source_name: L3 stage larvae,Light Blue Gut PS(3-6) (Celniker/RNA:450) 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.
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: L3 stage larvae, light blue gut PS(3-6) stage


title: Mouse retina_3 days_ rep1

status: Public on Aug 06 2010

type: RNA

city: Acton

first: Riccardo

last: Natoli

state: ACT

address: Sullivans Creek Road

department: CMBE

country: Australia

institute: ANU

description: Gene expression data from mouse retina exposued to 3 days 75% hyperoxia

hyb_protocol: Standard Affymetrix protocols were followed in the hybridisation, blocking and washing (GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 3)).

scan_protocol: The arrays were scanned on the GCS 3000 Affymetrix high resolution scanner and analyzed using the GeneChip Operating Software v1.4 (GCOS; Affymetrix) and GeneSpring v 7.3.1 (Agilent Technologies).

data_processing: RMA normalization performed in GeneSpring v 7.3.1. Log2 RMA data was quantile transformed to median sample baseline.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: retina, 3 days exposure to 75% hyperoxia

label_protocol: Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 500ng total RNA (Affymetrix manual, P/N 702646 Rev. 7).

growth_protocol: Animals were raised in cyclic light conditions using 12hrs dim (5 lux) and 12hrs dark (no light).

extract_protocol: Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.

treatment_protocol: Animals were placed in an oxygen chamber and exposed to 75% oxygen for a period of either 3, 7 or 14 days.

tag: strain

tag: tissue

value: Retina

tag: age

value: Adult P80 - 120


title: Mouse retina_Control_ rep2

description: Gene expression data from mouse retina exposued to normal oxygen levels

source_name: retina, no hyperoxia


status: Public on Aug 05 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

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

scan_protocol: Scanned at 0.7 microns/pixel.

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

organism: Drosophila melanogaster

source_name: L3 stage larvae,Light Blue Gut PS(3-6) (Celniker/RNA:446) extraction2_array1 channel_1

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

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

value: Y cn bw sp

tag: developmental stage

tag: genotype

tag: sex

value: Unknown


molecule: nuclear RNA

source_name: ML-DmBG3-c2 (Celniker/RNA:488) extraction1_array1 channel_1

growth_protocol: instructions for growth of BG3-c2 cells for RNA isolation.

extract_protocol:
For isolation of nuclear RNA from cell cultures.  Nuclei are isolated by differential centrifugation and RNA is collected using the TRIzol protocol for cell lines. This protocol is modified from Zimmerman et al 1982 (PNAS 79:3148) and used to prepare nuclear RNA from cell lines
cDNA Synthesis and Labeling: Note that this protocol gives you labeled dsDNA, as such the array results are not stranded.* ug cDNA hybed per chip: 10 ug if template was total RNA or Poly-A-, 2.5 ug if Poly-A+ RNAFIRST-STRAND SYNTHESIS  - 10 ug of Total RNA (DNAsed,Cleaned-up and ETOH precipitated)  - 1.25 ug of 250ng/ul random primers (Invitrogen)  - diH2O to 60 ul Vf.Incubate at 70C for 10 mins (fast ramp) then cool to 15C over the course of 20 minutes. Once it reaches 15C add:  - 20 ul of 5X First-Strand Buffer (Invitrogen)  - 10 ul of 100mM DTT (Invitrogen)  - 5 ul of 10mM dNTPs (Invitrogen)Incubate at 15C for 30 minutes then heat to 42C over the course of 20 minutes.  Once it reaches 42C add:  - 10 ul Superscript RT II (Invitrogen)Incubate at 42C for 60 minutes, then heat rapidly to 70C and incubate for 15 minutes, then park it at 4C.SECOND-STRAND SYNTHESISTo the First strand synthesis reaction above add while at 4C:  - 450 ul diH2O  - 150 ul 5X Second-Strand Buffer (Invitrogen)  - 15 ul 10mM dNTPs (Invitrogen)  - 5 ul 10U/ul E. coli DNA Ligase (Invitrogen)  - 20 ul 10U/ul E. coli DNA Polymerase (Invitrogen)  - 5 ul 2U/ul E. coli RNAseH (Invitrogen)Incubate at 16C for 120 minutes, then 70C for 15 minutes, then park it at 4C.RNA REMOVAL and cDNA PURIFICATIONAdd:  - 3 ul of 10U/ul RNaseH (Ambion)  - 3 ul of 5 and 20U/ul RNAseA/T1 (Ambion)Incubate at 37C for 20 minutesUse a Qiagen PCR Clean-up kit (two columns per reaction), ETOH precipitate the eluate and 70% ETOH rinse.  Redissolve in 35 ul diH2O.  Measure the OD600 on a Nanodrop.cDNA FRAGMENTATION*** NEED TO ADD ***Check the fragmentation on an agarose gel. Want it to be around 100 nucleotides.

