title: patient 1385

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description:
breast tumor biopsy
sample name: hw1385.U133A

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized on U133A GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-2v4.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: dChip version 2006

source_name: human breast tumor

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

tag: disease state

value: breast cancer

tag: age

tag: race

value: b

tag: menopause

value: PERI

tag: bmi

tag: bmi status

value: obese

tag: grade

tag: lymph

value: n

tag: er

value: N

tag: pr


title: patient 1841

status: Public on Jul 18 2011

type: RNA

city: Houston

state: TX

country: USA

description:
breast tumor biopsy
sample name: hw1841.U133A

label: biotin

molecule: total RNA

organism: Homo sapiens

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

value: w

value: POST

value: P

value: U


title: patient 1390

description:
breast tumor biopsy
sample name: hw1390.U133A

value: PRE


title: patient 1811

description:
breast tumor biopsy
sample name: hw1811.U133A


title: patient 1798

description:
breast tumor biopsy
sample name: hw1798.run2.U133A


title: 24h EGF versus Control replicate 3 dye swap (Operon)

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: 24h time point, biological replicate 3 of 3. Technical replicate 2 of 2. HeLa cells treated with EGF compared to untreated controls.

hyb_protocol: Three biological replicate experiments were performed, each comparing EGF treated with untreated control HeLa cells. Each experimental pair of labelled samples was co-hybridized on two separate microarrays with dye swapping to correct for dye bias effects. Thus, six microarray hybridizations were processed for each of three biological replicates for the two time points, totalling 12 array datasets.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization using 0.3 as the span parameter with reduced weights in control and poor quality spots, followed by scaling across chips. Differentially expressed genes for each time point were chosen using as cut off criteria a SAM FDR of 5% and an average absolute fold change (|FC|) above 1.2 .

source_name: Cervical cancer cell line (HeLa)

label_protocol: First and second strand cDNA were synthesized from total RNA (1 ug) with the Aminoallyl Message Amp II Kit (Ambion). cDNA was purified and in vitro transcribed for aRNA synthesis. aRNA was purified and coupled to the Cy ester, and further purified, to remove unincorporated dye. Arrays were hybridized on a Maui hybridization station washed and dried following Operon’s instructions (2/7/2007 Oparray protocol).

growth_protocol: HeLa cells were cultured at 37ºC in a 95/5 Air/CO2 water saturated  atmosphere in Dulbecco’s  modified  Eagle’s medium (DMEM) containing 10% heat inactivated foetal bovine serum (FBS), 2 mM  L-glutamine and 100U/ml Penicilin/streptomycine (complete growth medium).

extract_protocol: Total RNA from HeLa cells was extracted using the RNeasy RNA Isolation kit (Qiagen) followed by treatment with RNase-free DNase I (Ambion, Austin, TX) following manufacturers instructions. RNA quantification was performed with a Nanodrop spectrophotometer, and the RNA integrity was assessed using the Bioanalyzer 2100 nanoelectrophoresis Lab-on-a–chip system (Agilent, Wilmington, DE). All RNAs used had RIN (RNA integrity number) ranging between 9.3 and 10, and 28S/18S ratios between 1.67 and 2.07.

treatment_protocol: For treatments, the cells were transferred  to 60 mm dishes and cultured for 48h in complete growth medium, after which they were starved for 24h in DMEM containing 2% FBS. After serum deprivation cells were stimulated with EGF (150 ng/ml) for the indicated times.

tag: treatment

value: serum deprived for 24 hours, followed by exposure to EGF for 24 hours

tag: cell line

value: HeLa

value: serum deprived for 24 hours, followed by culture without EGF addition into the medium for 24 additional hours


title: patient 1363

description:
breast tumor biopsy
sample name: hw1363.U133A


title: 6h EGF versus Control replicate 2 (Operon)

description: 6h time point, biological replicate 2 of 3. Technical replicate 1 of 2. HeLa cells treated with EGF compared to untreated controls.

value: serum deprived for 24 hours, followed by exposure to EGF for 6 hours

value: serum deprived for 24 hours, followed by culture without EGF addition into the medium for 6 additional hours


title: patient 1804

description:
breast tumor biopsy
sample name: hw1804.U133A


title: patient 1585

description:
breast tumor biopsy
sample name: hw1585.U133A


title: patient 1371

description:
breast tumor biopsy
sample name: hw1371.U133A


title: 24h EGF versus Control replicate 2 dye swap (Operon)

description: 24h time point, biological replicate 2 of 3. Technical replicate 2 of 2. HeLa cells treated with EGF compared to untreated controls.


title: patient 1701

description:
breast tumor biopsy
sample name: hw1701.run2.U133A


title: patient 1356

description:
breast tumor biopsy
sample name: hw1356.run2.U133A


title: 6h EGF versus Control replicate 2 dye swap (Operon)

description: 6h time point, biological replicate 2 of 3. Technical replicate 2 of 2. HeLa cells treated with EGF compared to untreated controls.


title: 24h EGF versus Control replicate 2 (Operon)

description: 24h time point, biological replicate 2 of 3. Technical replicate 1 of 2. HeLa cells treated with EGF compared to untreated controls.


title: patient 1584

description:
breast tumor biopsy
sample name: hw1584.U133A

value: a


title: patient 1329

description:
breast tumor biopsy
sample name: hw1329.U133A

value: breast cancer


title: 6h EGF versus Control replicate 1 dye swap (Operon)

description: 6h time point, biological replicate 1 of 3. Technical replicate 2 of 2. HeLa cells treated with EGF compared to untreated controls.


title: 6h EGF versus Control replicate 1 (Operon)

description: 6h time point, biological replicate 1 of 3. Technical replicate 1 of 2. HeLa cells treated with EGF compared to untreated controls.


title: patient 1581

description:
breast tumor biopsy
sample name: hw1581.U133A


title: patient 1299

description:
breast tumor biopsy
sample name: hw1299.U133A

value: b


title: patient 1699

description:
breast tumor biopsy
sample name: hw1699.U133A


title: 6h EGF versus Control replicate 3 dye swap (Operon)

description: 6h time point, biological replicate 3 of 3. Technical replicate 2 of 2. HeLa cells treated with EGF compared to untreated controls.


title: patient 1286

description:
breast tumor biopsy
sample name: hw1286.U133A

value: PERI


title: patient 1291

description:
breast tumor biopsy
sample name: hw1291.U133A

value: obese


title: 6h EGF versus Control replicate 3 (Operon)

description: 6h time point, biological replicate 3 of 3. Technical replicate 1 of 2. HeLa cells treated with EGF compared to untreated controls.


title: patient 1173

description:
breast tumor biopsy
sample name: hw1173.U133A

value: y


title: patient 1073

description:
breast tumor biopsy
sample name: hw1073.U133A

value: n

value: N


title: patient 1233

description:
breast tumor biopsy
sample name: hw1233.U133A

value: w

value: POST


title: patient 1138

description:
breast tumor biopsy
sample name: hw1138.U133A

value: P


title: patient 913

description:
breast tumor biopsy
sample name: hw913.U133A


title: patient 919

description:
breast tumor biopsy
sample name: hw919.U133A


title: patient 642

description:
breast tumor biopsy
sample name: hw642.U133A

value: PRE


title: patient 961

description:
breast tumor biopsy
sample name: hw961.U133A


title: patient 993

description:
breast tumor biopsy
sample name: hw993.U133A


title: patient 1170

description:
breast tumor biopsy
sample name: hw1170.U133A


title: patient 868

description:
breast tumor biopsy
sample name: hw868.U133A


title: patient 646

description:
breast tumor biopsy
sample name: hw646.U133A


title: patient 676

description:
breast tumor biopsy
sample name: hw676.U133A


title: patient 687

description:
breast tumor biopsy
sample name: hw687.U133A


title: patient 1022

description:
breast tumor biopsy
sample name: hw1022.spore5.U133A


title: patient 786

description:
breast tumor biopsy
sample name: hw786.U133A


title: patient 635

description:
breast tumor biopsy
sample name: hw635.U133A


title: patient 738

description:
breast tumor biopsy
sample name: hw738.run2.U133A


title: patient 996

description:
breast tumor biopsy
sample name: hw996.U133A


title: patient 1812

description:
breast tumor biopsy
sample name: hw1812.U133A

value: overweight

value: U


title: patient 1832

description:
breast tumor biopsy
sample name: hw1832.U133A


title: patient 1831

description:
breast tumor biopsy
sample name: hw1831.U133A


title: patient 1809

description:
breast tumor biopsy
sample name: hw1809.U133A


title: patient 828

description:
breast tumor biopsy
sample name: hw828.U133A


title: patient 1807

description:
breast tumor biopsy
sample name: hw1807.U133A


title: patient 1805

description:
breast tumor biopsy
sample name: hw1805.U133A


title: patient 1840

description:
breast tumor biopsy
sample name: hw1840.run2.U133A


title: patient 1703

description:
breast tumor biopsy
sample name: hw1703.U133A


title: patient 1700

description:
breast tumor biopsy
sample name: hw1700.U133A


title: patient 1136

description:
breast tumor biopsy
sample name: hw1136.U133A


title: patient 1586

description:
breast tumor biopsy
sample name: hw1586.U133A


title: patient 1087

description:
breast tumor biopsy
sample name: hw1087.run2.U133A


title: patient 1698

description:
breast tumor biopsy
sample name: hw1698.U133A


title: patient 982

description:
breast tumor biopsy
sample name: hw982.spore5.U133A


title: patient 1219

description:
breast tumor biopsy
sample name: hw1219.U133A


title: patient 1839

description:
breast tumor biopsy
sample name: hw1839.U133A

value: normal


title: patient 1842

description:
breast tumor biopsy
sample name: hw1842.U133A


title: patient 849

description:
breast tumor biopsy
sample name: hw849.U133A


title: patient 657

description:
breast tumor biopsy
sample name: hw657.U133A


title: patient 1583

description:
breast tumor biopsy
sample name: hw1583.U133A


title: patient 1146

description:
breast tumor biopsy
sample name: hw1146.run2.U133A


title: patient 742

description:
breast tumor biopsy
sample name: hw742.U133A


title: patient 1245

description:
breast tumor biopsy
sample name: hw1245.U133A


title: patient 747

description:
breast tumor biopsy
sample name: hw747.U133A


title: patient 1695

description:
breast tumor biopsy
sample name: hw1695.U133A


title: patient 854

description:
breast tumor biopsy
sample name: hw854.U133A


title: patient 1702

description:
breast tumor biopsy
sample name: hw1702.U133A


title: patient 1837

description:
breast tumor biopsy
sample name: hw1837.U133A


title: patient 1833

description:
breast tumor biopsy
sample name: hw1833.U133A


title: patient 1838

description:
breast tumor biopsy
sample name: hw1838.U133A


title: patient 1836

description:
breast tumor biopsy
sample name: hw1836.run2.U133A


title: patient 1808

description:
breast tumor biopsy
sample name: hw1808.U133A


title: patient 1704

description:
breast tumor biopsy
sample name: hw1704.U133A


title: patient 1835

description:
breast tumor biopsy
sample name: hw1835.U133A


title: 24h EGF versus Control replicate 3 dye swap  (Agilent)

description: 24h time point, biological replicate 3 of 3. Technical replicate 2 of 2. HeLa cells treated with EGF compared to untreated controls.

label_protocol: 500 ng of total RNA were reverse transcribed, amplified, labelled by in vitro transcription using the Low Input Linear Amplification Kit (Agilent 5184-3523), and hybridized following the manufacturer’s instructions (SSC wash Agilent 60-mer oligo microarray processing protocol, Version 4.1, April 2004).

