title: Wobbler modifier/Wobbler_testis_rep2

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

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

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

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

source_name: Testis wr mod

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

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

tag: Strain

value: Wobbler modifier, Background:Castaneus, Gender:Male, RNApool of 3 individuals

source_name: Testis wr

value: Wobbler, Background:Castaneus, Gender:Male, RNApool of 3 individuals


title: MCF7 LMO4 high Replicate2B

status: Public on Apr 01 2007

type: RNA

city: Irvine

first: Kevin

middle: K

last: Lin

state: CA

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

country: USA

institute: University of California, Irvine

description: LMO4 - LIM-only protein 4

hyb_protocol: Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG-U133A array.

scan_protocol: The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip Scanner 3000. The results were quantified and analyzed using GCOS 1.1.1 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

data_processing: MAS 5.0

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MCF7-LMO4-TetOff cells

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA  present in the isolated total RNA (10 ug total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY).  15ug of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

extract_protocol: Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA). In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up. Eluted total RNAs were quantified with a portion of the recovered total RNA adjusted to a final concentration of 1 ug/ul. All starting total RNA samples were quality assessed prior to beginning target preparation/processing steps by running out a small amount of each sample (typically 25-250 ng/well) onto a RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) that was evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

tag: Without doxycycline treatment results in high LMO4 level.


title: MCF7 LMO4 high Replicate1B

description: LMO4 - LIM-only protein 4


title: MCF7 LMO4 low Replicate3B

description: LMO4 - LIM-only protein 4

tag: Treatment with doxycycline results in low LMO4 level.


title: Wobbler modifier/Wobbler_testis_rep1

organism: Mus musculus


title: Wobbler modifier/wt_testis_rep4

source_name: Testis wt

value: wildtype Background:Castaneus, Gender:Male, RNApool of 3 individuals


title: Wobbler modifier/Wobbler_testis_rep3


title: MCF7 LMO4 high Replicate3B

description: LMO4 - LIM-only protein 4


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. TAF1-(delta)TAND and spt3 del in Y13.2 w/ p2uLF-T(V161E F182V) (5-045B-700730)

city: Ithaca

first: B. Franklin

last: Pugh

email: fp265@cornell.edu, bfp2@psu.edu

state: NY

address: 465 Biotechnology Bldg.

department: Molecular Biology and Genetics

institute: Cornell University

description: one of at least 2 independent biological replicates, Test/Ref with Ref=WT strain with M1stop mutant

hyb_protocol: Chitikila et al.  2002. Mol Cell. 10:871-82

data_processing: MeanFRG- MedianBCK>S.D. BCK, <26% saturation.  Log2 Ratio of Test/Ref; see publication for normalized data

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Transformants carrying the TBP plasmids were grown in CSM-Leu-Trp + 3% raffinose liquid media until they reached an OD600 = 0.65-0.8. Expression of the TBP was induced by addition of galactose to a final concentration of 2%.

treatment_protocol: Galactose induction (see below)

tag: WT Y13.2 derivative strain transformed with p2uLF-T(M1Stop)(Gal10) plasmid

tag: TAF1-(delta)TAND and spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(V161E F182V)(Gal10) plasmid


title: Wobbler modifier/Wobbler_testis_rep4


title: Wobbler modifier/wt_testis_rep3


title: B-lineage ALL 1

city: Lund

first: Thoas

middle: Anna

address: Lund University Hospital

country: Sweden

institute: Dept of Clinical Genetics

description: cDNA microarray data

hyb_protocol: Arrays were hybridized and washed as described in Andersson et al et al. (Leukemia 2005)

scan_protocol: Arrays were scanned in an Agilent Microarray scanner

data_processing: Image analysis was performed using Genepix v4.0. Resultsfile were uploaded into BASE where they were filtered, normalized using pin-based lowess,  mean centered with respect to hospital and filtered for presence (40% required)

source_name: Case 2

label_protocol: Samples were labeled using the CyScribe Post-labeling Kit (Amersham Biosciences)

extract_protocol: Trizol extraction followed by purification using RNeasy

tag: High Hyperdiploidy

source_name: Stratagene Universal Human Reference RNA

tag: RNA pooled from ten human cell lines


title: MCF7 LMO4 low Replicate1B

description: LMO4 - LIM-only protein 4


title: AML 2

description: cDNA microarray data

source_name: Case 4


title: Wobbler/wt_testis_rep4


title: TAF1-(delta)TAND and spt3 del in Y13.2 deriv w/ p2uLF-T(V161E) vs. Y13.2 w/ p2uLF-T(M1Stop) (5-045A-700710)

scan_protocol: Chitikila et al.  2002. Mol Cell. 10:871-82

tag: TAF1-(delta)TAND and spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(V161E)(Gal10) plasmid

tag: Y13.2 strain transformed with p2uLF-T(M1Stop)(Gal10) plasmid


title: AML 1

description: cDNA microarray data

source_name: Case 1


title: Wobbler modifier/wt_testis_rep1


title: TAF1-(delta)TAND and spt3 del in Y13.2 deriv w/ p2uLF-T(K145E V161R F182V) vs. Y13.2 w/ p2uLF-T(M1Stop) (5-044B-700730)

label_protocol: Chitikila et al.  2002. Mol Cell. 10:871-82

tag: TAF1-(delta)TAND and spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(K145E V161R F182V)(Gal10) plasmid


title: Wobbler modifier/wt_testis_rep2


title: Wobbler/wt_testis_rep3


title: Wobbler/wt_testis_rep2


title: TAF1-(delta)TAND and spt3 del in Y13.2 deriv w/ p2uLF-T(M1Stop) vs. Y13.2 w/ p2uLF-T(M1Stop) (5-042A-700720)

extract_protocol: Chitikila et al.  2002. Mol Cell. 10:871-82

tag: TAF1-(delta)TAND and spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(M1Stop)(Gal10) plasmid


title: TAF1-(delta)TAND and spt3 del in Y13.2 deriv w/ p2uLF-T(V161E F182V) vs. Y13.2 w/ p2uLF-T(M1Stop) (5-042B-700720)


title: MCF7 LMO4 low Replicate2B

description: LMO4 - LIM-only protein 4


title: Lym_ES cell line_rep15

source_name: Treated Lymphoid ES cell line

tag: Treated Lymphoid ES cell line

source_name: Untreated Lymphoid ES cell line

tag: Untreated Lymphoid ES cell line


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. TAF1-(delta)TAND and spt3 del in Y13.2 w/ p2uLF-T(V161E) (5-039B-710710)


title: Wobbler/wt_testis_rep1


title: TAF1-(delta)TAND and spt3 del in Y13.2 deriv w/ p2uLF-T(K145E V161R) vs. Y13.2 w/ p2uLF-T(M1Stop) (5-043B-710710)

tag: TAF1-(delta)TAND and spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(K145E V161R)(Gal10) plasmid


title: TAF1-(delta)TAND and spt3 del in Y13.2 deriv w/ p2uLF-T(K145E F182V) vs. Y13.2 w/ p2uLF-T(M1Stop) (5-044A-700730)

tag: TAF1-(delta)TAND and spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(K145E F182V)(Gal10) plasmid


title: TAF1-(delta)TAND and spt3 del in Y13.2 deriv w/ p2uLF-T(V161R F182V) vs. Y13.2 w/ p2uLF-T(M1Stop) (5-034B-710730)

tag: TAF1-(delta)TAND and spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(V161R F182V)(Gal10) plasmid


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. TAF1-(delta)TAND and spt3 del in Y13.2 w/ p2uLF-T(K145E) (5-037A-720690)

tag: TAF1-(delta)TAND and spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(K145E)(Gal10) plasmid


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. TAF1-(delta)TAND + spt3 del in Y13.2 w/ p2uLF-T(K145E V161R F182V) (5-031B-720680)


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. TAF1-(delta)TAND + spt3 del in Y13.2 w/ p2uLF-T(K145E V161E F182V) (5-037B-720680)

tag: TAF1-(delta)TAND and spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(K145E V161E F182V)(Gal10) plasmid


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. TAF1-(delta)TAND and spt3 del in Y13.2 w/ p2uLF-T(M1Stop) (5-039A-710720)


title: Lym_ES cell line_rep11


title: Lym_ES cell line_rep14


title: Lym_ES cell line_rep10


title: Lym_ES cell line_rep7


title: Lym_ES cell line_rep12


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. TAF1-(delta)TAND and spt3 del in Y13.2 w/ p2uLF-T(V161R F182V) (5-030B-720690)


title: Lym_ES cell line_rep6


title: Lym_ES cell line_rep4


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. TAF1-(delta)TAND and spt3 del in Y13.2 w/ p2uLF-T(K145E V161E) (5-028B-710710)

tag: TAF1-(delta)TAND and spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(K145E V161E)(Gal10) plasmid


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. TAF1-(delta)TAND and spt3 del in Y13.2 w/ p2uLF-T(F182V) (5-028A-720700)

tag: TAF1-(delta)TAND and spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(F182V)(Gal10) plasmid


title: TAF1-(delta)TAND and spt3 del in Y13.2 deriv w/ p2uLF-T(K145E V161E) vs. Y13.2 w/ p2uLF-T(M1Stop) (4-018B-730680)


title: TAF1-(delta)TAND and spt3 del in Y13.2 deriv w/ p2uLF-T(K145E V161E F182V) vs. Y13.2 w/ p2uLF-T(M1Stop) (4-020B-720720)


title: TAF1-(delta)TAND and spt3 del in Y13.2 deriv w/ p2uLF-T(K145E) vs. Y13.2 w/ p2uLF-T(M1Stop) (4-021B-720720)


title: Lym_ES cell line_rep13


title: Lym_ES cell line_rep5


title: TAF1-(delta)TAND and spt3 del in Y13.2 deriv w/ p2uLF-T(F182V) vs. Y13.2 w/ p2uLF-T(M1Stop) (4-018A-720720)


