source_name: embryos,16-18 hr after egg laying (Celniker/RNA:262) extraction3_array1 channel_1


status: Public on Jun 02 2009

type: RNA

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: 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   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   genome version is r5

label: Biotin

molecule: total RNA

organism: Drosophila melanogaster

source_name: embryos,16-18 hr after egg laying (Celniker/RNA:427) 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.''All Drosophila tissue collections were made from the sequenced ''D. melanogaster'' isogenic strain containing the mutations; ''yellow'' (y1), ''cinnabar'' (cn1), ''brown'' (bw1), and ''speck'' (sp1) [1].  Synchronized embryos were collected from population cages that were less than one week old and maintained at 24 C.  At least one ? two hour pre-lay was made prior to the start of timed collections each day. Embryos were collected for two hours on 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.Staged embryos were passed through an 850 micron screen and collected on a 75 micron screen to remove adults and yeast paste.  Embryos were then dechorionated by treatment with 50% bleach (3% sodium hypochlorite), 0.2% sodium chloride, and 0.02% Triton-X-100 for five minutes.  Embryos were washed twice with 0.2% NaCl, 0.02% Triton buffer and split into two samples.  Most of the sample (approximately 95%) was rinsed with de-ionized water in a buchner funnel under mild vacuum, dried briefly, immediately frozen on dry ice and stored at -80 C for RNA preparations.  The small aliquot was transferred to a clean tube and fixed for staging.  Fixation was accomplished in 0.1 M Pipes (pH 6.9), 2 mM EGTA, 1 mM MgSO4, 4% paraformaldehyde, 0.1% glutaraldehyde (percentages are relative to aqueous volumes), and 50% heptane, as describe previously [2].  Samples were shaken for five minutes in the fixative, centrifuged briefly and the aqueous fraction was removed.  An equal volume of methanol containing 2 mM EGTA was added and the sample was shaken for five additional minutes.  Tissue was washed twice in methanol with 2 mM EGTA and saved at -80 C for the characterization of developmental stages. Fixed embryos were used to determine the embryonic stages present in each biological sample X (BS#X). Each biological sample was washed in 0.2% sodium chloride, and 0.02% Triton-X-100 for five minutes and placed in a P0042G Sedgewick Rafter Grid slide. The developmental stages present in each sample were counted under a dissecting scope. The criteria used for stage identifications are describe in detail at FlyBase [3] and Campos Ortega, J. A. and Hartenstein, V (1997)[4]. Embryonic stages were not assessed by morphology associated with head involution due to the observed defects in this process associated with the isogenic strain. Data were entered into a Microsoft Exel worksheet for graphing. Biological samples that required pooled collections for adequate RNA yields were staged independently and normalized according to the fraction of the final mass of tissue in the pooled biological sample

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.Materials	TRIzol® reagent: Invitrogen, cat. no. 15596-026 (100 ml) or 15596-018 (200 ml).	DNase/RNase-free water: Invitrogen cat. no. 10977.	75% ethanol, prepared with DNase/RNase-free water.	RNase-free DNase: Qiagen cat. no. 79254.	RNeasy® spin columns: RNeasy midi kit, Qiagen cat. no. 75144.	TenBroeck homogenizer: Bellco biotechnology cat no. 1982-10002.Procedure1.	Homogenize insect samples in TRIzol reagent using a TenBroeck tissue homogenizer. The sample volume should not exceed 10% of the volume of TRIzol reagent used for homogenization.2.	Incubate at room temperature for 5 minutes.  3.	Aliquot samples into 1.5 ml microcentifuge tubes.4.	Add 0.267 ml chloroform per ml of TRIzol used.5.	Shake tubes vigorously for 15 seconds.6.	Incubate at room temperature for 2 minutes.7.	Centrifuge for 15 minutes at 4degC at 12,000 x g.8.	Transfer the top (aqueous) phases to clean tubes.9.	Precipitate the RNA from the aqueous phase by adding 0.67 ml of isopropanol per ml of TRIzol used in step 5.10.	Invert tubes once to mix gently.11.	Incubate samples at room temperature for 10 minutes.12.	Centrifuge for 10 minutes at 4degC at 12,000 x g.13.	Remove the supernatant.14.	Wash RNA pellet once with 75% ethanol, using 0.7 ml per microcentrifuge tube.15.	Vortex briefly.16.	Centrifuge at 7,500 x g for 5 minutes at 4degC.17.	Let the pellet air dry for 10 minutes. Note: DO NOT let the pellet dry completely.18.	Dissolve in RNase-free water. 19.	Incubate at 37degC overnight to dissolve the RNA. Determine concentration using a Nanodrop® ND-1000 Spectrophotometer. RNA may be stored at -80degC at this point if desired.20.	Purify up to 1 mg of RNA on an RNeasy spin column, with DNase treatment, precisely as described in Qiagen's RNeasy Midi/Maxi Handbook, supplied with the RNeasy kit. Do the optional second wash on the column. Elute twice using DNase/RNase-free water.21.	Determine concentration by absorbance, using a Nanodrop® ND-1000 Spectrophotometer. If necessary, the RNA can be concentrated on a SpeedVac. Store at -80degC.
Poly (A)+ RNA isolation: Qiagen Oligotex mRNA Spin-Column procedureThis protocol is used to prepare poly (A)+ RNA from total RNA.  It utilizes the Oligotex mRNA Midi kit (Qiagen Cat# 70042), and the procedure is unmodified from Qiagen Oligotex Handbook Second Edition, May 2002.Materials?	Oligotex mRNA Midi kit (Qiagen Cat# 70042)?	Oligotex Suspension: 10% (w/v) suspension Oligotex particles in: 10 mM Tris?Cl, pH 7.5; 500 mM NaCl; 1 mM EDTA; 0.1% SDS; 0.1% NaN3 (sodium azide)?	Wash Buffer OW2: 10 mM Tris?Cl, pH 7.5; 150 mM NaCl; 1 mM EDTA?	Elution Buffer OEB: 5 mM Tris?Cl, pH 7.5?	Buffer OBB: 20 mM Tris?Cl, pH 7.5; 1 M NaCl; 2 mM EDTA; 0.2% SDSProcedure1.	Determine the concentration of the starting total RNA solution.  Add 250 ? 500 microgram total RNA (maximum volume 500 microliters) to a 1.5 ml microcentifuge tube and adjust the volume to 500 microliters with RNase-free water.2.	Add 500  microliters buffer OBB and mix.3.	Add 30 microliters Oligotex suspension (ensure that the resin is in suspension), and mix.4.	Incubate the sample for 3 minutes at 70degC in a heating block.5.	Remove the sample from heating block and place at 20 to 30degC for 10 minutes.6.	Centrifuge for 2 minutes at 15,000 g to pellet the Oligotex:mRNA, and carefully remove the supernatant.7.	Resuspend the Oligotex:mRNA pellet in 400 microliters of Buffer OW2 by pipetting up and down.  Transfer the suspension onto a small spin column placed in a 1.5 ml microcentrifuge tube.8.	Centrifuge for 1 minute at 15,000 g.9.	Transfer the spin column to a new RNase-free 1.5 ml microcentrifuge tube, and apply 400 microliters of Buffer OW2 to the column.10.	Centrifuge for 1 minute at 15,000 g.  11.	Transfer the spin column to a new RNase-free 1.5 ml microcentrifuge tube. Add 50-80 microliters pre-heated (70degC) Buffer OEB to the column and resuspend the resin by pipetting up and down 3 or 4 times.12.	Centrifuge for 1 minute at 15,000 g.13.	Add another 40-50 microliters pre-heated (70degC) Buffer OEB onto the column resuspend the resin by pipetting up and down 3 or 4 times.14.	Centrifuge for 1 min at 15,000 g. 15.	Determine concentration by absorbance, using a Nanodrop® ND-1000 Spectrophotometer. Store at -80degC.
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.

tag: strain

value: Y cn bw sp

tag: developmental stage

value: Embryo 16-18h

tag: genotype

tag: sex

value: Unknown


source_name: embryos,18-20 hr after egg laying (Celniker/RNA:266) extraction2_array1 channel_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.Materials	TRIzol® reagent: Invitrogen, cat. no. 15596-026 (100 ml) or 15596-018 (200 ml).	DNase/RNase-free water: Invitrogen cat. no. 10977.	75% ethanol, prepared with DNase/RNase-free water.	RNase-free DNase: Qiagen cat. no. 79254.	RNeasy® spin columns: RNeasy midi kit, Qiagen cat. no. 75144.	TenBroeck homogenizer: Bellco biotechnology cat no. 1982-10002.Procedure1.	Homogenize insect samples in TRIzol reagent using a TenBroeck tissue homogenizer. The sample volume should not exceed 10% of the volume of TRIzol reagent used for homogenization.2.	Incubate at room temperature for 5 minutes.  3.	Aliquot samples into 1.5 ml microcentifuge tubes.4.	Add 0.267 ml chloroform per ml of TRIzol used.5.	Shake tubes vigorously for 15 seconds.6.	Incubate at room temperature for 2 minutes.7.	Centrifuge for 15 minutes at 4degC at 12,000 x g.8.	Transfer the top (aqueous) phases to clean tubes.9.	Precipitate the RNA from the aqueous phase by adding 0.67 ml of isopropanol per ml of TRIzol used in step 5.10.	Invert tubes once to mix gently.11.	Incubate samples at room temperature for 10 minutes.12.	Centrifuge for 10 minutes at 4degC at 12,000 x g.13.	Remove the supernatant.14.	Wash RNA pellet once with 75% ethanol, using 0.7 ml per microcentrifuge tube.15.	Vortex briefly.16.	Centrifuge at 7,500 x g for 5 minutes at 4degC.17.	Let the pellet air dry for 10 minutes. Note: DO NOT let the pellet dry completely.18.	Dissolve in RNase-free water. 19.	Incubate at 37degC overnight to dissolve the RNA. Determine concentration using a Nanodrop® ND-1000 Spectrophotometer. RNA may be stored at -80degC at this point if desired.20.	Purify up to 1 mg of RNA on an RNeasy spin column, with DNase treatment, precisely as described in Qiagen's RNeasy Midi/Maxi Handbook, supplied with the RNeasy kit. Do the optional second wash on the column. Elute twice using DNase/RNase-free water.21.	Determine concentration by absorbance, using a Nanodrop® ND-1000 Spectrophotometer. If necessary, the RNA can be concentrated on a SpeedVac. Store at -80degC.
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 18-20h


