4+_Act+IL-4_1h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 1h


title: Cord blood CD4+_Act+IL-4_0.5h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 0.5h


title: Cord blood CD4+_Act_0.5h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act+IL-4_2h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act+IL-4_4h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act+IL-4_2h_rep1

description: biological replicate 1


title: Cord blood CD4+_Act_6h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act_72h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ cell, activated, 72h


title: Cord blood CD4+_Act_4h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act_1h_rep2

description: biological replicate 2

source_name: human cord blood CD4+ cell, activated, 1h


title: Cord blood CD4+_Act_2h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act+IL-4_6h_rep1

description: biological replicate 1


title: Cord blood CD4+_Act+IL-4_0.5h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act+IL-4_1h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act_4h_rep1

description: biological replicate 1


title: WT versus KO NSCs, H3K27me3 ChIP-chip (2/2)

first: Yi

last: Sun

address: 635, Charles E. Young Dr. South

department: Molecular and Medical Pharmacology

hyb_protocol: 5 ug Cy3- or Cy5-labelled DNA were combined and hybridized to the Agilent 244K mouse extended promoter microarray (G4490A, 2-array set, genomic build: mm7) for 40 h at 65 ˚C (10 r.p.m.). Microarrays were washed according to Agilent's standard procedures.

scan_protocol: Microarry slides were scanned on at 5-micron resolution using an Agilent Technologies Scanner G2505B (US23502366).

data_processing:
Final processed data file by ChIP Analytics 1.3: WTvsKO_NSC_H3K27me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by H3K27me3 antibodies

label_protocol: Whole cell extract and immunoprecipitated DNA were amplified using the Whole Genome Amplification Kit (Sigma), and 2 ug of amplified products was labeled with Cy3- and Cy5-dUTP (Perkin Elmer) using Bioprime DNA labeling system (Invitrogen).

growth_protocol: Postnatal day 14-21 day mouse lateral ventricle walls were dissected and mechanically dissociated. Single cell suspensions were plated at low density (10,000~20,000 cells cm-2) on cell culture dishes coated with poly-L-ornithine (PO)/fibronectin (FN), allowing individual cells to form spatially distinct colonies. Serial passage (less than 2 passages, or 2 weeks) allowed us to enrich undifferentiated NSCs to high purity (>95% Nestin+/Sox2+). The NSCs were maintained in serum-free B27 medium in presence of 10 ng/ml FGF-2/bFGF (Peprotech) and 10 ng/ml EGF (Invitrogen). The monolayer cultures were serially passaged every 4-7 days. To avoid the potential non-specific effect induced by prolonged culturing, only NSCs with limited in vitro culturing (less than 3 weeks) were used in the study. J1 ESCs were maintained in standard culture conditions in presense of irradiated mouse embryonic fibroblasts.

extract_protocol: Each ChIP-chip assay was performed with about 20 million cells following Agilent mammalian ChIP-on-chip protocol (March, 2006). Briefly, cells were cross-linked with formaldehyde for 10 min at room temperature. Sonicated chromatin was immunoprecipitated overnight at 4 C with 10 ug immobilized (on 100 ul Dynal protein-G beads, Invitrogen) antibodies to Dnmt3a (Santa Cruz, sc-20703), H3K4me3 (Millipore, 07-473), H3K27me3 (Millipore, 07-449), total histone H3 (Millipore, 07-690), Ezh2 (Active Motif, 39103) and Suz12 (A kind gift from Dr. Yi Zhang). MeDIP-chip was perfromed as previously described with minor modifications (Weber et al., 2005). Briefly, 5 ug sonicated, heat-denatured genomic DNA was immunoprecipitated with 5 ul of monoclonal antibody against 5-methylcytidine (Eurogentec) at 4 C overnight. Immunoprecipitated methylated DNA was collected with 30 ul Dynal protein-G beads for 2 h at 4 C.