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. TAF1-(delta)TAND and spt3 del in Y13.2 w/ p2uLF-T(K145E V161R) (5-029A-720720)

tag: WT Y13.2 derivative strain transformed with p2uLF-T(M1Stop)(Gal10) plasmid


title: TAF1-(delta)TAND and spt3 del in Y13.2 deriv w/ p2uLF-T(V161R) vs. Y13.2 w/ p2uLF-T(M1Stop) (4-016B-700720)

tag: TAF1-(delta)TAND and spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(V161R)(Gal10) plasmid


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. TAF1-(delta)TAND and spt3 del in Y13.2 w/ p2uLF-T(K145E F182V) (5-029B-720700)


title: Lym_ES cell line_rep3


title: Lym_ES cell line_rep2


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. TAF1-(delta)TAND and spt3 del in Y13.2 w/ p2uLF-T(V161R) (5-027B-730720)


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(V161R F182V) (5-036A-720700)

source_name: spt3(delta)_p2uLF-T(V161R F182V)(Gal10)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(V161R F182V)(Gal10) plasmid


title: Lym_ES cell line_rep8


title: Lym_ES cell line_rep1


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(K145E F182V) (5-035B-710710)

source_name: spt3(delta)_p2uLF-T(K145E F182V)(Gal10)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(K145E F182V)(Gal10) plasmid


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(V161E) (5-043A-710720)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(V161E)(Gal10) plasmid


title: Lym_ES cell line_rep9


title: spt3 del in Y13.2 deriv w/ p2uLF-T(K145E V161R F182V) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (5-033B-700730)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(K145E V161R F182V)(Gal10) plasmid


title: spt3 del in Y13.2 deriv w/ p2uLF-T(V161E) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (5-038B-710730)


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. TAF1-(delta)TAND and spt3 del in Y13.2 w/ p2uLF-T(wt) (5-026B-710690)

tag: TAF1-(delta)TAND and spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(wt)(Gal10) plasmid


title: TAF1-(delta)TAND and spt3 del in Y13.2 deriv w/ p2uLF-T(wt) vs. Y13.2 w/ p2uLF-T(M1Stop) (4-015B-710690)

tag: Y13.2 strain transformed with p2uLF-T(M1Stop)(Gal10) plasmid


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(K145E V161R F182V) (5-025A-740700)


title: spt3 del in Y13.2 deriv w/ p2uLF-T(K145E) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (5-032B-720720)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(K145E)(Gal10) plasmid


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(K145E V161E F182V) (5-024B-730730)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(K145E V161E F182V)(Gal10) plasmid


title: spt3 del in Y13.2 deriv w/ p2uLF-T(V161R F182V) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (5-033A-720730)


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(V161R F182V) (5-024A-730730)


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(K145E V161E) (5-023A-750720)

source_name: spt3(delta)_p2uLF-T(K145E V161E)(Gal10)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(K145E V161E)(Gal10) plasmid


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(V161E F182V) (5-023B-720690)

source_name: spt3(delta)_p2uLF-T(V161E F182V)(Gal10)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(V161E F182V)(Gal10) plasmid


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(K145E) (5-022B-750720)


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(K145E V161R) (4-058B-750690)

source_name: spt3(delta)_p2uLF-T(K145E V161R)(Gal10)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(K145E V161R)(Gal10) plasmid


title: spt3 del in Y13.2 deriv w/ p2uLF-T(K145E V161E F182V) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (5-020B-680720)


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(V161R) (4-057B-710730)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(V161R)(Gal10) plasmid


title: spt3 del in Y13.2 deriv w/ p2uLF-T(V161R) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (5-017A-700710)


title: spt3 del in Y13.2 deriv w/ p2uLF-T(M1Stop) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (4-051A-740680)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(M1Stop)(Gal10) plasmid


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(M1Stop) (4-057A-750720)


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(wt) (5-021B-740720)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(wt)(Gal10) plasmid


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-Toa2-TBP(N2-1) vs. WT Y13.2 w/ pCALF-T(M1Stop) (5-015A-700730)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-Toa2-TBP(N2-1)(Gal10) plasmid

tag: WT Y13.2 derivative strain transformed with pCALF-T(M1Stop)(Gal10) plasmid


title: spt3 del in Y13.2 deriv w/ p2uLF-T(wt) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (5-016B-700710)

tag: WT Y13.2 derivative strain transformed with p2uLF-T(M1Stop)(Gal10) plasmid


title: spt3 del in Y13.2 deriv w/ p2uLF-T(F182V) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (4-051B-750690)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(F182V)(Gal10) plasmid


title: spt3 del in Y13.2 deriv w/ p2uLF-T(V161E F182V) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (5-019B-680700)


title: spt3 del in Y13.2 deriv w/ p2uLF-T(V161R F182V) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (5-020A-690710)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(V161R F182V)(Gal10) plasmid


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. spt3 del in Y13.2 w/ p2uLF-T(F182V) (4-058A-710750)


title: spt3 del in Y13.2 deriv w/ p2uLF-T(K145E V161E) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (5-018A-670700)


title: spt3 del in Y13.2 deriv w/ p2uLF-T(K145E F182V) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (5-019A-680710)

tag: spt3 deletion in Y13.2 derivative strain transformed with p2uLF-T(K145E F182V)(Gal10) plasmid


title: spt3 del in Y13.2 deriv w/ p2uLF-T(K145E V161R) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (5-018B-700720)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-Toa2-TBP(N2-1) (5-010B-720700)

tag: TAF1-(delta)TAND Y13.2 derivative  strain transformed with pCALF-Toa2-TBP(N2-1)(Gal10) plasmid


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(R107E) vs. WT Y13.2 w/ pCALF-T(M1Stop) (5-013B-700710)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(R107E)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-Toa2-TBP(wt) (5-010A-720700)

tag: TAF1-(delta)TAND Y13.2 derivative  strain transformed with pCALF-Toa2-TBP(wt)(Gal10) plasmid


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(E93R) vs. WT Y13.2 w/ pCALF-T(M1Stop) (5-013A-700700)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(E93R)(Gal10) plasmid


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(V161E F182V) vs. WT Y13.2 w/ pCALF-T(M1Stop) (5-012A-700710)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(V161E F182V)(Gal10) plasmid


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(N2-1) vs. WT Y13.2 w/ pCALF-T(M1Stop) (5-014A-700740)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(N2-1)(Gal10) plasmid


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(K145E V161E) vs. WT Y13.2 w/ pCALF-T(M1Stop) (5-011B-700720)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(K145E V161E)(Gal10) plasmid


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(K145E V161E F182V) vs. WT Y13.2 w/ pCALF-T(M1Stop) (5-012B-700720)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(K145E V161E F182V)(Gal10) plasmid


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-Toa2-TBP(wt) vs. WT Y13.2 w/ pCALF-T(M1Stop) (5-014B-700730)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-Toa2-TBP(wt)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(N2-1) (5-009B-700710)

tag: TAF1-(delta)TAND Y13.2 derivative  strain transformed with pCALF-T(N2-1)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(E93R) (5-008B-720700)

tag: TAF1-(delta)TAND Y13.2 derivative  strain transformed with pCALF-T(E93R)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(R107E) (5-009A-700700)

tag: TAF1-(delta)TAND Y13.2 derivative  strain transformed with pCALF-T(R107E)(Gal10) plasmid


title: K562 Day 4 sample

type: other

city: Singapore

first: Meng Ling

last: Choong

address: 31 Biopolis Way, #03-01 Nanos

department: Drug Discovery

country: Singapore

institute: Experimental Therapeutics Centre

description: miRNA expression profiling was performed on ex vivo differentiating erythroid cultures derived from human K562 cells. Day 0 samples were non-stimulated cells. This is used as the baseline for comparison with ex vivo induced erythroid differentiation cultures from Day 2, 4, 6, 8, 10, 15 and 22.

hyb_protocol: Hybridization protocols as described in Ambion Probeset (Cat#1561v1) and Ambion miRNA Labeling Kit (Cat#1562)

scan_protocol: Processed slides were scanned using the microarray scanner GenePix 4000B (Axon), with the lasers power set at maximum with fixed PMT value and a scan resolution of 10 um.

data_processing: Data in VALUE column are median signal intensity after background subtraction, and normalized by dividing with the average signal (after background subtraction) of the sample

label: Cy3 (Amersham Pharmacia)

molecule: other

source_name: K562 cell line (ATCC#CCL-243)

label_protocol: Labeling protocol as described in Ambion miRNA Labeling Kit (Cat#1562)

growth_protocol:
For erythropoietic induction, the cells were adapted to the serum free defined media StemLineII (Sigma) first and then induced to differentiate in the StemLineII media supplemented with 50 ng/ml IL3 and 7.5 U/ml EPO (Mahdi et al. 1998).
Mahdi, T., Alcalay, D., Cognard, C., Tanzer, J., and Kitzis, A. 1998. Rescue of K562 cells from MDM2-modulated p53-dependent apoptosis by growth factor-induced differentiation. Biol. Cell 90: 615-627.

extract_protocol: miRNA extracted from CD34 cells using Ambion miRNA Isolation Kit (Cat#1560)

treatment_protocol: K562 cells are maintained in IMDM with 10% fetal calf serum (Hyclone).

