title: KO/WT CB, histone H3/4 acetylation ChIP-chip

city: Los Angeles

first: Yi

last: Sun

state: CA

address: 635, Charles E. Young Dr. South

department: Molecular and Medical Pharmacology

institute: UCLA

description: ChIP/ChIP

hyb_protocol: Hybridization was performed by NimbleGen as per their standard protocol. Briefly, Cy5- and Cy3-labeled samples were combined and hybridized to each custom NimbleGen microRNA promoter tiling microarrays for 16-20 h at 42 ˚C using NimbleGen hybridization System.

scan_protocol: Microarray scanning was performed by NimbleGen as per their standard protocol.

data_processing: Data extraction and peak detection were performed using NimbleScan v2.5 (Roche/NimbleGen). The log2 ratio between Cy3 and Cy5 signals is computed and scaled. Scaling is performed by subtracting the Tukey bi-weight mean for the log2 ratio values for all features on the array from each log2 ratio value. Genomic regions significantly enriched with Mecp2 or H3/4 acetylation were identified by a sliding window-base statistical algorithm in NimbleScan v2.5 (a non-parametric one-sided Kolmogorov-Smirno (KS) test, KS score>2).

source_name: WT CB, immunoprecipitated DNA by acetylated H3/4 antibodies

label_protocol: Whole cell extract and immunoprecipitated DNA were amplified using the Whole Genome Amplification Kit (Sigma). 4ug amplified ChIP/MeDIP or input samples were sent to NimbleGen and labeled (5’ Cy5- or Cy3-random nonamers, TriLink Biotechnologies) using the standard protocol (NimbleGen Arrays User’s Guide for ChIP-chip analysis).

extract_protocol: Cerebellar tissues (postnatal 6-8 week) were isolated, snap-frozen and stored in -80 freezer before use. Frozen tissues (pooled from four WT or KO littermates) were dissociated by dounce homogenizer and cross-linked with 1% formaldehyde for 10 min at room temperature. Sonicated chromatin was immunoprecipitated overnight at 4 C with 10 ul immobilized (on 100 ul Dynal protein-G beads, Invitrogen) anti-Mecp2 polyclonal antibodies, which were generated and characterized previously (Hu et al., 2006). MeDIP-chip was performed as previously described with minor modifications (Weber et al., 2005). Briefly, 5 ug sonicated, heat-denatured cerebellar genomic DNA was immunoprecipitated with 5 ul of monoclonal antibody against 5-methylcytidine (Eurogentec) at 4 C overnight.  Immunoprecipitated methylated DNA was collected with 30 ul Dynal protein-G beads for 2 h at 4 C.

value: postnatal cerebella

tag: antibody

value: acetylated H3/4

tag: vendor

value: Millipore/Upstate

tag: catalogue#

tag: lot#

value: Mecp2tm1.1Jae/+, mix background (129, C57BL/6 and BALB/c) backcrossed with BALB/c for >6 generations

source_name: KO CB, immunoprecipitated DNA by acetylated H3/4 antibodies


title: MTB_mpa_CDC1551_Samples 4

status: Public on Sep 29 2010

type: RNA

city: Rockville

first: PFGRC

last: JCVI

state: MD

address: 9704 Medical Center Drive

department: PFGRC

country: USA

institute: J. Craig Venter Institute

description: Channel 1 (cy3): M. tuberculosis mpa strain Cy3 cell culture growing in the suplemented with Cu. Channel 2 (cy5): M. tuberculosis CDC1551 strain Cy5 cell culture growing in the suplemented with Cu

hyb_protocol: Slide was hybridized for 12 hours at 42 in Water Bath with volume of 100 in solution of 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin, and blocked in 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate. After hybridization, the slide was washed with 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air. Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95 C degree  prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html)

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: Mtb mpa mutant cells

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

growth_protocol: The wildtype cells were grown in 7H9 minimal media to stationary phase (OD580 = 4). The mutant cells were grown in 7H9 minimal media to stationary phase (OD580 = 4)

extract_protocol: RNA was extracted from Mtb as follows: an equal volume of 4 M guanidinium isothiocyanate (GTC), 0.5% sodium N-lauryl sarcosine, 25 mM trisodium citrate) was added to cultures to arrest transcription, and cells were collected by centrifugation at 2,885 x g. Bacterial were resuspended in 1 ml TRIzol reagent (Invitrogen) and bead beat with zirconia silica beads (BioSpec Products) in a BioSpec Mini Bead Beater two times for 30 s, with 1 min cooling on ice in between. Samples were either stored at -80 C degree or used immediately. Samples were centrifuged for 5 min at 16,100 5 g at 4 C degree to pellet cellular debris. 300 ml of chloroform was added to PhaseLock tubes (Heavy 2 ml, 5Prime) after which the TRIzol samples were added. Tubes were vigorously inverted for 15 s and allowed to rest at RT for 5 min. Tubes were centrifuged for 10 min at 10,500 g at 4 C degree. The aqueous phases were added to microfuge tubes containing 270 ml isopropanol and 270 ml high salt solution (0.8 M  trisodium citrate, 1.2 M NaCl) and vortexed for 5 s. After a 10 min incubation at RT, tubes were microcentrifuged at 16,100 g for 10 min at 4 C degree to pellet RNA. RNA pellets were washed with 1 ml of 75% ethanol and centrifuged at 7,500 g for 5 min at 4 C degree. Pellets were allowed to dry by air and resuspended in 50 µl of RNA storage buffer (Ambion). 2 µl were used for quantification and another 2 µl were added to 80% formamide/ 20% loading dye to check RNA integrity on an (1.6%) agarose gel. The purification process was repeated two times to obtain DNA-free RNA. RNA aliquots were stored at -80 C degree.

tag: strain

value: mpa

source_name: Mtb CDC1551 cells

growth_protocol: The wildtype cells were grown in 7H9 minimal media to  stationary phase (OD580 = 4); The mutant cells were grown in 7H9 minimal media to stationary phase (OD580 = 4)


title: MTB_607_CDC1551_Samples 3

description: Channel 1 (cy3): M. tuberculosis 607 strain Cy3 cell culture growing in the suplemented with Cu. Channel 2 (cy5): M. tuberculosis CDC1551 strain Cy5 cell culture growing in the suplemented with Cu

source_name: Mtb 607 mutant cells


title: MTB_mpa_CDC1551_Samples 1

description: Channel 1 (cy3): M. tuberculosis CDC1551 strain Cy3 cell culture growing in the suplemented with Cu. Channel 2 (cy5): M. tuberculosis mpa strain Cy5 cell culture growing in the suplemented with Cu

growth_protocol: The wildtype cells were grown in 7H9 minimal media to stationary phase (OD580 = 2). The mutant cells were grown in 7H9 minimal media to stationary phase (OD580 = 2)

growth_protocol: The wildtype cells were grown in 7H9 minimal media to stationary phase (OD580 = 2)      The mutant cells were grown in 7H9 minimal media to stationary phase (OD580 = 2)


title: MTB_607_CDC1551_Samples 2

description: Channel 1 (cy3): M. tuberculosis CDC1551 strain Cy3 cell culture growing in the suplemented with Cu. Channel 2 (cy5): M. tuberculosis 607 strain Cy5 cell culture growing in the suplemented with Cu

growth_protocol: The wildtype cells were grown in 7H9 minimal media to  stationary phase (OD580 = 2); The mutant cells were grown in 7H9 minimal media to stationary phase (OD580 = 2)


title: MTB_607_CDC1551_Samples 4


title: MTB_pafA_CDC1551_Samples 1

description: Channel 1 (cy3): M. tuberculosis CDC1551 strain Cy3 cell culture growing in the suplemented with Cu. Channel 2 (cy5): M. tuberculosis pafA strain Cy5 cell culture growing in the suplemented with Cu

source_name: Mtb pafA mutant cells

growth_protocol: The wildtype cells were grown in 7H9 minimal media to stationary phase (OD580 = 2), The mutant cells were grown in 7H9 minimal media to stationary phase (OD580 = 2)

value: pafA


title: SUP-B15 Imatinib-treated

status: Public on Sep 10 2010

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

description: SUP-B15 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours. For more information about the cell line, please check: www.dsmz.de

hyb_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

data_processing: RMA

label: Biotin

organism: Homo sapiens

source_name: Cell line: SUP-B15

extract_protocol: Extraction Method: Qiagen RNeasy Kit

tag: cell line

tag: tissue

value: Human B cell precursor leukemia


status: Public on Aug 05 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: For array hybridization, 2ug of the labeled DNA material was hybridized per chip for 18 h at 45C in a 3 M tetramethyl ammonium chloride/1x MES-based solution containing 100?g/mL Herring Sperm DNA, 0.02% Triton and 30pM of biotinylated control oligo B2 (Affymetrix). All reagents were from Invitrogen, except where noted otherwise.

scan_protocol: Scanned at 0.7 microns/pixel.

data_processing:
Data_Normalization_for_Expression_Arrays protocol. Three biological replicates were hybridized for this experiment. The data from replicate arrays were quantile-normalized (Bolstad et al., 2003) and all arrays were scaled to a median array intensity given (e.g. 361).  Processed data are obtained using following parameters: median value is 361   Signal Graph generation protocol. The sliding window approach (bandwidth 50) has been used to estimate RNA abundance (signal which is listed in column #2). It was found by calculating the median of all pairwise average PM-MM values, where PM is a perfect match and MM is a mismatch.  Processed data are obtained using following parameters: bandwidth is 50

CEL file currently unavailable

organism: Drosophila melanogaster

source_name: embryos,6-8 hr after egg laying (Celniker/RNA:230) extraction1_array1 channel_1

label_protocol: Double-stranded cDNA was treated with RNase H (Epicentre Technologies) and RNases A/T1 (Ambion), extracted by using a QIAquick PCR purification kit (Qiagen), and subjected to further fragmentation to 50-100 bp by DNase I (1 unit/ul; Epicentre Technologies; size distribution of fragmented DNA was verified on a 2% agarose gel).The fragmented cDNA was then end-labeled with 2.5mM biotinylated DNA labeling reagent (Affymetrix) by using 100 units of terminal deoxynucleotidyltransferase (TdT; Roche Diagnostics) in 1x TdT buffer (Roche Diagnostics) and 5 mM CoCl2 (Roche Diagnostics) for 2 h at 37C.