value: Postnatal day 14-21

value: neural stem cells

tag: experimental design

value: IP/IP

source_name: WT NSC, immunoprecipitated DNA by H3K27me3 antibodies

value: wild type


title: Cord blood CD4+_Act+IL-4_6h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act_1h_rep3

description: biological replicate 3


title: Cord blood CD4+_Act_6h_rep1

description: biological replicate 1


title: WT versus KO NSCs, total histone H3 ChIP-chip (2/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: WTvsKO_NSC_panH3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by total histone H3 antibodies

source_name: WT NSC, immunoprecipitated DNA by total histone H3 antibodies


title: WT NSCs, Ezh2 ChIP-chip (2/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_NSC_Ezh2_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: WT NSC, whole cell extract

value: IP/WCE

source_name: WT NSC, immunoprecipitated DNA by Ezh2 antibodies


title: WT versus KO NSCs, H3K4me3 ChIP-chip (2/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: WTvsKO_NSC_H3K4me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by H3K4me3 antibodies

source_name: WT NSC, immunoprecipitated DNA by H3K4me3 antibodies


title: Cord blood CD4+_Act+IL-4_4h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 4h


title: KO NSCs, Ezh2 ChIP-chip (2/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: KO_NSC_Ezh2_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, whole cell extract

source_name: KO NSC, immunoprecipitated DNA by Ezh2 antibodies


title: KO NSCs, Suz12 ChIP-chip (2/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: KO_NSC_Suz12_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by Suz12 antibodies


title: WT embryonic stem cells (ESCs, J1), H3K27me3 ChIP-chip (2/2), exp1

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_ESC_H3K27me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: WT ESC, whole cell extract

value: embryonic stem cells

source_name: WT ESC, immunoprecipitated DNA by H3K27me3 antibodies


title: WT versus KO NSCs, DNA methylatyion by MeDIP-chip (2/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: WTvsKO_NSC_MeDIP_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by 5-methylcytosine antibodies

source_name: WT NSC, immunoprecipitated DNA by 5-methylcytosine antibodies


title: Cord blood CD4+_Act_0.5h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ cell, activated, 0.5h


title: Cord blood CD4+_Act+IL-4_0.5h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 0.5h


title: Cord blood CD4+_Act_1h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ cell, activated, 1h


title: WT embryonic stem cells (ESCs, J1), DNA methylatyion by MeDIP-chip (2/2), exp1

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_ESC_MeDIP_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: WT ESC, immunoprecipitated DNA by 5-methylcytosine antibodies


title: KO NSCs, H3K27me3 ChIP-chip (2/2), exp1

data_processing:
Final processed data file by ChIP Analytics 1.3: KO_NSC_H3K27me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by H3K27me3 antibodies


title: WT NSCs, H3K4me3 ChIP-chip (2/2), exp1

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_NSC_H3K4me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: WT NSC, whole cell extract


title: WT NSCs, Suz12 ChIP-chip (2/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_NSC_Suz12_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: WT NSC, immunoprecipitated DNA by Suz12 antibodies


title: WT NSCs, H3K4me3 ChIP-chip (2/2), exp2


title: WT NSCs, H3K27me3 ChIP-chip (2/2), exp1

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_NSC_H3K27me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: WT NSC, immunoprecipitated DNA by H3K27me3 antibodies


title: WT NSCs, H3K27me3 ChIP-chip (2/2), exp2


title: KO NSCs, H3K4me3 ChIP-chip (2/2), exp2

data_processing:
Final processed data file by ChIP Analytics 1.3: KO_NSC_H3K4me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by H3K4me3 antibodies


title: WT embryonic stem cells (ESCs, J1), DNA methylatyion by MeDIP-chip (2/2), exp2


title: KO NSCs, Dnmt3a ChIP-chip (2/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: KO_NSC_Dnmt3a_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by Dnmt3a antibodies


title: KO NSCs, H3K4me3 ChIP-chip (2/2), exp1

source_name: KO NSC, whole cell extract


title: WT NSCs, DNA methylatyion by MeDIP-chip (2/2), exp1_3-week

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_NSC_MeDIP_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.


title: Cord blood CD4+_Act+IL-4_1h_rep1

description: biological replicate 1

data_processing: The PM probe intensities were quantile-normalized using the R/Bioconductor package affy and log2-transformed. To identify consistent changes across the biological replicates, the probe-level expression change averaging procedure (PECA) was applied (Elo et al., Nucleic Acids Res 33:e193, 2005). The benefit of this approach is that is that the reliability of estimation can be improved by considering the distribution of probe-level expression changes instead of a single probeset-level value. Specifically, linear modeling with moderated F- and t-statistics was first applied to the probe-level time series data using the R/Bioconductor package limma and the obtained probe-level estimates were then summarized into probeset-level values using the Tukey biweight average. The probe-level estimates are contained in the sample (57) data tables. Since the PECA-estimation requires always at least two samples to be compared, the probeset-level data is represented as a supplemental file on the Series record and contains the PECA-estimates for the signal log-ratios between each non-Thp sample (54) and the corresponding Th cell precursor-samples (0h timepoint).