tag: K-562 blasts are multipotential, hematopoietic malignant cells that spontaneously differentiate into recognizable progenitors of the erythrocytic, granulocytic and monocytic series. [Lozzio BB , et al. A multipotential leukemia cell line (K-562) of human origin. Proc. Soc. Exp. Biol. Med. 166


title: K562 Day 15 sample


title: K562 Day 6 sample


title: K562 Day 10 sample


title: K562 Day 0 sample


title: K562 Day 2 sample


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(V161E F182V) (5-007B-720700)

tag: WT Y13.2 derivative strain transformed with pCALF-T(M1Stop)(Gal10) plasmid

tag: TAF1-(delta)TAND Y13.2 derivative  strain transformed with pCALF-T(V161E F182V)(Gal10) plasmid


title: K562 Day 22 sample


title: UCB Day 4 sample

description: miRNA expression profiling was performed on ex vivo differentiating erythroid cultures derived from human UCB-CD34 cells. Day 0 samples were freshly isolated CD34 cells. This is used as the baseline for comparison with ex vivo induced erythroid differentiation cultures from Day 2, 4, 6, 9 and 12.

source_name: Fresh UCB CD34 cells

growth_protocol:
The fresh CD34 cells were subjected to ex vivo erythroid differentiation culture as described in:
Carlile, G.W., Smith, D.H., and Wiedmann, M. 2004. Caspase-3 has a nonapoptotic function in erythroid maturation. Blood 103: 4310-4316.

treatment_protocol: Cord blood mononuclear cells were extracted by standard ficoll method and CD34 cells were isolated from mononuclear cells by flow cytometry using mouse anti-human CD34 antibody (BD Biosciences)

tag: Donated cord blood from informed consent subjects


title: UCB Day 9 sample


title: UCB Day 2 sample


title: UCB Day 12 sample


title: Y13.2 strain w/ p2uLF-T(M1Stop) vs. Y13.2 w/ p2uLF-T(M1Stop) (5-032A-720720)

description: homotypic hyb- Used in Null data set, Test & Ref different biological samples of same genotype

tag: Y13.2 strain transformed with p2uLF-T(M1Stop)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(M1Stop) (5-001A-720680)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(K145E V161E) (5-007A-720700)

tag: TAF1-(delta)TAND Y13.2 derivative  strain transformed with pCALF-T(K145E V161E)(Gal10) plasmid


title: UCB Day 6 sample


title: UCB Day 0 sample

growth_protocol: No culture required


title: K562 Day 8 sample


title: Y13.2 strain w/ pCALF-T(M1Stop) vs. Y13.2 w/ pCALF-T(M1Stop) (5-011A-700720)

tag: Y13.2 strain transformed with pCALF-T(M1Stop)(Gal10) plasmid


title: Y13.2 strain w/ p2uLF-T(M1Stop) vs. Y13.2 w/ p2uLF-T(M1Stop) (4-015A-700730)


title: Y13.2 strain w/ pCALF-T(M1Stop) vs. Y13.2 w/ pCALF-T(M1Stop) (5-006A-720700)


title: Y13.2 strain w/ p2uLF-T(M1Stop) vs. Y13.2 w/ p2uLF-T(M1Stop) (5-016A-700710)

description: homotypic hyb- Used in Null data set, Test & Ref different biological samples of identical genotypes


title: Y13.2 strain w/ p2uLF-T(M1Stop) vs. Y13.2 w/ p2uLF-T(M1Stop) (5-021A-700740)


title: Y13.2 strain w/ p2uLF-T(M1Stop) vs. Y13.2 w/ p2uLF-T(M1Stop) (5-025B-760720)


title: Y13.2 strain w/ p2uLF-T(M1Stop) vs. Y13.2 w/ p2uLF-T(M1Stop) (5-026A-700750)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(K145E V161E F182V) (5-006B-720700)

tag: TAF1-(delta)TAND Y13.2 derivative  strain transformed with pCALF-T(K145E V161E F182V)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(K145E) vs. WT Y13.2 w/ pCALF-T(M1Stop) (5-001B-680680)

tag: WT Y13.2 derivative strain transformed with pCALF-T(K145E)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(K145E V161R) vs. WT Y13.2 w/ pCALF-T(M1Stop) (5-004B-680750)

source_name: WT_pCALF-T(K145E V161R)(Gal10)

tag: WT Y13.2 derivative strain transformed with pCALF-T(K145E V161R)(Gal10) plasmid


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (4-050A-700700)

tag: WT Y13.2 derivative strain transformed with p2uLF-T(M1Stop)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(M1Stop) (5-004A-680750)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(K145E V161R) (5-005A-720680)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-Toa2-TBP(wt) (5-008A-720700)

tag: WT Y13.2 derivative strain transformed with pCALF-Toa2-TBP(wt)(Gal10) plasmid


title: Liver (Zebrafish EE2 experiment: slide 2)

status: Public on Mar 31 2007

city: Ottawa

first: Emily

middle: R

last: Gerrie

state: ON

address: 20 Marie Curie

department: Biology

country: Canada

institute: University of Ottawa

description: Oligonucleotide array

hyb_protocol: Genisphere Array 900MPX cDNA microarray labeling kit; 2X formamide based hybridization buffer for the microarray pre-hybridization step; 2X SDS based hybridization buffer for the light capture reaction (3DNA hybridization step)

scan_protocol: ScanArray 5000XL system; Images obtained using ScanArray Express software; Images opened using Quantarray

data_processing: Cluster analysis; Genowiz

organism: Danio rerio

source_name: Danio rerio; liver; control (EtOH) for ethinylestradiol

extract_protocol: TRIzol reagent as per the manufacturer's protocol

tag: Male adult zebrafish;

tag: Liver;

tag: Slide #2

source_name: Danio rerio; liver; treated; 10 ng/L EE2 in EtOH

tag: Exposed 3 weeks to 10ng/EE2;


title: WT Y13.2 deriv w/ p2uLF-T(M1Stop) vs. WT Y13.2 w/ p2uLF-T(M1Stop) (4-056A-730700)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(K145E) (5-005B-680780)


title: Telencephalon (Zebrafish EE2 experiment: slide 5)

description: Oligonucleotide array

source_name: Danio rerio; telencephalon; control (EtOH) for ethinylestradiol

label_protocol: Genisphere Array 900MPX cDNA microarray labeling kit

tag: Telencephalon;

tag: Slide #1

source_name: Danio rerio; telencephalon; treated; 10 ng/L EE2 in EtOH


title: Comparing between stage 46 anterior and posterior endoderm

city: POHANG

first: JIN-KWAN

last: HAN

state: KYUNGBUK

address: SAN 31, HYOJA-DONG, NAM GU

department: LIFE SCIENCE

country: South Korea

institute: POSTECH

description: Xenopus endoderms were isolated from three different stages during organogenesis (St. 30, 39, and 46) and separated to anterior and posterior region. Total RNA was extracted form the each endoderm region using TRIZOL reagent and used in reverse transcription reactions with oligo(dT)20 in the presence of Cy3-dUTP or Cy5-dUTP. The cDNA derived from the anterior endoderm was labeled with Cy5, and that derived from the posterior endoderm was labeled with Cy3. After hybridization at 65°C for 20 h, slides were scanned with the Axon Instruments GenePix 4000B scanner (Axon Instruments), which generates Tiff images of both the Cy3 and Cy5 channels. GenePix PMT voltage was set from 700 to 900 V depending upon the first sign of a saturated signal. GeneData Refiner® software was used to normalize the original data form GenePix Pro (GPR) files, and GeneData Expressionist® software was used to analyze the microarray data.

hyb_protocol: The hybridization and washing steps were performed as described in Shin et al., 2005 (Shin Y, Kitayama A, Koide T, Peiffer DA, Mochii M, Liao A, Ueno N, Cho KW. 2005. Identification of neural genes using Xenopus DNA microarrays. Dev Dyn 232:432-444) and Tran et al., 2002 (Tran PH, Peiffer DA, Shin Y, Meek LM, Brody JP, Cho KW. 2002. Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals. Nucleic Acids Res 30:e54). To reduce background, spotted slides were soaked for 45 min in a 400 ml solution of 5× SSC, 0.1% SDS and 1% BSA with shaking at 42°C. Then, the slides were washed five times with sterile water and once in isopropanol before drying in a tabletop centrifuge (Sorvall RT6000B) at 700 r.p.m. The cDNA probes were heated to 100°C for 1 min, applied to the glass slides, and sealed in a Corning hybridization chamber. After hybridization at 65°C for 20 h, the slides were washed for 5 min in each solution containing 2× SSC and 0.01% SDS, 1× SSC and 0.1× SSC.

scan_protocol: Hybridized slides were scanned with the Axon Instruments GenePix 4000B scanner (Axon Instruments), which generates Tiff images of both the Cy3 and Cy5 channels. GenePix PMT voltage was set from 700 to 900 V depending upon the first sign of a saturated signal.

data_processing: GeneData Refiner® software was used to normalize the original data form GenePix Pro (GPR) files, and GeneData Expressionist® software was used to analyze the microarray data. To eliminate cDNA spots with low signal, signal to noise ration of 2.5 was applied for the stage 30 and 1.0 for the stage 39 and 46. To select the cDNA spots that show constant values between duplicate microarray experiments, the ‘Filter by Variance’ analysis was performed and the cDNA spots less than variance score of 0.05 were selected. To select genes with up-regulated in the Xenopus anterior endoderm, ‘Filter by Average Signal’ analysis was used.

organism: Xenopus laevis

source_name: Stage 46 anterior endoderm

label_protocol: 50 µg of total RNA isolated from the explants was used in reverse transcription reactions with oligo(dT)20 using Superscript II enzyme (Gibco) in a total reaction volume of 30 µl. Also included in the mixture was Cy3-dUTP or Cy5-dUTP (Amersham) at 0.1 mM, dATP, dGTP and dCTP at 0.5 mM, and dTTP at 0.1 mM. The reaction mixture was incubated at 42°C for 2 h. The cDNA derived from the anterior endoderm was labeled with Cy5, and that derived from the posterior endoderm was labeled with Cy3. The RNA was degraded by incubation with 1 µl of 1 M NaOH for 10 min at 65°C, then neutralized by 1 µl of 1 M HCl. The fluorescent labeled samples were combined and diluted to 500 µl with TE (pH 8). A PCR purification kit (Qiagen) and Microcon YM-30 spin column filters (Amicon) were used to remove the unincorporated dyes and free nucleotides. After three washing and drying cycles, the probes were resuspended in a solution of 0.3% SDS, 3.5× SSC and yeast tRNA at 0.6 µg/µl.