source_name: embryos,14-16 hr after egg laying (Celniker/RNA:425) extraction2_array1 channel_1

value: Embryo 14-16h


source_name: embryos,14-16 hr after egg laying (Celniker/RNA:424) extraction1_array1 channel_1


source_name: embryos,16-18 hr after egg laying (Celniker/RNA:428) extraction3_array1 channel_1


source_name: embryos,16-18 hr after egg laying (Celniker/RNA:260) extraction1_array1 channel_1


source_name: embryos,14-16 hr after egg laying (Celniker/RNA:258) extraction2_array1 channel_1


source_name: embryos,12-14 hr after egg laying (Celniker/RNA:422) extraction2_array1 channel_1

value: Embryo 12-14h


source_name: embryos,14-16 hr after egg laying (Celniker/RNA:254) extraction1_array1 channel_1


source_name: embryos,16-18 hr after egg laying (Celniker/RNA:264) extraction2_array1 channel_1


title: Normoxia-HIF1-6

type: genomic

city: Boston

first: Xiaobo

last: Xia

state: MA

address: 44 Binney St, Mayer 649

department: Pediatric Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: HIF-1 ChIP Normoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 6

hyb_protocol: Approximately 2ug of DNA was hybridzed per array.

scan_protocol: Both hybridization and scan were performed by Microarray Core at Dana-Farber Cancer Institute.

data_processing: The model-based analysis of tiling-array (MAT) algorithm was used to identify regions enriched by ChIP-chip (‘‘hits’’) on Affymetrix whole-genome or promoter tiling arrays. MAT was used to identify probe intensity peaks comparing triplicate hypoxic ChIP vs. hypoxic input (‘‘Hypoxic’’) and normoxic ChIP vs. normoxic input (‘‘Normoxic’’). MAT was run with the same parameters for each: bandwidth = 200, maximum gap = 400, minimum probes  = 10, and P value cutoff  = 1e - 5. Hits appearing solely in the hypoxic samples were retained as hypoxia-unique. In cases where hypoxic and normoxic hits overlapped, hits for which the MAT score of hypoxic subtracted by that of normoxic samples were above the cutoff were also retained. The MAT library and mapping files were based on the March 2006 Human Genome Assembly (HG18). Hits flagged by MAT as mapping to repeat  regions were excluded from consideration.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: IP: HepG2 cells under normoxic condition

label_protocol: Amplified ChIP and Input samples were fragmented with DNase to 50~100bp size and labeled using the Terminal transferase (TdT, Promega) to add biotinylated-ddATP to the ends of the fragments.

extract_protocol: HepG2 cells were cultured under normoxic (ambient) or hypoxic (0.5% O2, 4 h) conditions. Cells were cross-linked with 1% formaldehyde for 10 minutes at 37ºC, washed with cold PBS, and lysed with 0.5% SDS Buffer. Chromatins were then sonicated in 0.5% SDS Buffer using 3 x 10 second pulses on setting 5 with a Fisher Scientific Sonic Dismembrator (model 100) into 500bp~1kb fragments. Lysates were then diluted with dilution buffer into final SDS concentration being 0.1%. Three ChIP biological replicates were performed for both normoxic and hypoxic samples with HIF-1a pAb (Novus, NB 100-134). A small aliquot for each biological sample are reserved for an input control. Both Chiped DNA and Input samples were amplified by LM-PCR.

tag: cell line

tag: cell type

value: hepatocellular carcinoma

tag: cell tissue

value: liver

tag: antibody

value: HIF-1 polyclonal

source_name: Input: HepG2 cells under normoxic condition


source_name: embryos,14-16 hr after egg laying (Celniker/RNA:256) extraction3_array1 channel_1


source_name: embryos,12-14 hr after egg laying (Celniker/RNA:252) extraction3_array1 channel_1


source_name: embryos,12-14 hr after egg laying (Celniker/RNA:421) extraction1_array1 channel_1


source_name: embryos,18-20 hr after egg laying (Celniker/RNA:432) extraction1_array1 channel_1


source_name: embryos,12-14 hr after egg laying (Celniker/RNA:248) extraction1_array1 channel_1


source_name: embryos,12-14 hr after egg laying (Celniker/RNA:250) extraction2_array1 channel_1


source_name: embryos,10-12 hr after egg laying (Celniker/RNA:244) extraction3_array1 channel_1

value: Embryo 10-12h


source_name: embryos,10-12 hr after egg laying (Celniker/RNA:419) extraction3_array1 channel_1


title: Hypoxia-HIF1-6

description: HIF-1 ChIP Hypoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 6

source_name: IP: HepG2 cells under hypoxic condition (0.5%O2, 4 hours)

source_name: Input: HepG2 cells under hypoxic condition (0.5%O2, 4 hours)


source_name: embryos,10-12 hr after egg laying (Celniker/RNA:420) extraction2_array1 channel_1


source_name: embryos,10-12 hr after egg laying (Celniker/RNA:246) extraction2_array1 channel_1


source_name: embryos,10-12 hr after egg laying (Celniker/RNA:418) extraction1_array1 channel_1


source_name: embryos,10-12 hr after egg laying (Celniker/RNA:242) extraction1_array1 channel_1


source_name: embryos,12-14 hr after egg laying (Celniker/RNA:423) extraction3_array1 channel_1


source_name: embryos,8-10 hr after egg laying (Celniker/RNA:236) extraction3_array1 channel_1

value: Embryo 8-10h


source_name: embryos,8-10 hr after egg laying (Celniker/RNA:240) extraction1_array1 channel_1


source_name: embryos,8-10 hr after egg laying (Celniker/RNA:415) extraction1_array1 channel_1


source_name: embryos,8-10 hr after egg laying (Celniker/RNA:238) extraction2_array1 channel_1


source_name: embryos,8-10 hr after egg laying (Celniker/RNA:417) extraction2_array1 channel_1


source_name: embryos,8-10 hr after egg laying (Celniker/RNA:416) extraction3_array1 channel_1


source_name: embryos,0-2 hr after egg laying (Celniker/RNA:403) extraction3_array1 channel_1

value: Embryo 0-2h


source_name: embryos,0-2 hr after egg laying (Celniker/RNA:404) extraction1_array1 channel_1


source_name: L3 stage larvae,Dark Blue Gut PS(1-2) (Celniker/RNA:440) extraction3_array1 channel_1

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.
All Drosophila larval collections were made from the sequenced D. melanogaster isogenic strain containing the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. Fly stocks were reared in 250ml bottles containing standard Drosophila medium at 24oC supplemented with bromophenol blue dye (BPB). Each pint bottle contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). Additionally, the medium contained 0.05% bromphenol blue (BPB) to stage late L3 larvae according to the previously described gut stages associated with differential gut staining [2, 3]. In summary, L3 larvae were collected by gut staging based on the intensity of blue dye retained in the gut of the L3 larvae. The intensity of the BPB in the gut is inversely related to the length of time the third instar larvae have been wandering. Dark blue gut staged animals correspond to L3 larvae that will pupariate in 12-24 hours and exhibit a puff stage (PS) 1 polytene chromosome puffing pattern. Light blue gut staged larvae correspond to L3 larvae with PS2-6 puffing patterns that will pupariate in 5-12 hours. Clear gut staged L3 larvae correspond to PS7-9 puffing stages and typically pupariate in 1-6 hours. Wandering third instar larvae collected at these three stages were sorted into separate tubes and placed immediately on dry ice. Samples were stored at -80oC prior to RNA isolation.

value: L3 stage larvae, Dark Blue Gut


source_name: embryos,0-2 hr after egg laying (Celniker/RNA:214) extraction3_array1 channel_1


source_name: embryos,0-2 hr after egg laying (Celniker/RNA:216) extraction2_array1 channel_1


title: RCCT 35-NA (SNP)

first: Rameen

last: Beroukhim

address: 450 Brookline Ave

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Genotyping was performed using Affymetrix Genotyping Tools Version 2.0.  dChip was used to normalize probe-level signal intensities to a baseline array with median intensity using invariant set normalization and obtain SNP-level signal intensities using a model-based (PM/MM) method,

source_name: normal renal cortex

label_protocol: biotin

extract_protocol: Genomic DNA was isolated from tissue or cell pellets using SDS/proteinase K followed by phenol/chloroform and isopropanol precipitation, and quantified using Picogreen.