growth_protocol:
Fly population cages contained the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. Two homemade Plexiglas cages approximately 25cm x 25cm x 25cm, were used for staged embryo collections. These population cages were constructed from ¼ inch solid Plexiglas except for the open front panel. The fronts of the cages were covered with sleeves constructed of muslin cloth that were attached to the Plexiglas sides using Velcro strips. Each muslin sleeve was then twisted and held closed with a hose clamp. Flies were fed with three hard egg lay collection plates made in 150 X 15 mm Petri dishes containing a substrate of 3.3% agar, 13% unsulfured molasses, and 0.15% Tegasept. The hard egg lay plates were completely covered with a thin layer of moist yeast paste (Fleischmann?s Baker?s Dry Yeast) and placed horizontally on a short 1cm raised Plexiglas bar in the bottom of each cage to avoid crushing flies. The two population cages were maintained at 24? C in a controlled environment on a 24-hour light cycle (14 hours light / 10 hours dark) using three 60W bulbs on a timer. Flies were introduced to the cages at least four days prior to collections and fertility counts. These animals were initially grown in bottles at the same controlled environment described above. Each population cage was established from four trays with 35 bottles per tray containing newly eclosed adult flies. Each 250ml (pint) bottle contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). The isogenic Drosophila mutant strain was propagated in bottles (A) starting with approximately 40-50 adults per bottle on day zero. New bottles (B) were generated from these bottles (A) on day 14. Cages were established by clearing the ?A? bottles into an empty bottle (without food) and transferring the newly eclosed adult flies in the ?A? bottles into the two population cages on day 18. The next round of cages and bottles (C) were established from the ?B? bottles in the same manner. Two-hour embryo collections were made during the light cycles following at least one two-hour pre-lay.
This protocol was used for staging and collection of Drosophila melanogaster embryos by Dave Miller(Kaufman Lab, IU Bloomington) for transcriptome analysis by the Celniker group.

extract_protocol:
RNA extraction: TRIzol procedure for Insects followed by DNase and RNeasyNote: This protocol is used to prepare RNA that will be used for microarray hybridization or RT-PCR.
First-strand cDNA synthesis was performed by using SuperScript II reverse transcriptase in the reaction volume of 105 ul for 15 ug of starting RNA material. The RNA was mixed with random hexamers (83.3 ng/g mRNA), heated to 70C for 10 min, and cooled to 15C after which 5x SuperScript II First Strand buffer, DTT (10 mM), and dNTPs (0.5 mM) were added. SuperScript II was added after a 20-min incubation (200 units/ug RNA) followed by a 20-min ramp to 42C and 60-min incubation at 420C. SuperScript II was inactivated at 75C for 15 min.The second-strand cDNA was synthesized by addition of 50 units of Escherichia coli DNA ligase, 200 units of E. coli DNA polymerase I, 10 units of E. coli RNase H, and 0.2 mM dNTPs to the first-strand synthesis reaction at 16C for 2 h.

value: Y cn bw sp

tag: developmental stage

value: Embryo 6-8h

tag: genotype


title: WT CB, DNA methylation by MeDIP-chip

status: Public on Sep 30 2010

type: genomic

description: MeDIP/IP

molecule: genomic DNA

organism: Mus musculus

source_name: WT CB, whole cell extract

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

value: Eurogentec


title: TOM-1 non-treated

description:
TOM-1 leukemia cells were cultured without STI571 (Imatinib).
For more information about the cell line, please check: www.dsmz.de

scan_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

source_name: Cell line: TOM-1


title: SUP-B15 non-treated

description:
SUP-B15 leukemia cells were cultured without STI571 (Imatinib).
For more information about the cell line, please check: www.dsmz.de

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)


title: KO CB, Mecp2 ChIP-chip (1/2)

description: ChIP/WCE

data_processing: Data extraction and peak detection were performed using NimbleScan v2.5 (Roche/NimbleGen). The log2 ratio between Cy3 and Cy5 signals is computed and scaled. Scaling is performed by subtracting the Tukey bi-weight mean for the log2 ratio values for all features on the array from each log2 ratio value.  Two separate hybridizations using biological independent samples were performed and yielded similar results.  We combined and averaged log2 ratio values from replicate arrays.  Mecp2 binding sites were identified by a sliding window-base statistical algorithm in NimbleScan v2.5 (a non-parametric one-sided Kolmogorov-Smirno (KS) test, KS score>2).

source_name: KO CB, whole cell extract

source_name: KO CB, immunoprecipitated DNA by Mecp2 antibodies

tag: antibody source

value: rabbit polyclonal (Hu et al, 2006; Nature Genetics)


source_name: pupae,WPP + 2 days (Celniker/RNA:346) extraction2_array1 channel_1

label_protocol: Double-stranded cDNA was treated with RNase H (Epicentre Technologies) and RNases A/T1 (Ambion), extracted by using a QIAquick PCR purification kit (Qiagen), and subjected to further fragmentation to 50-100 bp by DNase I (1 unit/ul; Epicentre Technologies; size distribution of fragmented DNA was verified on a 2% agarose gel).The fragmented cDNA was then end-labeled with 2.5mM biotinylated DNA labeling reagent (Affymetrix) by using 100 units of terminal deoxynucleotidyltransferase (TdT; Roche Diagnostics) in 1x TdT buffer (Roche Diagnostics) and 5 mM CoCl2 (Roche Diagnostics) for 2 h at 37C. TdT LABELING; Perform in 20 ul for 5 ug of DNA, 35 ul for 10 ug of DNA, and 70 ul for 10-15 ug of DNA.  - 40 ul of fragmented DNA  - 14 ul of 5X TdT buffer (Roche)  - 7 ul of 20mM CoCl2 (Roche)  - 2.3 ul of DNA Labeling Reagents (Affymetrix)  - 0.5 ul of Terminal deoxytransferase, 8000U (Roche)  - 6.2 ul of diH2OIncubate at 37C for 2 hours in water bath.The labeled cDNA is now ready to be hybridized.

growth_protocol:
Fly population cages contained the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. Two homemade Plexiglas cages approximately 25cm x 25cm x 25cm, were used for staged embryo collections. These population cages were constructed from ¼ inch solid Plexiglas except for the open front panel. The fronts of the cages were covered with sleeves constructed of muslin cloth that were attached to the Plexiglas sides using Velcro strips. Each muslin sleeve was then twisted and held closed with a hose clamp. Flies were fed with three hard egg lay collection plates made in 150 X 15 mm Petri dishes containing a substrate of 3.3% agar, 13% unsulfured molasses, and 0.15% Tegasept. The hard egg lay plates were completely covered with a thin layer of moist yeast paste (Fleischmann?s Baker?s Dry Yeast) and placed horizontally on a short 1cm raised Plexiglas bar in the bottom of each cage to avoid crushing flies. The two population cages were maintained at 24? C in a controlled environment on a 24-hour light cycle (14 hours light / 10 hours dark) using three 60W bulbs on a timer. Flies were introduced to the cages at least four days prior to collections and fertility counts. These animals were initially grown in bottles at the same controlled environment described above. Each population cage was established from four trays with 35 bottles per tray containing newly eclosed adult flies. Each 250ml (pint) bottle contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). The isogenic Drosophila mutant strain was propagated in bottles (A) starting with approximately 40-50 adults per bottle on day zero. New bottles (B) were generated from these bottles (A) on day 14. Cages were established by clearing the ?A? bottles into an empty bottle (without food) and transferring the newly eclosed adult flies in the ?A? bottles into the two population cages on day 18. The next round of cages and bottles (C) were established from the ?B? bottles in the same manner. Two-hour embryo collections were made during the light cycles following at least one two-hour pre-lay.
Protocol for collecting pre-pupal, pupal and pharate adult stages from the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1].

extract_protocol:
RNA extraction: TRIzol procedure for Insects followed by DNase and RNeasyNote: This protocol is used to prepare RNA that will be used for microarray hybridization or RT-PCR.
cDNA Synthesis and Labeling: Note that this protocol gives you labeled dsDNA, as such the array results are not stranded.* ug cDNA hybed per chip: 10 ug if template was total RNA or Poly-A-, 2.5 ug if Poly-A+ RNAFIRST-STRAND SYNTHESIS  - 10 ug of Total RNA (DNAsed,Cleaned-up and ETOH precipitated)  - 1.25 ug of 250ng/ul random primers (Invitrogen)  - diH2O to 60 ul Vf.Incubate at 70C for 10 mins (fast ramp) then cool to 15C over the course of 20 minutes. Once it reaches 15C add:  - 20 ul of 5X First-Strand Buffer (Invitrogen)  - 10 ul of 100mM DTT (Invitrogen)  - 5 ul of 10mM dNTPs (Invitrogen)Incubate at 15C for 30 minutes then heat to 42C over the course of 20 minutes.  Once it reaches 42C add:  - 10 ul Superscript RT II (Invitrogen)Incubate at 42C for 60 minutes, then heat rapidly to 70C and incubate for 15 minutes, then park it at 4C.SECOND-STRAND SYNTHESISTo the First strand synthesis reaction above add while at 4C:  - 450 ul diH2O  - 150 ul 5X Second-Strand Buffer (Invitrogen)  - 15 ul 10mM dNTPs (Invitrogen)  - 5 ul 10U/ul E. coli DNA Ligase (Invitrogen)  - 20 ul 10U/ul E. coli DNA Polymerase (Invitrogen)  - 5 ul 2U/ul E. coli RNAseH (Invitrogen)Incubate at 16C for 120 minutes, then 70C for 15 minutes, then park it at 4C.RNA REMOVAL and cDNA PURIFICATIONAdd:  - 3 ul of 10U/ul RNaseH (Ambion)  - 3 ul of 5 and 20U/ul RNAseA/T1 (Ambion)Incubate at 37C for 20 minutesUse a Qiagen PCR Clean-up kit (two columns per reaction), ETOH precipitate the eluate and 70% ETOH rinse.  Redissolve in 35 ul diH2O.  Measure the OD600 on a Nanodrop.cDNA FRAGMENTATION*** NEED TO ADD ***Check the fragmentation on an agarose gel. Want it to be around 100 nucleotides.

value: Pupae, WPP + 2 days


title: WT CB, histone H3/4 acetylation ChIP-chip

description: ChIP/WCE


title: MTB_607_CDC1551_Samples 1


source_name: pupae,WPP + 2 days (Celniker/RNA:348) extraction3_array1 channel_1


molecule: polyA RNA

source_name: embryos,4-6 hr after egg laying (Celniker/RNA:410) extraction2_array1 channel_1

extract_protocol:
Protocol for extraction of polyA+ RNA starting from staged whole insects.
First-strand cDNA synthesis was performed by using SuperScript II reverse transcriptase in the reaction volume of 105 ul for 15 ug of starting RNA material. The RNA was mixed with random hexamers (83.3 ng/g mRNA), heated to 70C for 10 min, and cooled to 15C after which 5x SuperScript II First Strand buffer, DTT (10 mM), and dNTPs (0.5 mM) were added. SuperScript II was added after a 20-min incubation (200 units/ug RNA) followed by a 20-min ramp to 42C and 60-min incubation at 420C. SuperScript II was inactivated at 75C for 15 min.The second-strand cDNA was synthesized by addition of 50 units of Escherichia coli DNA ligase, 200 units of E. coli DNA polymerase I, 10 units of E. coli RNase H, and 0.2 mM dNTPs to the first-strand synthesis reaction at 16C for 2 h.