tag: cell line

value: CNS-derived cell-line

value: third instar larval stage

value: y v f mal


source_name: S2-DRSC (Celniker/RNA:482) extraction1_array1 channel_1

growth_protocol: Description of the growth and maintenance of S2-DRSC cells used by modENCODE for RNA preparations.

value: embryo-derived cell-line

value: late embryonic stage

value: Male


source_name: S2-DRSC (Celniker/RNA:484) extraction3_array1 channel_1


molecule: polyA RNA

source_name: ML-DmBG2-c3 (Celniker/RNA:486) extraction2_array1 channel_1

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


source_name: L3 stage larvae,Clear Gut PS (7-9) (Celniker/RNA:454) 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 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, clear gut PS(7-9) stage


source_name: L3 stage larvae,Clear Gut PS (7-9) (Celniker/RNA:452) extraction1_array1 channel_1


source_name: L3 stage larvae,12 hr post-molt (Celniker/RNA:300) extraction3_array1 channel_1

value: L3 stage larvae, 12 hr post-molt


source_name: L3 stage larvae,12 hr post-molt (Celniker/RNA:298) extraction2_array1 channel_1


source_name: L3 stage larvae,12 hr post-molt (Celniker/RNA:296) extraction1_array1 channel_1


source_name: L3 stage larvae,Dark Blue Gut PS(1-2) (Celniker/RNA:444) extraction1_array1 channel_1

value: L3 stage larvae, dark blue gut PS(1-2) stage


hyb_protocol: Array hybridization and processing was performed at the Vanderbilt Shared Microarray Resource (VMSR) http://array.mc.vanderbilt.edu/. Briefly, targets in Hyb cocktail were received in the VMSR for hybridization services. Affymetrix targets in hyb cocktail were heat denatured at 99C for 5', and then held at 45C for at least 5 minutes. Targets were loaded on the Affymetrix Tiling arrays and the arrays were hybridized for 16 h at 45C in a rotisserie oven. After hybridization, arrays were washed using the Affymetrix fluidics station and the Affymetrix HWS kit (cat#900720), which provides pre-made stains (SAPE and antibody) as well as final holding buffer, including wash buffers A and B.  All steps were completed according to the Affymetrix technical manual. Washed arrays were scanned on an Affymetrix GeneChip Scanner 3000.  Cel files were posted to the investigator.

data_processing: Tiling_Array_Signal_Extraction protocol. Mismatch (MM) probe values are subtracted from their corresponding perfect match (PM) probes.  Processed data are obtained using following parameters: BPMap is BPmap:GPL5634:RW:1&oldid=22907   Tiling_Array_Normalization_and_Smoothing protocol. Biological replicates (usually 3 but sometimes 2) are normalized using quantile normalization.  The normalized signal from multiple replicates are then smoothed to produce a composite signal. Each probe's value is replaced by the psuedomedian of all probes in a window around it from all replicates. This is done in a sliding window fashion shifted one probe at a time. The window size is set to 110bp, which corresponds to about 4 probes.  Processed data are obtained using following parameters: window size is 110

organism: Caenorhabditis elegans

source_name: embryo A-class motor neurons tiling array extraction2_array1 channel_1

label_protocol: The NuGEN WT Pico RNA amplification kit was used to generate amplified single stranded cDNA from RNA samples. Starting material is 10 ng of RNA for mRNA tagging experiments and 1-5 ng of RNA for embryonic cells isolated by FACS.  The NuGEN WT-Ovation Exon Module was used to synthesize double stranded cDNA from the amplified single stranded cDNA template.   This was followed by fragmentation and labeling with the NuGEN FL-Ovation cDNA Biotin Module.