extract_protocol: Total RNA was extracted form the each endoderm region using TRIZOL reagent (Invitrogen) and further purified by LiCl precipitation.

tag: The anterior endoderm will later become major organs such as the lung, oesophagus, duodenum, stomach, pancreas, liver, and gallbladder.

source_name: Stage 46 posterior endoderm

tag: The posterior endoderm will later become the intestine.


title: Liver (Zebrafish EE2 experiment: slide 1)

description: Oligonucleotide array


title: Telencephalon (Zebrafish EE2 experiment: slide 8)

description: Oligonucleotide array

tag: Slide #4


title: Comparing between stage 39 anterior and posterior endoderm

source_name: Stage 39 anterior endoderm

source_name: Stage 39 posterior endoderm


title: Quercetin treated cardiomyocytes for 6 hours (Q6-A).

city: Bologna

first: Cristina

last: Angeloni

state: BO

address: Via Irnerio 48

department: Biochemistry

country: Italy

institute: University of Bologna

description: Data normalization was performed with the Agilent Feature Extraction software. Raw result files were then loaded into the Resolver SE System (Rosetta Biosoftware, Seattle, WA - USA) for data processing and normalization using the Agilent platform-specific error model. Replicated expression profiles were combined to form ratio experiments where each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value  <= 0.001 were considered as differentially expressed.

hyb_protocol: The same quantity of differentially labeled sample and reference (0.75 μg) was put together, fragmented and hybridized to high-density rat arrays containing 22,575 (60 mer) oligo-nucleotide probes representing over 20,000 well characterized rat genes, ESTs, and EST cluster. All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed with the SSC wash procedure (Agilent Technologies).

scan_protocol: The array was scanned with the dual-laser microarray scanner Agilent B (Agilent Technologies) at 5 μm resolution.

data_processing: Feature extraction was performed with the Agilent Feature Extraction software. LogRatio was calculated as Log of ratio channel 2/channel 1.

organism: Rattus norvegicus

source_name: Rat cardiomyocytes

label_protocol: For each sample, mRNA was amplified starting from 1.5 μg of totRNA by Amino Allyl MessageAmp I aRNA Kit (Ambion Inc.) to obtain amino allyl antisense RNA following the method developed by Van Gelder et al. (Proc Natl Acad Sci USA 1990,87:1663-1667) Only one round of amplification was performed, according to the manufacturer’s protocol, with minor modification. Briefly: mRNA was reverse transcribed into cDNA single strand; after the second strand synthesis, cDNA was in vitro transcribed in aaRNA including an amino allyl modified nucleotide (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. Labeling was performed using NHS ester Cy3 dye (Amersham Biosciences, Piscataway, NJ - USA) able to react with the modified RNA. At least 5 μg of mRNA, for each sample, were labeled and purified with columns.

growth_protocol: Cells were seeded at a density of 1.2x106 cells/mL and were grown in Ham F10 nutrient mixture supplemented with 10 % v/v FCS and 10 % v/v HS (complete medium), 1% sodium pyruvate, and kept in this medium at 37 °C, 5 % CO2 and 95 % humidity until complete confluence.

extract_protocol: Total RNA was extracted using Total RNA Isolation Mini Kit (Agilent Technologies, Palo Alto, CA), following the manufacturer’s protocol. The yield and purity of the RNA were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., Rockland, Del, USA). The 28s and 18s ribosomal bands were checked using Agilent 2100 bioanalyzer with an RNA 6000 Nano LabChip Kit.

tag: Primary heart cells were obtained by isolation of cardiomyocytes from the ventricles of 2–4 day old Wistar rats.

source_name: Rat cardiomyocytes treated with quercetin for 6 hours

label_protocol: For each sample, mRNA was amplified starting from 1.5 μg of totRNA by Amino Allyl MessageAmp I aRNA Kit (Ambion Inc.) to obtain amino allyl antisense RNA following the method developed by Van Gelder et al. (Proc Natl Acad Sci USA 1990,87:1663-1667) Only one round of amplification was performed, according to the manufacturer’s protocol, with minor modification. Briefly: mRNA was reverse transcribed into cDNA single strand; after the second strand synthesis, cDNA was in vitro transcribed in aaRNA including an amino allyl modified nucleotide (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. Labeling was performed using NHS ester Cy5 dye (Amersham Biosciences, Piscataway, NJ - USA) able to react with the modified RNA. At least 5 μg of mRNA, for each sample, were labeled and purified with columns.

treatment_protocol: 30 μM quercetin was added to the culture medium for 6 hours.


title: Telencephalon (Zebrafish EE2 experiment: slide 7)

description: Oligonucleotide array

tag: Slide #3


title: Liver (Zebrafish EE2 experiment: slide 4)

description: Oligonucleotide array


title: Liver (Zebrafish EE2 experiment: slide 3)

description: Oligonucleotide array


title: Telencephalon (Zebrafish EE2 experiment: slide 6)

description: Oligonucleotide array


title: Quercetin treated cardiomyocytes for 6 hours (Q6-B).


title: Comparing between stage 30 anterior and posterior endoderm

source_name: Stage 30 anterior endoderm

source_name: Stage 30 posterior endoderm


title: Maythorpe shoot Salt, biological rep 3

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

institute: University of Nebraska

description: Gene expression data from barley shoot

hyb_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method.

organism: Hordeum vulgare

source_name: Maythorpe shoot

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

growth_protocol: hydroponics

extract_protocol: Trizol extraction of total RNA

treatment_protocol: salt shoot

tag: Genotype

value: Maythorpe


title: Maythorpe shoot Salt, biological rep 2

description: Gene expression data from barley shoot


title: Maythorpe shoot Control, biological rep 3

description: Gene expression data from barley shoot

treatment_protocol: control shoot


title: Maythorpe shoot Salt, biological rep 1

description: Gene expression data from barley shoot


title: Quercetin treated cardiomyocytes for 24 hours (Q24-A).

source_name: Rat cardiomyocytes treated with quercetin for 24 hours

treatment_protocol: 30 μM quercetin was added to the culture medium for 24 hours.


title: Quercetin treated cardiomyocytes for 12 hours (Q12-B).

source_name: Rat cardiomyocytes treated with quercetin for 12 hours

treatment_protocol: 30 μM quercetin was added to the culture medium for 12 hours.


title: Maythorpe shoot Control, biological rep 2

description: Gene expression data from barley shoot


title: Quercetin treated cardiomyocytes for 24 hours (Q24-B).


title: Quercetin treated cardiomyocytes for 12 hours (Q12-A).


title: Golden Promise shoot Salt, biological rep 1

description: Gene expression data from barley shoot

source_name: Golden Promise shoot

value: Golden Promise


title: Golden Promise Root Control, biological rep 3

description: Gene expression data from barley root

source_name: Golden Promise Root

treatment_protocol: control root


title: Golden Promise Root Salt, biological rep 3

description: Gene expression data from barley root

treatment_protocol: salt root


title: Golden Promise shoot Control, biological rep 3

description: Gene expression data from barley shoot


title: Golden Promise Root Salt, biological rep 2

description: Gene expression data from barley root


title: Maythorpe Root Salt, biological rep 2

description: Gene expression data from barley root

source_name: Maythorpe Root


title: Maythorpe Root Salt, biological rep 3

description: Gene expression data from barley root


title: Golden Promise shoot Salt, biological rep 2

description: Gene expression data from barley shoot


title: Golden Promise Root Control, biological rep1

description: Gene expression data from barley root


title: Maythorpe shoot Control, biological rep1

description: Gene expression data from barley shoot


title: Golden Promise Root Control, biological rep 2

description: Gene expression data from barley root


title: Lung cancer 156

status: Public on Mar 30 2007

city: Chuo-ku, Chiba

first: YASUMITSU

last: MORIYA

address: 1-8-1, Inohana

department: Thoracic surgery

country: Japan

institute: Chiba University

hyb_protocol: Hybridized for 16 h at 42 C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitach Software Engineering Co., Ltd. http://www.dna-chip.co.jp/thesis/AceGeneProtocol.pdf

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array (Hitachi Software Engineering Co., Ltd.).

data_processing: This data were analyzed by DNASIS array software(Hitachi Software Engineering), which converted the signal intensity of each spot into text format. Log2-ratios of the median subtracted background intensity levels were analyzed. Data from each microarray were normalized by LOWESS normalization.