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 1h


title: WT NSCs, DNA methylatyion by MeDIP-chip (2/2), exp3_1-week


title: Cord blood CD4+_Act_2h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ cell, activated, 2h


title: WT NSCs, Dnmt3a ChIP-chip (1/4)

hyb_protocol: 34 ug of Cy5- and Cy3-labeled samples were combined and hybridized to each mouse whole genome tiling microarray (Roche/NimbleGen 4-array set) for 16-20 h at 42 ˚C using NimbleGen hybridization System 4.

scan_protocol: Microarrays were scanned using the Agilent scanner at 5 micron resolution.

data_processing:
Data were extracted and analyzed using NimbleScan v2.5 (Roche/NimbleGen). Dnmt3a binding sites were identified by a sliding window-base statistical algorithm in NimbleScan v2.5 (FDR<1% or <5%). For identifying probes associated with a significant increase in H3K27me3 levels or a significant decrease in DNA methylation level in KO NSCs as compared to WT NSCs, a non-parametric one-sided Kolmogorov-Smirno (KS) test was used (KS score>2).
Processed data VALUE definition: Log2 (ch2_signal / ch1_signal)

label_protocol: Whole cell extract and immunoprecipitated DNA were amplified using the Whole Genome Amplification Kit (Sigma), and 5 ug of amplified ChIP/MeDIP or input samples were labeled (5’ Cy5- or Cy3-random nonamers, TriLink Biotechnologies) using the standard protocol (NimbleGen Arrays User’s Guide for ChIP-chip analysis).

growth_protocol: postnatal SVZ NSCs were maintained in undifferentiated states in presence of mitogens (10 ng/ml EGF and 10 ng/ml bFGF)

extract_protocol: Each ChIP-chip assay was performed with about 20 million cells following Agilent mammalian ChIP-on-chip protocol (March, 2006). Briefly, cells were cross-linked with formaldehyde for 10 min at room temperature. Sonicated chromatin was immunoprecipitated overnight at 4 C with 10 ug immobilized (on 100 ul Dynal protein-G beads, Invitrogen) antibodies to Dnmt3a (Santa Cruz, sc-20703) or H3K27me3 (Millipore, 07-449). MeDIP-chip was perfromed as previously described with minor modifications (Weber et al., 2005). Briefly, 5 ug sonicated, heat-denatured genomic DNA was immunoprecipitated with 5 ul of monoclonal antibody against 5-methylcytidine (Eurogentec) at 4 C overnight. Immunoprecipitated methylated DNA was collected with 30 ul Dynal protein-G beads for 2 h at 4 C.

value: postnatal SVZ

source_name: WT NSC, immunoprecipitated DNA by Dnmt3a antibodies


title: WTvsKO NSCs, DNA methylation by MeDIP-chip (1/4), exp1


title: WTvsKO NSCs, DNA methylation by MeDIP-chip (1/4), exp2


title: WT NSCs, DNA methylatyion by MeDIP-chip (2/2), exp2_3-week


title: Chronic Lymphocytic Leukemia (CLL) sample 40 Jel106U133A

city: Rochester

first: Brian

last: Bot

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

description: Gene expression data from peripheral blood B cells from patients diagnosed with CLL prior to treatment

hyb_protocol: 15ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human U133 A and B GeneChips® . GeneChips were washed and stained following the Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA

scan_protocol: Hybridized arrays were scanned using a GeneChip® 3000 scanner

data_processing: Affymetrix GeneChip® Operating System software v.1.3 (Santa Clara, CA) were used to quantitatively analyze the scanned image

source_name: Purified CLL B cells from peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Enzo, New York, NY).