value: Embryo 4-6h


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:411) extraction3_array1 channel_1


title: NALM-1 non-treated

description:
NALM-1 leukemia cells were cultured without STI571 (Imatinib).
For more information about the cell line, please check: www.dsmz.de

source_name: Cell line: NALM1


source_name: pupae,WPP + 2 days (Celniker/RNA:344) extraction1_array1 channel_1


title: Young_16_Basal

status: Public on Oct 01 2010

city: Galveston

first: micah

last: Drummond

state: TX

address: 301 University Boulevard

institute: University of Texas Medical Branch

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Background is determined using a regression-based background mapping method.  The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots.  Raw data matrix is then subtracted by the background matrix.
Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data.  The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) "A comparison of normalization methods for high density oligonucleotide array data based on variance and bias", Bioinformatics, 19 (2), 185-193].
A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5.  CV is calculated by (standard deviation)/(signal intensity).  When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
t-Test is performed between “control” and “test” sample groups.   T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution.  miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis.  The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.
All data processes, except clustering plot, are carried out using in-house developed computer programs.  The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.

extract_protocol: Tri-Reagent

value: vastus lateralis basal skeletal muscle

tag: gender

value: male

tag: age

value: 19 years


title: WT CB, Mecp2 ChIP-chip

description: ChIP/WCE

source_name: WT CB, immunoprecipitated DNA by Mecp2 antibodies


title: BV-173 Imatinib-treated

description:
BV-173 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours.
For more information about the cell line, please check: www.dsmz.de

source_name: Cell line: BV-173


title: TOM-1 Imatinib-treated

description: TOM-1 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours. For more information about the cell line, please check: www.dsmz.de


title: KO CB, Mecp2 ChIP-chip (2/2)

description: ChIP/WCE


title: WT CB, DNA methylation by MeDIP-chip (2/2)

description: MeDIP/IP


title: BV-173 non-treated

description:
BV-173 leukemia cells were cultured without STI571 (Imatinib).
For more information about the cell line, please check: www.dsmz.de


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:409) extraction1_array1 channel_1


title: WT CB, Mecp2 ChIP-chip (1/2), exp2

description: ChIP/WCE


title: NALM-1 Imatinib-treated

description: NALM-1 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours. For more information about the cell line, please check: www.dsmz.de


title: WT CB, Mecp2 ChIP-chip (1/2), exp1

description: ChIP/WCE


title: WT CB, Mecp2 ChIP-chip (2/2), exp1

description: ChIP/WCE


title: WT CB, Mecp2 ChIP-chip (2/2), exp2

description: ChIP/WCE


title: WT CB, DNA methylation by MeDIP-chip (1/2)

description: MeDIP/IP


title: 9C: Letrozole, 2.5mg/day,oral, 90 days; responder

status: Public on Jul 28 2010

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: breast tumor biopsy

hyb_protocol: standard Affymetrix procedures except for use of a custom 24-channel fluidics machine

scan_protocol: standard Affymetrix procedures

label: biotin

label_protocol: Approximately 500 ng of total RNA was processed to produce biotinylated cRNA targets using protocol described in Biotechniques. 2003 Mar;34(3):546-50, 552-4, 556

extract_protocol: Biopsies were snap-frozen after collection and stored in liquid nitrogen.  Frozen sections were taken prior to RNA extraction to confirm the presence of cancerous tissue within the specimens.  Only samples in which the malignant component comprised at least 20% of the section area were used in further analyses.  Immediately before RNA extraction the biopsies were pulverised using U2 micro-dismembranator U (Braun Biotech).  Total RNA was extracted from the resultant frozen tissue powder using TRI-reagent (Sigma) according to the manufacturer's recommendations.  Extracted RNA was additionally purified on RNeasy mini columns (Qiagen).  RNA quantity and quality was verified on Bioanalyser 2100 (Agilent).

treatment_protocol: breast biopsies were taken from subjects after 90 days Letrozol, 2.5 mg

tag: subject

value: female

value: breast tumor

tag: agent

value: Letrozol

tag: dose

tag: administration

value: oral

tag: time

value: 90 days


title: 20C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 24C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 28C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 7C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 25C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 13C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 18C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 21C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 22C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 10C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 16C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 12C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 8C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 15C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 27C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 14C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 19C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 11C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 23C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 69C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 17C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 67C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 68C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


source_name: embryos,6-8 hr after egg laying (Celniker/RNA:232) extraction2_array1 channel_1


title: 64C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 65C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 57C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 58C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 60C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 63C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 59C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 46C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 50C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 52C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 44C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 56C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 53C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 49C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 51C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 43C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 42C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 47C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 37C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 45C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 35C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 31C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 36C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 41C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 40C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 39C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 34C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 30C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 33C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 29C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 6C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 3C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 5C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 4C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 2C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: EPT304 ependynoma [human miRNA]

status: Public on Jul 19 2010

city: Memphis

first: Richard

middle: James

last: Gilbertson

state: TN

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St Jude Children's Research Hospital

description: analyzed at St. Jude Hartwell Center

hyb_protocol: Per the protocol, the dried labeled product was resuspended in nuclease-free water, followed by addition of Agilent GE Blocking Agent and Agilent Hi-RPM Hybridization Buffer. The labeled miRNA was then heated to 100°C for 5 minutes, followed by 5 minutes in an ice-water bath. The entire volume (45 µl) of eight, individual reactions was hybridized to Human 8x15K miRNA Microarrays (V2), Agilent #G4470B, for 20 hours at 55°C, 20 rpm, in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minutes with 37°C GE Wash Buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were immediately scanned after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 8x15k array slides, using the following scan settings: 20-bit, scan area 61x21.6 mm, single pass, scan resolution 5 µm, 100% PMT, green dye channel only, and eXtended Dynamic range (XDR) not enabled

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1 (Agilent) using default parameters (protocol miRNA_105_Dec08 and Grid: 019118_D_20080215) to obtain background detrended processed signal intensities, which was then normalized, scaled and averaged. The minimum detecting miRNA expression signal was set at a threshold with less than 1% of the negative control probes.

source_name: patient sample

label_protocol: Cyanine-3 labeled miRNA was prepared from 100 ng total RNA using the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit, v.2.0  (June 2008) according to the manufacturer's instructions. No post labeling purification was performed, followed by vacuum drying of the labeled reactions, per the protocol.

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

treatment_protocol: tumors excised and flash frozen at distinct sites, storage and freezing method varies

tag: disease state

value: ependynoma primary tumor

tag: Sex

value: F


title: EPT290 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center

value: M


title: EPT291 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT297 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT289 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT292 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT295 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT302 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT298 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT303 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT293 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT294 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT286 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT306 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT307 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT309 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT314 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT285 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT315 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT310 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT296 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT313 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT278 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT281 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT284 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT277 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT283 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: 55C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: EPT276 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT272 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT094 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT093 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT103 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT102 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT101 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT100 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT095 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT257 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT107 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT275 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT260 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT273 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT256 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT105 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT104 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT274 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT089 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT255 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT099 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT091 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT084 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT254 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT079 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT078 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT071 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT087 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT032 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT068 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT070 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT065 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT026 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT064 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT002 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: EPT011 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: pmh256 cell line [mouse mRNA]

description: Gene expression data from mouse model tumor models

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCOS v1.4 software (Affymetrix, Santa Clara, CA). Signals were normalized for each array by scaling to a 2% trimmed mean of 500.

source_name: mouse tumor model

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix One-Cycle protocol from 1 ug of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

growth_protocol: mouse tumors and cell lines

treatment_protocol: tumor exicision or cell line suspension extraction

value: mouse ependymoma model

value: Spinal

value: WT

value: adult


title: pmh242 cell line [mouse mRNA]

value: Posterior fossa

value: embryonic


title: pmh196 cell line [mouse mRNA]

value: Cerebrum


title: pmh237 cell line [mouse mRNA]

value: Arf null


title: pmh247 cell line [mouse mRNA]


title: pmh235 cell line [mouse mRNA]


title: pmh241 cell line [mouse mRNA]


title: pmh236 cell line [mouse mRNA]


title: pmh209 cell line [mouse mRNA]


title: pmh190 cell line [mouse mRNA]


title: EPT066 ependynoma [human miRNA]

description: analyzed at St. Jude Hartwell Center


title: pmh193 cell line [mouse mRNA]


title: pmh185 cell line [mouse mRNA]


title: pmh192 cell line [mouse mRNA]


title: pmh186 cell line [mouse mRNA]


title: pmh181 cell line [mouse mRNA]


title: pmh175 cell line [mouse mRNA]


title: pmh154 cell line [mouse mRNA]


title: pmh130 cell line [mouse mRNA]


title: pmh129 cell line [mouse mRNA]


title: pmh112 cell line [mouse mRNA]


title: pmh101 cell line [mouse mRNA]


title: pmh152 cell line [mouse mRNA]


title: pmh131 cell line [mouse mRNA]


title: pmh137 cell line [mouse mRNA]


title: pmh151 cell line [mouse mRNA]


title: pmh107 cell line [mouse mRNA]


title: pmh141 cell line [mouse mRNA]


title: pmh070 cell line [mouse mRNA]


title: pmh044 cell line [mouse mRNA]


title: pmh042 cell line [mouse mRNA]


title: hmp460 tumor [mouse mRNA]


title: pmh026 cell line [mouse mRNA]


title: pmh033 cell line [mouse mRNA]


title: hmp459 tumor [mouse mRNA]


title: hmp453 tumor [mouse mRNA]


title: hmp452 tumor [mouse mRNA]


title: hmp458 tumor [mouse mRNA]


title: pmh030 cell line [mouse mRNA]


title: pmh053 cell line [mouse mRNA]


title: pmh096 cell line [mouse mRNA]


title: hmp457 tumor [mouse mRNA]


title: hmp450 tumor [mouse mRNA]


title: hmp444 tumor [mouse mRNA]


title: hmp259 cell line [mouse mRNA]


title: hmp261 cell line [mouse mRNA]