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp?  aRNA Amplification Kit (Ambion). CyeDye Coupling and fragmentation were performed as the protocol supplied by Hitach Software Engineering Co., Ltd. http://www.dna-chip.co.jp/thesis/AceGeneProtocol.pdf

extract_protocol: TriZol procedure

tag: Non-tumorus tissue

tag: Right lung

tag: Tissue

value: resected Adenocarcinoma

tag: tumor tissue

tag: Histlogical Type:Adenocarcinoma

tag: Right lung cancer

tag: LN Metastasis:Negative


title: Maythorpe Root Control, biological rep 2

description: Gene expression data from barley root


title: Lung cancer 158


title: Lung cancer 177


title: Maythorpe Root Salt, biological rep 1

description: Gene expression data from barley root


title: Lung cancer 157

tag: Left lung

tag: Left lung cancer


title: Golden Promise Root Salt, biological rep 1

description: Gene expression data from barley root


title: Lung cancer 171

tag: LN Metastasis:Positive


title: Lung cancer 161

value: resected Squamous cell carcinoma

tag: Histlogical Type:Squamous cell carcinoma


title: Lung cancer 167

value: resected Large cell carcinoma

tag: Histlogical Type:Large cell carcinoma


title: Golden Promise shoot Salt, biological rep 3

description: Gene expression data from barley shoot


title: Lung cancer 173


title: Golden Promise shoot Control, biological rep 2

description: Gene expression data from barley shoot


title: Lung cancer 170


title: Lung cancer 160


title: Maythorpe Root Control, biological rep 3

description: Gene expression data from barley root


title: Golden Promise shoot Control, biological rep1

description: Gene expression data from barley shoot


title: Maythorpe Root Control, biological rep1

description: Gene expression data from barley root


title: Lung cancer 153

tag: Postperative Tumor Recurrence:Unknown


title: Lung cancer 148


title: Lung cancer 142


title: Lung cancer 152

value: resected Small cell carcinoma

tag: Histlogical Type:Small cell carcinoma


title: Lung cancer 178


title: Lung cancer 143


title: Lung cancer 151


title: Lung cancer 154


title: Lung cancer 149


title: Lung cancer 140


title: Lung cancer 133


title: Lung cancer 150


title: Lung cancer 134


title: Lung cancer 136


title: Lung cancer 137


title: Lung cancer 130


title: Lung cancer 141


title: Lung cancer 118


title: Lung cancer 125


title: Lung cancer 131


title: Lung cancer 128


title: Lung cancer 126


title: Lung cancer 121


title: Lung cancer 109


title: Lung cancer 113


title: Lung cancer 114


title: Lung cancer 122


title: Lung cancer 119


title: Lung cancer 120


title: Lung cancer 123


title: Lung cancer 102


title: Lung cancer 101


title: Lung cancer 96


title: Lung cancer 107


title: Lung cancer 91


title: Lung cancer 99


title: Lung cancer 103


title: Lung cancer 95


title: Lung cancer 94


title: Lung cancer 88


title: Lung cancer 84


title: Lung cancer 108


title: Lung cancer 86


title: Lung cancer 105


title: Lung cancer 92


title: Lung cancer 100


title: Lung cancer 89


title: Lung cancer 98


title: Lung cancer 80


title: Lung cancer 77


title: Lung cancer 78


title: Lung cancer 82


title: Lung cancer 76


title: Lung cancer 75


title: Lung cancer 73


title: Lung cancer 83


title: Lung cancer 72


title: Lung cancer 74


title: Lung cancer 68


title: Lung cancer 87


title: Lung cancer 97


title: Lung cancer 59


title: Lung cancer 69


title: Lung cancer 64


title: Lung cancer 63


title: Lung cancer 62


title: Lung cancer 66


title: Lung cancer 65


title: Lung cancer 61


title: Lung cancer 70


title: Lung cancer 56


title: Lung cancer 58


title: Lung cancer 57

value: resected Other

tag: Histlogical Type:Other


title: Lung cancer 15


title: Lung cancer 51


title: Lung cancer 39


title: Lung cancer 07


title: Lung cancer 47


title: Lung cancer 08


title: Lung cancer 09


title: Lung cancer 38


title: Lung cancer 10


title: Lung cancer 05


title: Lung cancer 11


title: Lung cancer 03


title: Lung cancer 04


title: Lung cancer 02


title: Lung cancer 48


title: Lung cancer 54


title: Lung cancer 01


title: Amanitin2_Cy5

status: Public on Mar 29 2007

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

description: Total RNA was treated with DNase I (RNeasy - Qiagen) before labeling

hyb_protocol: In situ Hybridization Kit Plus (Agilent Technologies)

scan_protocol: GenePix 4000B microarray scanner (Axon Instruments)

data_processing: We employed in our analyses the Median-based Trimmed Mean density value (MTM) for each spot by Arrayvision. The reported value represents the mean of all the pixels remaining in a target, after first removing pixels with density values that exceed four median absolute deviations (MADs) above or below the median intensity of the target. This measure moderates the influence of image artifacts (e.g., dust particles) on density estimation. The MTM density for each spot was subtracted by the individual background surrounding the spot (size 4 pixels). Spot quantization matrixes (the �raw� output of the image analysis software) were obtained from all hybridizations. Measurements correspond to the raw data generated by the Image analysis software. We have consolidated in a single tab-delimited text file all measurements obtained in all hybridizations in order to facilitate subsequent normalization and averaging of signal intensities from each tissue. Microarray data intensities from spots representing controls were removed and raw quantization matrixes from each tissue samples were normalized using a robust locally weighted linear regression algorithm (lowess), implemented into the R package, to correct for systematic biases on the data originated from small differences in the labeling and/or detection efficiencies between the fluorescent dyes. Next, in order to make experiments comparable, we used the average signal intensity derived from spots that hybridized to spike mRNA to normalize signal intensities of all spots. A parallel analysis was performed to detect spots with signal intensity above the detection cutoff, which was determined by the average intensity plus 3 standard-deviations of 1,198 negative controls of microarray platform. The raw intensity of each spot was compared to detection cutoff of the corresponding dye. A spot was considered �expressed� if 3 out of 4 signals from treated cells or control cells were above the detection cutoff. Significance Analysis of Microarray (SAM) approach was employed, using as parameters: two-class unpaired response, t-statistic test, 1000 permutations, K-Nearest Neighbors Imputer, and false discovery rates (FDR) ranging from 0.2% to 3.5%; a signal-to-noise ratio (SNR) analysis with 10k permutations (p-value less than 0.05) was performed. Gene sets identified by both SAM and SNR were combined in order to identify a more restrict set of spots that showed statistically significant expression changes upon alpha-amanitin treatment by both analyses.

source_name: Alpha-amanitin-treated cell, 24hs

label_protocol: Low RNA Input Linear Amplification Kit (Agilent Technologies)

growth_protocol: Maintained in RPMI 1640 medium (Gibco) supplemented with 10% (vol/vol) fetal calf serum (FCS), 3 mM L-glutamine, 100 �g/ml streptomycin and 100 U/ml penicillin, at 37�C and 5% CO2

extract_protocol: RNeasy Mini Kit (QIAGEN) extraction

treatment_protocol: 8 x 105 LNCaP cells were plated in 60mm-diam. (p60) dishes and cultured in RPMI 1640 medium for two days when the medium was replaced by fresh medium with or without (mock) 50 �g/mL alpha-amanitin (Roche). After 24 h cells were washed with ice-cold PBS, harvested, pelleted and stored at -80�C

tag: Prostate carcinoma cell line LNCaP


title: Cervical cancer tissue (India: CaCx69)

city: Navi Mumbai

first: Chandan

last: Kumar

state: Maharashtra

address: Kharghar Node

department: ACTREC

country: India

institute: Tata Memorial Center

description: Superficial Fragments of Squamous cell carcinoma In-Situ involving condyloma accuminate

hyb_protocol: Hybridization in 2XHyb buffer containing 50%formamide, 10X SSC and 0.2%SDS (adapted from Quackenbush protocol) in a 42 degrees Centigrade waterbath overnight in a Hyb chamber, with the probe under a coverslip, as described by Pat Brown Lab http://cmgm.stanford.edu/pbrown/protocols/index.html

scan_protocol: Scanned in Axon 4200A Professional according to the manufacturer's instructions

data_processing: Slides have been scanned by Axon scanner 4200A and data analyzed by GenePix Version 5.0. 'Value' column represents normalized, log transformed, ratio of medians of CH1/CH2. Normalization has been carried out with respect to 'all normalization features' using GenePix software. Normalization features meet the following criteria:[F532 Median]>= 250 And [F635 Median]>= 250 And [F Pixels]>=30 And [Dia.]>=50 And[% >B635+1SD]>55 And[% >B532+1SD]>55

source_name: Cervical cancer tissue

label_protocol: Amino-allyl dUTP based indirect labelling protocol described by Pat Brown Lab, available at http://cmgm.stanford.edu/pbrown/protocols/index.html

extract_protocol: TriZol Extraction protocol with an additional chloroform extraction step followed by quantitation in spectrophotometer and checking on formaldehyde-agarose gel. RNA stored in 10mM Sodium Citrate Buffer (Ambion).

tag: Lab ID

tag: Age

tag: Gender

value: Female

value: cervical cancer biopsy

tag: Tumor Stage

value: IIB/IB

source_name: Human Universal Reference RNA

extract_protocol: Commercial RNA

tag: Purchased from (Stratagene, Cat No. 740000),the Human Universal Reference RNA comprises of a pool of RNA made from 10 different human cell lines including

value: Adenocarcinoma, mammary gland Melanoma, Hepatoblastoma, liver Liposarcoma Adenocarcinoma, cervix Histiocytic lymphoma; macrophage; histocyte, Embryonal carcinoma, testis Lymphoblastic leukemia, T lymphoblast, Glioblastoma, brain, Plasmacytoma; myeloma; B lymphocyte


title: Kidney1_Cy5

data_processing: We employed in our analyses the Median-based Trimmed Mean density value (MTM) for each spot by Arrayvision. The reported value represents the mean of all the pixels remaining in a target, after first removing pixels with density values that exceed four median absolute deviations (MADs) above or below the median intensity of the target. This measure moderates the influence of image artifacts (e.g., dust particles) on density estimation. The MTM density for each spot was subtracted by the individual background surrounding the spot (size 4 pixels). Spot quantization matrixes (the “raw” output of the image analysis software) were obtained from all hybridizations. Measurements correspond to the raw data generated by the Image analysis software. We have consolidated in a single tab-delimited text file all measurements obtained in all hybridizations in order to facilitate subsequent normalization and averaging of signal intensities from each tissue. Microarray data intensities from spots representing controls were removed and raw quantization matrixes from each tissue samples were normalized using a robust locally weighted linear regression algorithm (lowess), implemented into the R package, to correct for systematic biases on the data originated from small differences in the labeling and/or detection efficiencies between the fluorescent dyes. Next, in order to make experiments comparable, expression profiles were scaled to a reference, based on the trimmed mean intensity of all intensities measured in each sample that were expressed in at least one tissue, where the highest and the lowest 20% of the values were excluded from the calculated mean. A parallel analysis was performed to detect spots with signal intensity above the detection cutoff, which was determined by the average intensity plus 2 standard-deviations of 1,198 negative controls present in microarray platform. The raw intensity of each spot was compared to the detection cutoff of the corresponding dye. A spot was considered “expressed” if all 4 signals from a tissue were above the detection cutoff. For statistical analyses, Significance Analysis of Microarray (SAM) approach was employed using as parameters: multi-class response, 1000 permutations, K-Nearest Neighbors Imputer, and false discovery rate (FDR)  0.00001%; analysis of variance (ANOVA) implemented in the SpotFire Decision Site for Functional Genomics (SpotFire Inc.) with a cutoff of p less than 0.001. Gene sets identified by both SAM and ANOVA were combined in order to identify a more restrict set of spots that showed statistically significant expression changes in a tissue by both analyses.