extract_protocol: Total RNA isolation by the Trizol method following manufacturer's protocol from purified B cells

tag: disease state

value: CLL


title: Normal B Cell Control 8 Jel066U133A

description: Gene expression data from peripheral blood  B cells age matched normal controls

source_name: Purified B cells from peripheral blood from donors 60 years of age and older

value: normal


title: Chronic Lymphocytic Leukemia (CLL) sample 35 Jel067U133A

value: Purified CLL B cells from peripheral blood


title: Chronic Lymphocytic Leukemia (CLL) sample 39 Jel105U133A


title: Chronic Lymphocytic Leukemia (CLL) sample 41 Jel107U133A


title: Normal B Cell Control 9 Jel100U133A

value: Purified B cells from peripheral blood from donors 60 years of age and older


title: Normal B Cell Control 10 Jel108U133A


title: Chronic Lymphocytic Leukemia (CLL) sample 36 Jel101U133A


title: KTCL26 5'AZA Treatment

city: Birmingham

first: Mark

middle: Richard

last: Morris

address: Medical School

department: Medical and Molecular Genetics

institute: Univeristy of Birmingham

description: Gene expression following global de-methylation

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

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.

source_name: RCC Cell line 5-Aza-2'-deoxycytidine treated

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

growth_protocol: Control Cells: Standard tissue culture, DMEM, 10%FCS (5 days). Aza Cells: Standard tissue culture, DMEM, 10%FCS suplimented with 5-Aza-2'-deoxycytidine (5 days)

extract_protocol: RNABee followed by Qiagen RNA column purification


title: UMRC3 CONTROL

description: Gene expression under normal culture conditions

source_name: RCC Cell line

treatment_protocol: Control Cells: Standard tissue culture, DMEM, 10%FCS (5 days). Aza Cells: Standard tissue culture, DMEM, 10%FCS suplimented with 5-Aza-2'-deoxycytidine (5 days)


title: KTCL26 CONTROL


title: SKRC54 5'AZA Treatment


title: WT NSCs, Dnmt3a ChIP-chip (2/2), exp2

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_NSC_Dnmt3a_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.


title: WT NSCs, Dnmt3a ChIP-chip (2/2), exp1


title: SKRC39 5'AZA Treatment


title: SKRC54 CONTROL


title: Chronic Lymphocytic Leukemia (CLL) sample 34 Jel065U133A


title: Chronic Lymphocytic Leukemia (CLL) sample 38 Jel104U133A


title: Chronic Lymphocytic Leukemia (CLL) sample 37 Jel102U133A


title: Chronic Lymphocytic Leukemia (CLL) sample 32 Jel063U133A


title: Chronic Lymphocytic Leukemia (CLL) sample 33 Jel064U133A


title: SKRC39 CONTROL


title: Chronic Lymphocytic Leukemia (CLL) sample 31 Jel060U133A


title: WTvsKO NSCs, H3K27me3 ChIP-chip (1/4)