tag: disease state

value: normal renal cortex


source_name: embryos,0-2 hr after egg laying (Celniker/RNA:212) extraction1_array1 channel_1


title: RCCT 206-C (SNP)


title: RCCT 373-NCA (SNP)


source_name: embryos,0-2 hr after egg laying (Celniker/RNA:405) extraction2_array1 channel_1


title: RCCT 168-C (SNP)


title: RCCT 158-C (SNP)


title: RCCT 162-C (SNP)


title: RCCT 171-C (SNP)


title: RCCT 037-NA (SNP)


source_name: pupae,WPP + 4 days (Celniker/RNA:356) extraction2_array1 channel_1

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.
Fly populations consisted of the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. These flies 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. These animals were grown in 250ml (pint) bottle that contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). Approximately seven days after being introduced into the bottles, white prepupa were collected by individually transferring staged animals to a tube on crushed dry ice. In order to collect synchronized pupal stages, white prepupa were marked on the overlaying glass with a Sharpie®. These marked bottles containing synchronized white prepupa were aged the indicated amount of time at 24C, and transferred to a tube on crushed dry ice. All frozen biological samples were stored at -80C until the RNA could be isolated. A yield of approximately 4 micrograms total RNA per milligram tissue was typical from these stages. Animals were staged according to Ashburner, et. al. (2005)[2].

value: Pupae, WPP + 4 days


source_name: pupae,WPP + 3 days (Celniker/RNA:350) extraction3_array1 channel_1

value: Pupae, WPP + 3 days


source_name: adult male,eclosion + 5 days (Celniker/RNA:380) extraction1_array1 channel_1

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.''All Drosophila tissue collections were made from the sequenced ''D. melanogaster'' isogenic strain containing the mutations; ''yellow'' (y1), ''cinnabar'' (cn1), ''brown'' (bw1), and ''speck'' (sp1) [1].  Synchronized embryos were collected from population cages that were less than one week old and maintained at 24 C.  At least one ? two hour pre-lay was made prior to the start of timed collections each day. Embryos were collected for two hours on 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.Staged embryos were passed through an 850 micron screen and collected on a 75 micron screen to remove adults and yeast paste.  Embryos were then dechorionated by treatment with 50% bleach (3% sodium hypochlorite), 0.2% sodium chloride, and 0.02% Triton-X-100 for five minutes.  Embryos were washed twice with 0.2% NaCl, 0.02% Triton buffer and split into two samples.  Most of the sample (approximately 95%) was rinsed with de-ionized water in a buchner funnel under mild vacuum, dried briefly, immediately frozen on dry ice and stored at -80? C for RNA preparations.  The small aliquot was transferred to a clean tube and fixed for staging.  Fixation was accomplished in 0.1 M Pipes (pH 6.9), 2 mM EGTA, 1 mM MgSO4, 4% paraformaldehyde, 0.1% glutaraldehyde (percentages are relative to aqueous volumes), and 50% heptane, as describe previously [2].  Samples were shaken for five minutes in the fixative, centrifuged briefly and the aqueous fraction was removed.  An equal volume of methanol containing 2 mM EGTA was added and the sample was shaken for five additional minutes.  Tissue was washed twice in methanol with 2 mM EGTA and saved at -80? C for the characterization of developmental stages.

value: Adult male, eclosion + 5 days

value: Male


source_name: adult male,eclosion + 1 day (Celniker/RNA:370) extraction3_array1 channel_1

value: Y cn bw sp

value: Adult male, eclosion + 1 day


title: RCCT 189-N (SNP)


title: RCCT 170-C (SNP)


title: RCC 81N (SNP)


source_name: adult male,eclosion + 5 days (Celniker/RNA:382) extraction2_array1 channel_1


title: RCCT 155-C (SNP)


source_name: adult male,eclosion + 5 days (Celniker/RNA:384) extraction3_array1 channel_1


title: RCCT 003-NCA (SNP)


source_name: adult male,eclosion + 1 day (Celniker/RNA:368) extraction1_array1 channel_1


source_name: adult female,eclosion + 5 days (Celniker/RNA:388) extraction3_array1 channel_1

value: Adult female, eclosion + 5 days

value: Female


title: TS047-D3-rep2

status: Public on Jun 22 2009

city: Osaka

first: Kayo

last: Sumida

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

department: Environmental Health Science Laboratory

country: Japan

institute: Sumitomo Chemical Co., Ltd.

description:
Biological replicate 1 of 5. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

hyb_protocol: Fragmented cRNA was obtained by heating the solution of 1× fragmentation buffer (Invitrogen), 0.75 μg of Cy3-labeled cRNA, and 0.75 μg of Cy5-labeled cRNA at 94 deg C for 15 min. 30 μl of the fragmented mixture, 46.5 μl of water, 37.5 μl of 20× SSC, 7.5 μl of 10% SDS, and 12 μl of 5× Denhardt's solution were mixed and heated at 95 deg C for 2 min. 1.5 μl of 10 mg/ml salmon sperm DNA solution and 15 μl of formamide were added and heated at 60 deg C for 3 min. 130 μl of hybridization mixture was injected into a microarray chamber and sealed. The microarray was transferred to a hybridization chamber and incubated at 60 deg C overnight with rotation at 6 rpm. After incubation, the microarray was washed for 10 min at 30 degb C in lowstringency wash buffer (5× SSC and 0.1% SDS), washed twice for 2 min at 30 deg C in high-stringency wash buffer (0.5× SSC), and finally rinsed with 0.5× SSC and 0.01% Tween20. The microarray was dried by centrifugation at 360×g for 1 min.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using GenePix Pro Software (version 4.0).

data_processing: LOWESS normalized, background subtracted data was calculated by an R package 'sma' using processed Red signal and processed Green signal.

organism: Rattus norvegicus

source_name: Total RNA from rat liver

label_protocol: Amino-allyl cRNA was synthesized from 5 μg of total RNA using the SuperScript Indirect RNA Amplification System (Invitrogen). Amino-allyl cRNA was amplified by in vitro transcription reaction for 3 h, purified using the RNeasy MinElute Kit (Qiagen), and used for the fluorescent dye coupling reaction with the Cy3 or Cy5 Post-Labeling Reactive Dye Pack (GE Healthcare). Amino-allyl cRNA from individual compound-treated rats and pooled time-matched control rats were labeled with Cy3 and Cy5, respectively.

growth_protocol: 4 week-old male Fischer 344 rats were purchased from Charles River Japan. They were housed in an air-conditioned room at 22±2 deg C and 55±15% humidity, with a 12 h light, 12 h dark cycle. Rats were maintained on a basal diet (CRF-1, Oriental Yeast Co.), with tap water ad libitum.

extract_protocol: Total RNA was extracted from liver using RNeasy Midi Kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Each group was composed of 4 rats. At each time point for each compound, there were a group that received the test compound and a control group. Compounds were administered once daily by oral gavage at a dose of 5 ml/kg for up to 1, 3, 7, 14, or 28 days. Control animals received corresponding volumes of vehicle.

tag: gender

tag: age

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: treatment

value: 3 days

tag: vehicle

value: Corn oil

value: 7,12-Dimethylbenz [a]anthracene (DMBA)


source_name: adult female,eclosion + 5 days (Celniker/RNA:390) extraction2_array1 channel_1

tag: strain


title: RCC 83N (SNP)


title: RCC 77N (SNP)


source_name: adult female,eclosion + 5 days (Celniker/RNA:386) extraction1_array1 channel_1

tag: developmental stage


source_name: adult female,eclosion + 1 day (Celniker/RNA:378) extraction3_array1 channel_1

value: Adult female, eclosion + 1 day

tag: genotype


title: RCC 80N SNP_02 (SNP)


source_name: adult female,eclosion + 1 day (Celniker/RNA:376) extraction2_array1 channel_1

tag: sex


title: RCC 65N (SNP)


source_name: white prepupae (WPP) (Celniker/RNA:328) extraction2_array1 channel_1

value: White prepupae (WPP)

value: Unknown


source_name: white prepupae (WPP) (Celniker/RNA:326) extraction3_array1 channel_1


source_name: adult female,eclosion + 1 day (Celniker/RNA:374) extraction1_array1 channel_1


source_name: white prepupae (WPP) (Celniker/RNA:330) extraction1_array1 channel_1


title: RCC 66N SNP_02 (SNP)

source_name: normal renal cortex

value: normal renal cortex


title: RCC 62N (SNP)


title: RCC 64N (SNP)


title: RCC 56N (SNP)


source_name: L3 stage larvae,Dark Blue Gut PS(1-2) (Celniker/RNA:444) extraction2_array1 channel_1

value: L3 stage larvae, Dark Blue Gut


title: RCC 61N SNP_02 (SNP)


source_name: L2 stage larvae (Celniker/RNA:290) extraction2_array1 channel_1

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.
All Drosophila larval collections were made from the sequenced D. melanogaster isogenic strain containing the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. First, second and early third instar larvae were staged and collected by this method. Synchronized embryos were collected from population cages that contained adult flies that were less than one week old and were maintained at 24 C. A two hour pre-lay was done prior to the start of timed collections each day. Embryos were collected for two hours on 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 (Baker?s Dry Yeast) and placed horizontally on a short 1cm raised Plexiglas bar in the bottom of each cage to avoid crushing flies. Embryos were aged 18 hours on the collection plates, washed from the plates with water, passed through an 850 micron screen to remove adults and collected on a 75 micron screen to remove yeast paste. Embryos were gently transferred onto a new hard egg-lay plate in rows and the rows surrounded by stripes of fresh yeast paste to tempt the larvae to migrate away from the unhatched embryos. The strips of unhatched embryos were cut out of the plate after a few hours and discarded. Feeding larvae in the yeast paste were aged appropriately and harvested by the screening procedure above. Larvae collected 42-44 hr after egg-lay were designated L1; larvae collected 66-70 hr after egg-lay were designated L2; larvae collected 83-85 hours after egg-lay were designated L3+12 hr. Collected larvae were washed briefly with de-ionized water in a buchner funnel, split into two samples and immediately frozen with dry ice. The staged animals were stored at minus 80oC for larval RNA production.