growth_protocol:
Animals were synchronized by treating a mixed stage hermaphrodite population with bleach to collect embryos.   The embryos surviving bleach treatment were incubated without food, causing the larvae to arrest at the L1 stage upon hatching.  Starved L1 larvae were plated in the presence of food and raised at 20 degrees Celsius (or indicated temperature) to desired stage.
For embryonic assays, embryonic cells were obtained using methods previously described [Christensen et al, 2002). Briefly, embryos were isolated from gravid adults following lysis in a hypochlorite solution. Intact embryos were separated from debris by flotation on 30% sucrose. For later stages, the embryos were incubated without food, causing the larvae to arrest at the L1 stage upon hatching. Starved L1 larvae were plated on standard NGM plates in the presence of food (OP50) and raised at 20 degrees Celsius. Staging was determined by examining a subset of animals under Nomarski optics at intervals for postdeirid, vulval and germline development. Animals were collected at the mid-L2, late L3-mid L4 and young adult (pre-gravid) stages and washed in M9 buffer. mid-L2 worms were collected when postdeirid divisions complete. L3/L4 animals were collected when a majority of animals diplayed a bilaterally symmetrical "christmas tree" vulval anatomy (See view at 40 hr, Fig 18, Sulston and Horvitz, Dev. Biol. 56, 110-156, 1977) Young Adult  were collected when vulvae fully formed and oocytes present in gonad, but no embryos. The worms were centrifuged on a sucrose cushion to remove debris and recovered in several washes of M9 buffer.
Embryonic cells were obtained using methods previously described [Christensen et al, 2002). Briefly, embryos were isolated from gravid adults following lysis in a hypochlorite solution. Intact embryos were separated from debris by flotation on 30% sucrose. Eggshells were removed by incubation in 0.5 ml chitinase (0.5 U/ml in egg buffer) for 45 minutes. Following resuspension in L-15 medium supplemented with 10% FBS (L15-10) and antibiotics, the embryos were dissociated by passage through a 5?m syringe filter (Durapore). Cells were plated on poly-L-lysine (0.01%, Sigma) coated single-well chambered coverglasses (Nalgene Nunc International) at a density of ~10 million cells/ml and maintained in L15-10 media. Cells were incubated at 25°C in a humidified chamber. Wildtype (N2) cells were isolated and treated similarly.FACSSorting experiments were performed on a FACStar Plus flow cytometer equipped with a 488 nm argon laser or on a FACS Aria (488nm, 633 nm lasers) (Becton Dickinson, San Jose, CA). Emission filters were 530 ± 30 nm for GFP fluorescence and 585 ± 22 nm for PI fluorescence. The machine was flushed with egg buffer [6] prior to sorting to enhance viability. 2 um fluorescent beads were used to calibrate light scattering parameters for the relatively small size of C. elegans embryonic cells. Cells were sorted at a rate of 4000-5000 cells per second through a 70 um nozzle. Immediately prior to sorting, supernatant from the 24 hour cultures was removed and discarded. 1 ml of egg buffer was added to the chamber coverglass. Cells are loosely adherent to poly-L-lysine and can be easily dislodged with gentle pipetting. 3 ml of egg buffer + cells were drawn into a 3 cc syringe and the suspension filtered with a 5 ?m Durapore  syringe filter. Propidium Iodide (PI) was added to the cell suspension at a final concentration of 5 ug/ml prior to sorting. Autofluorescence levels were established by flow cytometry of cells isolated from wildtype (i.e. non-GFP) embryos (See Fig 2A). Next, wildtype cells stained with PI were used to define the sorting gate for damaged cells. GFP+ cells containing no PI were sorted to establish the intensity range of GFP fluorescence. Finally, unc-4::GFP cells stained with PI were gated (Fig 2B) using the parameters established above. The sorting gate for size and granularity (Fig 2C) was empirically adjusted to exclude cell clumps and debris and to achieve ~90% enrichment for GFP-labeled cells. unc-4::GFP cells were collected in a 15 ml conical tube containing 1 ml of L15-10 media. Cells were pelleted using low-speed cenrifugation (300 × g) and either plated on peanut lectincoated slides for visualization [6] or used for RNA isolation (see below). Reference cells were obtained from 1 day old cultures of embryonic blastomeres isolated from the non-GFP wildtype strain (N2). In this case, all viable cells (i.e. non-PI stained) were collected by FACS for RNA isolation.(from Fox et al.,2005)

extract_protocol: Add cells lysate/Trizol (from FACS) to Phase Lock Gel Heavy tubes, extract with phenol/chloroform and precipitate RNA with isopropanol. Wash pellet with 75% ethanol and dissolve pellet in DEPC dwater for purification and concentration with ZYMO DNA-free RNA kit(Detailed protocol: MAPCeL_RNA_isolation.doc)

value: NC300 (engineered, target gene unc-119 tagged by GFP)

value: unc-4 neurons (embryonic)