source_name: Normal kidney tissue

extract_protocol: TRIZOL (Invitrogen) extraction

tag: Tissue

value: normal Kidney


title: Kidney2_Cy5

data_processing: We employed in our analyses the Median-based Trimmed Mean density value (MTM) for each spot by Arrayvision. The reported value represents the mean of all the pixels remaining in a target, after first removing pixels with density values that exceed four median absolute deviations (MADs) above or below the median intensity of the target. This measure moderates the influence of image artifacts (e.g., dust particles) on density estimation. The MTM density for each spot was subtracted by the individual background surrounding the spot (size 4 pixels). Spot quantization matrixes (the �raw� output of the image analysis software) were obtained from all hybridizations. Measurements correspond to the raw data generated by the Image analysis software. We have consolidated in a single tab-delimited text file all measurements obtained in all hybridizations in order to facilitate subsequent normalization and averaging of signal intensities from each tissue. Microarray data intensities from spots representing controls were removed and raw quantization matrixes from each tissue samples were normalized using a robust locally weighted linear regression algorithm (lowess), implemented into the R package, to correct for systematic biases on the data originated from small differences in the labeling and/or detection efficiencies between the fluorescent dyes. Next, in order to make experiments comparable, expression profiles were scaled to a reference, based on the trimmed mean intensity of all intensities measured in each sample that were expressed in at least one tissue, where the highest and the lowest 20% of the values were excluded from the calculated mean. A parallel analysis was performed to detect spots with signal intensity above the detection cutoff, which was determined by the average intensity plus 2 standard-deviations of 1,198 negative controls present in microarray platform. The raw intensity of each spot was compared to the detection cutoff of the corresponding dye. A spot was considered �expressed� if all 4 signals from a tissue were above the detection cutoff. For statistical analyses, Significance Analysis of Microarray (SAM) approach was employed using as parameters: multi-class response, 1000 permutations, K-Nearest Neighbors Imputer, and false discovery rate (FDR)  0.00001%; analysis of variance (ANOVA) implemented in the SpotFire Decision Site for Functional Genomics (SpotFire Inc.) with a cutoff of p less than 0.001. Gene sets identified by both SAM and ANOVA were combined in order to identify a more restrict set of spots that showed statistically significant expression changes in a tissue by both analyses.


title: Normal (non-malignant) cervical tissue (India: NCx 126)

description: It is important to note that the data provides comparison of test sample against the universal reference RNA, and not cancer versus normal ratios.

scan_protocol: Scanned in Axon 4200A Professional according to the manufacturer's instructions.

source_name: Normal (non-malignant) cervical tissue

value: Non-malignant cervical tissue obtained from radical hysterectomy


title: Mock1_Cy3

data_processing: We employed in our analyses the Median-based Trimmed Mean density value (MTM) for each spot by Arrayvision. The reported value represents the mean of all the pixels remaining in a target, after first removing pixels with density values that exceed four median absolute deviations (MADs) above or below the median intensity of the target. This measure moderates the influence of image artifacts (e.g., dust particles) on density estimation. The MTM density for each spot was subtracted by the individual background surrounding the spot (size 4 pixels). Spot quantization matrixes (the “raw” output of the image analysis software) were obtained from all hybridizations. Measurements correspond to the raw data generated by the Image analysis software. We have consolidated in a single tab-delimited text file all measurements obtained in all hybridizations in order to facilitate subsequent normalization and averaging of signal intensities from each tissue. Microarray data intensities from spots representing controls were removed and raw quantization matrixes from each tissue samples were normalized using a robust locally weighted linear regression algorithm (lowess), implemented into the R package, to correct for systematic biases on the data originated from small differences in the labeling and/or detection efficiencies between the fluorescent dyes. Next, in order to make experiments comparable, we used the average signal intensity derived from spots that hybridized to spike mRNA to normalize signal intensities of all spots. A parallel analysis was performed to detect spots with signal intensity above the detection cutoff, which was determined by the average intensity plus 3 standard-deviations of 1,198 negative controls of microarray platform. The raw intensity of each spot was compared to detection cutoff of the corresponding dye. A spot was considered “expressed” if 3 out of 4 signals from treated cells or control cells were above the detection cutoff. Significance Analysis of Microarray (SAM) approach was employed, using as parameters: two-class unpaired response, t-statistic test, 1000 permutations, K-Nearest Neighbors Imputer, and false discovery rates (FDR) ranging from 0.2% to 3.5%; a signal-to-noise ratio (SNR) analysis with 10k permutations (p-value less than 0.05) was performed. Gene sets identified by both SAM and SNR were combined in order to identify a more restrict set of spots that showed statistically significant expression changes upon alpha-amanitin treatment by both analyses.

source_name: Mock-treated cell, 24hs

growth_protocol: Maintained in RPMI 1640 medium (Gibco) supplemented with 10% (vol/vol) fetal calf serum (FCS), 3 mM L-glutamine, 100 µg/ml streptomycin and 100 U/ml penicillin, at 37ºC and 5% CO2

treatment_protocol: 8 x 105 LNCaP cells were plated in 60mm-diam. (p60) dishes and cultured in RPMI 1640 medium for two days when the medium was replaced by fresh medium with or without (mock) 50 µg/mL alpha-amanitin (Roche). After 24 h cells were washed with ice-cold PBS, harvested, pelleted and stored at -80ºC


title: Mock1_Cy5


title: Cervical cancer tissue (India: CaCx83)

description: Pathology: Large cell non keratinising squamous carcinoma


title: Kidney2_Cy3


title: Kidney1_Cy3


title: Normal (non-malignant) cervical tissue (India: NCx 123)


title: Mock2_Cy5


title: Amanitin2_Cy3


title: Normal (non-malignant) cervical tissue (India: NCx 125)


title: Mock2_Cy3


title: Amanitin1_Cy3


title: Amanitin1_Cy5


title: Liver18_Cy3

source_name: Normal liver tissue

value: normal Liver


title: Prostate75_Cy5

source_name: Tumor prostate tissue

value: Prostate tumor


title: Liver11_Cy3


title: Normal (non-malignant) cervical tissue (India: NCx 202)

description: It is important to note that the data provides comparison of test sample against the universal reference RNA, and not cancer versus normal ratios


title: Liver11_Cy5


title: Liver18_Cy5


title: Prostate73_Cy5


title: Prostate75_Cy3


title: Prostate73_Cy3


title: Terminal duct lobular units (S04-80568-A5-TDLU)

status: Public on Mar 28 2007

city: St Louis

first: Sangjun

last: Lee

state: MO

address: 4940 Parkview Place

department: Pathology

institute: Washington University at St. Louis

description: Gene expression data from benign hyperplastic breast epithelial cells

hyb_protocol: Following fragmentation, 20 mg cRNA were hybridized to the microarrays for 16 hours at 45C.

scan_protocol: The chips were washed in a fluidic station and the phycoerythrin-stained array was scanned as a digital image file as described in the Affymetrix GeneChip protocol

data_processing: Data was processed and analyzed with GCOS 1.2 using affymetrix default settings.

source_name: non-cancerous adult female human breast

label_protocol: The cDNA was in vitro transcribed to biotin-labeled cRNA using IVT Labeling Kit.

extract_protocol: Total RNA extracted using the Optimum Kit, which is based on proteinase K digestion followed by phase separation in a proprietary micro-filter cartridge and incubation with DNase to remove contaminating genomic DNA.

tag: Formalin-fixed paraffin-embedded tissue (FFPET) biopsies containing paired normal TDLUs and well-developed HELUs from non-cancerous adult female human breasts obtained within the past 3 years


title: Rv-D981[mpr]-control(4) vs Rv-D981[mpr]-SDS(4)

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

hyb_protocol: Slides were blocked prior to hybridization using BSA The purified cDNA probes were added to the arrays together with a hybridization solution mix resulting in a final concentration of 0.5ug/ul tRNA (Invitrogen), 2.0X SSC (Ambion), 0.25% Formamide (Sigma) and 0.1% SDS (Ambion).  The probes were covered by a flat 22x22mm coverslip (Corning) and hybridized in sealed hybridization chambers (Genemachines) for sixteen hours in a 50oC water bath.

scan_protocol: The slides were scanned using an Axon 4000B scanner

data_processing: The images were processed using GenePix 5.1 and resulting text files were exported to Microsoft Excel

organism: Mycobacterium tuberculosis

source_name: Mpr treated with SDS

label_protocol: cDNA was synthesized using random primers and labeled with Cyanine-3 or Cyanine-5 dUTP (PerkinElmer, Wellesley, MA) by a modification of the procedure described by Voskuil et. al. {Voskuil, 2003 #137} and hybridized to the arrays overnight.