value: L2 stage larvae


source_name: L2 stage larvae (Celniker/RNA:294) extraction3_array1 channel_1


source_name: L2 stage larvae (Celniker/RNA:292) extraction1_array1 channel_1


title: RCC 53N (SNP)


title: RCC 55N_02 (SNP)


title: RCC 50N (SNP)


source_name: L3 stage larvae,Dark Blue Gut PS(1-2) (Celniker/RNA:442) extraction1_array1 channel_1


source_name: L1 stage larvae (Celniker/RNA:288) extraction3_array1 channel_1

value: L1 stage larvae


title: RCC 41N-a SNP_02 (SNP)


source_name: L1 stage larvae (Celniker/RNA:286) extraction1_array1 channel_1

value: Y cn bw sp


title: RCC 29N (SNP)


source_name: L1 stage larvae (Celniker/RNA:284) extraction2_array1 channel_1


source_name: ML-DmD16-c3 (Celniker/RNA:136) extraction2_array1 channel_1

extract_protocol:
This protocol is used by the IU Bloomington labs to prepare RNA from cell lines that will be used for for microarray hybridization or RT-PCR.This is a standard TRIzol purification procedure, followed by DNase and RNeasy (Qiagen).  Concentration was determined by Nanodrop absorbance.
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.

tag: cell line

value: dorsal mesothoracic disc

value: y v f mal


title: RCC 32N (SNP)


title: RCC 2N SNP_02 (SNP)


source_name: ML-DmD16-c3 (Celniker/RNA:134) extraction1_array1 channel_1

value: Female


source_name: adult male,eclosion + 1 day (Celniker/RNA:372) extraction2_array1 channel_1

value: Adult male, eclosion + 1 day

value: Male


title: RCC 51N (SNP)


source_name: Sg4 (Celniker/RNA:204) extraction3_array1 channel_1

value: embryo-derived cell-line


source_name: Sg4 (Celniker/RNA:200) extraction1_array1 channel_1


source_name: embryos,6-8 hr after egg laying (Celniker/RNA:230) extraction2_array1 channel_1

growth_protocol: ''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.''All Drosophila tissue collections were made from the sequenced ''D. melanogaster'' isogenic strain containing the mutations; ''yellow'' (y1), ''cinnabar'' (cn1), ''brown'' (bw1), and ''speck'' (sp1) [1].  Synchronized embryos were collected from population cages that were less than one week old and maintained at 24 C.  At least one ? two hour pre-lay was made prior to the start of timed collections each day. Embryos were collected for two hours on 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.Staged embryos were passed through an 850 micron screen and collected on a 75 micron screen to remove adults and yeast paste.  Embryos were then dechorionated by treatment with 50% bleach (3% sodium hypochlorite), 0.2% sodium chloride, and 0.02% Triton-X-100 for five minutes.  Embryos were washed twice with 0.2% NaCl, 0.02% Triton buffer and split into two samples.  Most of the sample (approximately 95%) was rinsed with de-ionized water in a buchner funnel under mild vacuum, dried briefly, immediately frozen on dry ice and stored at -80? C for RNA preparations.  The small aliquot was transferred to a clean tube and fixed for staging.  Fixation was accomplished in 0.1 M Pipes (pH 6.9), 2 mM EGTA, 1 mM MgSO4, 4% paraformaldehyde, 0.1% glutaraldehyde (percentages are relative to aqueous volumes), and 50% heptane, as describe previously [2].  Samples were shaken for five minutes in the fixative, centrifuged briefly and the aqueous fraction was removed.  An equal volume of methanol containing 2 mM EGTA was added and the sample was shaken for five additional minutes.  Tissue was washed twice in methanol with 2 mM EGTA and saved at -80? C for the characterization of developmental stages.

value: Embryo 6-8h


source_name: Sg4 (Celniker/RNA:202) extraction2_array1 channel_1


title: RCC 25N (SNP)


source_name: S3 (Celniker/RNA:108) extraction3_array1 channel_1


title: RCC 141N (SNP)

source_name: normal renal cortex


source_name: S3 (Celniker/RNA:106) extraction2_array1 channel_1


source_name: S3 (Celniker/RNA:104) extraction1_array1 channel_1


source_name: S2R+ (Celniker/RNA:24) extraction3_array1 channel_1


title: RCC 117N (SNP)


title: RCC 14N SNP_02 (SNP)


title: RCC 116N (SNP)


source_name: S2R+ (Celniker/RNA:22) extraction2_array1 channel_1


title: RCC 01N (SNP)


title: RCC 11N (SNP)


source_name: S2R+ (Celniker/RNA:20) extraction1_array1 channel_1


source_name: S2-DRSC (Celniker/RNA:18) extraction3_array1 channel_1


title: RCC 101N (SNP)


source_name: S2-DRSC (Celniker/RNA:16) extraction2_array1 channel_1


title: RCC 10N SNP_02 (SNP)


title: CC 17N (SNP)


title: RCC 0006N (SNP)


source_name: S2-DRSC (Celniker/RNA:14) extraction1_array1 channel_1


title: S1 (Celniker/RNA:30) extraction3_array1

source_name: S1 (Celniker/RNA:30) extraction3_array1 channel_1


title: RCC 13N (SNP)


title: CC 7N (SNP)


title: RCC 132N SNP_02 (SNP)


title: CC 15N (SNP)


title: S1 (Celniker/RNA:26) extraction1_array1

source_name: S1 (Celniker/RNA:26) extraction1_array1 channel_1


source_name: ML-DmD9 (Celniker/RNA:74) extraction2_array1 channel_1


source_name: ML-DmD9 (Celniker/RNA:76) extraction3_array1 channel_1


title: gra3-D, biological rep2

city: Gent

first: Nathalie

last: Gonzalez

address: Technologiepark 927

department: Plant System Biology

country: Belgium

institute: VIB

description: gra3-D mutant, vegetative part of seedlings at stage 1.03

hyb_protocol: Standard affymetrix protocol

scan_protocol: Standard affymetrix protocol

data_processing: Expression data were processed using RMA (background correction, normalization and summarization) in BioConductor (Gentleman et al. 2004; Irizarry et al. 2003a; 2003b). An alternative CDF (tinesath1cdf) was used, where each probe is assigned uniquely to one transcript and is excluded if it aligns to a different transcript with 24 or more perfect matches (Casneuf et al. 2007; http://www.bioconductor.org/packages/release/data/experiment/html/tinesath1cdf.html)

organism: Arabidopsis thaliana

source_name: gra3-D mutant

label_protocol: Standard affymetrix protocol

growth_protocol: plant were grown on MS medium under 16 h light/ 8 h dark cycle at 22°C

extract_protocol: RNeasy plant mini kit (Qiagen) , according to manufacturer protocol

tag: ecotype

value: vegetative part

value: stage 1.03


title: CC 9N (SNP)


source_name: ML-DmD9 (Celniker/RNA:72) extraction1_array1 channel_1


title: gra3-D, biological rep3


title: gra3-D, biological rep1


title: gra2-D, biological rep3

description: gra2-D mutant, vegetative part of seedlings at stage 1.03

source_name: gra2-D mutant


source_name: ML-DmD8 (Celniker/RNA:210) extraction3_array1 channel_1


title: CC 119N (SNP)

source_name: normal renal cortex


title: gra2-D, biological rep2


source_name: ML-DmD16-c3 (Celniker/RNA:138) extraction3_array1 channel_1


title: 769-P (SNP)

source_name: renal cancer cell line

value: renal cancer cell line


title: S1 (Celniker/RNA:28) extraction2_array1

source_name: S1 (Celniker/RNA:28) extraction2_array1 channel_1


source_name: ML-DmD8 (Celniker/RNA:206) extraction1_array1 channel_1


source_name: ML-DmD8 (Celniker/RNA:208) extraction2_array1 channel_1


source_name: ML-DmD4-c1 (Celniker/RNA:144) extraction3_array1 channel_1

value: imaginal disc-derived cell-line


source_name: ML-DmD4-c1 (Celniker/RNA:142) extraction2_array1 channel_1

value: Unknown


source_name: ML-DmD4-c1 (Celniker/RNA:140) extraction1_array1 channel_1


source_name: ML-DmD32 (Celniker/RNA:168) extraction3_array1 channel_1


title: gra2-D, biological rep1


title: RCC 129N (SNP)

value: normal renal cortex


source_name: ML-DmD32 (Celniker/RNA:166) extraction2_array1 channel_1


title: Caki-2 (SNP)


source_name: ML-DmD32 (Celniker/RNA:164) extraction1_array1 channel_1


title: UMRC2 (SNP)


source_name: ML-DmD21 (Celniker/RNA:52) extraction2_array1 channel_1


title: gra1-D, biological rep3

description: gra1-D mutant, vegetative part of seedlings at stage 1.03

source_name: gra1-D mutant


source_name: ML-DmD21 (Celniker/RNA:54) extraction3_array1 channel_1


source_name: ML-DmD21 (Celniker/RNA:50) extraction1_array1 channel_1


title: gra1-D, biological rep1


source_name: ML-DmD20-c5 (Celniker/RNA:192) extraction3_array1 channel_1

value: antenna disc-derived cell-line


title: gra1-D, biological rep2


title: SW 156 (SNP)


title: wild type, biological rep3

description: Wild type, vegetative part of seedlings at stage 1.03

source_name: Wild type

value: WT


source_name: ML-DmD20-c5 (Celniker/RNA:190) extraction2_array1 channel_1


title: wild type, biological rep2


title: UMRC6 (SNP)

source_name: renal cancer cell line


source_name: ML-DmD20-c2 (Celniker/RNA:184) extraction2_array1 channel_1


title: JL00004_MIX1_N2_MXemb_3 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: lab: Lieb; short description: Recombinant protein was cloned and expressed with Novagen's Pet30-EkLIC system. Rabbit polyclonal antibodies were produced at Covance Immunology Services. DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.; catalog: Jason Lieb; company: Covance; clonal: Polyclonal; purified: Affinity; antigen: 837-1244; host: Rabbit; species: C. elegans; target id: mix-1; target name: MIX-1; aliases: anti-MIX-1; official name: JL0004_MIX1;
channel ch2 is input DNA;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

data_processing: ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes. Processed data are obtained using following parameters: genome version is WS180

label: Cy5 dye

organism: Caenorhabditis elegans

growth_protocol: Worm_embryo_growth_and_harvest_vSE1. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature. Embryos were then washed once with 100 mM Tris, twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSE1. Embryos were resuspended in FA buffer and dounced 30 times (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.