extract_protocol: Total RNA from HeLa cells was extracted using the RNeasy RNA Isolation kit (Qiagen) followed by treatment with RNase-free DNase I (Ambion, Austin, TX) following manufacturer's instructions. RNA quantification was performed with a Nanodrop spectrophotometer, and the RNA integrity was assessed using the Bioanalyzer 2100 nanoelectrophoresis Lab-on-a–chip system (Agilent, Wilmington, DE). All RNAs used had RIN (RNA integrity number) ranging between 9.3 and 10, and 28S/18S ratios between 1.67 and 2.07.

value: serum deprived for 24 hours, followed by exposure to EGF for 24 hours

value: HeLa

value: serum deprived for 24 hours, followed by culture without EGF addition into the medium for 24 additional hours


title: patient 1394

description:
breast tumor biopsy
sample name: hw1394.U133A

value: breast cancer


title: 24h EGF versus Control replicate 3  (Agilent)

description: 24h time point, biological replicate 3 of 3. Technical replicate 1 of 2. HeLa cells treated with EGF compared to untreated controls.


title: patient 1814

description:
breast tumor biopsy
sample name: hw1814.run2.U133A


title: patient 1810

description:
breast tumor biopsy
sample name: hw1810.U133A


title: ZF-TF 7, 2nd infection

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description:
ZF-TF.7.b4
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 7, 2nd infection

hyb_protocol: Microarray = Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2

scan_protocol: Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS

data_processing: MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.

label_protocol: Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)

growth_protocol: MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541

extract_protocol: QIAGEN RNeasy protocol and reagents for extraction of total RNA

treatment_protocol: 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene.  Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days.  Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only.  T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.

tag: retroviral transduction

value: zinc finger transcription factor 7


title: patient 1803

description:
breast tumor biopsy
sample name: hw1803.U133A


title: patient 1813

description:
breast tumor biopsy
sample name: hw1813.U133A


title: patient 1802

description:
breast tumor biopsy
sample name: hw1802.U133A


title: patient 1806

description:
breast tumor biopsy
sample name: hw1806.U133A


title: patient 1697

description:
breast tumor biopsy
sample name: hw1697.U133A


title: patient 1696

description:
breast tumor biopsy
sample name: hw1696.U133A


title: 24h EGF versus Control replicate 1 dye swap  (Agilent)

description: 24h time point, biological replicate 1 of 3. Technical replicate 2 of 2. HeLa cells treated with EGF compared to untreated controls.


title: patient 1799

description:
breast tumor biopsy
sample name: hw1799.U133A


title: patient 1589

description:
breast tumor biopsy
sample name: hw1589.run3.U133A


title: patient 1801

description:
breast tumor biopsy
sample name: hw1801.U133A


title: 24h EGF versus Control replicate 2  (Agilent)

description: 24h time point, biological replicate 2 of 3. Technical replicate 1 of 2. HeLa cells treated with EGF compared to untreated controls.


title: patient 1800

description:
breast tumor biopsy
sample name: hw1800.U133A

value: b


title: ZF-TF 70, 2nd infection

description:
ZF-TF.70.b3
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 70, 2nd infection

value: zinc finger transcription factor 70


title: ZF-TF 19, 2nd infection

description:
ZF-TF.19.b3
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 19, 2nd infection

value: zinc finger transcription factor 19


title: ZF-TF 83, 2nd infection

description:
ZF-TF.83.b3
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 83, 2nd infection

value: zinc finger transcription factor 83


title: ZF-TF 64, 2nd infection

description:
ZF-TF.64.b4
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 64, 2nd infection

value: zinc finger transcription factor 64


title: Control, 2nd infection

description:
Control.b3
fulvestrant sensitive MCF7 clone retroviraly induced with control plasmid encoding only the NF-kappaB p65 activation domain, 2nd infection

value: control


title: 6h EGF versus Control replicate 3  (Agilent)

description: 6h time point, biological replicate 3 of 3. Technical replicate 1 of 2. HeLa cells treated with EGF compared to untreated controls.

value: serum deprived for 24 hours, followed by exposure to EGF for 6 hours

value: serum deprived for 24 hours, followed by culture without EGF addition into the medium for 6 additional hours


title: 24h EGF versus Control replicate 1  (Agilent)

description: 24h time point, biological replicate 1 of 3. Technical replicate 1 of 2. HeLa cells treated with EGF compared to untreated controls.


title: 6h EGF versus Control replicate 3 dye swap  (Agilent)

description: 6h time point, biological replicate 3 of 3. Technical replicate 2 of 2. HeLa cells treated with EGF compared to untreated controls.


title: ZF-TF 83, 1st infection

description:
ZF-TF.83.b1
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 83, 1st infection


title: HeLa versus Control Pool dye swap (Agilent)

type: genomic

description: Technical replicate 2 of 2. Dye swap. HeLa cell DNA compared to euploid control DNA.

hyb_protocol: Slides hybridized and washed as recommended by Agilent.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings.

data_processing: Default CGH-v4_95 Agilent Feature extraction normalization protocol used. For detection of gains and losses data was further analyzed using the DNA Analytics software in aCGH mode

molecule: genomic DNA

label_protocol: 1 μg of reference and sample DNA were digested with AluI and RsaI restriction enzymes (Life Technologies; Rockville, MD). Digested samples were enzyme inactivated and labeled with Cy3-dUTP and Cy5-dUTP using the Agilent Genomic DNA Labeling Kit PLUS (50) (Agilent Technologies) following the manufacturer’s instructions.

extract_protocol: Genomic DNA from HeLa cells was extracted using the Chemagen kit following manufacturer's instructions. DNA quantification was performed with a Nanodrop spectrophotometer, and the DNA integrity was assessed by akaline gel electrophoresis.

source_name: Human peripheral blood

tag: tissue

value: blood


title: ZF-TF 115, 2nd infection

description:
ZF-TF.115.b3
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 115, 2nd infection

value: zinc finger transcription factor 115


title: 24h EGF versus Control replicate 2 dye swap  (Agilent)

description: 24h time point, biological replicate 2 of 3. Technical replicate 2 of 2. HeLa cells treated with EGF compared to untreated controls.


title: patient 1588

description:
breast tumor biopsy
sample name: hw1588.U133A

value: w

value: PRE

value: n

value: P

value: U


title: 24h EGF replicate 3 repetition (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 24 hours
24h time point, EGF, biological replicate 3 of 3. Technical replicate 2 of 2.

hyb_protocol: Microarrays were hybridized with 15 µg of fragmented cRNA. Hybridizations were carried out at 45°C for 16 h without agitation. Arrays were washed and the hybridized RNA was fluorescence-stained by incubating with streptavidin–phycoerythrin.

scan_protocol: Detection and feature readout were performed using the CCD-based detection system of the Geniom device (Cy3 filter set).

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The single channel intensity data were quantile normalized to scaling across chips. Differentially expressed genes for each time point were chosen using as cut off criteria a SAM FDR of 5% and an average absolute fold change (|FC|) above 1.2 .

label: biotin / streptavidin-phycoerythrin

label_protocol: 5 µg of total RNA was converted into double-stranded cDNA using the Superscript II system for cDNA synthesis (Invitrogen). Double-stranded cDNA was purified and in vitro transcribed. Biotinylated cRNA was purified and fragmented randomly to an average length of ~100 nt by incubating at 94°C for 35 min.

treatment_protocol: For treatments, the cells were transferred to 60 mm dishes and cultured for 48h in complete growth medium, after which they were starved for 24h in DMEM containing 2% FBS. After serum deprivation cells were stimulated with EGF (150 ng/ml) for the indicated times. Three biological replicate experiments were performed, each comparing EGF treated with untreated control HeLa cells.

value: HeLa


title: 24h EGF replicate 3 (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 24 hours
24h time point, EGF, biological replicate 3 of 3. Technical replicate 1 of 2.


title: 6h EGF versus Control replicate 1 dye swap  (Agilent)

description: 6h time point, biological replicate 1 of 3. Technical replicate 2 of 2. HeLa cells treated with EGF compared to untreated controls.


title: patient 1587

description:
breast tumor biopsy
sample name: hw1587.U133A

value: breast cancer

value: normal

value: N


title: 6h EGF versus Control replicate 2 dye swap  (Agilent)

description: 6h time point, biological replicate 2 of 3. Technical replicate 2 of 2. HeLa cells treated with EGF compared to untreated controls.


title: ZF-TF 70, 1st infection

description:
ZF-TF.70.b1
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 70, 1st infection

value: zinc finger transcription factor 70


title: HeLa versus Control Pool (Agilent)

description: Technical replicate 1 of 2. HeLa cell DNA compared to diploid control DNA.


title: intestine, BlimpKO, rep8

city: Amsterdam

first: Jarom

last: Heijmans

address: Meibergdreef 69-71

department: Tytgat Institute for liver and intestinal research

country: Netherlands

institute: Academic Medical Center

description:
5388876090_H.AVG_Signal
VillinCre-Blimpflox

hyb_protocol: According to illumina instructions.

scan_protocol: According to illumina instructions on a BeadArray 500GX scanner.

data_processing: All transcripts were taken from data with standard background subtraction in illumina Beadstudio, and all genes that had low intensity values (<5) were omitted. Subsequently, quantile normalization was performed.

label: Biotin

organism: Mus musculus

source_name: Mid-intestine, KO

label_protocol: Ambion cRNA synthesis for illumina.

growth_protocol: Specific pathogen-free (SPF) caging.

extract_protocol: Trizol, followed by Qiagen RNeasy cleanup.

treatment_protocol: Conditional knockout of Prdm1 (Blimp1) crossed into the VillinCre allele.

tag: strain

tag: genotype

value: Blimp knockout

value: mid-intestine

value: postnatal day 7


title: intestine, BlimpKO, rep4

description:
5388876105_H.AVG_Signal
VillinCre-Blimpflox


title: intestine, BlimpKO, rep2

description:
5388876105_C.AVG_Signal
VillinCre-Blimpflox


title: intestine, BlimpKO, rep7

description:
5388876090_F.AVG_Signal
VillinCre-Blimpflox


title: intestine, BlimpKO, rep6

description:
5388876090_C.AVG_Signal
VillinCre-Blimpflox


title: 6h EGF versus Control replicate 2  (Agilent)

description: 6h time point, biological replicate 2 of 3. Technical replicate 1 of 2. HeLa cells treated with EGF compared to untreated controls.

value: serum deprived for 24 hours, followed by exposure to EGF for 6 hours


title: 24h Control replicate 3 repetition (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 24 additional hours
24h time point, Control, biological replicate 3 of 3. Technical replicate 2 of 2.


title: patient 1580

description:
breast tumor biopsy
sample name: hw1580.U133A

value: POST

value: y


title: intestine, BlimpKO, rep5

description:
5388876090_A.AVG_Signal
VillinCre-Blimpflox


title: ZF-TF 7, 1st infection

description:
ZF-TF.7.b1
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 7, 1st infection

value: zinc finger transcription factor 7


title: 24h Control replicate 3 (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 24 additional hours
24h time point, Control, biological replicate 3 of 3. Technical replicate 1 of 2.


title: patient 1387

description:
breast tumor biopsy
sample name: hw1387.U133A

value: w


title: patient 1388

description:
breast tumor biopsy
sample name: hw1388.U133A

value: PRE


title: intestine, BlimpKO, rep3

description:
5388876105_G.AVG_Signal
VillinCre-Blimpflox


title: 24h EGF replicate 1 repetition (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 24 hours
24h time point, EGF, biological replicate 1 of 3. Technical replicate 2 of 2.