title: hmp451 tumor [mouse mRNA]


title: hmp260 cell line [mouse mRNA]


title: hmp449 tumor [mouse mRNA]


title: hmp257 cell line [mouse mRNA]


title: hmp445 tumor [mouse mRNA]


title: hmp249 cell line [mouse mRNA]


title: hmp248 cell line [mouse mRNA]


title: hmp239 cell line [mouse mRNA]


title: hmp447 tumor [mouse mRNA]


title: hmp446 tumor [mouse mRNA]


title: hmp231 cell line [mouse mRNA]


title: hmp250 cell line [mouse mRNA]


title: hmp240 cell line [mouse mRNA]


title: pmh090 cell line [mouse mRNA]


title: hmp252 cell line [mouse mRNA]


title: hmp233 cell line [mouse mRNA]


title: hmp230 cell line [mouse mRNA]


title: hmp232 cell line [mouse mRNA]


title: hmp243 cell line [mouse mRNA]


title: pmh065 cell line [mouse mRNA]


title: hmp246 cell line [mouse mRNA]


title: hmp228 cell line [mouse mRNA]


title: hmp234 cell line [mouse mRNA]


title: hmp226 cell line [mouse mRNA]


title: hmp229 cell line [mouse mRNA]


title: hmp224 cell line [mouse mRNA]


title: hmp221 cell line [mouse mRNA]


title: hmp214 cell line [mouse mRNA]


title: hmp227 cell line [mouse mRNA]


title: hmp223 cell line [mouse mRNA]


title: hmp210 cell line [mouse mRNA]


title: hmp211 cell line [mouse mRNA]


title: hmp212 cell line [mouse mRNA]


title: hmp206 cell line [mouse mRNA]


title: hmp207 cell line [mouse mRNA]


title: hmp198 cell line [mouse mRNA]


title: hmp199 cell line [mouse mRNA]


title: hmp197 cell line [mouse mRNA]


title: hmp195 cell line [mouse mRNA]


title: hmp208 cell line [mouse mRNA]


title: hmp192 cell line [mouse mRNA]


title: hmp219 cell line [mouse mRNA]


title: hmp205 cell line [mouse mRNA]


title: hmp204 cell line [mouse mRNA]


title: hmp193 cell line [mouse mRNA]


title: hmp194 cell line [mouse mRNA]


title: hmp191 cell line [mouse mRNA]


title: hmp188 cell line [mouse mRNA]


title: hmp184 cell line [mouse mRNA]


title: hmp183 cell line [mouse mRNA]


title: hmp189 cell line [mouse mRNA]


title: hmp180 cell line [mouse mRNA]


title: hmp179 cell line [mouse mRNA]


title: hmp178 cell line [mouse mRNA]


title: hmp173 cell line [mouse mRNA]


title: hmp187 cell line [mouse mRNA]


title: hmp171 cell line [mouse mRNA]


title: hmp177 cell line [mouse mRNA]


title: hmp172 cell line [mouse mRNA]


title: hmp167 cell line [mouse mRNA]


title: hmp160 cell line [mouse mRNA]


title: hmp159 cell line [mouse mRNA]


title: hmp158 cell line [mouse mRNA]


title: hmp156 cell line [mouse mRNA]


title: hmp145 cell line [mouse mRNA]


title: hmp142 cell line [mouse mRNA]


title: hmp140 cell line [mouse mRNA]


title: hmp135 cell line [mouse mRNA]


title: hmp134 cell line [mouse mRNA]


title: hmp149 cell line [mouse mRNA]


title: hmp136 cell line [mouse mRNA]


title: hmp127 cell line [mouse mRNA]


title: hmp128 cell line [mouse mRNA]


title: hmp123 cell line [mouse mRNA]


title: hmp133 cell line [mouse mRNA]


title: EPT061 ependynoma [human mRNA]

description: Gene expression data from human primary tumors

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: ependynoma primary tumor

growth_protocol: human primary tumors

tag: subgroup

value: C

tag: age in years


title: hmp120 cell line [mouse mRNA]


title: EPT051 ependynoma [human mRNA]

value: not grouped


title: EPT050 ependynoma [human mRNA]


title: hmp122 cell line [mouse mRNA]


title: EPT053 ependynoma [human mRNA]


title: EPT057 ependynoma [human mRNA]


title: hmp117 cell line [mouse mRNA]


title: EPT056 ependynoma [human mRNA]

value: H


title: hmp113 cell line [mouse mRNA]


title: EPT152 ependynoma [human mRNA]


title: EPT015 ependynoma [human mRNA]

value: B


title: hmp105 cell line [mouse mRNA]


title: hmp098 cell line [mouse mRNA]


title: EPT032 ependynoma [human mRNA]

value: I


title: EPT018 ependynoma [human mRNA]

value: G


title: hmp093 cell line [mouse mRNA]


title: EPT010 ependynoma [human mRNA]

value: ependynoma primary tumor


title: hmp111 cell line [mouse mRNA]


title: hmp109 cell line [mouse mRNA]


title: EPT025 ependynoma [human mRNA]


title: hmp091 cell line [mouse mRNA]


title: EPT026 ependynoma [human mRNA]


title: hmp115 cell line [mouse mRNA]


title: hmp108 cell line [mouse mRNA]


title: hmp097 cell line [mouse mRNA]


title: EPT023 ependynoma [human mRNA]


title: ept313 ependynoma [human mRNA]


title: hmp080 cell line [mouse mRNA]


title: ept310 ependynoma [human mRNA]


title: hmp089 cell line [mouse mRNA]


title: ept315 ependynoma [human mRNA]

value: F

value: E


title: ept314 ependynoma [human mRNA]

value: M


title: hmp088 cell line [mouse mRNA]

value: mouse ependymoma model


title: ept308 ependynoma [human mRNA]


title: hmp079 cell line [mouse mRNA]

value: Spinal

value: WT


title: ept309 ependynoma [human mRNA]


title: ept307 ependynoma [human mRNA]


title: hmp078 cell line [mouse mRNA]


title: ept298 ependynoma [human mRNA]

value: Posterior fossa


title: ept306 ependynoma [human mRNA]


title: ept305 ependynoma [human mRNA]

value: A


title: hmp076 cell line [mouse mRNA]

value: embryonic


title: ept304 ependynoma [human mRNA]

value: Cerebrum


title: hmp077 cell line [mouse mRNA]


title: hmp071 cell line [mouse mRNA]


title: ept302 ependynoma [human mRNA]


title: hmp065 cell line [mouse mRNA]


title: hmp064 cell line [mouse mRNA]


title: ept296 ependynoma [human mRNA]


title: hmp069 cell line [mouse mRNA]


title: hmp073 cell line [mouse mRNA]


title: hmp068 cell line [mouse mRNA]


title: hmp100 cell line [mouse mRNA]

value: Arf null

value: adult


title: ept297 ependynoma [human mRNA]

value: H


title: ept294 ependynoma [human mRNA]

value: B


title: hmp067 cell line [mouse mRNA]


title: ept293 ependynoma [human mRNA]


title: hmp072 cell line [mouse mRNA]


title: ept295 ependynoma [human mRNA]


title: ept292 ependynoma [human mRNA]


title: ept291 ependynoma [human mRNA]


title: hmp063 cell line [mouse mRNA]


title: ept289 ependynoma [human mRNA]

value: not grouped


title: ept290 ependynoma [human mRNA]

value: I


title: hmp062 cell line [mouse mRNA]


title: ept303 ependynoma [human mRNA]

value: ependynoma primary tumor


title: hmp056 cell line [mouse mRNA]


title: hmp059 cell line [mouse mRNA]


title: hmp057 cell line [mouse mRNA]


title: ept286 ependynoma [human mRNA]

value: G


title: hmp060 cell line [mouse mRNA]


title: hmp066 cell line [mouse mRNA]


title: hmp055 cell line [mouse mRNA]


title: hmp050 cell line [mouse mRNA]


title: hmp054 cell line [mouse mRNA]


title: hmp052 cell line [mouse mRNA]


title: hmp058 cell line [mouse mRNA]


title: ept276 ependynoma [human mRNA]

value: F


title: ept284 ependynoma [human mRNA]

value: M

value: C


title: ept281 ependynoma [human mRNA]


title: ept283 ependynoma [human mRNA]


title: ept278 ependynoma [human mRNA]


title: hmp049 cell line [mouse mRNA]

value: mouse ependymoma model


title: ept275 ependynoma [human mRNA]


title: ept274 ependynoma [human mRNA]


title: ept285 ependynoma [human mRNA]

value: Spinal


title: ept277 ependynoma [human mRNA]


title: hmp041 cell line [mouse mRNA]

value: Posterior fossa


title: hmp043 cell line [mouse mRNA]


title: ept260 ependynoma [human mRNA]


title: ept257 ependynoma [human mRNA]


title: hmp047 cell line [mouse mRNA]


title: hmp046 cell line [mouse mRNA]


title: ept254 ependynoma [human mRNA]

value: A


title: ept255 ependynoma [human mRNA]


title: hmp036 cell line [mouse mRNA]

value: WT


title: hmp035 cell line [mouse mRNA]


title: hmp039 cell line [mouse mRNA]

value: embryonic


title: hmp029 cell line [mouse mRNA]


title: hmp028 cell line [mouse mRNA]


title: ept106 ependynoma [human mRNA]


title: ept107 ependynoma [human mRNA]


title: ept273 ependynoma [human mRNA]

value: Cerebrum


title: ept272 ependynoma [human mRNA]


title: hmp048 cell line [mouse mRNA]

value: Arf null


title: hmp034 cell line [mouse mRNA]

value: adult


title: ept256 ependynoma [human mRNA]


title: ept105 ependynoma [human mRNA]


title: ept103 ependynoma [human mRNA]


title: EPT009 ependynoma [human mRNA]


title: ept102 ependynoma [human mRNA]

value: E


title: ept104 ependynoma [human mRNA]


title: hmp027 cell line [mouse mRNA]


title: hmp022 cell line [mouse mRNA]


title: hmp017 cell line [mouse mRNA]


title: hmp019 cell line [mouse mRNA]


title: hmp020 cell line [mouse mRNA]


title: hmp024 cell line [mouse mRNA]


title: hmp018 cell line [mouse mRNA]


title: ept095 ependynoma [human mRNA]


title: ept101 ependynoma [human mRNA]

value: B


title: ept093 ependynoma [human mRNA]


title: ept094 ependynoma [human mRNA]

value: I


title: ept100 ependynoma [human mRNA]

value: ependynoma primary tumor


title: hmp013 cell line [mouse mRNA]


title: ept099 ependynoma [human mRNA]