value: embryo

label: Cy3 dye


title: JL00004_MIX1_N2_MXemb_2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: lab: Lieb; short description: Recombinant protein was cloned and expressed with Novagen's Pet30-EkLIC system. Rabbit polyclonal antibodies were produced at Covance Immunology Services. DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.; catalog: Jason Lieb; company: Covance; clonal: Polyclonal; purified: Affinity; antigen: 837-1244; host: Rabbit; species: C. elegans; target id: mix-1; target name: MIX-1; aliases: anti-MIX-1; official name: JL0004_MIX1;

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.


title: wild type, biological rep1


source_name: ML-DmD20-c2 (Celniker/RNA:182) extraction1_array1 channel_1


source_name: ML-DmD20-c2 (Celniker/RNA:186) extraction3_array1 channel_1


source_name: ML-DmD20-c5 (Celniker/RNA:188) extraction1_array1 channel_1


source_name: ML-DmD17-c3 (Celniker/RNA:198) extraction3_array1 channel_1


title: SN12-PM6 (SNP)


title: SLR 25 (SNP)


title: SLR 26 (SNP)


title: JL00004_MIX1_N2_MXemb_1 extraction1_array1

value: wild type


title: SLR 24 (SNP)


source_name: ML-DmD17-c3 (Celniker/RNA:196) extraction2_array1 channel_1

value: dorsal mesothoracic disc


source_name: ML-DmD17-c3 (Celniker/RNA:194) extraction1_array1 channel_1

value: y v f mal


source_name: ML-DmD11 (Celniker/RNA:174) extraction3_array1 channel_1

value: eye-antenna disc-derived cell-line


title: SLR 22 (SNP)


source_name: ML-DmD11 (Celniker/RNA:170) extraction1_array1 channel_1


source_name: ML-DmBG3-c2 (Celniker/RNA:126) extraction3_array1 channel_1

value: CNS-derived cell-line


source_name: ML-DmD11 (Celniker/RNA:172) extraction2_array1 channel_1


source_name: ML-DmBG3-c2 (Celniker/RNA:124) extraction2_array1 channel_1


title: SLR 23 (SNP)


source_name: ML-DmBG3-c2 (Celniker/RNA:122) extraction1_array1 channel_1


source_name: ML-DmBG1-c1 (Celniker/RNA:120) extraction3_array1 channel_1


source_name: ML-DmBG1-c1 (Celniker/RNA:118) extraction2_array1 channel_1


title: SLR 21 (SNP)


title: SOD1G93A triceps-14w, biol rep4

city: Cusano Milanino

first: Antonia

last: Ratti

state: Milan

address: Via Zucchi, 18

department: Dept. Neurological Sciences

country: Italy

institute: IRCCS Istituto Auxologico Italiano, University of Milan

description: Gene expression data from symptomatic SODG93A triceps

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on murine 430A2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

organism: Mus musculus

source_name: 14week-old triceps from SODG93A mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA.

growth_protocol: Mice were maintained at 21C with relative humidity 55+10% and 12hrs of light; Food (standard pellet) and water were supplied ad libitum.

extract_protocol: Total RNA was extracted with Trizol reagent and subsequently purified on Qiagen RNeasy mini-columns; quality was assessed on a BioAnalyzer instrument (Agilent).

treatment_protocol: Mice were sacrificed according to national and international laws on animal care; gastrocenemius and triceps muscles were removed and immediately frozen in liquid nitrogen.

value: female

tag: genetic modification

value: transgenic humanSODG93A

value: 14 week-old triceps


title: SOD1G93A gastro-14w, biol rep4

description: Gene expression data from symptomatic SODG93A gastrocnemius

source_name: 14week-old gastrocnemius from SODG93A mice

value: 14 week-old gastrocnemius


title: Crushed-gastro-14w, biol rep2

description: Gene expression data from 14week-old nerve-crushed gastrocnemius

source_name: 14week-old gastrocnemius from nerve-crushed mice

value: To anesthetised 12week-old mice, the sciatic nerves at the midtight level were crushed by compression with Martin 20-307-14 forceps for 30sec. Animals were killed after 2 weeks (14weeks-old).


source_name: ML-DmBG1-c1 (Celniker/RNA:116) extraction1_array1 channel_1


title: NTg-gastro-14w, biol rep4

description: Gene expression data from 14week-old NTg gastrocnemius

source_name: 14week-old gastrocnemius from NTg mice

value: non-transgenic mice


title: SLR 20 (SNP)

source_name: renal cancer cell line

value: renal cancer cell line


title: Crushed-gastro-14w, biol rep4

value: 14week-old gastrocnemius from nerve-crushed mice


title: SOD1G93A gastro-14w, biol rep3


source_name: Kc167 (Celniker/RNA:6) extraction3_array1 channel_1

value: embryo-derived cell-line

value: se/e

value: Female


title: Crushed-gastro-14w, biol rep3


title: SOD1G93A triceps-14w, biol rep3


source_name: Kc167 (Celniker/RNA:2) extraction1_array1 channel_1


source_name: Kc167 (Celniker/RNA:4) extraction2_array1 channel_1


title: UT04 455 #9_04 (SNP)

source_name: clear cell renal cell carcinoma

value: clear cell renal cell carcinoma

value: VHL biallelically inactivated


title: NTg-triceps-14w, biol rep4

source_name: 14week-old triceps from NTg mice


title: SK-RC 52 (SNP)


title: KC 12 (SNP)


title: UT04 455 #8_03 (SNP)


title: SK-RC 42 (SNP)


source_name: GM2 (Celniker/RNA:12) extraction3_array1 channel_1

value: Unknown


title: SOD1G93A triceps-14w, biol rep2


title: NTg-triceps-14w, biol rep2

description: Gene expression data from 14week-old NTg triceps


title: SOD1G93A gastro-14w, biol rep2


title: UT04 145 #6 (SNP)


title: SK-RC 29 (SNP)


title: SK-RC 38 (SNP)


title: Crushed-gastro-14w, biol rep1


title: SK-RC 31 (SNP)


source_name: GM2 (Celniker/RNA:10) extraction2_array1 channel_1


title: GM2 (Celniker/RNA:8) extraction1_array1

source_name: GM2 (Celniker/RNA:8) extraction1_array1 channel_1


title: NTg-gastro-14w, biol rep3


source_name: CME W1 Cl.8+ (Celniker/RNA:64) extraction3_array1 channel_1

value: dorsal mesothoracic disc

value: Male


title: NTg-gastro-14w, biol rep2


title: KU 19-20 (SNP)


title: UT04 0021 #1 (SNP)


title: UT04 0046 #10 (SNP)


title: NTg-triceps-14w, biol rep3


source_name: CME W1 Cl.8+ (Celniker/RNA:62) extraction2_array1 channel_1


title: A-704 (SNP)


title: NTg-triceps-14w, biol rep1


title: UT04 0046 #20_03 (SNP)


title: NTg-gastro-14w, biol rep1


title: Exp E7 vs. Control C8, skeletal muscle

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: Skeletal muscle

hyb_protocol: According to Agilent protocol

scan_protocol: Agilent Scanner, according to Agilent protocol

data_processing: Feature Extraction Software, then log2 transformation and lowess normalization using Bioconductor packages

source_name: KIKO, E7, skeletal muscle

label_protocol: Agilent Low RNA Input FluorescentLinear Amplification Kit

growth_protocol: 6-month old mice

extract_protocol: Trizol

value: KIKO

value: skeletal muscle

source_name: Control, C8, skeletal muscle

value: WT


title: UT04 0046 #25_04 (SNP)


source_name: CME W1 Cl.8+ (Celniker/RNA:60) extraction1_array1 channel_1


title: Exp E7 vs. Control C8, heart

description: Heart

source_name: KIKO, E7, heart

value: heart

source_name: Control, C8, heart


source_name: CME L1 (Celniker/RNA:90) extraction3_array1 channel_1

value: ventral prothoracic disc


title: SOD1G93A gastro-14w, biol rep1

source_name: 14week-old gastrocnemius from SODG93A mice

value: female

value: transgenic humanSODG93A

value: 14 week-old gastrocnemius


title: Exp E6 vs. Control C3, skeletal muscle

description: Skeletal muscle

source_name: KIKO, E6, skeletal muscle

source_name: Control, C3, skeletal muscle


title: RCCT 155-T2B (SNP)

value: sporadic tumor


source_name: CME L1 (Celniker/RNA:88) extraction2_array1 channel_1


source_name: CME L1 (Celniker/RNA:86) extraction1_array1 channel_1


title: SOD1G93A triceps-14w, biol rep1

source_name: 14week-old triceps from SODG93A mice

value: 14 week-old triceps


title: UT04 0046 #14_02 (SNP)