growth_protocol: M. tuberculosis mutants and parental strain H37Rv were grown in either Middlebrook 7H9 broth containing 0.05% Tween 80, or Middlebrook 7H10 agar (Difco), both enriched with 10% oleic acid-albumin-dextrose-catalase (OADC; Difco). Broth cultures were incubated at 37oC with gentle shaking, under normal atmospheric conditions (without additional CO2), except where indicated. Escherichia coli Novablue and Rosetta(DE3)pLysS (Novagen) were used as host strains for general cloning and gene expression, respectively. E. coli strains were grown on L agar or in L broth. Antibiotics were added to growth media as required.

extract_protocol: Mycobacterial strains were cultured in 7H9 medium to mid-log phase (OD600nm of 0.4-0.5) at 37oC with shaking. Cultures for the DNA microarray experiments were grown in the absence of CO2. For other experiments, cultures were grown with or without 5% CO2 as indicated. Total RNA was isolated using TRIzol LS Reagent (Invitrogen) according to the manufacturer's instruction, except that lysing matrix B and a FastPrep FP120 shaker (BIO 101) were used to disrupt the mycobacteria. With large culture volumes, bacteria were first pelleted by centrifugation and resuspended in a small volume of 0.2% Tween, prior to adding to the lysing tubes. Chromosomal DNA was removed with DNA-free reagents (Ambion), according to the manufacturer's instructions. For experiments with detergent stress, cultures were grown to log phase (O.D.600 of 0.3-0.4), SDS was added to a final concentration of 0.05%, and RNA was extracted from control and SDS-treated samples after 90 min incubation at 37?.

treatment_protocol: Cultures were grown to early log phase (O.D.600 < 0.2), and divided into two 25 ml samples. SDS was added to one sample for each strain to a final concentration of 0.05%. Samples were incubated at 37oC, and then aliquots were removed at 2 hr or 5 hr, centrifuged to remove SDS, and then diluted in PBS prior to plating in duplicate. Coloines were counted after 2 weeks to determine percent survival in the stress-treated samples compared to untreated controls. No additional increase in colony number was observed after further incubation.

tag: mpr mutant (Rv-D981)

tag: Mpr treated with SDS for 90 min

source_name: Mpr control

tag: Time

value: Mpr grown under control conditions


title: Hyperplastic enlarged lobular units (S04-11578-HELU)


title: Rv-D981[mpr]-control(3) vs Rv-D981[mpr]-SDS(3)

tag: Mpr grown under control conditions

value: Mpr treated with SDS for 90 min


title: Terminal duct lobular units (S04-11578-TDLU)


title: Terminal duct lobular units (S04-21945-TDLU)


title: Hyperplastic enlarged lobular units (S04-25290-HELU)


title: Hyperplastic enlarged lobular units (S04-2376-A01-HELU)


title: Rv-SDS(5) vs Rv-D981[mpr]-SDS(5)

description: Rv-SDS(5) vs Rv-D981[mpr]-SDS(5)

source_name: Rv treated with SDS

tag: strain H37Rv

tag: Rv treated with SDS for 90 min


title: Hyperplastic enlarged lobular units (S04-21945-HELU)


title: Rv-SDS(6) vs Rv-D981[mpr]-SDS(6)

description: Rv-SDS(6) vs Rv-D981[mpr]-SDS(6)

value: Rv treated with SDS for 90 min


title: Rv-D981[mpr]-control(1) vs Rv-D981[mpr]-SDS(1)


title: Rv-D981[mpr]-control(5) vs Rv-D981[mpr]-SDS(5)


title: Rv-D981[mpr]-control(6) vs Rv-D981[mpr]-SDS(6)


title: Rv-D981[mpr]-control(2) vs Rv-D981[mpr]-SDS(2)


title: Rv-SDS(1) vs Rv-D981[mpr]-SDS(1)

description: Rv-SDS(1) vs Rv-D981[mpr]-SDS(1)


title: Rv-SDS(2) vs Rv-D981[mpr]-SDS(2)

description: Rv-SDS(2) vs Rv-D981[mpr]-SDS(2)


title: Terminal duct lobular units (S04-0280-TDLU)


title: Rv-SDS(4) vs Rv-D981[mpr]-SDS(4)

description: Rv-SDS(4) vs Rv-D981[mpr]-SDS(4)


title: Terminal duct lobular units (S04-2412-TDLU)


title: Terminal duct lobular units (S04-6016-TDLU)


title: Hyperplastic enlarged lobular units (S04-80568-A2-HELU)


title: Rv-Control(6)  vs. Rv-D981[mpr]-control(6)

source_name: Rv control

value: Rv grown under control conditions


title: Hyperplastic enlarged lobular units (S04-2412-HELU)


title: Hyperplastic enlarged lobular units (S04-0280-HELU)


title: Terminal duct lobular units (S04-25290-TDLU)


title: Terminal duct lobular units (S04-2376-TDLU)


title: E10.5 (FVB/NJ x C57BL/6)F1

type: genomic

city: Forest Hill

first: Russell

middle: Leigh

last: McInnes

state: Vic

address: 347 Burwood Hwy

department: LSCA

country: Australia

institute: Agilent Technologies

description: E10.5 female C57BL/6 Dnmt3L+/+ V E10.5 female C57BL/6 Dnmt3L+/+

hyb_protocol: Agilent oligo hyb protocol for array comparative genomic hybridisation version 4.0

scan_protocol: Microarrays were scanned using the Agilent DNA microarray scanner (G2565BA)

data_processing: Agilent Feature Extraction software ver 9.1

molecule: genomic DNA

source_name: whole embryo genomic DNA from control cross

label_protocol: Agilent genomic DNA Labeling Kit PLUS

extract_protocol: Sambrook, J. and Russell, D. W. (2001) Molecular cloning: a laboratory manual, 3rd edn (Cold Spring Harbor, N. Y.:Cold Spring Harbor Laboratory Press)

source_name: whole embryo genomic DNA from wildtype offspring of heterozygous Dnmt3L sire


title: Rv-SDS(3) vs Rv-D981[mpr]-SDS(3)

description: Rv-SDS(3) vs Rv-D981[mpr]-SDS(3)


title: Hyperplastic enlarged lobular units (S04-6016-HELU)


title: Rv-Control(4)  vs. Rv-D981[mpr]-control(4)


title: Rv-Control(1)  vs. Rv-D981[mpr]-control(1)


title: Rv-Control(3)  vs. Rv-D981[mpr]-control(3)


title: Adult females

description: Adult female C57BL/6 Dnmt3L+/+ V Adult female C57BL/6 Dnmt3L+/+

source_name: tail genomic DNA from wildtype offspring of heterozygous Dnmt3L sire

source_name: tail genomic DNA from unrelated C57BL/6 colony


title: Rv-Control(2)  vs. Rv-SDS treated(2)

description: Rv-Control(2)  vs. Rv-SDS treated(2)

tag: Rv grown under control conditions


title: Rv-Control(6)  vs. Rv-SDS treated(6)

description: Rv-Control(6)  vs. Rv-SDS treated(6)


title: Rv-Control(4)  vs. Rv-SDS treated(4)

description: Rv-Control(4)  vs. Rv-SDS treated(4)


title: Rv-Control(5)  vs. Rv-SDS treated(5)

description: Rv-Control(5)  vs. Rv-SDS treated(5)


title: Rv-Control(2)  vs. Rv-D981[mpr]-control(2)


title: Rv-Control(1)  vs. Rv-SDS treated(1)

description: Rv-Control(1)  vs. Rv-SDS treated(1)

growth_protocol: M. tuberculosis mutants and parental strain H37Rv were grown in either Middlebrook 7H9 broth containing 0.05% Tween 80, or Middlebrook 7H10 agar (Difco), both enriched with 10% oleic acid-albumin-dextrose-catalase (OADC; Difco). Broth cultures were incubated at 37C with gentle shaking, under normal atmospheric conditions (without additional CO2), except where indicated. Escherichia coli Novablue and Rosetta(DE3)pLysS (Novagen) were used as host strains for general cloning and gene expression, respectively. E. coli strains were grown on L agar or in L broth. Antibiotics were added to growth media as required.


title: Rv-Control(3)  vs. Rv-SDS treated(3)

description: Rv-Control(3)  vs. Rv-SDS treated(3)


title: Rv-Control(5)  vs. Rv-D981[mpr]-control(5)


title: CXCL4+oxLDL #1

city: Charlottesville

first: Christian

middle: Albert

last: Gleissner

state: VA

address: MR5 Building, Rm. 1133

department: Cardiovascular Research Center

institute: University of Virginia

description: Gene expression in monocyte derived macrophages from healthy donors treated with oxLDL for 2 days

hyb_protocol: Hybridization of cRNA was performed according to standard Affymetrix protocols.

scan_protocol: Scanning was performed according to standard Affymetrix protocols.

data_processing: Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).

source_name: peripheral blood CXCL4+oxLDL #1

label_protocol: Labeling of samples was performed according to standard Affymetrix protocols.

growth_protocol: Monocytes were incubated with CXCL4 (100 nM) for 6 days to obtain macrophage differentiation. Macrophages were treated with oxidized LDL (oxLDL) (100 µg/ml) for 2 days to induce foam cell formation.

extract_protocol: Media was aspirated and cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.

treatment_protocol:
Human blood was drawn from the antecubital veins of healthy blood donors and provided
as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in
monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.

tag: healthy blood donors


title: CXCL4 #2

description: Gene expression in monocyte derived macrophages from healthy donors

source_name: peripheral blood CXCL4 #2

growth_protocol: Monocytes were incubated with CXCL4 (100 nM) for 6 days to obtain macrophage differentiation.


title: oxLDL #1

description: Gene expression in monocyte-derived macophages stimulated with oxLDL for two days.

source_name: peripheral blood oxLDL #1

growth_protocol: Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. Human monocyte-derived macrophages (MDM) were incubated with minimally oxidized LDL (oxLDL) (100 µg/ml) for 2 days to induce foam cell formation.