title: 6h EGF versus Control replicate 1 (Agilent)

description: 6h time point, biological replicate 1 of 3. Technical replicate 1 of 2. HeLa cells treated with EGF compared to untreated controls.

value: serum deprived for 24 hours, followed by culture without EGF addition into the medium for 6 additional hours


title: intestine, BlimpKO, rep1

description:
5388876105_B.AVG_Signal
VillinCre-Blimpflox


title: patient 1314

description:
breast tumor biopsy
sample name: hw1314.U133A

value: n

value: P


title: Control, 1st infection

description:
Control.b1
fulvestrant sensitive MCF7 clone retroviraly induced with control plasmid encoding only the NF-kappaB p65 activation domain, 1st infection

value: control


title: ZF-TF 64, 1st infection

description:
ZF-TF.64.b1
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 64, 1st infection

value: zinc finger transcription factor 64


title: 24h EGF replicate 3 (Illumina)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 24 hours
24h time point, EGF, biological replicate 3 of 3

hyb_protocol: For each sample, 750 ng of biotinylated cRNA were hybridized in a BeadChip Hyb Chamber with rocking 16 h at 58ºC. The day after the bead arrays were washed with Illumina proprietary washing solutions in a Hybex waterbath: first with static incubation for 10 min at 55ºC in E1BC solution, followed by 10 rinses by dipping in the same solution and shaking 5 min at 90 rpm in an orbital shaker; the next wash was by dipping 10 times in 100% ethanol and shaking 10 min at 110 rpm in an orbital shaker; this was followed by another wash in E1BC solution with 10 dippings followed by 2 min shaking at 90 rpm. Washed bead arrays were blocked in E1 buffer 10 min in rocking incubator and 10 additional minutes with 2 ml of E1 buffer plus streptavidin-Cy3. The fluorescent reagent was washed away with E1BC solution with 10 dippings plus 5 min shaking at 140 rpm. Finally beadarrays were dried by centrifugation 4 min at 275 rcf, followed by scanning in a Illumina Beadstation.

scan_protocol: The Beadscan software was used to control de scanner, generate .tif images and extract the raw data as tabulated text files. Default settings for DirectHyb Gene Expression were used.

data_processing: The raw data was summarized per probe using BeadStudio software Gene Expression module and the summary data file was processed using the PILLA web einterface tool (Lozano et al, unpublished), an implementation of the Lumi package (Du et al, 2008) developed within the Bioconductor project in the R statistical programming environment (Gentleman et al, 2004). Data were normalized using the rsn method and vst as the variance stabilization method. The log2 intensities were median centered and log ratios were computed as differences in log2 intensities for each probe. The SAM  (significance analysis of microarrays) two class unpaired comparison test was applied with 100 permutations to detect statistically significant differences in gene expression between treated and control conditions (Tusher et al, 2001).

label: biotin / streptavidin-Cy3

label_protocol: For each sample 200 ng of total RNA were reverse transcribed, amplified by in vitro transcription and labelled with biotin-UTP using the Illumina Total Prep RNA amplification kit (IL1791, Ambion) following the manufacturer's instructions. Labelled sample quality was assessed by spectrophotometry and bioanalyzer. After preheating at 65ºC for 5 min.

value: HeLa


title: ZF-TF 19, 1st infection

description:
ZF-TF.19.b1
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 19, 1st infection

value: zinc finger transcription factor 19


title: ZF-TF 115, 1st infection

description:
ZF-TF.115.b1
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 115, 1st infection

value: zinc finger transcription factor 115


title: patient 1582

description:
breast tumor biopsy
sample name: hw1582.spore5.U133A

value: breast cancer

value: normal

value: N

value: U


title: intestine, BlimpWT, rep8

description:
5388876090_G.AVG_Signal
VillinCre-Blimpwt

source_name: Mid-intestine, WT

value: Blimp wild type

value: mid-intestine

value: postnatal day 7


title: patient 1283

description:
breast tumor biopsy
sample name: hw1283.U133A

value: w


title: 24h EGF replicate 1 (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 24 hours
24h time point, EGF, biological replicate 1 of 3. Technical replicate 1 of 2.


title: 24h Control replicate 1 (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 24 additional hours
24h time point, Control, biological replicate 1 of 3. Technical replicate 1 of 2.


title: 6h EGF replicate 3 repetition (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 6 hours
6h time point, EGF, biological replicate 3 of 3. Technical replicate 2 of 2.


title: 24h Control replicate 1 repetition (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 24 additional hours
24h time point, Control, biological replicate 1 of 3. Technical replicate 2 of 2.


title: 6h EGF replicate 3 (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 6 hours
6h time point, EGF, biological replicate 3 of 3. Technical replicate 1 of 2.


title: 6h Control replicate 3 (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 6 additional hours
6h time point, Control, biological replicate 3 of 3. Technical replicate 1 of 2.


title: patient 873

description:
breast tumor biopsy
sample name: hw873.U133A

value: a

value: PRE


title: intestine, BlimpWT, rep5

description:
5388876090_B.AVG_Signal
VillinCre-Blimpwt


title: 6h Control replicate 3 repetition (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 6 additional hours
6h time point, Control, biological replicate 3 of 3. Technical replicate 2 of 2.


title: patient 675

description:
breast tumor biopsy
sample name: hw675.U133A

value: POST

value: n


title: patient 1059

description:
breast tumor biopsy
sample name: hw1059.U133A

value: PERI

value: P


title: 24h Control replicate 3 (Illumina)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 24 additional hours
24h time point, Control, biological replicate 3 of 3

value: HeLa


title: 24h EGF replicate 2 (Illumina)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 24 hours
24h time point, EGF, biological replicate 2 of 3


title: patient 1251

description:
breast tumor biopsy
sample name: hw1251.U133A


title: intestine, BlimpWT, rep4

description:
5388876105_F.AVG_Signal
VillinCre-Blimpwt


title: intestine, BlimpWT, rep6

description:
5388876090_D.AVG_Signal
VillinCre-Blimpwt


title: patient 973

description:
breast tumor biopsy
sample name: hw973.U133A


title: patient 837

description:
breast tumor biopsy
sample name: hw837.U133A

value: b


title: intestine, BlimpWT, rep2

description:
5388876105_D.AVG_Signal
VillinCre-Blimpwt


title: intestine, BlimpWT, rep1

description:
5388876105_A.AVG_Signal
VillinCre-Blimpwt


title: 24h EGF replicate 1 (Illumina)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 24 hours
24h time point, EGF, biological replicate 1 of 3


title: 24h Control replicate 1 (Illumina)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 24 additional hours
24h time point, Control, biological replicate 1 of 3


title: 24h Control replicate 2 (Illumina)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 24 additional hours
24h time point, Control, biological replicate 2 of 3


title: 6h EGF replicate 1 (Illumina)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 6 hours
6h time point, EGF, biological replicate 1 of 3


title: 6h EGF replicate 3 (Illumina)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 6 hours
6h time point, EGF, biological replicate 3 of 3


title: intestine, BlimpWT, rep7

description:
5388876090_E.AVG_Signal
VillinCre-Blimpwt


title: 6h EGF replicate 2 (Illumina)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 6 hours
6h time point, EGF, biological replicate 2 of 3


title: 6h EGF replicate 1 (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 6 hours
6h time point, EGF, biological replicate 1 of 3. Technical replicate 1 of 2.


title: 6h EGF replicate 1 repetition (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 6 hours
6h time point, EGF, biological replicate 1 of 3. Technical replicate 2 of 2.


title: 6h Control replicate 1 repetition (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 6 additional hours
6h time point, Control, biological replicate 1 of 3. Technical replicate 2 of 2.


title: 6h Control replicate 1 (IMPPC)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 6 additional hours
6h time point, Control, biological replicate 1 of 3. Technical replicate 1 of 2.


title: patient 665

description:
breast tumor biopsy
sample name: hw665.U133A


title: patient 633

description:
breast tumor biopsy
sample name: hw633.U133A

value: y


title: intestine, BlimpWT, rep3

description:
5388876105_E.AVG_Signal
VillinCre-Blimpwt


title: 6h Control replicate 3 (Illumina)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 6 additional hours
6h time point, Control, biological replicate 3 of 3


title: T47D-CrkII Cell Replicate 2

city: Montreal

first: Sean

last: Cory

state: QC

address: 3649 Promenade Sir William Osler

department: Goodman Cancer centre

country: Canada

institute: McGill

description: T47D-CrkII Cell Replicate 2

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: T47D-CrkII Cell Replicate 2

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: ES cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemicon, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder layer inactivated by 10 ug/ml of mitomycin C (Sigma, St. L)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: cell type

value: T47D-CrkII Cell

source_name: Universal Human Refence RNA

tag: reference

value: Universal Human Refence RNA


title: 6h Control replicate 2 (Illumina)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 6 additional hours
6h time point, Control, biological replicate 2 of 3


title: Bj USDA110 elevated CO2 condition vs ambient condition (non-root) rep1

status: Public on Jul 16 2011

city: Saint Paul

first: Masayuki

last: Sugawara

state: MN

address: 250 Borloug Hall, 1991 Upper Buford Circle

department: Soil, Water, and Climate

institute: University of Minnesota

hyb_protocol: Both Cy3 and Cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 70 ul of preheated hybridization buffer (nuclease free water:formamide:20X SSC:1% SDS = 4:2.5:2.5:1) at 42°C. After adding 0.7 ul salmon sperm DNA (10 mg/ml) to prevent non-specific binding to the array, the mixture was hybridized at 42 C for 16 to 18 h. Hybridized arrays were washed with 1X SSC, 0.2% SDS at 42°C for 6 min, and, subsequently, with 0.1X SSC, 0.2% SDS at room temperature for 6 min, and twice with 0.1X SSC at room temperature for 3 min.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices Corp., Sunnyvale, CA). Signal intensities were analyzed using GenePix Pro 6.0 software (Molecular Devices Corp., Sunnyvale, CA).

data_processing: Signal intensities were normalized for spot and slide abnormalities using spatial lowess. Lowess adjusted data were subsequently analyzed by mixed effect microarray analysis of variance (MAANOVA) (Kerr et al. 2000). The resulting variety-by-gene interaction (VG) values were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Kerr et al. 2000; Kerr and Churchill 2001). Both lowess and MAANOVA are part of the R/maanova microarray statistical analysis package (http://www.jax.org/staff/churchill/labsite/). Expression values from two technical replicates in each array were combined, averaged, and subsequently subjected to significance analysis of microarray (SAM) data using the SAM package (Tusher et al. 2001). Significant genes were selected based on a 1.5-fold cut off threshold with a false discovery rate lower than 5%.

organism: Bradyrhizobium japonicum

source_name: cells grown in a plant growth box under elevated CO2 condition for 3 days

label_protocol: 10 ug of total RNA was used for cDNA synthesis with Superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Invtrogen), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined.