value: Mixed stage of embryos 20dC

value: Hermaphrodite


scan_protocol: Array hybridization and processing was performed at the Vanderbilt Shared Microarray Resource (VMSR) http://array.mc.vanderbilt.edu/. Briefly, targets in Hyb cocktail were received in the VMSR for hybridization services. Affymetrix targets in hyb cocktail were heat denatured at 99C for 5', and then held at 45C for at least 5 minutes. Targets were loaded on the Affymetrix Tiling arrays and the arrays were hybridized for 16 h at 45C in a rotisserie oven. After hybridization, arrays were washed using the Affymetrix fluidics station and the Affymetrix HWS kit (cat#900720), which provides pre-made stains (SAPE and antibody) as well as final holding buffer, including wash buffers A and B.  All steps were completed according to the Affymetrix technical manual. Washed arrays were scanned on an Affymetrix GeneChip Scanner 3000.  Cel files were posted to the investigator.

source_name: embryo germline precursor cells tiling array extraction1_array1 channel_1

value: SS747 (engineered, target gene pie-1 tagged by GFP)

value: germ line precursor (embryonic)

value: bnIs1 (pie-1p8::GFP::PGL-1+unc119)


source_name: embryo hypodermal cells tiling array extraction1_array1 channel_1

value: DM8001 (engineered, target gene dpy-7 tagged by GFP)

value: hypodermis


source_name: embryo hypodermal cells tiling array extraction3_array1 channel_1


source_name: embryo A-class motor neurons tiling array extraction3_array1 channel_1


hyb_protocol: Array hybridization and processing performed at the Keck Facility at Yale University. Briefly, array hybridization buffer (100 mM MES, 1M [Na+], 20 mM EDTA, 0.01 % Tween 20) is used to prehybridize the array for 10-15 minutes at 450C. The prehybridized solution is removed and replaced with 80 ul of hybridization mixture containing hybridization buffer, fragmented cRNA (0.05ìg/ìl) and herring sperm DNA (0.1 mg/ml; Promega). Also included in the hybridization buffer are acetylated BSA (0.5 mg/ml, Invitrogen) and four control bacterial and phage cRNA (1.5 pM BioB, 5 pM Bio C, 25 pM BioD, and 100 pM Cre) samples to serve as internal controls for hybridization efficiency. The arrays are hybridized for 16 h at 450 in a rotisserie oven. After hybridization, arrays are washed using the Affymetrix fluidics station and stained with streptavidin-phycoerythrin (10 ìg/ml, Molecular Probes) according to the Affymetrix technical manual. Washed arrays will be scanned on a Affymetrix GeneChip Scanner 3000. Scanned output files will be visually inspected for hybridization artifacts and then analyzed by using Affymetrix GeneChip Operating Software (GCOS).

label: biotin

source_name: pathogen control OP50 25dC 48hr exposure post-adulthood N2 tiling array extraction3_array1 channel_1

growth_protocol:
Animals were synchronized by treating a mixed stage hermaphrodite population with bleach to collect embryos.   The embryos surviving bleach treatment were incubated without food, causing the larvae to arrest at the L1 stage upon hatching.  Starved L1 larvae were plated in the presence of food and raised at 20/25 degrees Celsius (as specified).
The embryos were incubated without food, causing the larvae to arrest at the L1 stage upon hatching. Starved L1 larvae were plated on standard NGM plates in the presence of food (OP50) and raised at 25 degrees Celsius. Staging was determined by examining a subset of animals under Nomarski optics at intervals for vulval and germline development. Animals were collected at the mid-L2, mid-L3, mid-L4, and young adult (pre-gravid) stages and washed in S basal buffer. Exact times for growth after plating of starved L1s (all at 25 degrees C) were as follows: (1) L1 worms were grown for 4 hours (2) L2 worms were grown for 17.75 hours (Pn.p cells visible but not divided, gonad just starting to proliferate); (3) L3 for 26.75 hours (Pn.p cells divided once or twice; gonad just starting to turn up); (4) L4 for 34.25 hours (vulvae are in Christmas tree stage gonad has passed bend, sperm are present); and (5) Young Adult for 46 hours (vulvae fully formed and oocytes present in gonad, but no embryos). The worms were centrifuged on a sucrose cushion to remove debris and recovered in several washes of S basal.
Bacterial strains included E. coli OP50, E. faecalis OG1RF, S. marcescens Db11, and P. luminescens Hb. Liquid cultures of E. coli,  P. luminescens and S. marcescens were grown in LB, E. faecalis in BHI. We spread 50-150 ul of overnight bacterial liquid culture (concentrated 10-fold), depending on size of the assay plate (35 or 90 mm diameter), onto fresh NGM agar plates and incubated them for 24 h.  P. luminescens were cultured at 30°C; E. coli, S. marcescens and E. faecalis at 37°C. We used 90 mm plates.Aliquots of synchronized larvae were transferred after 16-20 h to NGM plates spread with OP50 and cultivated at 25°C until just reaching adulthood. Worms were then transferred to assay plates. After 24 h or 48 h at 25°C, the worms were collected, washed three times in M9 buffer and pelleted and suspended in 10 volumes of Trizol.(Samples received as worms-in-trizol from Jonathan Ewbank's lab.)