value: not grouped


title: ept089 ependynoma [human mRNA]


title: ept087 ependynoma [human mRNA]

value: F


title: hmp015 cell line [mouse mRNA]


title: hmp008 cell line [mouse mRNA]


title: ept084 ependynoma [human mRNA]

value: M


title: hmp014 cell line [mouse mRNA]


title: hmp012 cell line [mouse mRNA]


title: hmp010 cell line [mouse mRNA]


title: hmp011 cell line [mouse mRNA]


title: ept092 ependynoma [human mRNA]


title: ept091 ependynoma [human mRNA]


title: hmp009 cell line [mouse mRNA]


title: ept082 ependynoma [human mRNA]

value: G


title: ept079 ependynoma [human mRNA]


title: hmp007 cell line [mouse mRNA]

value: mouse ependymoma model


title: hmp002 cell line [mouse mRNA]


title: ept068 ependynoma [human mRNA]

value: C


title: hmp004 cell line [mouse mRNA]


title: ept067 ependynoma [human mRNA]

value: Posterior fossa

value: H


title: ept070 ependynoma [human mRNA]


title: ept071 ependynoma [human mRNA]


title: hmp003 cell line [mouse mRNA]

value: WT


title: ept078 ependynoma [human mRNA]


title: ept011 ependynoma [human mRNA]


title: Low protein diet, rep5

status: Public on Jul 02 2010

city: Nantes

first: Francisco

last: Bolanos

address: CHU-Hôtel Dieu. Place Alexis Ricordeau

country: France

institute: INRA-Université de Nantes

hyb_protocol: Hybridization was performed at NimbleGen.

scan_protocol: Scanning was performed at NimbleGen.

data_processing: Lowess procedure using raw calls files and an in-house R script (ref for normalisation = median virtual sample).

organism: Rattus norvegicus

source_name: hypothalamus, low-protein diet

label_protocol: DscDNA synthesis and DNA end-labeling were performed at NimbleGen.

extract_protocol: Extracted using the TRIzol reagent (Invitrogen) and subsequently purified using the mini-column purification kit NucleoSpin® from Macherey-Nagel according to the manufacturer’s instructions.

treatment_protocol: Exposure to a low-protein (80 g/kg) or control (200 g/kg) diet during gestation and lactation. Gene expression in the hypothalamus was analyzed at 6 months old.

tag: strain

value: Sprague Dawley

value: male

value: 180 days

value: hypothalamus

tag: treatment

value: low-protein diet


title: ept002 ependynoma [human mRNA]

tag: tissue


title: ept066 ependynoma [human mRNA]


title: Low protein diet, rep4


title: ept065 ependynoma [human mRNA]

value: Spinal

value: E


title: Low protein diet, rep3


title: Control diet, rep5

source_name: hypothalamus, control diet

value: control diet


title: ept064 ependynoma [human mRNA]

value: ependynoma primary tumor


title: Low protein diet, rep2


title: Low protein diet, rep1


title: Control diet, rep1


title: eBOP43_glycerolM9_mid-log_rep3

status: Public on Apr 01 2010

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

description: The purpose of the experiment was to observe gene expression differences in mid-log phase growth of E. coli K-12 in glycerol M9 minimal media resulting from certain RNA polymerase (rpoC) mutations which had appeared during adaptive evolution in glycerol M9 minimal media.

hyb_protocol: Hybridization was performed using an Affymetrix Hybridization Oven 320.  Chip washing and staining was performed using a GeneChip Fluidics Station 450.

scan_protocol: The microarray was scanned at 500nm pixel resolution to get an image file by the GeneChip Scanner 3000 (Affymetrix).

data_processing: The twelve .cel files representing the expression measurements for triplicates of wild-type E. coli K-12 MG1655 and three related RNAP mutants were normalized together using RMAExpress and written to file using log-scale.  Gene names were assigned to results by mapping the gene probe ID to annotation using the Probe Set Data provided by Affymetrix.  Only probes which mapped to a gene synonym (three or four letters, such as hfq or rpoC) or a Blattner number (a "b" followed by a four-digit number, such as b1234) were considered in further analysis.  There were 4070 such probes.  Therefore, the VALUEs in the processed file are RMA-normalized log-scale values for the signal of probes on the GeneChip that corresponded to a gene synonym or Blattner number in the Probe Set Data file.

label: GeneChip DNA Labeling Reagent (Affymetrix, P/N 900542)

organism: Escherichia coli

source_name: Escherichia K-12 rpoC mutant: eBOP43

label_protocol: Approximately 10 ug of total RNA extract was used for cDNA synthesis (SuperScript II).  RNA was then removed by addition of NaOH and heat.  cDNA was purified using QIAquick PCR Purification kit and then fragmented using DNase I.  Fragments were visualized on a 2% agarose gel to confirm most fragments were 50-200 bp.  cDNA was 3'-terminal labeled using the GeneChip DNA Labeling Reagent.

growth_protocol: A small amount of frozen stock was inoculated into a flask of glycerol (2g/L) M9 minimal media and incubated at 30 degrees C.  After the culture reached stationary phase, it was diluted 1:100 into three separate flasks containing glycerol minimal media -- again these were incubated @ 30 degrees C.  These cultures were the three replicates used to extract mRNA for hybridization to the GeneChips.  mRNA was extracted when the cultures reached an OD of 0.3 (mid-log phase)

extract_protocol: Three mL of culture was mixed with 6 mL of RNAprotect reagent (Qiagen).  After sitting for 5 minutes at room temperature the tubes are centrifuged.  The pellets are frozen at -80 C.  mRNA is extracted from the pellets using an RNeasy kit (Qiagen) and using the recommended protocol.

value: isogenic to MG1655

tag: mutation

value: deletion in the rpoC gene at base positions 3611 through 3619

tag: rnap mutant


title: Control diet, rep3


title: eBOP43_glycerolM9_mid-log_rep1


title: Gastrolith disk of premolt alpha-ecdysone-injected males vs. sham-injected intermolt males

status: Public on May 27 2010

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

country: Israel

institute: Israel Oceanographic and Limnological Research

description: Evaluated Gene expression ratio between gastrolith disk tissues of alpha-ecdysone injected late premolted and sham-injected intermolt males was part of a broader experiment which includes also another control of intact intermolt males. Individual variability was integrated into the hybridization design, by using RNA populations of 4 individual crayfish males for each of the experimental and control conditions, namely, alpha-ecdysone injected, sham-injected and intact males. Four hybridization sets, each composed of 3 slides, were carried out. In each set, one individual from the treatment was compared to one intact and sham-injected male. In addition the two controls were also compared. The design was balanced with respect to the dye labeling of the RNA populations, such that each individual RNA population was labeled with one dye on one slide and with the other dye in two other slides. The data table of this sample, comparing gastrolith disk of alpha-ecdysone injected-premolted males to sham-injected males, is part of an integrative analysis of the entire 12 slides set, resulting with three binary comparisons among experimental groups (see data processing below). Only two important comparisons are presented as samples here and only valid M values were included in the data file.

hyb_protocol: The Hybridization protocol followed: Yudkovski, Y., Shechter, A., Chalifa-Caspi, V., Auslander, M., Ophir, R., Dauphin-Villemant, C., Waterman, M., Sagi, A. & Tom, M. (2007). Hepatopancreatic multi-transcript expression patterns in the crayfish Cherax quadricarinatus during the moult cycle. Insect Mol. Biol. 16, 661-674.

scan_protocol: The slides were scanned by Axon 4000B laser scanner in two wavelengths, corresponding to the Cy3 and Cy5 emissions. The TIF imaged dual fluorescence was quantified by the GENEPIX software (Axon), which also provided weight index of the quality for each hybridized spot.

data_processing:
Data analysis was generally conducted according to: Yudkovski, Y., Shechter, A., Chalifa-Caspi, V., Auslander, M., Ophir, R., Dauphin-Villemant, C., Waterman, M., Sagi, A. & Tom, M. (2007). Hepatopancreatic multi-transcript expression patterns in the crayfish Cherax quadricarinatus during the moult cycle. Insect Mol. Biol. 16, 661-674.
Briefly, analysis was accomplished using the LIMMA package (Linear Models for Microarray data Analysis; Smyth, G.K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3. http//www.bepress.com/sagmb/vol3/iss1/art3). The Cy5 and Cy3 intensities within each slide were normalized using global Loess method and background correction was applied. LIMMA calculated for each spot on an individual slide an M-value [M=log2(Cy5/Cy3); Cy5/Cy3 was calculated using the normalized emission intensities of the spot] and an emission intensity A-value [A=(log2(Cy5)*Cy3))/2]. Subsequently, LIMMA fitted a linear model to the expression data followed by Empirical Bayes smoothing. Inter-duplicate correlation method was used at the linear modeling step. A meanA value, which is the average spot emission intensity across the analyzed experiment, was calculated for each unique spot and only spots with meanA>9 were included in the analysis, avoiding faint emissions. The LIMMA summary statistics of each unique spot included an estimated average M-value across each binary comparison associated to the p-value, derived from a moderated t-statistic after multiple testing correction. All these parameters are found in the sample data table.

label: Cy3 and Cy5 alternatively on different slides (see hybridization description below).

organism: Cherax quadricarinatus

source_name: Gastrolith disks from premolt alpha-ecdysone-injected males

label_protocol: The labeling protocol followed: Yudkovski, Y., Shechter, A., Chalifa-Caspi, V., Auslander, M., Ophir, R., Dauphin-Villemant, C., Waterman, M., Sagi, A. & Tom, M. (2007). Hepatopancreatic multi-transcript expression patterns in the crayfish Cherax quadricarinatus during the moult cycle. Insect Mol. Biol. 16, 661-674.

growth_protocol: C. quadricarinatus males were maintained in captivity before and during the experiment at 28°C with a photoperiod of 14L:10D.

extract_protocol: EZ-RNA II Kit (Biological Industries, Israel) was used for total RNA extraction. PolyTtract kit (Promega) was used for mRNA extraction from total RNA solutions.

treatment_protocol: 20-OH-ecdysone of 1 μg/μl in a 10% ethanol saline solution was administered to intermolt males by repetitive injections to the sinus at the base of the fifth walking leg. Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph. The entire injection and molt monitoring procedure followed Shechter, A., Tom, M., Yudkovski, Y., Weil, S., Chang, S. A., Chang, E. S., Chalifa-Caspi, V., Berman, A. & Sagi, A. (2007). Search for hepatopancreatic ecdysteroid-responsive genes during the crayfish molt cycle, from a single gene to multigenicity. J. Exp. Biol. 210, 3525-3537. Treated males were sacrificed ten days from the first injection.