growth_protocol: Bradyrhizobium japonicum strain was grown in 10 ml of AG medium (Sadowsky et al. 1987) until stationary phase, collected by centrifugation at 8,000 ×g for 10 min, and washed twice with sterilized, nitrogen-free, plant growth medium (Franco and Munns 1982). The resultant cells were re-suspended in 10 ml of the same plant growth medium to a final concentration of approximately 10^9 cells/ml. Germinated soybean seedlings (60 – 70) were each aseptically transferred into holes in the growth boxes filled with 300 ml of plant growth medium, and 3 ml washed bacterial suspension was added to provide approximately 107 cells/ml of growth medium. Three replicates seedling growth boxes were used for each CO2 treatment. Seedling boxes were covered with aluminum foil, transferred to a plant growth chamber, and the aeration pump (Luft Pump; Oceanic systems Inc. Dallas, TX) was immediately started. Each pump supplied aeration of three growth boxes, at a rate of 1.3 L /min. The seedling boxes were incubated for 3 days at 27°C in the dark. Kyoto, Japan). To investigate a directly influence of atmospheric elevated CO2 on gene expression in Bradyrhizobium cells, 3 ml of washed bacterial suspension was added in a growth boxes without plant seedlings, and the boxes were incubated at the same condition as above.

extract_protocol: Standard hot-phenol method

treatment_protocol: Germinated soybean seedlings in the growth boxes were incubated for 3 days at 27°C in the dark under elevated or amibient CO2 conditions. The elevated CO2 concentration in growth chambers was controlled by an APBA-250E indoor CO2 monitor (HORIBA, Kyoto, Japan), and maintained at 550 ppm or ambient CO2 concentration. All of the roots from three replicate hydroponic boxes were gently rinsed, several times in sterile fresh plant growth medium to remove loosely-adhering or non-attached bradyrhizobia. Rinsed roots were randomly cut with a sterilized scissor, and placed into 500 ml bottles containing 180 ml of ice- cold extraction buffer (0.1 % Na-pyrophosphate, pH 7.0, and 0.1 % Tween 20) and 20 ml of stop solution (5 % H2O-saturated phenol, pH 4.3, in 95% Ethanol). Bottles were agitated at approximately 220 strokes per min for 30 min by using an Eberbach model 6000 horizontal shaker (Eberbach Corp., Ann Arbor, MI). Extracts were filtered through three layers of Miracloth (Calbiochem Inc. LaJolla, CA) to remove plant cells and debris and filtrates were centrifuged at 8,000 ×g for 12 min. The resulting cell pellet were immediately flash frozen in liquid nitrogen, and stored in the freezer at -80 °C until RNA extraction.

tag: co2 condition

value: USDA 110

value: elevated (550ppm)

source_name: cells grown in a plant growth box under ambient CO2 condition for 3 days

value: ambient


title: 6h Control replicate 1 (Illumina)

description:
HeLa cells, serum deprived for 24 hours, followed by culture without EGF addition into the medium for 6 additional hours
6h time point, Control, biological replicate 1 of 3


title: T47D Cell Replicate 1

description: T47D Cell Replicate 1

source_name: T47D Cell Replicate 1

value: T47D Cell


title: Bj USDA110 elevated CO2 condition vs ambient condition (non-root) rep4


title: Root-attached Bj USDA110 elevated CO2 condition vs ambient condition rep1

source_name: cells grown in the soybean rhizosphere under elevated CO2 condition for 3 days

source_name: cells grown in the soybean rhizosphere under ambient CO2 condition for 3 days


title: Bj USDA110 elevated CO2 condition vs ambient condition (non-root) rep3


title: Root-attached Bj USDA110 elevated CO2 condition vs ambient condition rep4


title: Root-attached Bj USDA110 elevated CO2 condition vs ambient condition rep2


title: Bj USDA110 elevated CO2 condition vs ambient condition (non-root) rep2


title: T47D-CrkII Cell Replicate 1

description: T47D-CrkII Cell Replicate 1

source_name: T47D-CrkII Cell Replicate 1


title: patient 644

description:
breast tumor biopsy
sample name: hw644.U133A

tag: disease state

value: breast cancer

tag: age

tag: race

value: normal

value: N


title: Root-attached Bj USDA110 elevated CO2 condition vs ambient condition rep3


title: patient 671

description:
breast tumor biopsy
sample name: hw671.U133A

value: w

tag: menopause

value: PRE

tag: bmi

tag: bmi status


title: T47D Cell Replicate 2

description: T47D Cell Replicate 2

source_name: T47D Cell Replicate 2


title: Jurkat PMA CD3 PD98059 2

city: Ede

first: Wynand

last: Alkema

address: Kernhemseweg 2

institute: NIZO Food Research

hyb_protocol: After fragmentation, cRNA (10μg) was hybridized at 45°C for 16-17 hours to the Human Genome U133A 2.0 Array or the Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Following hybridization, the arrays were washed, stained with phycoerythrin-streptavidin conjugate (Molecular Probes, Eugene, OR), and the signals were amplified by staining the array with biotin-labeled anti-streptavidin antibody (Vector Laboratories, Burlingame, CA) followed by phycoerythrin-streptavidin.

scan_protocol: The arrays were laser scanned with an GeneChip Scanner 3000 6G (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions.

data_processing: Data was saved as raw image file and quantified using GCOS (Affymetrix).

source_name: Jurkat T cells

label_protocol: Double-stranded cDNA was synthesized from 1.5 μg total RNA using the One-Cycle Target Labeling Kit (Affymetrix Santa Clara, CA), and used as a template for the preparation of biotin-labeled cRNA using the GeneChip IVT Labeling Kit (Affymetrix Santa Clara, CA). Biotin-labeled cRNA was fragmented at 1 μg/μl following the manufacturer’s protocol.

growth_protocol: Jurkat E6.2.11 T cells were cultured in DMEM F12 medium (#041-94895M, Gibco) supplemented with 10% FBS (#10099-141, Invitrogen) and 80 U/ml penicillin/80 μg/ml streptomycin (#15140-122 Gibco).

extract_protocol: Total RNA was isolated from Jurkat T cells using the RNeasy mini extraction kit (Qiagen # 74106) according to the manufactures’ protocol. RNA was dissolved and diluted in RNAse free water and the RNA concentration was determined via Nanodrop analysis. The quality of total RNA was evaluated by capillary electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Calif.).

treatment_protocol: For gene expression profiling Jurkat T cells were seeded in T25 culture flasks at a concentration of 1x106 cells/ml (1x107 cells in total) and cultured overnight at 37°C/5%CO2, one day prior to stimulation. On the day of the experiment cells were preincubated with the compound of interest for 30 minutes, followed by a stimulation with either CD3/CD28, PMA/CD28 or PMA/CD3, at concentrations of 10 ng/ml PMA, 1 μg/ml CD3 and 1 μg/ml CD28. Jurkat T cells were cultured in the presence or absence of stimulation for one or eight hours in total, after which the cells were washed in ice cold PBS. Thereafter cell pellets were collected and snap frozen at -80°C. Cell pellets were stored until further processing.

value: Jurkat E6.2.11 T cells


title: Jurkat PMA CD3 Org48762 1

value: PMA, CD3, Org48762


title: Jurkat PMA CD3 SP600125 2


title: Jurkat PMA CD3 Org48762 2


title: Jurkat PMA CD3 CsA 2

value: PMA, CD3, CsA


title: Jurkat PMA CD3 PD98059 1


title: Jurkat PMA CD3 A 420983 2


title: Jurkat PMA CD3 CsA 1


title: Jurkat CD28 CD3 PD98059 2


title: Jurkat CD28 CD3 PD98059 1


title: Jurkat PMA CD3 AEB 071 1

value: PMA, CD3, AEB, 071


title: Jurkat CD28 CD3 SP600125 1


title: Jurkat CD28 CD3 Org48762 1


title: Jurkat PMA CD3 AEB 071 2


title: Jurkat CD28 CD3 SP600125 2


title: Jurkat PMA CD3 SP600125 1


title: Jurkat PMA CD3 A 420983 1


title: Jurkat CD28 CD3 Org48762 2


title: Jurkat CD28 CD3 CsA 2

value: CD28, CD3, CsA


title: Jurkat CD28 CD3 AEB 071 2


title: Jurkat CD28 PMA PD98059 2


title: Jurkat CD28 CD3 A 420983 2


title: Jurkat CD28 PMA PD98059 1


title: Jurkat CD28 CD3 CsA 1


title: Jurkat CD28 PMA SP600125 2


title: Jurkat CD28 PMA SP600125 1


title: Jurkat CD28 PMA Org48762 2


title: Jurkat CD28 CD3 A 420983 1


title: Jurkat CD28 PMA CsA 1

value: CD28, PMA, CsA


title: Jurkat PMA CD3 Control 2

value: PMA, CD3, Control


title: Jurkat CD28 PMA A 420983 2


title: Jurkat CD28 PMA Org48762 1


title: Jurkat CD28 PMA CsA 2


title: Jurkat CD28 PMA AEB 071 1

value: CD28, PMA, AEB, 071


title: Jurkat CD28 PMA AEB 071 2


title: Jurkat PMA CD3 Control 3


title: Jurkat CD28 PMA Control 2

value: CD28, PMA, Control


title: Jurkat CD28 CD3 Control 2

value: CD28, CD3, Control


title: Jurkat PMA CD3 Control 1


title: Jurkat CD28 CD3 Control 1


title: Jurkat CD28 CD3 AEB 071 1


title: Jurkat CD3 3


title: Jurkat PMA 1

value: PMA


title: Jurkat CD28 CD3 Control 3


title: Jurkat PMA 3


title: Jurkat CD28 PMA Control 1


title: Jurkat PMA 2


title: Jurkat CD28 PMA A 420983 1


title: Jurkat CD28 PMA Control 3


title: Jurkat CD3 2


title: Jurkat CD28 2


title: 14165070

city: Cerdanyola

first: Carlos

last: Casado

address: Edifici IBB, Campus Bellaterra

department: Departament Bioquimica i Biologia Molecular

institute: Universitat Autònoma de Barcelona

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42 oC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 ul of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five ug of salmon sperm DNA was added to the mix before denaturation for 3 min at 95 ºC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42 ºC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 um. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices).  Spots with either a diameter smaller than 120 um, or fluorescence intensity for Cy3 and Cy5 lower than 100 units, were not considered for further analysis.

data_processing: The GEPAS server (http://www.gepas.org) was used to preprocess the data: merge replicates and remove inconsistent replicates (Maximum distance to median of replicates=1). The normalization method we used to generate the data reported in the VALUE columns was the ratio of medians for the non-flagged genes.

organism: Saccharomyces cerevisiae

source_name: MCY5278 mutant in exponential phase culture treated with 20 mM KOH, 30 min

label_protocol: Fluorescent labeled cDNA was prepared from 8 ug of purified total RNA by the indirect dUTP-labeling method using the CyScribe post-labeling kit (GE Healthcare) and oligo(dT) as a primer.

growth_protocol: Grown at 28 ºC in 50 ml of YPD rich medium until A660=0.6. KOH was added to a final concentration of 20 mM and the culture was grown for 30 more minutes before cells were harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 ºC until RNA purification.

extract_protocol: Total RNA purification using the Ambion RiboPure™-Yeast Total RNA Isolation Kit.

treatment_protocol: 20mM KOH for 30 min

value: msn2::kanMX4 msn4::hphMX4

value: KOH

tag: treatment duration

value: 30 min

source_name: MCY5278 mutant in exponential phase culture treated with 20 mM KCl, 30 min

growth_protocol: Grown at 28 ºC in 50 ml of YPD rich medium until A660=0.6. KCl was added to a final concentration of 20 mM and the culture was grown for 30 more minutes before cells were harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 ºC until RNA purification.