extract_protocol:
RNA isolation from medium- to large-scale preparations of staged C. elegans nematodes. The worms were centrifuged on a sucrose cushion to remove debris and recovered in several washes of S basal.  Total RNA isolation was performed by adding 4 volumes of Trizol (Gibco) per volume of packed worms.  After two rounds of freeze/thaw and vortexing, the slurry was extracted with 2 volumes of chloroform. The aqueous layer was precipitated with one volume of isopropanol and the pellet washed with 70% ethanol.  The pellet was resuspended in water and the concentration determined by UV spectrometry.  RNA quality was assessed by examining an aliquot run on an ethidium bromide stained gel for discrete ribosomal and transfer RNA bands, as well as an mRNA "smear".
RNA is DNase treated as follows:  using the Ambion DNA-free kit, add 5ul of 10x DNAse I buffer and 1ul of DNAse I to 10ug total RNA in 50ul volume.  Incubate at 37deg C for 30'.  Add 5ul DNase inactivation reagent and mix well.  Incubate 2-3' at RT.  Spin 1.5' at 10K.  Put supernatant in clean RNAase-free tube.  Measure concentration by spectrophotometer. We follow the standard Affymetrix protocol for cDNA synthesis, using the GeneChip® WT Double-Stranded cDNA Synthesis Kit (#900813).  Everything is according to manufacturer.

value: Young Adult (pre-gravid) 25dC 46 hrs post-L1

value: wild type


scan_protocol: Array hybridization and processing performed at the Keck Facility at Yale University. Briefly, array hybridization buffer (100 mM MES, 1M [Na+], 20 mM EDTA, 0.01 % Tween 20) is used to prehybridize the array for 10-15 minutes at 450C. The prehybridized solution is removed and replaced with 80 ul of hybridization mixture containing hybridization buffer, fragmented cRNA (0.05ìg/ìl) and herring sperm DNA (0.1 mg/ml; Promega). Also included in the hybridization buffer are acetylated BSA (0.5 mg/ml, Invitrogen) and four control bacterial and phage cRNA (1.5 pM BioB, 5 pM Bio C, 25 pM BioD, and 100 pM Cre) samples to serve as internal controls for hybridization efficiency. The arrays are hybridized for 16 h at 450 in a rotisserie oven. After hybridization, arrays are washed using the Affymetrix fluidics station and stained with streptavidin-phycoerythrin (10 ìg/ml, Molecular Probes) according to the Affymetrix technical manual. Washed arrays will be scanned on a Affymetrix GeneChip Scanner 3000. Scanned output files will be visually inspected for hybridization artifacts and then analyzed by using Affymetrix GeneChip Operating Software (GCOS).

source_name: pathogen control OP50 25dC 24hr exposure post-adulthood N2 tiling array extraction1_array1 channel_1


source_name: pathogen control OP50 25dC 24hr exposure post-adulthood N2 tiling array extraction2_array1 channel_1

label_protocol: Array hybridization and processing performed at the Keck Facility at Yale University. Briefly, array hybridization buffer (100 mM MES, 1M [Na+], 20 mM EDTA, 0.01 % Tween 20) is used to prehybridize the array for 10-15 minutes at 450C. The prehybridized solution is removed and replaced with 80 ul of hybridization mixture containing hybridization buffer, fragmented cRNA (0.05ìg/ìl) and herring sperm DNA (0.1 mg/ml; Promega). Also included in the hybridization buffer are acetylated BSA (0.5 mg/ml, Invitrogen) and four control bacterial and phage cRNA (1.5 pM BioB, 5 pM Bio C, 25 pM BioD, and 100 pM Cre) samples to serve as internal controls for hybridization efficiency. The arrays are hybridized for 16 h at 450 in a rotisserie oven. After hybridization, arrays are washed using the Affymetrix fluidics station and stained with streptavidin-phycoerythrin (10 ìg/ml, Molecular Probes) according to the Affymetrix technical manual. Washed arrays will be scanned on a Affymetrix GeneChip Scanner 3000. Scanned output files will be visually inspected for hybridization artifacts and then analyzed by using Affymetrix GeneChip Operating Software (GCOS).