value: gastrolith disks

value: alpha-ecdysone injected

value: males

tag: developmental stage

value: premolt

source_name: Gastrolith disks from sham-injected intermolt males

treatment_protocol: 10% ethanol saline solution was administered to intermolt males by repetitive injections to the sinus at the base of the fifth walking leg. Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph. The entire injection and molt monitoring procedure followed Shechter, A., Tom, M., Yudkovski, Y., Weil, S., Chang, S. A., Chang, E. S., Chalifa-Caspi, V., Berman, A. & Sagi, A. (2007). Search for hepatopancreatic ecdysteroid-responsive genes during the crayfish molt cycle, from a single gene to multigenicity. J. Exp. Biol. 210, 3525-3537. Sham-treated males were sacrificed ten days from the first injection.

value: sham-injected

value: intermolt


title: Control diet, rep2

value: Sprague Dawley

tag: gender


title: Hypodermis of alpha-ecdysone injected premolt males vs. sham-injected premolt males

description: Evaluated Gene expression ratio between hypodermal tissues of alpha-ecdysone injected premolted and sham-injected intermolted males was part of a broader experiment which includes also a control of intact intermolted males. Individual variability was integrated into the hybridization design, by using RNA populations of 5 individual crayfish males for each of the experimental and control conditions, namely, alpha-ecdysone injected, sham-injected and intact intermolt males. Five hybridization sets, each composed of 3 slides, were carried out. In each set, one individual from the treatment was compared to one intact and sham-injected male. In addition the two controls were also compared. The design was balanced with respect to the dye labeling of the RNA populations, such that each individual RNA population was labeled with one dye on one slide and with the other dye in two other slides. The data table of this sample, comparing gastrolith disk of alpha-ecdysone injected-premolted males to sham-injected males, is part of an integrative analysis of the entire 15 slides set, resulting with three binary comparisons among experimental groups (see data processing below). Only two important comparisons are presented as samples here and only valid M values were included in the data file.

label: EZ-RNA II Kit (Biological Industries, Israel) was used for total RNA extraction. PolyTtract kit (Promega) was used for mRNA extraction from total RNA solutions.

source_name: Hypodermis from Alpha-ecdysone injected premolt males

treatment_protocol: Alpha-ecdysone in 10% ethanol saline solution was administered to intermolt males by repetitive injections to the sinus at the base of the fifth walking leg. Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph. The entire injection and molt monitoring procedure followed Shechter, A., Tom, M., Yudkovski, Y., Weil, S., Chang, S. A., Chang, E. S., Chalifa-Caspi, V., Berman, A. & Sagi, A. (2007). Search for hepatopancreatic ecdysteroid-responsive genes during the crayfish molt cycle, from a single gene to multigenicity. J. Exp. Biol. 210, 3525-3537. Sham-treated males were sacrificed ten days from the first injection.

value: hypodermis beneath the carapax

source_name: Hypodermis from sham-injected intermolt males


title: Hypodermis of sham-injected intermolt males vs. intact intermolt males

description: Evaluated Gene expression ratio between hypodermal tissues of sham-injected intermolted and intact intermolt males was part of a broader experiment which includes also alpha-ecdysone injected premolted males. Individual variability was integrated into the hybridization design, by using RNA populations of 5 individual crayfish males for each of the experimental and control conditions, namely, alpha-ecdysone injected, sham-injected and intact intermolt males. Five hybridization sets, each composed of 3 slides, were carried out. In each set, one individual from the treatment was compared to one intact and sham-injected male. In addition the two controls were also compared. The design was balanced with respect to the dye labeling of the RNA populations, such that each individual RNA population was labeled with one dye on one slide and with the other dye in two other slides. The data table of this sample, comparing gastrolith disk of alpha-ecdysone injected-premolted males to sham-injected males, is part of an integrative analysis of the entire 15 slides set, resulting with three binary comparisons among experimental groups (see data processing below). Only two important comparisons are presented as samples here and only valid M values were included in the data file.

source_name: Hypodermis from intact intermolt males

treatment_protocol: No treatment was applied. Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph According to Shechter, A., Tom, M., Yudkovski, Y., Weil, S., Chang, S. A., Chang, E. S., Chalifa-Caspi, V., Berman, A. & Sagi, A. (2007). Search for hepatopancreatic ecdysteroid-responsive genes during the crayfish molt cycle, from a single gene to multigenicity. J. Exp. Biol. 210, 3525-3537.


title: eBOP43_glycerolM9_mid-log_rep2


title: B cell ctrl Expression (Cy3)

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description:
Biological replicates of B cell Expression (untreated).
raw data file: Slide1.US22502657_251486819798_S01_GE2-v5_95_Feb07_1_1.txt

hyb_protocol: 4x 44 k Agilent arrays were hybridized with 825 ng of each cDNA using the manufacturer's hybridization kit according to the instructions.

scan_protocol: Scanned on an Agilent Technologies Scanner using the extended dynamic range scan mode with a 5 µm pitch. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing:
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. Data was further normalized between arrays using a multi-loess technique described in Corbeil et al (Journal of Molecular Endocrinology (2004) 33:1–9).
Dual-channel hybridization was analyzed as single-channel (ratios were not used).  Each channel is therefore represented as a single Sample and the same raw data file is linked to two Sample records.

source_name: resting splenic B cells

label_protocol: Total RNA (250 ng) of two biological replicates was amplified and labeled using the Agilent Quick-Amp labeling kit according to the manufacturer's instructions.

growth_protocol: CD43-negative splenic B cells were isolated by magnetic depletion of CD43- and CD11b-expressing cells using MACS (Miltenyi, Bergisch Gladbach, Germany) according to the manufacturer's instructions. Peritoneal macrophages were harvested by peritoneal lavage with 10 ml ice-cold PBS 3 days after peritoneal injection of 3 ml thioglycollate broth. Peritoneal cells were washed once with PBS, and seeded in 10% fetal calf serum (FCS)/DMEM containing 100 U/ml penicillin/streptomycin in tissue culture-treated petri dishes overnight. Non-adherent cells were washed off with room temperature PBS.

extract_protocol: Total RNA was extracted from 5 Mio cells on Rneasy columns (Qiagen) with on-column DNase digestion following the manufacturer's instructions. RNA quality was assessed on an Agilent 2100 BioAnalyzer .

tag: cell type

value: resting splenic B cells


title: Control diet, rep4

value: male

tag: age

value: 180 days

value: hypothalamus


title: 3576 SN Cm

status: Public on Mar 12 2010

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

hyb_protocol: Standard method (Affymetrix Expression Analysis Technical Manual 701021 rev 5)

data_processing: To obtain the most stringent normalization possible on the dataset, we implemented the Robust Multichip Analysis method [Irizarry et al., [2003]] for the complete set of chips derived from each brain area. These robust multi-array analysis (RMA)-normalized data were imported into GeneSpring 7.0 (Silicon Genetics) for significance analysis and pattern analysis (clustering). To obtain the most accurate cross-gene error model for subsequent statistical analyses, the individual transcript data were further normalized within each respective brain area to the mean intensity measurements of the control subject samples for that brain area and transcript.

source_name: Postmortem brain whole substantia nigra

label_protocol: Standard Two-Cycle cRNA IVT method (Affymetrix Expression Analysis Technical Manual 701021 rev 5)

extract_protocol: RNeasy (Qiagen)

value: Control

tag: brain region

value: Whole substantia nigra from postmortem brain


title: Macrophage ctrl Expression (Cy5)

description:
Biological replicates of Macrophage Expression (untreated).
raw data file: Slide2.US22502657_251486819799_S01_GE2-v5_95_Feb07_1_1.txt


title: B cell ctrl Expression (Cy5)


title: Macrophage ctrl Expression (Cy3)


title: T98 SN Cm

scan_protocol: Standard method (Affymetrix Expression Analysis Technical Manual 701021 rev 5)


title: T55 SN Cm


title: Gastrolith disk of sham-injected intermolt males vs. intact intermolt males

description: Evaluated Gene expression ratio between gastrolith disk tissues of sham-injected intermolted and intact intermolt males was part of a broader experiment which includes also males induced to enter premolt by alpha-ecdysone injections. Individual variability was integrated into the hybridization design, by using RNA populations of 4 individual crayfish males for each of the experimental and control conditions, namely, alpha-ecdysone injected, sham-injected and intact males. Four hybridization sets, each composed of 3 slides, were designed. In each set, one individual from the treatment was compared to one intact and sham-injected male. In addition the two controls were also compared. The design was balanced with respect to the dye labeling of the RNA populations, such that each individual RNA population was labeled with one dye on one slide and with the other dye in two other slides. The data table of this sample, comparing gastrolith disks of sham-injected males to inta cct intermolted males is part of an integrative analysis of the entire 12 slides set, resulting with three binary comparisons among experimental groups (see data processing below). Only two important comparisons are presented as samples here and only valid M values were included in the data file.

source_name: Gastrolith disks from intermolt sham-injected males

source_name: Gastrolith disks from intact intermolt males

treatment_protocol: No treatment, intact intermolt males. Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph according to: Shechter, A., Tom, M., Yudkovski, Y., Weil, S., Chang, S. A., Chang, E. S., Chalifa-Caspi, V., Berman, A. & Sagi, A. (2007). Search for hepatopancreatic ecdysteroid-responsive genes during the crayfish molt cycle, from a single gene to multigenicity. J. Exp. Biol. 210, 3525-3537.