treatment_protocol: 20mM KCl for 30 min

value: KCl


title: 13905786


title: 14164790

source_name: Wild type in exponential phase culture treated with 20 mM KOH, 30 min

value: wild type

source_name: Wild type in exponential phase culture treated with 20 mM KCl, 30 min


title: 14164936

source_name: MCY5278 mutant in exponential phase culture treated with 20 mM KOH, 10 min

growth_protocol: Grown at 28 ºC in 50 ml of YPD rich medium until A660=0.6. KOH was added to a final concentration of 20 mM and the culture was grown for 10 more minutes before cells were harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 ºC until RNA purification.

treatment_protocol: 20mM KOH for 10 min.

value: 10 min

source_name: MCY5278 mutant in exponential phase culture treated with 20 mM KCl, 10 min

growth_protocol: Grown at 28 ºC in 50 ml of YPD rich medium until A660=0.6. KCl was added to a final concentration of 20 mM and the culture was grown for 10 more minutes before cells were harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 ºC until RNA purification.

treatment_protocol: 20mM KCl for 10 min.


title: 13905730


title: Jurkat CD3 1

value: Jurkat E6.2.11 T cells


title: 13905618


title: 14164935

source_name: Wild type in exponential phase culture treated with 20 mM KOH, 10 min

source_name: Wild type in exponential phase culture treated with 20 mM KCl, 10 min


title: Jurkat Control  1

value: Control


title: PASMC_BMP4_24h

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

hyb_protocol: Array hybridization was performed as described previously (Ishii et al., Genomics 68:136-143, 2000 [PMID 10964511]).

scan_protocol: Array scanning was performed as described previously (Ishii et al., Genomics 68:136-143, 2000 [PMID 10964511]).

data_processing: Microarray Suite software 5.0 of GCOS (Affymetrix) was used with target intensity of 100.

source_name: PASMCs stimulated with BMP-4 for 24 h

label_protocol: Double-stranded cDNA was synthesized with the SuperScript Choice system (GIBCO) and a T7-(dT) 24 Primer (GE Amersham) from the total RNA. In vitro transcription was performed to produce biotin-labeled cRNA by using a BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) according to the manufacturer’s instructions (Ishii et al, Genomics 68:136-143, 2000 [PMID 10964511]).

growth_protocol: PASMCs were maintained in SmGM-2 medium (Lonza).  Cells were grown in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: Total RNAs were extracted using the RNeasy mini kit (QIAGEN).

treatment_protocol: Cells were starved overnight and stimulated with 50 ng/ml BMP-4 for the indicated times.

value: pulmonary arterial smooth muscle cells (PASMCs)

value: 24 hrs


title: 13905658


title: 13905787


title: 13905659


title: 13905732


title: 13905733


title: 13905672


title: Jurkat CD3 PMA t8 3

hyb_protocol: After fragmentation, cRNA (10μg) was hybridized at 45°C for 16-17 hours to the Human Genome U133A 2.0 Array. Following hybridization, the arrays were washed, stained with phycoerythrin-streptavidin conjugate (Molecular Probes, Eugene, OR), and the signals were amplified by staining the array with biotin-labeled anti-streptavidin antibody (Vector Laboratories, Burlingame, CA) followed by phycoerythrin-streptavidin.

treatment_protocol: For gene expression profiling Jurkat T cells were seeded in T25 culture flasks at a concentration of 1x106 cells/ml (1x107 cells in total) and cultured overnight at 37°C/5%CO2, one day prior to stimulation. On the day of the experiment cells stimulated with either CD3/CD28, PMA/CD28 or PMA/CD3, at concentrations of 10 ng/ml PMA, 1 μg/ml CD3 and 1 μg/ml CD28. Jurkat T cells were cultured in the presence or absence of stimulation for one or eight hours in total, after which the cells were washed in ice cold PBS. Thereafter cell pellets were collected and snap frozen at -80°C. Cell pellets were stored until further processing.

value: CD3 PMA

tag: time

value: 8 hr


title: Jurkat CD3 PMA t8 1

tag: treatment


title: Jurkat CD3 PMA t8 2

tag: cell line


title: Jurkat Control  3


title: HUVEC_BMP9_24h

hyb_protocol: Array hybridization was performed as described previously (Ishii et al, Genomics 68:136-143, 2000)

scan_protocol: Array scanning was performed as described previously (Ishii et al, Genomics 68:136-143, 2000)

source_name: HUVECs stimulated with BMP-9 for 24 h

label_protocol: Double-stranded cDNA was synthesized with the SuperScript Choice system (GIBCO) and a T7-(dT) 24 Primer (GE Amersham) from the total RNA. In vitro transcription was performed to produce biotin-labeled cRNA by using a BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) according to the manufacturer’s instructions (Ishii et al, Genomics 68:136-143, 2000).

growth_protocol: HUVECs were maintained in EGM-2 medium (Lonza).  Cells were grown in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: Total RNAs were extracted using RNeasy mini kit (QIAGEN).

treatment_protocol: Cells were starved overnight and stimulated with either 50 ng/ml of BMP-6 or 1 ng/ml of BMP-9 for the indicated times.

value: human umbilical vein endothelial cells (Lonza)

value: stimulated with 1 ng/ml of BMP-9 for 24 h


title: PASMC_0h

source_name: PASMCs without BMP stimulation

value: 0 hrs


title: HUVEC_BMP9_2h

source_name: HUVECs stimulated with BMP-9 for 2 h

value: stimulated with 1 ng/ml of BMP-9 for 2 h


title: 13905734


title: PASMC_BMP4_2h

source_name: PASMCs stimulated with BMP-4 for 2 h

value: 2 hrs


title: Jurkat CD28 1


title: Jurkat Control  2


title: HUVEC_BMP6_2h

source_name: HUVECs stimulated with BMP-6 for 2 h

value: stimulated with 50 ng/ml of BMP-6 for 2 h


title: HUVEC_BMP6_24h

source_name: HUVECs stimulated with BMP-6 for 24 h

value: stimulated with 50 ng/ml of BMP-6 for 24 h


title: HUVEC_0h

source_name: HUVECs without BMP stimulation


title: Jurkat CD3 PMA t1 3

source_name: Jurkat T cells

value: 1 hr


title: Jurkat CD3 PMA t1 2


title: 13905657

value: KOH

value: KCl


title: 13905655

value: wild type

value: 10 min


title: Jurkat CD3 PMA t1 1

value: Jurkat E6.2.11 T cells


title: Jurkat CD28 PMA t8 2

value: CD28 PMA


title: Jurkat CD28 PMA t1 2


title: Jurkat CD28 CD3 t8 3

value: CD28 CD3


title: Jurkat CD28 PMA t8 3


title: Jurkat CD28 CD3 t1 1


title: Jurkat CD28 CD3 t8 1


title: Jurkat CD28 CD3 t1 3


title: mammary gland at L1, biological rep3

city: Guangzhou

first: D P

last: Shu

address: 483 Wushan Avenue, Tianhe District

country: China

institute: South China Agricultural University

description:
Porcine_L1-3
Gene expression data from mammary gland at d 1  relative to parturition

hyb_protocol: Molecules of cRNA were hybridized to each GeneChip array according to the standard procedures provided by the manufacturer.

scan_protocol: The arrays were scanned with the Affymetrix GeneChip Scanner 3000.

data_processing: Raw data from the .CEL files were converted to gene signal files using MAS 5.0 software.

organism: Sus scrofa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA .

growth_protocol: Six Large White sows were managed by standard procedures. The diets were corn and soybean meal-based and were formulated to meet or exceed all nutrient concentrations recommended by the National Research Council (NRC, 1998).

treatment_protocol: Each sow underwent three mammary gland biopsies from the right side of the anterior three mammary glands at -17(-17 ± 2), 1, and 17(-17 ± 2) d relative to parturition.

tag: breed

value: Large White

tag: Sex

value: sow

value: mammary gland tissues


title: mammary gland at L-17, biological rep3

description:
Porcine_L-17-3
Gene expression data from mammary gland at d -17 relative to parturition

tag: tissue


title: Jurkat CD28 PMA t8 1

value: 8 hr


title: Jurkat CD28 CD3 t8 2


title: Jurkat Control  t8 1

value: Control


title: Jurkat Control  t8 2


title: mammary gland at L17, biological rep1

description:
Porcine_L17-1
Gene expression data from mammary gland at d 17  relative to parturition


title: mammary gland at L17, biological rep3

description:
Porcine_L17-3
Gene expression data from mammary gland at d 17  relative to parturition


title: Jurkat Control  t8 3


title: Jurkat CD28 CD3 t1 2


title: Jurkat CD28 PMA t1 3


title: mammary gland at L1, biological rep2

description:
Porcine_L1-2
Gene expression data from mammary gland at d 1  relative to parturition


title: mammary gland at L-17, biological rep1

description:
Porcine_L-17-1
Gene expression data from mammary gland at d -17 relative to parturition


title: mammary gland at L-17, biological rep2

description:
Porcine_L-17-2
Gene expression data from mammary gland at d -17 relative to parturition


title: Jurkat Control  t1 3


title: mammary gland at L17, biological rep2

description:
Porcine_L17-2
Gene expression data from mammary gland at d 17  relative to parturition


title: Jurkat Control  t1 1


title: Jurkat CD28 PMA t1 1


title: mammary gland at L1, biological rep1

description:
Porcine_L1-1
Gene expression data from mammary gland at d 1  relative to parturition


title: Jurkat Control  t1 2


status: Public on Jul 15 2011

city: Vienna

first: Andreas

last: Bracher

state: Vienna

address: Lazarettgasse 14, Floor 4, Lab 6

department: General Dermatology

country: Austria

institute: Medical University of Vienna

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: RMA

source_name: tumor negative axillary sentinel lymph node from M24met tumor bearing SCID mouse

label_protocol: Affymetrix

growth_protocol: Total RNAs of SLNs were isolated and 5µg of total RNA were then used for preparation of cRNA, hybridization to Mouse Genome 430A 2.0 Arrays(Affymetrix).

extract_protocol: DNA/RNA Mini Kit and RNeasy Micro Kit

tag: strain

value: CB17 scid/scid (SCID) mice

value: negative axillary lymph node

tag: tumor

value: yes


title: Pou3f1 knockdown rep1

city: Philadelphia

first: xin

last: wu

state: PA

address: 3850 baltimore Ave,

department: Animal Biology

institute: School of Veterinary Medicine, University of Pennsylvania

description: Pou3f1 siRNA transient knockdown

hyb_protocol: Fragmented and biotinylated cDNA was added to Affymetrix hybridization cocktails and hybridized for 16 hr at 45°C to Affymetrix Mouse 430 2.0

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Affymetrix .cel files were imported into Partek Genomics Suite (v6.4, Partek Inc., St. Louis, MO) where GCRMA was applied yielding normalized, log2-transformed intensities. Preliminary principal components analysis and pair-wise correlation analysis revealed one sample (B1) from Bcl6b knockdown group to be an outlier. GCRMA was repeated on the remaining fifteen samples.  The resulting probe-set list was filtered to retain those flagged as “Present” by the MAS5 algorithm (Affymetrix Expression Console, v1.1) yielding 29,277 probe-sets for subsequent analysis.