source_name: clear cell renal cell carcinoma


title: SOD1G93A triceps-7w, biol rep4

description: Gene expression data from presymptomatic SODG93A triceps

source_name: 7week-old triceps from SODG93A mice

value: female mice

value: 7 week-old triceps


source_name: 1182-4H (Celniker/RNA:42) extraction3_array1 channel_1

value: embryo-derived cell-line

value: mh


title: RCCT 162-T1C (SNP)

value: clear cell renal cell carcinoma

value: VHL biallelically inactivated


title: Exp E3 vs. Control C4, heart

description: Heart

source_name: KIKO, E3, heart

source_name: Control, C4, heart


title: RCCT 35-T1 (SNP)


title: Exp E3 vs. Control C4, skeletal muscle

description: Skeletal muscle

source_name: KIKO, E3, skeletal muscle

source_name: Control, C4, skeletal muscle


title: Exp E6 vs. Control C3, heart

description: Heart

source_name: KIKO, E6, heart

source_name: Control, C3, heart


title: NTg-triceps-7w, biol rep4

description: Gene expression data from NTg triceps (7weeks)

source_name: 7week-old triceps from NTg mice

value: non-transgenic mice


title: Control C8 vs. Exp E7, skeletal muscle

description: Skeletal muscle

source_name: Control, C8, skeletal muscle

source_name: KIKO, E7, skeletal muscle

value: KIKO


title: SOD1G93A gastro-7w, biol rep3

description: Gene expression data from presymptomatic SODG93A gastrocnemius

source_name: 7week-old gastrocnemius from SODG93A mice

value: 7 week-old gastrocnemius


title: SOD1G93A triceps-7w, biol rep3


title: SOD1G93A gastro-7w, biol rep4


title: CC 5058T (SNP)


source_name: 1182-4H (Celniker/RNA:40) extraction2_array1 channel_1

value: Unknown


title: CC 5580T (SNP)


title: CC 5043T (SNP)


source_name: 1182-4H (Celniker/RNA:38) extraction1_array1 channel_1


title: Control C4 vs. Exp E3, skeletal muscle

description: Skeletal muscle

value: WT

value: skeletal muscle


title: CC 5389T (SNP)


title: UT03 0530 #18 (SNP)


title: NTg-triceps-7w, biol rep3


title: Control C4 vs. Exp E3, heart

description: Heart

value: heart


title: RCC 114T (SNP)

value: VHL not biallelicall inactivated


title: NTg-gastro-7w, biol rep3

description: Gene expression data from NTg gastrocnemius (7weeks)

source_name: 7week-old gastrocnemius from NTg mice


title: NTg-triceps-7w, biol rep2


title: Control C8 vs. Exp E7, heart

description: Heart

source_name: Control, C8, heart

source_name: KIKO, E7, heart


title: NTg-gastro-7w, biol rep4


title: RCC 80N SNP_02 (expression)

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: normal renal cortex

extract_protocol: For total RNA extraction, tumor regions containing at least 70% of tumor cells were isolated from the frozen blocks utilizing a 2mm punch.   Frozen tissue fragments were pulverized with a chilled mortar and pestle and homogenized in 1 ml of Triazol reagent (Gibco/BRL).

value: normal renal cortex


title: RCC 65N (expression)


title: NTg-gastro-7w, biol rep2


title: Prop_30h_C

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: S. pastorianus 30hrs

hyb_protocol: Hybridization, washing, staining procedures were conducted with Affymetrix Fluidics Station as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

scan_protocol: Scanning done with GeneChip Scanner as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

data_processing: CEL files were generated using the GeneChip® operating system (GCOS version 5.0; Affymetrix). The data were analyzed with Affymetrix MAS5 software.

organism: Saccharomyces pastorianus

source_name: propagation, 30h

label_protocol: Biotinylated cRNA was prepared from total RNA with Affymetrix GeneChip Labeling and Control Reagents.

extract_protocol: RNA extraction was carried out following the method of Lyne et al. RNA yield and purity were determined using an Agilent 2100 Bioanalyser (Agilent Technologies Inc., Santa Clara, California).

treatment_protocol: yeast sampling: Triplicate samples of the lager yeast strain CB11 were sampled from a 140 hl (14,000 l) propagation vessel immediately after inoculation and at intervals throughout a 30-hour propagation period. The yeast batch was incubated aerobically in an 8 hl propagation vessel prior to incubation in the principal (140 hl) vessel. Propagation wort (80% malt and 20% maltose adjunct) supplement_protocoled to 0.5 mg l-1 Zn2+ (added as zinc sulphate heptahydrate) and was oxygenated with a ramped supply of molecular oxygen (5-100 l min-1) to give a constant dissolved oxygen concentration of 7-8 mg l-1. Temperature of the wort was maintained throughout at 20°C. Specific gravity of the wort was 17° Plato. Cells and wort were separated by centrifugation at 4°C. Cell pellets for RNA extraction were flash-frozen in liquid nitrogen and stored at -80°C until required.

tag: timepoint

value: 30 hours


title: Prop_30h_B

institute: Nottingham Arabidopsis Stock Centre (NASC)

description: S. pastorianus 30hrs


title: NTg-triceps-7w, biol rep1


title: CC 5001T (SNP)

source_name: clear cell renal cell carcinoma

tag: disease state

value: sporadic tumor


title: RCC 64N (expression)


title: RCC 56N (expression)


title: SOD1G93A triceps-7w, biol rep2

source_name: 7week-old triceps from SODG93A mice

tag: gender

value: female mice

value: transgenic humanSODG93A


title: 008 RCC needle_03 (SNP)


title: Prop_8h_C

description: S. pastorianus 8hrs

source_name: propagation, 8h

value: 8 hours


title: CC 2932T (SNP)


title: CC 5466T (SNP)


title: UT03 0064 #32_02 (SNP)


title: SOD1G93A gastro-7w, biol rep2


title: NTg-gastro-7w, biol rep1


title: CC 5534T (SNP)


title: RCC 14N SNP_02 (expression)


title: SOD1G93A triceps-7w, biol rep1

value: 7 week-old triceps


title: SOD1G93A gastro-7w, biol rep1


title: RCC 50N (expression)


title: Prop_30h_A

description: S. pastorianus 30hrs


title: Prop_8h_A

description: S. pastorianus 8hrs


title: RCC 117N (expression)


title: Prop_4h_C

description: S. pastorianus 4hrs

source_name: propagation, 4h

value: 4 hours


title: RCC 129N (expression)


title: RCC 118N (expression)


title: Prop_4h_A

description: S. pastorianus 4hrs


title: 011 RCC needle_05 (SNP)

value: clear cell renal cell carcinoma

value: VHL biallelically inactivated


title: CC 2943T (SNP)


title: Prop_8h_B

description: S. pastorianus 8hrs


title: 006 RCC needle_02 (SNP)


title: Prop_0h_B

description: S. pastorianus 0hrs

source_name: propagation, 0h

value: 0 hours


title: RCC 141N (expression)


title: Prop_4h_B

description: S. pastorianus 4hrs


title: CC 5475T (SNP)


title: UT03 0064 #31 (SNP)


title: 004 RCC needle (SNP)


title: 010 RCC needle_04 (SNP)


title: Prop_0h_A

description: S. pastorianus 0hrs

data_processing: Four time points from the fermentation (0, 4, 8, and 30 hours after pitching) were chosen for microarray analysis. All analyses were carried out in triplicate, with each replicate processed separately. In total, therefore, 12 samples were used in this investigation. CEL files were generated using the GeneChip® operating system (GCOS version 5.0; Affymetrix). The data were analyzed with Affymetrix MAS5 software.


title: UT04 0046 #10 (expression)


title: UT04 455 #8_03 (expression)


title: UT04 455 #9_04 (expression)


title: Prop_0h_C

description: S. pastorianus 0hrs


title: UT04 0046 #20_03 (expression)


title: UT04 145 #6 (expression)


title: Lymphoblasts ALD vs. control fam5 rep16

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description:
- RNA quality control with Agilent Bioanalyzer 2100
- Dye incorporation with NanoDrop ND-1000
Keywords = ALD, lymphoblasts

hyb_protocol: - hybridization according to Agilent 60-mer oligo microarray processing protocol v2.1 with the following modifications: 2 micro gram labeled DNA per channel were mixed no fractionation probes were denatured for 3 min at 98 degree celcius hybridization at 65 degree celcius SSPE washes as recommended slides were dipped in acetonitril (10 s) then dried

scan_protocol: - scanned with a G2505B Microarray Scanner (Agilent Technologies) - quantification software: Feature Extraction 9.1.3.1 (GE2-v4_91, Agilent Technologies)

data_processing:
- Normalization of the log2(cy3/cy5)-ratios with pinwise non-linear loess regression
- variance homogenisation by division of each value with the standard deviation
of the normalized log2-ratios
- statistical software: R

source_name: lymphoblasts from control patient N15

label_protocol:
- totalRNA was transcribed, amplified and labeled according to BD Atlas SMART fluorescent probe amplification kit with following modifications:
- RNA template was hydrolized after transcription (high pH, 30 min/70 degree celcius)
- PCR amplification progress was monitored and stopped before reaching saturation

extract_protocol:
- Trizol (Invitrogen) isolation according to the manufactures standard protocol
- Subsequent DNase I treatment

tag: immortalized lymphoblasts from N15

source_name: lymphoblasts from ALD patient B13

tag: immortalized lymphoblasts from B13


title: UT04 0046 #25_04 (expression)


title: CC 9T (SNP)

tag: tissue


title: RCC 65T (SNP)


title: RCC 101T (SNP)


title: UT03 0064 #34_03 (SNP)