title: 5476 SN Pm

value: Parkinsons disease


title: 5498 SN Cm


title: 5138 SN Pm


title: 5220 SN Cm


title: 5441 SN Pf

value: female


title: 3406 SN Cf


title: 3401 SN Cm


title: 3397 SN Cf


title: 3543 SN Cf


title: 3216 SN Cm


title: 2977 SN Pm


title: 2515 SN Pf


title: 2729 SN Pm


title: 3276 SN Cm


title: 2829 SN Cf


title: 2685 SN Pm


title: 1401 SN Pf


title: 1647 SN Pf


title: 5398 SN Cf


title: 3236 SN Cm


title: 1206 SN Cm


title: T72 PT Pm

source_name: Postmortem brain putamen

value: Putamen from postmortem brain


title: T55 PT Cm


title: 5498 PT Cm


title: 5476 PT Pm


title: T98 PT Cm


title: 5138 PT Pm


title: 5329 PT Pm


title: 5220 PT Cm


title: 1364 SN Pm


title: 5441 PT Pf


title: T127 PT Pm


title: 5398 PT Cf


title: 2525 SN Pf


title: 3543 PT Cf


title: 3401 PT Cm


title: 3236 PT Cm


title: 3276 PT Cm


title: 2525 PT Pf


title: 2977 PT Pm


title: 3406 PT Cf


title: 3397 PT Cf


title: 2729 PT Pm


title: 2829 PT Cf


title: 2685 PT Pm


title: 3688 PT Cm


title: 2515 PT Pf


title: 1516 PT Pf


title: 1647 PT Pf


title: 3216 PT Cm


title: 1206 PT Cm


title: LPS 10d (Rag-1 null) A

status: Public on Dec 31 2009

city: Baltimore

first: Dmitry

middle: N

last: Grigoryev

institute: JHU

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using in-house software described in Grigoryev et, Identification of candidate genes in scleroderma-related pulmonary arterial hypertension. Transl Res 151(4):197-207.  Briefly, the significance (P>0.95) of hybridization signals were tested and “Present” and “Absent” transcripts identified.  The chip background and brightness were computed using high quartile and whole set of “Absent” hybridization signals, respectively.  The expression data was stratified by experimental conditions (n=3) and hybridization of each transcript was evaluated.  The transcripts that had P>0.95 and produced signal at least twice as high as that of background in at least 75% of hybridizations in any given group of mice were considered Present. The signal intensity values of these transcripts from each chip were background adjusted and divided by a chip brightness coefficient for normalization.  Only Present values are reported and used for Significance Analysis of Microarrays (SAM) analysis.

source_name: mouse lung

label_protocol: Biotinylated cRNA was prepared using the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent followed by purification and DNase I treatment using QIAGEN RNeasy mini kit according to manufacturer's protocol. Quality control was performed with an Agilent Bioanalyzer.

tag: genotype/variation

value: Rag-1 null

value: 6-8 wks old

value: whole lung

value: LPS


title: LPS 4d (Rag-1 null) C

description: replicate 3


title: LPS 10d (Rag-1 null) B

description: replicate 2


title: Contol (Rag-1 null) C

description: replicate 3


title: LPS 10d (Rag-1 null) C

description: replicate 3


title: 1401 PT Pf


title: 1364 PT Pm


title: LPS 1d (Rag-1 null) C

description: replicate 3


title: LPS 1d (Rag-1 null) A

description: replicate 1


title: Contol (Rag-1 null) B

description: replicate 2


title: LPS 1d (Rag-1 null) B

description: replicate 2


title: LPS 4d (Rag-1 null) B

description: replicate 2


title: LPS 10d (WT) C

description: replicate 3

value: wild type


title: Contol (Rag-1 null) A

description: replicate 1


title: LPS 4d (WT) B

description: replicate 2


title: LPS 4d (Rag-1 null) A

description: replicate 1


title: LPS 1d (WT) C

description: replicate 3


title: LPS 4d (WT) A

description: replicate 1


title: LPS 10d (WT) A

description: replicate 1


title: LPS 1d (WT) A

description: replicate 1


title: Control (WT) A

description: replicate 1


title: LPS 10d (WT) B

description: replicate 2


title: LPS 1d (WT) B

description: replicate 2


title: Control (WT) C

description: replicate 3


title: Control (WT) B

description: replicate 2


title: LPS 4d (WT) C

description: replicate 3


title: MR453 (MicMa381) Replicate 1

status: Public on Dec 16 2009

city: Cold Spring Harbor

first: Jude

last: Kendall

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: These samples were hybridized to two color-reversal arrays

hyb_protocol: Hybridizations consisted of 35 uL of hybridization solution (37% formamide, 4x SSC, 0.1%SDS, and labeled DNA). Samples were denatured in an MJ Research Tetrad (Bio-Rad, Hercules, CA) at 95 degrees C for 5 min, and then pre-annealed at 37 degrees C for no more than 30 min. The solution was then applied to the microarray and hybridized under a coverslip in an oven at 42 degrees C for 14 to 16 h. Thereafter, slides were washed 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC, and 30 sec in 0.05x SSC. Slides were dried by centrifugation and scanned immediately.

scan_protocol: Scanned on an Axon GenePix 4000B scanner using a pixel size of 5 um. Microarrays were scanned and gridded using GenePix Pro 4.0 software (MDS Analytical Technologies, Toronto, Canada).

data_processing: The data were normalized using a lowess curve-fitting algorithm, followed by a local normalization (previously described in Hicks et al.). After placement in genome order, the mean of log ratios was computed for color reversal experiments for each sample. Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. Our segmentation method is based on the minimization of the square-sum of differences between log-ratios and means (squared deviation) over segments larger than 6 probes in size. Initially, the segmenter searches for breakpoints that might be boundaries of segments. The first known breakpoint on a given chromosome is its first probe. For a given breakpoint, a 100-probe window to its right is selected. The sum of squared deviations of the flanking probes is calculated for each probe within this window. A probe whose squared deviation value produces a local minimum with respect to its neighbors, and is below a threshold of 95% of the square deviation within a window, is accepted as a new, known breakpoint. Whenever a probe is found below the threshold in the newly defined region, the segmenter recursively breaks said region into two pieces until it cannot find any further breakpoints therein. If no breakpoints are found, the 100- probe window is shifted by half its size and this procedure continues until a chromosome end is reached. Initial segments are constructed using found breakpoints. Each segment and its neighbors are validated for significance by the Kolmogorov-Smirnov (K-S) algorithm. If the p-value of compared segments is less than 10-5, then said segment is accepted as real. If not, the segments are merged. The segmenter also reports statistics such as mean, standard deviation, and median for each segment.

label_protocol: Complexity-reduced representations, consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrimelabeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide.