source_name: Pou3f1 knockdown

label_protocol: Total RNA was converted to cDNA using reverse transcriptase primed by a poly(T) oligomer

growth_protocol: Murine Spermatogonial stem cell cultures were established from Thy1+ enriched germ cell populations,Long-term SSC self-renewal and proliferation was supported in a chemically defined serum-free defined MEMα medium (mSFM) supplemented with 20 ng/ml GDNF (R&D Systems), 150 ng/ml GFRα1 (R&D Systems), and 1 ng/ml basic fibroblast growth factor (FGF2; BD Biosciences)

extract_protocol: RNA was harvested from transfected SSCs according to standard Trizol isolation protocols, and potential genomic DNA contamination was prevented by DNase treatment

treatment_protocol: Transient reduction in the expression of targeted genes within germ cells with 30 hr treatment of short interfering RNA oligonucleotides (siRNA)

tag: cell type

value: Spermatogonial stem cell

value: Pou3f1 siRNA transient knockdown

tag: genetic background


title: Etv5 knockdown rep4

description: Etv5 siRNA transient knockdown

source_name: Etv5 knockdown

value: Etv5 siRNA transient knockdown


title: Etv5 knockdown rep1

description: Etv5 siRNA transient knockdown


title: Bcl6b knockdown rep3

description: Bcl6b siRNA transient knockdown

source_name: Bcl6b knockdown

value: Bcl6b siRNA transient knockdown


title: Nc


title: Nb


title: Bcl6b knockdown rep1

description: Bcl6b siRNA transient knockdown


title: Etv5 knockdown rep3

description: Etv5 siRNA transient knockdown


title: P15 vestibular ganglion P15_VG_2

first: Lisa

last: Goodrich

address: 220 Longwood Avenue

department: Neurobiology

institute: Harvard Medical School

description: P15 vestibular ganglion

hyb_protocol: Fragmented, labeled probes were hybridized to Affymetrix Mouse 430 2.0 GeneChips using standard protocols at the Dana Farber Cancer Institute Microarray Core.

scan_protocol: GeneChips were scanned using standard protocols at the Dana Farber Cancer Institute Microarray Core

data_processing: We used the July 13, 2009 build of dChip and the July 1, 2009 Affymetrix gene info for MOE430v2 for normalization and modeling. Normalization parameters were invariant set and running median smoothing, and the baseline array was P0 SG1 (313, 46.6%).  The expression signal was obtained using the model-based expression method and mismatch probe (PM/MM) difference as background.  Note that two chips (E16 SG 4 and P15 SG 2) had significantly lower intensity than the rest.

source_name: Vestibular ganglion from P15 Rnx-cre; Z/EG pup

label_protocol: Amplified RNA (aRNA) was biotin labeled using the Enzo BioArray High Yield RNA Transcript Labeling (T7) kit, according to the manufacturer’s instructions, then fragmented by adding 15 µg of aRNA in a volume of 40 µl to 10 µl of 5X fragmentation buffer (200 mM Tris-Acetate pH 8.1, 150 mM MgOAc, 500 mM KOAc) and incubating at 95ºC for 35 minutes.

extract_protocol: Microdissected samples were thawed and pooled such that ~15-20 E12 or E13 SG or VG ganglia, or ~10-12 E16-P15 VG ganglia were processed for each of three replicates.  For FACS sorted samples, between 4,591-125,070 cells were processed for each of four replicates.  RNA was extracted using the Arcturus PicoPure RNA kit (Applied Biosystems), according to the manufacturer’s instructions.  Samples were stored at -80ºC until needed.  RNA was amplified using the Arcturus RiboAmp Plus 1.5 round RNA Amplification kit (Applied Biosystems), according to the manufacturer’s instructions.

treatment_protocol: E12 and E13 Rnx-Cre; Z/EG cochlear-vestibular ganglia were dissected in cold sterile PBS with 2% glucose and 2% BSA (PBS/glucose/BSA) under an epifluorescence stereomicroscope.  The SG and VG were separated from one another using a microblade, taking care to discard the region where the ganglia contact one another in order to avoid cross-contamination.  Ganglia were rinsed in fresh PBS/glucose/BSA and transferred to a microcentrifuge tube with 900 µl PBS with 10% BSA and 100 µl 0.5 M EDTA with a mouth pipetter fitted with a sterile pulled glass Pasteur pipet.  Samples were centrifuged for 10 minutes at 4ºC at 800g, PBS/glucose BSA was removed, and samples were quickly frozen in liquid nitrogen, where they were stored until RNA isolation.  Inferior VG from E16, P0, P6, and P15 Rnx-Cre; Z/EG animals were dissected in PBS with 0.5% glucose, then collected into PBS/glucose/BSA, briefly centrifuged, decanted, and frozen in liquid nitrogen.  Cochleae from 2-4 litters from CD1 X MafB-GFP-/+ matings were dissected in cold sterile PBS with 0.5% glucose under an epifluorescence stereomicroscope, rinsed in fresh PBS with 0.5% glucose, and transferred into a 1.5 ml tube on ice containing 1 ml PBS with 2% glucose and 2% BSA (PBS/glucose/BSA).  Non-fluorescent wild-type littermates (from 3-5 animals) were processed at the same time as controls to facilitate gating for FACS sorting.  Samples were centrifuged for 10 minutes at 4ºC at 800g.  PBS/glucose/BSA was pipetted off and dissociation solution was added.  E16 SG samples were dissociated in ~10 µg/ml each of collagenase type 4, papain (Worthington), and dispase (Gibco), and 2800 U/ml DNase (Worthington) in 1 ml PBS, while P0-P15 SG samples were dissociated in 0.05% trypsin, 1% chicken serum, 0.37 mM EDTA, ~5 µg/ml each of collagenase type 4, papain, and dispase, and 2800 U/mL DNase in PBS.  Tubes were rotated at 37ºC for 45 minutes, with gentle trituration 5-10 times every 15 minutes using a filtered P1000 tip.  At the end of 45 minutes, tissue was again triturated 5-10 times.  Cells were centrifuged for 10 minutes at 4ºC at 800g.  Dissociation medium was pipetted off and cells were resuspended gently in 1 ml cold PBS/glucose/BSA.  To generate a single-cell suspension, samples were passed through a 40 µm cell strainer (BD Falcon) into a sterile 5 ml round bottom tube (BD Falcon) on ice.  Cells were sorted on a BD MoFlo machine at the Dana Farber Cancer Institute Flow Cytometry Core using a chilled sample chamber and collection chamber with a sheath pressure of 24 psi, through a 100 µm nozzle at 500-1000 events/sec.  Gating was set by first running non-fluorescent littermate controls on the machine followed by a small amount of  MafB-GFP-/+ sample, and then choosing cells present only in the MafB-GFP-/+ sample.  The yield of GFP positive cells was as follows:  E16, 4,591-46,036 cells/sample; P0, 10,889-57,160 cells/sample; P6, 13,069-125,070 cells/sample; P15, 8,653-33,247 cells/sample. Cells were sorted into a chilled microcentrifuge tube with cold 450 µl PBS with 10% BSA and 50 µl 0.5 M EDTA.  Samples were centrifuged for 15 minutes at 4ºC at 1100g.  The PBS/BSA was removed, and samples were quick frozen in liquid nitrogen, where they were stored until RNA isolation.

tag: extraction procedure

value: microdissected

value: vestibular ganglion

tag: development stage

tag: genotype/variation

value: Rnx-cre; Z/EG


title: Cc

source_name: axillary lymph node (control) from non tumor bearing SCID mouse

value: axillary lymph node

value: no


title: P15 vestibular ganglion P15_VG_3

description: P15 vestibular ganglion


title: Pd

source_name: tumor positive axillary sentinel lymph node from M24met tumor bearing SCID mouse

value: positive axillary lymph node


title: Bcl6b knockdown rep2

description: Bcl6b siRNA transient knockdown


title: Pb


title: P15 vestibular ganglion P15_VG_1

description: P15 vestibular ganglion


title: P6 vestibular ganglion P6_VG_3

description: P6 vestibular ganglion

source_name: Vestibular ganglion from P6 Rnx-cre; Z/EG pup


title: Pa


title: Pou3f1 knockdown rep2

description: Pou3f1 siRNA transient knockdown


title: Ca


title: Negative control rep4

description: Negative siRNA treatment

source_name: Negative contol

value: Negative siRNA treatment


title: Negative control rep1

description: Negative siRNA treatment


title: Cb


title: Bcl6b knockdown rep4

description: Bcl6b siRNA transient knockdown


title: Etv5 knockdown rep2

description: Etv5 siRNA transient knockdown


title: Negative control rep3

description: Negative siRNA treatment


title: Negative control rep2

description: Negative siRNA treatment


title: Pou3f1 knockdown rep3

description: Pou3f1 siRNA transient knockdown


title: Pou3f1 knockdown rep4

description: Pou3f1 siRNA transient knockdown


title: P0 vestibular ganglion P0_VG_2

description: P0 vestibular ganglion

source_name: Vestibular ganglion from P0 Rnx-cre; Z/EG pup


title: P6 vestibular ganglion P6_VG_2

description: P6 vestibular ganglion


title: P6 vestibular ganglion P6_VG_1

description: P6 vestibular ganglion


title: E16 vestibular ganglion E16_VG_3

description: E16 vestibular ganglion

source_name: Vestibular ganglion from E16 Rnx-cre; Z/EG embryo


title: P6 spiral ganglion neurons P6_SG_4

description: P6 spiral ganglion neurons

source_name: Spiral ganglion neurons from P6 Mafb-GFP embryo

value: FACS sorted

value: spiral ganglion

value: CD1 X MafB-GFP-/+


title: E13 vestibular ganglion E13_VG_1

description: E13 vestibular ganglion

source_name: Vestibular ganglion from E13 Rnx-cre; Z/EG embryo


title: E12 vestibular ganglion E12_VG_1

description: E12 vestibular ganglion

source_name: Vestibular ganglion from E12 Rnx-cre; Z/EG embryo


title: E12 vestibular ganglion E12_VG_3

description: E12 vestibular ganglion


title: E16 spiral ganglion neurons E16_SG_4

description: E16 spiral ganglion neurons

source_name: Spiral ganglion neurons from E16 Mafb-GFP embryo


title: P15 spiral ganglion neurons P15_SG_1

description: P15 spiral ganglion neurons

source_name: Spiral ganglion neurons from P15 Mafb-GFP embryo


title: E16 vestibular ganglion E16_VG_2

description: E16 vestibular ganglion


title: P0 vestibular ganglion P0_VG_3

description: P0 vestibular ganglion


title: P0 spiral ganglion neurons P0_SG_2

description: P0 spiral ganglion neurons

source_name: Spiral ganglion neurons from P0 Mafb-GFP embryo


title: E12 vestibular ganglion E12_VG_2

description: E12 vestibular ganglion


title: P0 spiral ganglion neurons P0_SG_4

description: P0 spiral ganglion neurons


title: P15 spiral ganglion neurons P15_SG_3

description: P15 spiral ganglion neurons


title: E16 spiral ganglion neurons E16_SG_3

description: E16 spiral ganglion neurons


title: P15 spiral ganglion neurons P15_SG_2

description: P15 spiral ganglion neurons


title: P0 spiral ganglion neurons P0_SG_1

description: P0 spiral ganglion neurons

source_name: Spiral ganglion neurons from P0 Mafb-GFP pup


title: P0 vestibular ganglion P0_VG_1

description: P0 vestibular ganglion


title: E16 spiral ganglion neurons E16_SG_2

description: E16 spiral ganglion neurons


title: P6 spiral ganglion neurons P6_SG_2

description: P6 spiral ganglion neurons


title: E13 vestibular ganglion E13_VG_2

description: E13 vestibular ganglion


title: P15 spiral ganglion neurons P15_SG_4

description: P15 spiral ganglion neurons


title: E16 vestibular ganglion E16_VG_1

description: E16 vestibular ganglion


title: P6 spiral ganglion neurons P6_SG_3

description: P6 spiral ganglion neurons


title: P0 spiral ganglion neurons P0_SG_3

description: P0 spiral ganglion neurons


title: P6 spiral ganglion neurons P6_SG_1

description: P6 spiral ganglion neurons


title: E16 spiral ganglion neurons E16_SG_1

description: E16 spiral ganglion neurons


title: E13 spiral ganglion E13_SG_1

description: E13 spiral ganglion

source_name: Spiral ganglion from E13 Rnx-cre; Z/EG embryo


title: E12 spiral ganglion E12_SG_3

description: E12 spiral ganglion

source_name: Spiral ganglion from E12 Rnx-cre; Z/EG embryo


title: E12 spiral ganglion E12_SG_2

description: E12 spiral ganglion


title: Liver-Pseudo_Ag2

city: Ann Arbor

first: Jung

last: Kim

state: MI

address: 1400 E. Medical Center Drive

institute: University of Michigan

description: Gene expression data of agouti mouse with pseudo agouti coat color. Total RNA isolated from Liver tissue.

hyb_protocol: Biotin-labeled cRNA transcript was synthesized in vitro, fragmented, and hybridized to the array chip followed by washing and scanning for bound fluorescent tags by Duke University microarray core facility (Duke University, Durham, NC).

scan_protocol: Scanning was conducted by Duke University microarray core facility (Duke University, Durham, NC) using Affymetrix GeneChip Scanner.