title: Lymphoblasts ALD vs. control fam5 rep15

source_name: lymphoblasts from control patient B13

source_name: lymphoblasts from ALD patient N15


title: UT04 0021 #1 (expression)


title: UT04 0046 #14_02 (expression)


title: CC 17T_02 (SNP)


title: CC 15T (SNP)


title: CC 7T (SNP)


title: Lymphoblasts ALD vs. control fam5 rep11

source_name: lymphoblasts from ALD patient N12

tag: immortalized lymphoblasts from N12


title: RCC 83T (SNP)


title: Lymphoblasts ALD vs. control fam5 rep13

source_name: lymphoblasts from control patient B11

tag: immortalized lymphoblasts from B11

source_name: lymphoblasts from control patient N14

tag: immortalized lymphoblasts from N14


title: Lymphoblasts ALD vs. control fam5 rep10

source_name: lymphoblasts from control patient N10

tag: immortalized lymphoblasts from N10

source_name: lymphoblasts from ALD patient B11


title: 008 RCC needle_03 (expression)


title: Lymphoblasts ALD vs. control fam5 rep14


title: Lymphoblasts ALD vs. control fam5 rep12

source_name: lymphoblasts from control patient N12

tag: immortalized lymphoblasts  from N12


title: UT03 0530 #18 (expression)


title: UT03 0064 #32_02 (expression)


title: Lymphoblasts ALD vs. control fam5 rep8

source_name: lymphoblasts from control patient N9

tag: immortalized lymphoblasts from N9


title: UT03 0064 #31 (expression)

tag: genotype


title: CC 3M (SNP)


title: Lymphoblasts ALD vs. control fam5 rep9

tag: immortalized lymphoblast from N10


title: 004 RCC needle (expression)


title: UT04 464 #10 (SNP)


title: RCC 11T (SNP)


title: RCC 119T (SNP)


title: UT03 0064 #34_03 (expression)


title: Lymphoblasts ALD vs. control fam5 rep7


title: Lymphoblasts ALD vs. control fam5 rep6

source_name: lymphoblasts from control patient N8

tag: immortalized lymphoblasts from N8


title: Lymphoblasts ALD vs. control fam5 rep3

tag: immortalized lymphoblasts for B13

source_name: lymphoblasts from control patient N7

tag: immortalized lymphoblasts from N7


title: Lymphoblasts ALD vs. control fam5 rep2

source_name: lymphoblasts from control patient N6

tag: immortalized lymphoblasts from N6


title: UT04 455 #1 (SNP)

source_name: clear cell renal cell carcinoma

tag: disease state


title: CC 13M (SNP)


title: UT04 455 #5 (SNP)


title: UT04 464 #13_03 (SNP)


title: UT04 466 #1_04 (SNP)


title: UT04 455 #22_07 (SNP)


title: UT04 455 #10_05 (SNP)


title: Lymphoblasts ALD vs. control fam1 rep7

source_name: lymphoblasts from control patient N4

tag: immortalized lymphoblasts from N4

source_name: lymphoblasts from ALD patient B3

tag: immortalized lymphoblasts from B3


title: CC 4M (SNP)


title: UT04 455 #5 (expression)


title: UT04 455 #1 (expression)


title: UT04 464 #13_03 (expression)


title: Lymphoblasts ALD vs. control fam5 rep5


title: Lymphoblasts ALD vs. control fam1 rep8

source_name: lymphoblasts from control patient B3


title: Lymphoblasts ALD vs. control fam5 rep1

tag: lymphoblasts from ALD patient B11

tag: lymphoblasts from control patient N6


title: Lymphoblasts ALD vs. control fam5 rep4

source_name: lymphoblasts from ALD patient B13

tag: immortalized lymphoblasts from B13


title: Lymphoblasts ALD vs. control fam1 rep6

source_name: lymphoblasts from control patient B2

tag: immortalized lymphoblasts from B2


title: CC 12M (SNP)

tag: tissue


title: UT04 466 #1_04 (expression)


title: UT04 455 #22_07 (expression)


title: Lymphoblasts ALD vs. control fam1 rep5

source_name: lymphoblasts from ALD patient B2


title: UT04 455 #10_05 (expression)


title: Lymphoblasts ALD vs. control fam1 rep4

source_name: lymphoblasts from control patient N1

tag: immortalized lymphoblasts from N1


title: RCC 141T (SNP)


title: Normoxia-HIF1-1

description: HIF-1 ChIP Normoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 1

source_name: IP: HepG2 cells under normoxic condition

tag: cell line

tag: cell type

value: hepatocellular carcinoma

tag: cell tissue

value: liver

tag: antibody

value: HIF-1 polyclonal

source_name: Input: HepG2 cells under normoxic condition


title: Hypoxia-HIF1-1

description: HIF-1 ChIP Hypoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 1

source_name: IP: HepG2 cells under hypoxic condition (0.5%O2, 4 hours)

source_name: Input: HepG2 cells under hypoxic condition (0.5%O2, 4 hours)


title: RCC 14T (SNP)

tag: genotype


title: Lymphoblasts ALD vs. control fam1 rep3


title: Lymphoblasts ALD vs. control fam1 rep2


title: UT04 455 #13_06 (SNP)


title: Normoxia-HIF1-4

description: HIF-1 ChIP Normoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 4


title: RCC 55T (SNP)


title: UT04 455 #13_06 (expression)


title: Hypoxia-HIF1-4

description: HIF-1 ChIP Hypoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 4


title: RCC 66T (SNP)


title: Lymphoblasts ALD vs. control fam1 rep1


title: UT04 464 #12_02 (SNP)


title: Normoxia-HIF1-2

description: HIF-1 ChIP Normoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 2


title: UT04 464 #12_02 (expression)


title: Hypoxia-HIF1-2

description: HIF-1 ChIP Hypoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 2


title: Hypoxia-HIF1-3

description: HIF-1 ChIP Hypoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 3


title: RCC 61T (SNP)


title: RCC 2T (SNP)


title: RCC 80T (SNP)


title: Clostridium beijerinckii mutant BA101 time course (27hr fermentation)

city: Urbana

first: Zhen

last: Shi

state: IL

address: 1206 West Gregory Drive

department: Institute for Genomic Biology

institute: University of Illinois

description: Clostridium beijerinckii mutant BA101 was monitored from exponential growth to stationary phase.

hyb_protocol: The printed array slides were re-hydrated and UV cross-linked. The slides were then washed in 0.2% SDS (w/v) followed by a H2O rinse. Washed slides were pre-hybridized in 75 mM sodium citrate and 750 mM NaCl pH 7.0 (5X SSC), 0.1% SDS and 1% (w/v) bovine serum albumin (BSA) in a 42 oC water bath for 45 min. After pre-hybridization the slides were washed in H2O five times followed by a last wash in isopropanol. The slides were spun dry immediately in 50 ml conical tubes at 700 x g for 1 min and kept until hybridization. A set of oppositely labeled cDNA probes were mixed in 30 ul SlideHyb Glass Array Hybridization Buffer (Ambion) and heated at 95 oC for 2-3 min. The probe set solution was applied to an array slide placed in a Corning hybridization chamber. The slides were hybridized in a 42 oC water bath for 16-20 hr. After hybridization the slides were washed with 1X SSC and 0.2% SDS at 42 oC for 5 min, followed by a second wash in 0.1X SSC and 0.2% SDS at room temperature for 5 min and two washes in 0.1X SSC at room temperature for 5 min. The washed slides were spun dry immediately at 200 x g for 5 min.

scan_protocol: Slides were scanned using an Axon 4000B Microarray Scanner (Molecular Devices).

data_processing: Feature intensity statistics were extracted using GenePix Pro 6.0 (Molecular Devices). Median spot intensity was obtained by substracting median intensity of non-specific background from median intensity of each feature. Spot intensities for all the features on an array were normalized using TIGR MIDAS. Expression ratios for duplicate spots representing the same probe sequence were averaged after normalization.

organism: Clostridium beijerinckii NCIMB 8052

source_name: Clostridium beijerinckii NCIMB 8052 mixture of RNA samples collected at various time points

label_protocol: 3ug total RNA was spiked with 6 ug random hexamer primers (GE Healthcare) in a 20 ul reaction, incubated at 70 oC for 10 min and then cooled on ice. The spiked reaction was incubated with 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, 0.2 mM aminoallyl-dUTP and 400 units Superscript III reverse transcriptase (Invitrogen) in 1X First Strand Buffer (Invitrogen) in a total of 40 ul at 46 oC for 3-8 hr. Aminoallyl-labelled cDNA in the mixture was purified on a QIAquick PCR purification column (QIAGEN) and dried in a speedvac. Cy3 or Cy5 dye ester (Molecular Probes) was dissolved in 10 ul 100 mM Na2CO3 and mixed with dried cDNA sample. The dye-coupling reaction was incubated in the dark at room temperature for 1 hr. The reaction was neutralized with 395 ul of a 300 mM sodium acetate solution (pH 5.2). The mixture was loaded onto a QIAquick PCR purification column (QIAGEN) to purifiy dye-labelled cDNA. The quantity, quality and dye incorporation ratio of purified cDNA probes were determined by measuring A260, A280, A550 (for Cy3 probe) and A650 (for Cy5 probe) on a UV/vis-spectrophotometer. Probes with dye incorporation of at least 20 dyes per 1,000 nucleotides were used for array hybridization. Purified cDNAs were dried on a speedvac and used for hybridization within the same day.