extract_protocol: Qiagen Genomic DNA Isolation Kit

value: Ductal Breast Carcinoma

tag: cell line

value: EBV Immortalized Fibroblast Reference


title: MR393 (WZ121) Replicate 1


title: MR454 (MicMa381) Replicate 2


title: MR417 (MicMa388) Replicate 1


title: MR452 (MicMa247) Replicate 2


title: MR390 (MicMa119) Replicate 2


title: MR418 (MicMa388) Replicate 2


title: MR387 (MicMa112) Replicate 1


title: MR394 (WZ121) Replicate 2


title: MR382 (WZ120) Replicate 2


title: MR389 (MicMa119) Replicate 1


title: MR381 (WZ120) Replicate 1


title: MR384 (MicMa100) Replicate 2


title: MR372 (WZ115) Replicate 2


title: MR375 (WZ117) Replicate 1


title: MR371 (WZ115) Replicate 1


title: MR377 (WZ118) Replicate 1


title: MR373 (WZ116) Replicate 1


title: MR378 (WZ118) Replicate 2


title: MR370 (WZ114) Replicate 2


title: MR388 (MicMa112) Replicate 2


title: MR369 (WZ114) Replicate 1


title: MR380 (WZ119) Replicate 2


title: MR376 (WZ117) Replicate 2


title: MR383 (MicMa100) Replicate 1


title: MR379 (WZ119) Replicate 1


title: MR374 (WZ116) Replicate 2


title: MR368 (WZ113) Replicate 2


title: MR451 (MicMa247) Replicate 1


title: MR365 (WZ112) Replicate 1


title: MR358 (WZ108) Replicate 2


title: MR363 (WZ111) Replicate 1


title: MR364 (WZ111) Replicate 2


title: MR362 (WZ110) Replicate 2


title: MR346 (WZ103) Replicate 2


title: MR352 (WZ106) Replicate 2


title: MR366 (WZ112) Replicate 2


title: MR357 (WZ108) Replicate 1


title: MR351 (WZ106) Replicate 1


title: MR347 (WZ104) Replicate 1


title: MR349 (WZ105) Replicate 1


title: MR348 (WZ104) Replicate 2


title: MR350 (WZ105) Replicate 2


title: MR332 (WZ131) Replicate 2


title: MR361 (WZ110) Replicate 1


title: MR367 (WZ113) Replicate 1


title: MR359 (WZ109) Replicate 1


title: MR331 (WZ131) Replicate 1


title: MR328 (WZ129) Replicate 2


title: MR354 (WZ107) Replicate 2


title: MR327 (WZ129) Replicate 1


title: MR344 (WZ102) Replicate 2


title: MR343 (WZ102) Replicate 1


title: MR330 (WZ130) Replicate 2


title: MR353 (WZ107) Replicate 1


title: MR360 (WZ109) Replicate 2


title: MR345 (WZ103) Replicate 1


title: MR324 (WZ127) Replicate 2


title: MR325 (WZ128) Replicate 1


title: MR329 (WZ130) Replicate 1


title: MR321 (WZ126) Replicate 1


title: MR320 (WZ125) Replicate 2


title: MR319 (WZ125) Replicate 1


title: MR323 (WZ127) Replicate 1


title: MR326 (WZ128) Replicate 2


title: MR317 (WZ124) Replicate 1


title: CLL11

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: Human Promega control

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

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

label_protocol: manufacturer's instructions

extract_protocol: manufacturer's instructions

treatment_protocol: Total DNA extracted using manufacturer's instructions

value: 73 years

value: atypical CLL

source_name: Human Promega control

tag: type

value: promega control


title: CLL10

description: Human Promega control

value: male

value: 68 years

tag: disease state


title: MR311 (WZ136) Replicate 1


title: CLL9

description: Human Promega control

value: typical CLL


title: MR310 (WZ135) Replicate 2


title: MR322 (WZ126) Replicate 2


title: MR308 (WZ134) Replicate 2


title: MR303 (WZ132) Replicate 1


title: MR305 (WZ133) Replicate 1


title: MR304 (WZ132) Replicate 2


title: CLL7

description: Human Promega control

value: 56 years


title: MR314 (WZ122) Replicate 2


title: MR318 (WZ124) Replicate 2


title: CLL8

description: Human Promega control

value: 85 years


title: MR315 (WZ123) Replicate 1


title: MR300 (WZ140) Replicate 2


title: MR302 (WZ141) Replicate 2


title: MR298 (WZ139) Replicate 2


title: MR313 (WZ122) Replicate 1


title: MR297 (WZ139) Replicate 1


title: MR301 (WZ141) Replicate 1


title: CLL6

description: Human Promega control

value: 70 years


title: MR306 (WZ133) Replicate 2


title: MR316 (WZ123) Replicate 2


title: MR296 (WZ138) Replicate 2


title: CLL1

description: Human Promega control

value: 66 years


title: MR299 (WZ140) Replicate 1


title: MR307 (WZ134) Replicate 1


title: CLL3

description: Human Promega control


title: CLL2

description: Human Promega control

value: 65 years


title: MR295 (WZ138) Replicate 1


title: CLL5

description: Human Promega control

value: 63 years


title: CLL4

description: Human Promega control

value: female

value: 87 years


title: MR288 (MicMa283) Replicate 2


title: MR291 (MicMa300) Replicate 1


title: MR292 (MicMa300) Replicate 2


title: MR290 (MicMa298) Replicate 2


title: MR284 (MicMa275) Replicate 2


title: MR279 (MicMa256) Replicate 1


title: MR281 (MicMa264) Replicate 1


title: MR282 (MicMa264) Replicate 2


title: MR287 (MicMa283) Replicate 1


title: MR278 (MicMa250) Replicate 2


title: MR283 (MicMa275) Replicate 1


title: MR309 (WZ135) Replicate 1


title: MR270 (MicMa245) Replicate 2


title: MR280 (MicMa256) Replicate 2


title: MR267 (MicMa212) Replicate 1


title: MR277 (MicMa250) Replicate 1


title: MR255 (MicMa071) Replicate 1


title: MR268 (MicMa212) Replicate 2


title: MR269 (MicMa245) Replicate 1


title: MR252 (MicMa080) Replicate 2


title: MR254 (MicMa044) Replicate 2


title: MR265 (MicMa197) Replicate 1


title: MR312 (WZ136) Replicate 2


title: MR248 (MicMa057) Replicate 2


title: MR246 (MicMa055) Replicate 2


title: MR289 (MicMa298) Replicate 1


title: MR266 (MicMa197) Replicate 2


title: MR247 (MicMa057) Replicate 1


title: MR256 (MicMa071) Replicate 2


title: MR251 (MicMa080) Replicate 1


title: MR245 (MicMa055) Replicate 1


title: MR241 (MicMa034) Replicate 1


title: MR242 (MicMa034) Replicate 2


title: MR234 (MicMa006) Replicate 2


title: MR230 (MicMa004) Replicate 2


title: MR165 (MicMa024) Replicate 1


title: MR221 (MicMa002) Replicate 1


title: MR229 (MicMa004) Replicate 1


title: MR162 (MicMa023) Replicate 2


title: MR225 (MicMa003) Replicate 1


title: MR253 (MicMa044) Replicate 1


title: MR161 (MicMa023) Replicate 1


title: MR166 (MicMa024) Replicate 2


title: MR233 (MicMa006) Replicate 1


title: MR154 (MicMa017) Replicate 2


title: MR160 (MicMa019) Replicate 2


title: MR157 (MicMa018) Replicate 1


title: MR158 (MicMa018) Replicate 2


title: MR153 (MicMa017) Replicate 1


title: MR159 (MicMa019) Replicate 1


title: MR069 (WZ97) Replicate 1


title: MR096 (MicMa014) Replicate 2


title: MR072 (WZ98) Replicate 2


title: MR070 (WZ97) Replicate 2


title: MR226 (MicMa003) Replicate 2


title: MR095 (MicMa014) Replicate 1


title: MR071 (WZ98) Replicate 1


title: MR102 (MicMa015) Replicate 2


title: MR108 (MicMa022) Replicate 2


title: MR222 (MicMa002) Replicate 2


title: MR092 (WZ56) Replicate 2


title: MR079 (WZ94) Replicate 1


title: MR107 (MicMa022) Replicate 1


title: MR065 (WZ99) Replicate 1


title: MR068 (WZ96) Replicate 2


title: MR066 (WZ99) Replicate 2


title: MR060 (WZ100) Replicate 2


title: MR063 (WZ95) Replicate 1


title: MR061 (WZ101) Replicate 1


title: MR080 (WZ94) Replicate 2


title: MR059 (WZ100) Replicate 1


title: MR064 (WZ95) Replicate 2


title: MR091 (WZ56) Replicate 1


title: MR048 (WZ74) Replicate 2


title: MR062 (WZ101) Replicate 2


title: MR045 (WZ67) Replicate 1


title: MR037 (WZ90) Replicate 1


title: MR040 (WZ91) Replicate 2


title: MR043 (WZ93) Replicate 1


title: MR038 (WZ90) Replicate 2


title: MR044 (WZ93) Replicate 2


title: MR067 (WZ96) Replicate 1


title: MR041 (WZ92) Replicate 1


title: MR042 (WZ92) Replicate 2


title: MR039 (WZ91) Replicate 1


title: MR046 (WZ67) Replicate 2


title: MR047 (WZ74) Replicate 1


title: MR029 (WZ88) Replicate 1


title: MR030 (WZ88) Replicate 2


title: MR031 (WZ89) Replicate 1


title: MR032 (WZ89) Replicate 2


title: MR101 (MicMa015) Replicate 1


title: JBH561 (MicMa378) Replicate 1


title: JBH562 (MicMa378) Replicate 2


title: MR026 (WZ86) Replicate 2


title: MR025 (WZ86) Replicate 1


title: MR027 (WZ87) Replicate 1


title: JBH551 (MicMa355) Replicate 1


title: JBH557 (MicMa371) Replicate 1


title: JBH549 (MicMa341) Replicate 1


title: JBH552 (MicMa355) Replicate 2


title: JBH558 (MicMa371) Replicate 2


title: JBH556 (MicMa363) Replicate 2


title: JBH559 (MicMa373) Replicate 1


title: JBH555 (MicMa363) Replicate 1


title: JBH542 (MicMa309) Replicate 2


title: JBH541 (MicMa309) Replicate 1


title: JBH545 (MicMa334) Replicate 1


title: JBH540 (MicMa308) Replicate 2


title: MR028 (WZ87) Replicate 2


title: JBH547 (MicMa338) Replicate 1


title: JBH550 (MicMa341) Replicate 2


title: JBH538 (MicMa722) Replicate 2


title: JBH532 (MicMa579) Replicate 2


title: JBH535 (MicMa630) Replicate 1


title: JBH546 (MicMa334) Replicate 2


title: JBH548 (MicMa338) Replicate 2


title: JBH537 (MicMa722) Replicate 1


title: JBH536 (MicMa630) Replicate 2


title: JBH530 (MicMa551) Replicate 2


title: JBH529 (MicMa551) Replicate 1


title: JBH539 (MicMa308) Replicate 1


title: JBH531 (MicMa579) Replicate 1


title: JBH528 (MicMa512) Replicate 2


title: JBH522 (MicMa476) Replicate 2


title: JBH520 (MicMa470) Replicate 2


title: JBH521 (MicMa476) Replicate 1


title: JBH516 (MicMa451) Replicate 2


title: JBH500 (MicMa223) Replicate 2


title: JBH525 (MicMa493) Replicate 1


title: JBH526 (MicMa493) Replicate 2


title: JBH498 (MicMa222) Replicate 2


title: JBH527 (MicMa512) Replicate 1


title: JBH524 (MicMa488) Replicate 2


title: JBH514 (MicMa430) Replicate 2


title: JBH490 (MicMa185) Replicate 2


title: JBH491 (MicMa085) Replicate 1


title: JBH523 (MicMa488) Replicate 1


title: JBH407 (WZ24) Replicate 1


title: JBH515 (MicMa451) Replicate 1


title: JBH499 (MicMa223) Replicate 1


title: JBH489 (MicMa185) Replicate 1


title: JBH513 (MicMa430) Replicate 1


title: JBH406 (WZ23) Replicate 2


title: JBH497 (MicMa222) Replicate 1


title: JBH519 (MicMa470) Replicate 1


title: JBH404 (WZ22) Replicate 2


title: JBH560 (MicMa373) Replicate 2


title: JBH405 (WZ23) Replicate 1


title: JBH402 (WZ21) Replicate 2


title: JBH492 (MicMa085) Replicate 2


title: JBH401 (WZ21) Replicate 1


title: JBH376 (MicMa632) Replicate 2


title: JBH219 (WZ39) Replicate 1


title: JBH375 (MicMa632) Replicate 1


title: JBH222 (WZ81) Replicate 2


title: JBH368 (MicMa088) Replicate 2


title: JBH221 (WZ81) Replicate 1


title: JBH403 (WZ22) Replicate 1


title: JBH212 (WZ78) Replicate 2


title: JBH216 (WZ79) Replicate 2


title: JBH220 (WZ39) Replicate 2


title: JBH215 (WZ79) Replicate 1


title: JBH218 (WZ80) Replicate 2


title: JBH213 (WZ42) Replicate 1


title: JBH211 (WZ78) Replicate 1


title: JBH203 (WZ45) Replicate 1


title: JBH202 (WZ44) Replicate 2


title: JBH214 (WZ42) Replicate 2


title: JBH367 (MicMa088) Replicate 1


title: JBH206 (WZ47) Replicate 2


title: JBH205 (WZ47) Replicate 1


title: JBH408 (WZ24) Replicate 2


title: JBH204 (WZ45) Replicate 2


title: JBH105 (MicMa091) Replicate 1


title: JBH097 (MicMa067) Replicate 1


title: JBH106 (MicMa091) Replicate 2


title: JBH201 (WZ44) Replicate 1


title: JBH098 (MicMa067) Replicate 2


title: JBH093 (MicMa042) Replicate 1


title: JBH209 (WZ77) Replicate 1


title: JBH217 (WZ80) Replicate 1


title: JBH099 (MicMa079) Replicate 1


title: JBH210 (WZ77) Replicate 2


title: JBH100 (MicMa079) Replicate 2


title: JBH095 (MicMa065) Replicate 1


title: JBH096 (MicMa065) Replicate 2


title: JBH094 (MicMa042) Replicate 2


title: JBH091 (MicMa053) Replicate 1


title: JBH088 (MicMa020) Replicate 2


title: JA951 (WZ55) Replicate 1


title: JBH087 (MicMa020) Replicate 1


title: JBH092 (MicMa053) Replicate 2


title: JA952 (WZ57) Replicate 2


title: JA953 (WZ57) Replicate 1


title: JA949 (WZ53) Replicate 1


title: JA950 (WZ55) Replicate 2


title: JA948 (WZ53) Replicate 2


title: JA946 (WZ50) Replicate 2


title: JBH114 (MicMa267) Replicate 2


title: JA921 (WZ35) Replicate 1


title: JBH113 (MicMa267) Replicate 1


title: JA925 (WZ37) Replicate 1


title: JA945 (WZ46) Replicate 1


title: JA942 (WZ43) Replicate 2


title: JA926 (WZ38) Replicate 2


title: JA927 (WZ38) Replicate 1


title: JA923 (WZ36) Replicate 1


title: JA947 (WZ50) Replicate 1


title: JA918 (WZ34) Replicate 2


title: JA944 (WZ46) Replicate 2


title: JA920 (WZ35) Replicate 2