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.  Genes with average expression signals less than 30 units (background) were excluded from the analysis.

source_name: Mouse-Liver

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: Animals were housed in polycarbonate-free cages and provided ad libitum access to diet and water.  Mice were obtained from a colony that has been maintained with sibling mating and forced heterozygosity for the Avy allele for over 220 generations, resulting in a genetically invariant background. These mice were originally obtained from a colony at the Oak Ridge National Laboratory, in which the Avy mutation arose spontaneously in the C3H/HeJ strain. Animals used in this study were maintained in accordance with the Guidelines for the Care and Use of Laboratory Animals (Institute of Laboratory Animal Resources, 1996) and were treated humanely and with regard for alleviation of suffering. The study protocol was approved by the University of Michigan Committee on Use and Care of Animals and the Duke University Institutional Animal Care and Use Committee.

extract_protocol: Total RNA was isolated from frozen brain, kidney, and liver tissues by homogenization in RNA-Stat 60 (Tel-Test, Friendswood, TX), and subsequent processing was performed as recommended by the manufacturer. RNA quality and yield was checked on an agarose gel and with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA) before submission to Expression Analysis (EA) (Durham, NC).

value: Avy/a

tag: gender

value: male

tag: site

value: Liver

tag: coatcolor


title: Liver-Mottled2

description: Gene expression data of agouti mouse with mottled coat color. Total RNA isolated from Liver tissue.


title: E12 spiral ganglion E12_SG_1

description: E12 spiral ganglion


title: Brain-Pseudo_Ag2

description: Gene expression data of agouti mouse with pseudo agouti coat color. Total RNA isolated from Brain tissue.

source_name: Mouse-Brain

value: Brain


title: E13 spiral ganglion E13_SG_3

description: E13 spiral ganglion


title: E13 vestibular ganglion E13_VG_3

description: E13 vestibular ganglion


title: Liver-Slightly_Mottled2

description: Gene expression data of agouti mouse with slightly mottled coat color. Total RNA isolated from Liver tissue.


title: Kidney-Mottled2

description: Gene expression data of agouti mouse with mottled coat color. Total RNA isolated from Kidney tissue.

source_name: Mouse-Kidney

value: Kidney


title: Kidney-Pseudo_Ag2

description: Gene expression data of agouti mouse with pseudo agouti coat color. Total RNA isolated from Kidney tissue.


title: Liver-Heavily_Mottled2

description: Gene expression data of agouti mouse with heavily mottled coat color. Total RNA isolated from Liver tissue.


title: E13 spiral ganglion E13_SG_2

description: E13 spiral ganglion


title: Kidney-Slightly_Mottled2

description: Gene expression data of agouti mouse with slightly mottled coat color. Total RNA isolated from Kidney tissue.


title: Brain-Heavily_Mottled2

description: Gene expression data of agouti mouse with heavily mottled coat color. Total RNA isolated from Brain tissue.


title: Brain-Slightly_Mottled2

description: Gene expression data of agouti mouse with slightly mottled coat color. Total RNA isolated from Brain tissue.


title: Kidney-Pseudo_Ag1


title: Kidney-Yellow2

description: Gene expression data of agouti mouse with yellow coat color. Total RNA isolated from Kidney tissue.


title: Brain-Pseudo_Ag1


title: Kidney-Heavily_Mottled2

description: Gene expression data of agouti mouse with heavily mottled coat color. Total RNA isolated from Kidney tissue.


title: Kidney-Heavily_Mottled1


title: Liver-Yellow2

description: Gene expression data of agouti mouse with yellow coat color. Total RNA isolated from Liver tissue.


title: Brain-Mottled2

description: Gene expression data of agouti mouse with mottled coat color. Total RNA isolated from Brain tissue.


title: Liver-Pseudo_Ag1


title: Kidney-Mottled1


title: Brain-Heavily_Mottled1


title: Brain-Yellow2

description: Gene expression data of agouti mouse with yellow coat color. Total RNA isolated from Brain tissue.


title: Liver-Heavily_Mottled1


title: Brain-Mottled1


title: Liver-Mottled1


title: Brain-Slightly_Mottled1


title: Liver-Slightly_Mottled1


title: Liver-Yellow1


title: am1-pramsE_pramsF-Rep1-Cy5-pramsF

city: Stanford

first: John

middle: F

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

description:
Cy5-139-3
am1-pra allele ms anthers - 1.0mm vs 1.5mm Rep 1

hyb_protocol: 825 ng of each labeled target cRNA were hybridized for 17 h at 65C

scan_protocol: Slides were scanned on an Agilent G2565AA microarray scanner as indicated in the manual.  Images were processed with the Agilent Feature Extraction software.

data_processing: Text files from Feature Extraction software were processed using the limma package of R.  After removal of spots flagged by Feature Extraction as below background or saturated or outliers, dye normalized values for each channel from Feature Extraction were normalized again to the median array intensity.  Average intensities were then calculated for probes with at least 3 of 4 good intensities.

organism: Zea mays

label_protocol: Total RNA (1000 ng) was amplified & labeled with Cy3 or Cy5 using Agilent Low RNA Input Linear Amplification Kit.

growth_protocol: Plants were grown and dissected at the Stanford field; tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA was extracted from 30 - 60  of frozen anthers with Invitrogen Purelink RNA Mini kit with DNase I treatment.

value: anther

tag: anther length (mm)

tag: allele

tag: wild-type vs male-sterile

value: male-sterile


title: f98pl_2 with array type maize from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description: Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription, and eQTL.

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003) using R-2.6.2 version and AFFYMETRIX Bioconductor packages (Gentleman and Carey, 2002).

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: stem - Greenhouse conditions: - hygrometry 77% night and 63% day - temperature 20°C night and 22°C day - Light 10h night and 14h day

extract_protocol:
Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.
f98pl_2:120.7ng.

treatment_protocol: no treatment

tag: line

value: F98902 (line of bad digestibility)

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

value: f1-a (24 hours before ovulation), flowering stage


title: Brain-Yellow1


title: cm484pl_1 with array type maize from Affymetrix

growth_protocol: stem - - Greenhouse conditions: - hygrometry 77% night and 63% day - temperature 20°C night and 22°C day - Light 10h night and 14h day

extract_protocol:
Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.
cm484pl_1:416.8ng.

value: Cm484 (line of good digestibility)


title: cm484pl_2 with array type maize from Affymetrix

extract_protocol:
Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.
cm484pl_2:342.3ng.


title: Kidney-Slightly_Mottled1


title: am1-pramsE_prawtE-Rep2-Cy5-prawtE

description:
Cy5-138-4
am1-pra allele 1.0mm anthers - ms vs wt Rep 2

value: wild-type


title: am1-pramsE_pramsF-Rep2-Cy5-pramsE

description:
Cy5-139-4
am1-pra allele ms anthers - 1.0mm vs 1.5mm Rep 2


title: am1-pramsF_prawtF-Rep1-Cy5-prawtF

description:
Cy5-139-2
am1-pra allele 1.5mm anthers - ms vs wt Rep 1


title: f98pl_1 with array type maize from Affymetrix

type: other

extract_protocol:
Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.
f98pl_1:312.4ng.