source_name: WT NSC, immunoprecipitated DNA by H327me3 antibodies

source_name: KO NSC, immunoprecipitated DNA by H327me3 antibodies


title: SKRC47 CONTROL


title: Normal B Cell Control 11 Jel109U133A


title: Chronic Lymphocytic Leukemia (CLL) sample 30 Jel058U133A


title: SKRC47 5'AZA Treatment


title: Chronic Lymphocytic Leukemia (CLL) sample 26 Jel052A


title: Chronic Lymphocytic Leukemia (CLL) sample 29 Jel057U133A


title: SKRC45 CONTROL


title: Chronic Lymphocytic Leukemia (CLL) sample 28 Jel056U133A


title: SKRC45 5'AZA Treatment


title: Chronic Lymphocytic Leukemia (CLL) sample 27 Jel054A


title: UMRC3 5'AZA Treatment


title: KTCL 140 CONTROL

value: KTCL 140


title: Chronic Lymphocytic Leukemia (CLL) sample 23 Jel049A


title: KTCL 140 5'AZA Treatment


title: Chronic Lymphocytic Leukemia (CLL) sample 24 Jel050A


title: RCC4 CONTROL


title: CAKI-1 CONTROL


title: Normal B Cell Control 7 Jel055A


title: Chronic Lymphocytic Leukemia (CLL) sample 19 Jel045A


title: Chronic Lymphocytic Leukemia (CLL) sample 22 Jel048A


title: 786-O 5'AZA Treatment


title: 786-O CONTROL


title: CAKI-1 5'AZA Treatment


title: UMRC2 5'AZA Treatment


title: Chronic Lymphocytic Leukemia (CLL) sample 18 Jel044A


title: RCC4 5'AZA Treatment


title: Chronic Lymphocytic Leukemia (CLL) sample 17 Jel043A


title: Chronic Lymphocytic Leukemia (CLL) sample 20 Jel046A


title: Met 31

city: Dresden

first: Wuttig

last: Daniela

address: Fetscherstr. 74

department: Department of Urology

country: Germany

institute: Dresden, University of Technology

description: in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases

hyb_protocol: Following fragmentation, 20 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip HGU133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS3000 7G Scanner (Affymetrix).

data_processing:
data for analysis:
study I: Met1-9, Met11-18, Met20, Met23, Met25 (n=20); study II: all samples (n=48)
Global background correction, quantile normalization and signal calculation were carried out using the RMAExpress 4.1 software. Data of primary ccRCC were batch corrected using the combat modul after all probe sets with less than 5/48 present signals were excluded. Data of all samples were filtered (max-min > 100; max/min > 3; ceiling = 16000, threshold = 20).

source_name: pulmonary metastasis of clear-cell renal cell carcinoma (laser resection)

label_protocol: Biotinylated cRNA were prepared according to the One-Cycle Target Labeling and Control Reagents Kit protocol (Affymetrix, Santa Clara, USA) from 1.0 - 2.5 µg total RNA.

extract_protocol:
Metastases were obtained during precise laser-based resection (1318 nm neodynium-YAG, Coswig Specialized Hospital). Primary ccRCC were obtained by (partial) nephrectomy in the Departments of Urology in the University Hopitals Dresden or Jena.
Cryo-sections (4 um) of snap-frozen tissue samples were made and homogenized using QiaShredder (Qiagen, Hilden, Germany)
RNA was isolated with the RNeasy Mini Kit (Qiagen) with additional DNA digestion (RNase-Free DNase Set, Qiagen).

value: female

tag: dfs/follow-up

value: DFS = 0 month

tag: date of sample preparation and hybridisation


title: Met 29

value: pulmonary metastasis of clear-cell renal cell carcinoma (laser resection)

value: DFS = 36 months


title: Chronic Lymphocytic Leukemia (CLL) sample 16 Jel042A


title: Met 30


title: Normal B Cell Control 6 Jel041U133A


title: UMRC2 CONTROL


title: Chronic Lymphocytic Leukemia (CLL) sample 14 Jel039U133A


title: Met 25 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359496

value: male

value: DFS = 127 months

tag: no. of pulmonary metastases


title: Met 23 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359495

value: DFS = 11 months


title: Chronic Lymphocytic Leukemia (CLL) sample 25 Jel051A


title: Met 20 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359494

value: DFS = 114 months


title: Normal B Cell Control 5 Jel037U133A


title: Chronic Lymphocytic Leukemia (CLL) sample 13 Jel038U133A


title: Met 22

value: DFS = 2 months


title: Met 18 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359493

value: DFS = 8 months


title: Chronic Lymphocytic Leukemia (CLL) sample 15 Jel040U133A


title: Met 17 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359492

value: DFS = 90 months


title: Chronic Lymphocytic Leukemia (CLL) sample 12 Jel036U133A


title: Normal B Cell Control 4 Jel033U133A


title: Met 15 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359490

value: DFS = 156 months


title: Chronic Lymphocytic Leukemia (CLL) sample 11 Jel032U133A

value: CLL


title: Chronic Lymphocytic Leukemia (CLL) sample 9 Jel030U133A


title: Met 16 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359491


title: Chronic Lymphocytic Leukemia (CLL) sample 10 Jel031U133A


title: Met 13 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359488

value: DFS = 1 month


title: Met 14 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359489

value: DFS = 60 months


title: Met 12 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359487


title: Chronic Lymphocytic Leukemia (CLL) sample 5 Jel023U133A

value: Purified CLL B cells from peripheral blood


title: Met 5 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359481

value: DFS = 38 months


title: Met 8 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359484


title: Normal B Cell Control 3 Jel028U133A

value: normal

value: Purified B cells from peripheral blood from donors 60 years of age and older