growth_protocol: Clostridium beijerinckii NCIMB 8052 spore stock was stored at 4 oC in sterile H2O. Solid culture was prepared in agar-solidified TGY plates (TGY containing 30 g/L tryptone, 20 g/L glucose, 10 g/L yeast extract, 1 g/L L-cysteine and 4.5 g/L agar). Liquid cultures were inoculated with single colonies from plates. Cultures were grown in Cooked Meat Medium (CMM containing 100 g/L cooked meat medium and 10 g/L glucose) to late exponential phase at 35 °C in an anaerobic chamber. CMM culture was then inoculated into fresh TGY medium and grown at 35 °C for a few hours. TGY pre-culture was inoculated into Complete P2 Medium containing P2 stock solutions supplemented with 60 g/L glucose and 1 g/L yeast extract (P2 Medium, Qureshi, N. and Blaschek, H. P. 1999. Biomass Bioenergy 17:175-184) and grown at 35 °C into late stationary phase. Samples were taken at selected time points during the course of fermentation.

extract_protocol: 10 ml sample was collected at a specific time point from a batch fermentation culture. Cells were pelleted by centrifuging at 4,000 x g at 4 oC for 10 min. Total RNA was extracted from cell pellets using RNeasy Mini Kits (Qiagen) according to the manufacturer’s protocol. RNA quality was determined using nanochip on an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA concentration was quantified by A260 using a UV/vis spectrophotometer (Biotek Instruments). A RNA pool was generated by mixing equal amounts of RNA preparations obtained from samples taken at different time points during fermentation.

treatment_protocol: Samples were taken at different stages of fermentation from a batch culture of Clostridium beijerinckii NCIMB 8052 in Complete P2 Medium. Samples were combined to produce a pool for the generation of a reference probe for array hybridization.

tag: A pool of samples representating different stages of fermentation of Clostridium beijerinckii NCIMB 8052.

organism: Clostridium beijerinckii

source_name: Clostridium beijerinckii mutant BA101 27hr fermentaton sample

label_protocol: Same as Channel 1

growth_protocol: Same as Channel 1

extract_protocol: Same as Channel 1 except that total RNA was extracted from 27hr fermentation culture

treatment_protocol: A Sample was taken at 27hr after initiation of a batch fermentation culture of Clostridium beijerinckii BA101 in Complete P2 Medium.

tag: Sample collected 27 hours after fermentor inoculation


title: RCC 32T (SNP)


title: Normoxia-HIF1-3

description: HIF-1 ChIP Normoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 3


title: Liver_C8

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: BeadStudio, quantile normalization

source_name: Liver, control C8

label_protocol: Illumina protocol

value: WT


title: Clostridium beijerinckii mutant BA101 time course (24hr fermentation)

tag: A pool of samples representating different stages of fermentation of Clostridium beijerinckii NCIMB 8052

source_name: Clostridium beijerinckii mutant BA101 24hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 24hr fermentation culture

treatment_protocol: A Sample was taken at 24hr after initiation of a batch fermentation culture of Clostridium beijerinckii BA101 in Complete P2 Medium.

tag: Sample collected 24 hours after fermentor inoculation


title: Liver_E7

source_name: Liver, KIKO E7

value: KIKO


title: RCC 29T (SNP)

source_name: clear cell renal cell carcinoma

tag: disease state


title: RCC 132T (SNP)


title: RCC 41T (SNP)


title: Clostridium beijerinckii mutant BA101 time course (13hr fermentation)

source_name: Clostridium beijerinckii mutant BA101 13hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 13hr fermentation culture

treatment_protocol: A Sample was taken at 13hr after initiation of a batch fermentation culture of Clostridium beijerinckii BA101 in Complete P2 Medium.

tag: Sample collected 13 hours after fermentor inoculation


title: Liver_E6

source_name: Liver, KIKO E6


title: RCC 124T (SNP)


title: Liver_C4

source_name: Liver, control C4


title: RCCT 168-T1C (SNP)


title: Clostridium beijerinckii mutant BA101 time course (11hr fermentation)

source_name: Clostridium beijerinckii mutant BA101 11hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 11hr fermentation culture

treatment_protocol: A Sample was taken at 11hr after initiation of a batch fermentation culture of Clostridium beijerinckii BA101 in Complete P2 Medium.

tag: Sample collected 11 hours after fermentor inoculation


title: RCCT 170-T1A (SNP)


title: Clostridium beijerinckii mutant BA101 time course (7hr fermentation)

source_name: Clostridium beijerinckii mutant BA101 7hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 7hr fermentation culture.

treatment_protocol: A Sample was taken at 7hr after initiation of a batch fermentation culture of Clostridium beijerinckii BA101 in Complete P2 Medium.

tag: Sample collected 7 hours after fermentor inoculation


title: RCCT 171-T3 (SNP)

value: VHL not biallelicall inactivated


title: Clostridium beijerinckii mutant BA101 time course (6hr fermentation)

growth_protocol: Clostridium beijerinckii NCIMB 8052 spore stock was stored at 4 oC in sterile H2O. Solid culture was prepared in agar-solidified TGY plates (TGY containing 30 g/L tryptone, 20 g/L glucose, 10 g/L yeast extract, 1 g/L L-cysteine and 4.5 g/L agar). Liquid cultures were inoculated with single colonies from plates. Cultures were grown in Cooked Meat Medium (CMM containing 100 g/L cooked meat medium and 10 g/L glucose) to late exponential phase at 35 °C in an anaerobic chamber. CMM culture was then inoculated into fresh TGY medium and grown at 35 °C for a few hours. TGY pre-culture was inoculated into Complete P2 Medium containing P2 stock solutions supplemented with 60 g/L glucose and 1 g/L yeast extract (P2 Medium, Qureshi, N. and Blaschek, H. P. 1999. Bioenergy 17:175-184) and grown at 35 °C into late stationary phase. Samples were taken at selected time points during the course of fermentation.

source_name: Clostridium beijerinckii mutant BA101 6hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 6hr fermentation culture.

treatment_protocol: A Sample was taken at 6hr after initiation of a batch fermentation culture of Clostridium beijerinckii BA101 in Complete P2 Medium.

tag: Sample collected 6 hours after fermentor inoculation


title: RCCT 206-T1C (SNP)

extract_protocol: Genomic DNA was isolated from tissue or cell pellets using SDS/proteinase K followed by phenol/chloroform and isopropanol precipitation, and quantified using Picogreen.


title: RCC 10T (SNP)


title: RCCT 158-T1B (SNP)


title: Liver_C3

source_name: Liver, control C3


title: Clostridium beijerinckii mutant BA101 time course (5hr fermentation)

source_name: Clostridium beijerinckii mutant BA101 5hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 5hr fermentation culture.

treatment_protocol: A Sample was taken at 5hr after initiation of a batch fermentation culture of Clostridium beijerinckii BA101 in Complete P2 Medium.

tag: Sample collected 5 hours after fermentor inoculation


title: RCC 0006T (SNP)

tag: tissue


title: UT04 142 #6_03 (expression)


title: E4m

source_name: Skeletal muscle, KIKO E4

value: Skeletal Muscle


title: UT04 142 #5_02 (expression)


title: C6m

source_name: Skeletal muscle, control C6


title: Clostridium beijerinckii mutant BA101 time course (4hr fermentation)

source_name: Clostridium beijerinckii mutant BA101 4hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 4hr fermentation culture

treatment_protocol: A Sample was taken at 4hr after initiation of a batch fermentation culture of Clostridium beijerinckii BA101 in Complete P2 Medium.

tag: Sample collected 4 hours after fermentor inoculation


title: UT04 142 #8_04 (expression)


title: UT04 142 #6_03 (SNP)


title: Clostridium beijerinckii mutant BA101 time course (3hr fermentation)

source_name: Clostridium beijerinckii NCIMB 8052 mixture of RNA samples collected at various time points

source_name: Clostridium beijerinckii mutant BA101 3hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 3hr fermentation culture.

treatment_protocol: A Sample was taken at 3hr after initiation of a batch fermentation culture of Clostridium beijerinckii BA101 in Complete P2 Medium.

tag: Sample collected 3 hours after fermentor inoculation


title: Clostridium beijerinckii mutant BA101 time course (9hr fermentation)

source_name: Clostridium beijerinckii mutant BA101 9hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 9hr fermentation culture

treatment_protocol: A Sample was taken at 9hr after initiation of a batch fermentation culture of Clostridium beijerinckii BA101 in Complete P2 Medium.

tag: Sample collected 9 hours after fermentor inoculation


title: UT04 142 #5_02 (SNP)


title: C6h

source_name: Heart, control C6

value: Heart


title: UT04 142 #4 (expression)


title: UT04 142 #9_05 (expression)


title: Clostridium beijerinckii mutant BA101 time course (1hr fermentation)

source_name: Clostridium beijerinckii mutant BA101 1hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 1 hr fermentation culture.

treatment_protocol: A Sample was taken at 1hr after initiation of a batch fermentation culture of Clostridium beijerinckii BA101 in Complete P2 Medium.

tag: Sample collected 1 hour after fermentor inoculation


title: E4h

source_name: Heart, KIKO E4

extract_protocol: Trizol


title: UT03 0538 #7_02 (expression)

source_name: clear cell renal cell carcinoma

extract_protocol: For total RNA extraction, tumor regions containing at least 70% of tumor cells were isolated from the frozen blocks utilizing a 2mm punch.   Frozen tissue fragments were pulverized with a chilled mortar and pestle and homogenized in 1 ml of Triazol reagent (Gibco/BRL).


title: C8m

source_name: Skeletal muscle, control C8


title: C4m

source_name: Skeletal muscle, control C4


title: UT03 0599 #6_03 (expression)


title: UT04 142 #8_04 (SNP)


title: UT04 142 #10_06 (expression)


title: C3m

source_name: Skeletal muscle, control C3


title: UT04 142 #4 (SNP)