title: am1-489msF_489wtF-Rep3-Cy5-489msF

description:
Cy5-139-1
am1-489 allele 1.5mm anthers - ms vs wt Rep 3


title: am1-489msE_489msF-Rep1-Cy5-489msE

description:
Cy5-138-1
am1-489 allele ms anthers - 1.0mm vs 1.5mm Rep 1


title: am1-pramsE_prawtE-Rep1-Cy5-pramsE

description:
Cy5-138-3
am1-pra allele 1.0mm anthers - ms vs wt Rep 1


title: Kidney-Yellow1


title: am1-489msE_489msF-Rep2-Cy5-489msF

description:
Cy5-138-2
am1-489 allele ms anthers - 1.0mm vs 1.5mm Rep 2


title: am1-489msF_pramsF-Rep4-Cy3-489msF

description:
Cy3-147-4
1.5mm ms anthers - am1-489 allele vs am1-pra allele Rep 4


title: am1-489msE_pramsE-Rep3-Cy3-pramsE

description:
Cy3-147-1
1.0mm ms anthers - am1-489 allele vs am1-pra allele Rep 3


title: am1-pramsE_pramsF-Rep4-Cy3-pramsF

description:
Cy3-146-4
am1-pra allele ms anthers - 1.0mm vs 1.5mm Rep 4


title: am1-489msE_489wtE-Rep2-Cy5-489wtE

description:
Cy5-137-2
am1-489 allele 1.0mm anthers - ms vs wt Rep 2


title: am1-489msF_pramsF-Rep3-Cy3-pramsF

description:
Cy3-147-3
1.5mm ms anthers - am1-489 allele vs am1-pra allele Rep 3


title: am1-489msE_489wtE-Rep1-Cy5-489msE

description:
Cy5-137-1
am1-489 allele 1.0mm anthers - ms vs wt Rep 1


title: am1-489msF_489wtF-Rep2-Cy5-489wtF

description:
Cy5-137-4
am1-489 allele 1.5mm anthers - ms vs wt Rep 2


title: am1-489msE_pramsE-Rep4-Cy3-489msE

description:
Cy3-147-2
1.0mm ms anthers - am1-489 allele vs am1-pra allele Rep 4


title: am1-pramsF_prawtF-Rep4-Cy3-pramsF

description:
Cy3-146-2
am1-pra allele 1.5mm anthers - ms vs wt Rep 4


title: am1-489msE_489msF-Rep4-Cy3-489msF

description:
Cy3-145-2
am1-489 allele ms anthers - 1.0mm vs 1.5mm Rep 4


title: am1-pramsF_prawtF-Rep3-Cy3-prawtF

description:
Cy3-146-1
am1-pra allele 1.5mm anthers - ms vs wt Rep 3


title: am1-pramsE_prawtE-Rep4-Cy3-pramsE

description:
Cy3-145-4
am1-pra allele 1.0mm anthers - ms vs wt Rep 4


title: am1-489msF_489wtF-Rep1-Cy5-489msF

description:
Cy5-137-3
am1-489 allele 1.5mm anthers - ms vs wt Rep 1


title: am1-pramsF_prawtF-Rep2-Cy3-prawtF

description:
Cy3-144-4
am1-pra allele 1.5mm anthers - ms vs wt Rep 2


title: am1-489msF_pramsF-Rep2-Cy3-pramsF

description:
Cy3-140-4
1.5mm ms anthers - am1-489 allele vs am1-pra allele Rep 2


title: am1-489msE_489wtE-Rep4-Cy3-489msE

description:
Cy3-144-2
am1-489 allele 1.0mm anthers - ms vs wt Rep 4


title: am1-489msF_pramsF-Rep1-Cy3-489msF

description:
Cy3-140-3
1.5mm ms anthers - am1-489 allele vs am1-pra allele Rep 1


title: am1-pramsF_prawtF-Rep1-Cy3-pramsF

description:
Cy3-139-2
am1-pra allele 1.5mm anthers - ms vs wt Rep 1


title: am1-489msE_489msF-Rep3-Cy3-489msE

description:
Cy3-145-1
am1-489 allele ms anthers - 1.0mm vs 1.5mm Rep 3


title: am1-489msF_489wtF-Rep4-Cy3-489msF

description:
Cy3-144-3
am1-489 allele 1.5mm anthers - ms vs wt Rep 4


title: am1-pramsE_pramsF-Rep3-Cy3-pramsE

description:
Cy3-146-3
am1-pra allele ms anthers - 1.0mm vs 1.5mm Rep 3


title: am1-pramsE_prawtE-Rep2-Cy3-pramsE

description:
Cy3-138-4
am1-pra allele 1.0mm anthers - ms vs wt Rep 2


title: am1-pramsE_prawtE-Rep3-Cy3-prawtE

description:
Cy3-145-3
am1-pra allele 1.0mm anthers - ms vs wt Rep 3


title: am1-489msE_pramsE-Rep1-Cy3-489msE

description:
Cy3-140-1
1.0mm ms anthers - am1-489 allele vs am1-pra allele Rep 1


title: am1-pramsE_pramsF-Rep1-Cy3-pramsE

description:
Cy3-139-3
am1-pra allele ms anthers - 1.0mm vs 1.5mm Rep 1


title: am1-489msE_489wtE-Rep3-Cy3-489wtE

description:
Cy3-144-1
am1-489 allele 1.0mm anthers - ms vs wt Rep 3


title: am1-pramsE_pramsF-Rep2-Cy3-pramsF

description:
Cy3-139-4
am1-pra allele ms anthers - 1.0mm vs 1.5mm Rep 2


title: am1-489msE_pramsE-Rep2-Cy3-pramsE

description:
Cy3-140-2
1.0mm ms anthers - am1-489 allele vs am1-pra allele Rep 2


title: am1-489msF_489wtF-Rep1-Cy3-489wtF

description:
Cy3-137-3
am1-489 allele 1.5mm anthers - ms vs wt Rep 1


title: am1-489msE_489wtE-Rep2-Cy3-489msE

description:
Cy3-137-2
am1-489 allele 1.0mm anthers - ms vs wt Rep 2


title: am1-489msE_489msF-Rep2-Cy3-489msE

description:
Cy3-138-2
am1-489 allele ms anthers - 1.0mm vs 1.5mm Rep 2


title: am1-489msF_489wtF-Rep3-Cy3-489wtF

description:
Cy3-139-1
am1-489 allele 1.5mm anthers - ms vs wt Rep 3


title: am1-489msE_489msF-Rep1-Cy3-489msF

description:
Cy3-138-1
am1-489 allele ms anthers - 1.0mm vs 1.5mm Rep 1


title: am1-489msF_pramsF-Rep4-Cy5-pramsF

description:
Cy5-147-4
1.5mm ms anthers - am1-489 allele vs am1-pra allele Rep 4


title: am1-pramsE_prawtE-Rep1-Cy3-prawtE

description:
Cy3-138-3
am1-pra allele 1.0mm anthers - ms vs wt Rep 1


title: am1-489msF_pramsF-Rep3-Cy5-489msF

description:
Cy5-147-3
1.5mm ms anthers - am1-489 allele vs am1-pra allele Rep 3


title: Hoxb1b+Meis B

city: Aurora

first: Charles

last: Sagerstrom

state: CO

address: 12801 East 17th Avenue

department: Pediatrics

institute: University of Colorado Medical School

hyb_protocol: Hybridization was carried out in 6XSSPE, 50% formamide at 37C for 20hrs. Washing in 0.75X TNT at 46C for 1hr. Biotinylated probes were detected with avidin-Cy5. Hybridization was carried out by the Kimmel Cancer Center on a fee-for-service basis.

scan_protocol: Perkin Elmer ScanArray XL5000, software v3.1. Scanning was carried out by the Kimmel Cancer Center on a fee-for-service basis.

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. This normalized data is presented in the attached Matrix file.

organism: Danio rerio

source_name: Danio rerio, 14 hpf, hoxb1b+meis3 injected

label_protocol: 1 microgram of total RNA was linearly amplified and used to generate biotinylated cRNA probes. Probe synthesis was carried out by the Kimmel Cancer Center on a fee-for-service basis.

extract_protocol: The anterior 1/3 of injected zebrafish embryos (encompassing approximately the forebrain and midbrain) was dissected at 14hpf. Total RNA was prepared using Trizol.

tag: Stage

tag: treatment


title: gat201 KO vs. wt in YPAD CHM7-260

city: San Francisco

first: Cheryl

last: Chun

institute: UC San Francisco

hyb_protocol: as described in Chun, Brown, and Madhani.  Cell Host and Microbe 2011 9(3): 243-51

scan_protocol: scanned on an Axon 400B scanner with GenePix software and the images generated were analyzed using SpotReader software

data_processing: Array signals were bulk-normalized and filtered for flagged spots using NOMAD. Data were log-transformed (base 2) and filtered for genes that contained data for at least three out of four arrays from each strain, and missing values were calculated through K-nearest neighbor algorithm using Significance Analysis of Microarrays (SAM) software. Ratios were converted into log scale (base 2).

organism: Cryptococcus neoformans

source_name: gat201KO, grown in YPAD

tag: sample type

value: strain H99, knockout marked by NAT resistance

tag: genotype

value: gat201 KO

tag: media

value: YPAD

value: strain H99

source_name: wild-type, grown in YPAD

value: wild type


title: am1-489msF_489wtF-Rep2-Cy3-489msF

description:
Cy3-137-4
am1-489 allele 1.5mm anthers - ms vs wt Rep 2

tag: tissue


title: am1-489msE_489wtE-Rep1-Cy3-489wtE

description:
Cy3-137-1
am1-489 allele 1.0mm anthers - ms vs wt Rep 1


title: Hoxb1b+Meis A


title: am1-489msE_pramsE-Rep4-Cy5-pramsE

description:
Cy5-147-2
1.0mm ms anthers - am1-489 allele vs am1-pra allele Rep 4


title: gat201 KO vs. wt in YPAD CHM7-257

label_protocol: as described in Chun, Brown, and Madhani.  Cell Host and Microbe 2011 9(3): 243-51

tag: genetic background


title: gat201 KO vs. wt in YPAD CHM7-256

extract_protocol: as described in Chun, Brown, and Madhani.  Cell Host and Microbe 2011 9(3): 243-51


title: Hoxb1b+Meis


title: am1-489msE_pramsE-Rep3-Cy5-489msE

description:
Cy5-147-1
1.0mm ms anthers - am1-489 allele vs am1-pra allele Rep 3


title: gat201 KO vs. wt in YPAD CHM7-259 flip

source_name: wild-type, grown in DMEM

source_name: gat201KO, grown in DMEM


title: Meis only A

source_name: Danio rerio, 14hpf, meis3 injected


title: gat201 KO vs. wt in DMEM CHM7-254-flip

value: DMEM


title: gat201 KO vs. wt in YPAD CHM7-258


title: gat201 KO vs. wt in DMEM CHM7-253


title: am1-pramsE_pramsF-Rep3-Cy5-pramsF

description:
Cy5-146-3
am1-pra allele ms anthers - 1.0mm vs 1.5mm Rep 3


title: Meis only B


title: Meis only


title: am1-pramsE_pramsF-Rep4-Cy5-pramsE

description:
Cy5-146-4
am1-pra allele ms anthers - 1.0mm vs 1.5mm Rep 4


description: sample #2 from strain with tagged Gat201 ORF Median of Ratios (635/532)

hyb_protocol: see Nobile, C.J., Nett, J.E., Hernday, A.D., Homann, O.R., Deneault, J.S., Nantel, A., Andes, D.R., Johnson, A.D., and Mitchell, A.P. (2009). Biofilm matrix regulation by Candida albicans Zap1. PLoS Biol 7, e1000133.

data_processing: Median of Ratios (635/532) were further analyzed.  Analysis was performed by calculating the median of the top five probes in the 2kb flanking the start codon of each gene. The median value for the untagged strain was subtracted from the median value of the tagged strain, yielding the difference for the pair of untagged/tagged arrays. The calculation was repeated for a second duplicate pair of untagged/tagged arrays. The calculated differences were clustered using the software Cluster, and the cluster showing increased binding in both pairs was isolated for additional analysis.

label_protocol: generated DNA probes with incorporated aminoallyl-dUTP

growth_protocol: grown in DMEM, 37C, 5% CO2

extract_protocol: The cultures were fixed with 1% formaldehyde, followed by quenching with 125 mM glycine, then harvested by centrifugation and snap freezing. Samples were lyophilized, and chromatin immunoprecipitation performed as previously described (Nobile et al., 2009) with the following minor modifications: zirconia/silica beads (0.5 mm diameter) were used to lyse the cells via a Bead Beater-8, used for thirty minutes with frequent rests on ice. The chromatin in the cell pellet was sonicated for 1 hr in a Diagenode Bioruptor (settings: 4x15 min, 30 s on, 1 min off) at 4ºC. Immunoprecipitation was performed with an anti-FLAG antibody.

treatment_protocol: sonication settings: 4x15 min, 30 s on, 1 min off

tag: strain

value: CBP-FLAG tag at the Gat201 ORF

tag: antibody

value: anti-FLAG

tag: antibody manufacturer

value: Sigma

tag: antibody catalog #

source_name: whole cell extract

value: whole cell extract


title: untagged wild type sample replicate #1

description: untagged wild type sample replicate #1 Median of Ratios (635/532)

scan_protocol: see Nobile, C.J., Nett, J.E., Hernday, A.D., Homann, O.R., Deneault, J.S., Nantel, A., Andes, D.R., Johnson, A.D., and Mitchell, A.P. (2009). Biofilm matrix regulation by Candida albicans Zap1. PLoS Biol 7, e1000133.

source_name: untagged wild type sample replicate #1


description: sample #1 from strain with tagged Gat201 ORF Median of Ratios (635/532)


title: T21, sniSh, biological rep3

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: L4-L5 rat DRGs after sciatic SNISh lesion

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Array data were preprocessed with the robust multichip analysis algorithm (RMA)

organism: Rattus norvegicus

label_protocol: Affymetrix protocol

growth_protocol: Eight- to 12-week-old Wistar rats were subjected to crush lesion

extract_protocol: Qiagen Rneasy

treatment_protocol: L4/L5 DRG were dissected from lesioned animals at the indicated time points

tag: time after lesion (days)

tag: lesion

value: sniSh

value: Wistar

tag: age

value: 8 to 12 weeks old


title: T3, sniSh, biological rep3


title: T21, sniSh, biological rep1