extract_protocol: Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.

treatment_protocol:
Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.


title: Macrophages 8d #2

description: Gene expression in monocyte-derived macrophages from healthy donors

source_name: peripheral blood Macrophages 8d #2

growth_protocol: Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 8 days, after which the cells showed the expected morphological signs of macrophage differentiation.


title: oxLDL #2

source_name: peripheral blood oxLDL #2


title: CXCL4 #1

source_name: peripheral blood CXCL4 #1


title: CXCL4+oxLDL #2

source_name: peripheral blood CXCL4+oxLDL #2


title: LDL #2

description: Gene expression in monocyte-derived macrophages from healthy donors stimulated with LDL for 2 days

source_name: peripheral blood LDL #2

growth_protocol: Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. Human monocyte-derived macrophages (MDM) were incubated with native LDL (100 µg/ml) for 2 days to induce foam cell formation.


title: mmLDL #1

description: Gene expression in monocyte-derived macophages stimulated with mmLDL for two days.

source_name: peripheral blood mmLDL #1

growth_protocol: Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. Human monocyte-derived macrophages (MDM) were incubated with minimally modified LDL (mmLDL) (100 µg/ml) for 2 days to induce foam cell formation.


title: LDL #1

source_name: peripheral blood LDL #1


title: CCL2 #1

description: Gene expression in monocyte-derived macrophages from healthy donors stimulated with CCL2 for 5 hours

source_name: peripheral blood CCL2 #1

growth_protocol: Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. These macrophages were incubated with 100 nM CCL2 for 5 hours.


title: CXCL1 #1

description: Gene expression in monocyte-derived macrophages from healthy donors stimulated with CXCL1 for 5 hours

source_name: peripheral blood CXCL1 #1

growth_protocol: Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. These macrophages were incubated with 100 nM CXCL1 for 5 hours.


title: mmLDL #2

source_name: peripheral blood mmLDL #2


title: CXCL1 #2

source_name: peripheral blood CXCL1 #2


title: CCL2 #2

source_name: peripheral blood CCL2 #2


title: Macrophages 8d #1

source_name: peripheral blood Macrophages 8d #1


title: Monocytes #1

description: Gene expression in monocytes isolated from peripheral blood of healthy donors

source_name: peripheral blood Monocytes #1


title: Macrophages 6d #1

source_name: peripheral blood Macrophages 6d #1

growth_protocol: Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation.


title: PBMC #2

description: Gene expression in PBMC isolated from peripheral blood of healthy donors

source_name: peripheral blood PBMC #2

treatment_protocol: Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer.


title: Monocytes #2

source_name: peripheral blood Monocytes #2


title: Macrophages 6d #2

source_name: peripheral blood Macrophages 6d #2


title: PBMC #1

source_name: peripheral blood PBMC #1


title: PERH0423_CD4+_t0_aGVHD+_cGVHD+_17

status: Public on Mar 27 2007

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description: Peripheral blood was obtained from AHCT donors pre-transplant (referred to as day 0) and from recipients on day 365. Recipients were regarded as negative for acute GVHD (aGVHD) when they lived at least 100 days without presenting GVHD. Recipients were considered negative for chronic GVHD (cGVHD) when they remained cGVHD-free for 365 days post-AHCT. PBMC were isolated from blood by Ficoll separation. CD4 and CD8 T-cell subsets were purified with microbeads.

hyb_protocol: similar to direct labelling protocol lists at UHN Microarray facility web site.

scan_protocol: Scanned at 16 bits using the ScanArray Express Scanner (Packard Bioscience) at 10micro-meter resolution at 635 nm (Cy5) and 532 nm (Cy3) using Genepix Pro 6.0 analysis software (Molecular Divices Corporation)

data_processing: Each quantified output file was run though the following pre-processing steps using R (URL: www.r-project.org)and the Limma package. For Minimum Intensity filtering, R and G values were treated with a surrogate replacement policy for estimating sub-threshold values. For normalization within Arrays, the raw merged R and G channels were lowess-normalized (grouped by print-tip) and transformed to log2 ratios (70).

source_name: Universal RNA

tag: Tissue:Universal RNA

source_name: PBMC t0 (donor pre-graft)

extract_protocol: Total RNA was isolated from beads purified CD4 or CD8 T cell populations using TRIzol (Invitrogen/Life Technologies)


title: PERH0417_CD8+_t0_aGVHD+_cGVHD+_14


title: PERH0405_CD4+_t0_aGVHD+_cGVHD+_15


title: PERH0412_CD4+_t0_aGVHD+_cGVHD+_16


title: PERH0406_CD8+_t0_aGVHD+_cGVHD+_13


title: PERH0396_CD4+_t0_aGVHD+_cGVHD-_1


title: PERH0381_CD8+_t0_aGVHD-_cGVHD+_1


title: PERH0380_CD4+_t0_aGVHD-_cGVHD+_1


title: PERH0385_CD8+_t0_aGVHD-_cGVHD+_2


title: PERH0384_CD4+_t0_aGVHD-_cGVHD+_2


title: PERH0397_CD8+_t0_aGVHD+_cGVHD-_1


title: PERH0409_CD4+_t0_aGVHD-_cGVHD+_3


title: PERH0403_CD8+_t0_aGVHD+_cGVHD+_12


title: PERH0402_CD4+_t0_aGVHD+_cGVHD+_14


title: PERH0424_CD8+_t0_aGVHD+_cGVHD+_15


title: PERH0621_CD8+_t0_aGVHD+_cGVHD-_4


title: PERH0620_CD4+_t0_aGVHD+_cGVHD-_5


title: PERH0615_CD8+_t0_aGVHD-_cGVHD-_23


title: PERH0606_CD8+_t0_aGVHD-_cGVHD-_21


title: PERH0614_CD8+_t0_aGVHD-_cGVHD-_22


title: PERH0589_CD8+_t0_aGVHD+_cGVHD+_22


title: PERH0597_CD8+_t0_aGVHD-_cGVHD+_14


title: PERH0603_CD4+_t0_aGVHD+_cGVHD+_25


title: PERH0604_CD8+_t0_aGVHD+_cGVHD+_23


title: PERH0587_CD4+_t0_aGVHD+_cGVHD+_23


title: PERH0613_CD4+_t0_aGVHD-_cGVHD-_22


title: PERH0582_CD4+_t0_aGVHD+_cGVHD+_22


title: PERH0583_CD8+_t0_aGVHD+_cGVHD+_21


title: PERH0579_CD4+_t0_aGVHD+_cGVHD+_21


title: PERH0596_CD4+_t0_aGVHD-_cGVHD+_16


title: PERH0588_CD4+_t0_aGVHD+_cGVHD+_24


title: PERH0580_CD8+_t0_aGVHD+_cGVHD+_20


title: PERH0571_CD4+_t0_aGVHD-_cGVHD+_14


title: PERH0567_CD4+_t0_aGVHD-_cGVHD+_13


title: PERH0568_CD8+_t0_aGVHD-_cGVHD+_11


title: PERH0576_CD8+_t0_aGVHD-_cGVHD+_13


title: PERH0557_CD8+_t0_aGVHD-_cGVHD-_19


title: PERH0558_CD4+_t0_aGVHD-_cGVHD-_19


title: PERH0559_CD4+_t0_aGVHD-_cGVHD+_12


title: PERH0550_CD4+_t0_aGVHD-_cGVHD-_17


title: PERH0572_CD8+_t0_aGVHD-_cGVHD+_12


title: PERH0556_CD4+_t0_aGVHD-_cGVHD-_18


title: PERH0545_CD4+_t0_aGVHD-_cGVHD-_16


title: PERH0551_CD8+_t0_aGVHD-_cGVHD-_18


title: NRSF ChIP-ChIP from HeLaS3 Cells applied to the NimbleGen ENCODE Array Sample 3

city: New Haven

first: Guoneng

last: Zhong

state: CT

address: 300 George St

institute: Yale Med

description: Red Channel: NRSF ChIP DNA purified from HeLaS3 cells with polyclonal antibody; Green Channel: Normal rabbit IgG ChIP DNA purified from HeLaS3 cells

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: value = log_2(Signal for Cy5 / Signal for Cy3)

source_name: NRSF ChIP DNA from HeLaS3 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy5-coupled nonamers (for NRSF ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLaS3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 20 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of anti-NRSF rabbit polyclonal antibody (Upstate 07-579) per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

tag: Polyclonal antibody

source_name: normal rabbit IgG ChIP DNA from HeLaS3 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy3-coupled nonamers (for normal rabbit IgG ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLaS3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 20 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of normal rabbit IgG (Santa Cruz sc-2027) per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

tag: Normal rabbit IgG


title: NRSF ChIP-ChIP from HeLaS3 Cells applied to the NimbleGen ENCODE Array Sample 2


title: PERH0563_CD4+_t0_aGVHD-_cGVHD-_20


title: PERH0539_CD8+_t0_aGVHD-_cGVHD+_10


title: PERH0536_CD4+_t0_aGVHD-_cGVHD+_11


title: SMARCA6 ChIP-ChIP from HeLaS3 Cells applied to the NimbleGen ENCODE Array Sample 1

description: Red Channel: SMARCA6 ChIP DNA purified from HeLaS3 cells with polyclonal antibody; Green Channel: Normal rabbit IgG ChIP DNA purified from HeLaS3 cells

source_name: SMARCA6 ChIP DNA from HeLaS3 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy5-coupled nonamers (for SMARCA6 ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLaS3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 20 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 18 ug of anti-SMARCA6 rabbit polyclonal antibody (Abcam ab3851) per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

extract_protocol: HeLaS3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 20 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 18 ug of normal rabbit IgG (Santa Cruz sc-2027) per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).


title: PERH0527_CD8+_t0_aGVHD-_cGVHD+_9