source_name: pathogen control OP50 25dC 24hr exposure post-adulthood N2 tiling array extraction3_array1 channel_1


source_name: L3 stage larvae,Clear Gut PS (7-9) (Celniker/RNA:456) extraction3_array1 channel_1

value: Y cn bw sp

value: Unknown


source_name: pathogen control OP50 25dC 48hr exposure post-adulthood N2 tiling array extraction2_array1 channel_1


source_name: pathogen control OP50 25dC 48hr exposure post-adulthood N2 tiling array extraction1_array1 channel_1


source_name: pathogen Smarcescens 25dC 24hr exposure post-adulthood N2 tiling array extraction3_array1 channel_1


source_name: pathogen Smarcescens 25dC 24hr exposure post-adulthood N2 tiling array extraction2_array1 channel_1


source_name: embryo hypodermal cells tiling array extraction2_array1 channel_1


source_name: embryo germline precursor cells tiling array extraction3_array1 channel_1


source_name: pathogen Smarcescens 25dC 24hr exposure post-adulthood N2 tiling array extraction1_array1 channel_1


source_name: pathogen Smarcescens 25dC 48hr exposure post-adulthood N2 tiling array extraction3_array1 channel_1


source_name: embryo A-class motor neurons tiling array extraction1_array1 channel_1


source_name: pathogen Smarcescens 25dC 48hr exposure post-adulthood N2 tiling array extraction2_array1 channel_1


source_name: embryo germline precursor cells tiling array extraction2_array1 channel_1


source_name: pathogen Smarcescens 25dC 48hr exposure post-adulthood N2 tiling array extraction1_array1 channel_1


title: Bt_glyphosate induction_rep3

city: Honolulu

first: Tung

last: Hoang

state: HI

address: 1800 East-West Road

department: Microbiology

country: USA

institute: University of Hawaii at Manoa

hyb_protocol: 1. Prepare hybridization solution    Hybridization solution mix recipe for two-color B. thailandensis microarray assay  Component Volume Final Concentration  100% Formamide 400 μl 40%  20x SSC 250 μl 5x  10% SDS 10 μl 0.1%  0.1M DTT 1 μl 0.1 mM  Total Volume 1 ml     2. Filter the hybridization buffer using a 1 ml syringe and 0.45 μm filter.  3. Add 60 μl of Salmon Sperm DNA.  4. Add 50 μl of 1x hybridization buffer to the Cy3/Cy5 probe mixture, heat at 95°C for 10 minutes.  5. Apply the entire labeled probe mixture on to the microarray slides with coverslips, hybridize in the hybridization chamber for 20 hours at 42°C.   6. Following hybridization, the wash procedures are carried out as in the established protocols (http://pfgrc.jcvi.org/index.php/microarray/protocols.html).

scan_protocol: Scan slides immediately in a GenePix 4000B scanner using GenePix Pro software 5.1 at the resolution of 10 μm/pixel and wavelength of 532 nm and 635 nm.

data_processing: Individual TIFF images from each channel were processed with Spotfinder software 3.2.1 (available at http://www.tm4.org) to generate mev data. Microarray data were then normalized by low intensity filtering, LOWESS normalization, standard de+B38viation regularization, and in-slide replicate analysis using MIDAS software 2.21 (available at http://www.tm4.org).  Finally, the mev files from MIDAS were used to generate the data table in MEV software 4.5.1 (available at http://www.tm4.org). The fold-change (FC) data for all detected genes were then obtained by combining the triplicate samples. The GS-induced genes (FC ≥ 2, p ≤ 0.05) and the GS-inhibited genes (FC ≥ 2, p ≤ 0.05) were kept for the final lists.

organism: Burkholderia thailandensis

source_name: Uninduced

label_protocol: 10 μg of total RNA was used in reverse transcription reactions, and cDNA fragmented and labeled following the established protocols (http://pfgrc.jcvi.org/index.php/microarray/protocols.html).

growth_protocol: B. thailandensis wildtype strain E264  was cultured overnight in LB medium, cells were harvested by centrifugation, washed twice with 1x M9 minimal medium, and inoculated into MG medium. Two of these identical cultures were then incubated at 37°C with shaking speed of 200 rpm.

extract_protocol: After induction, cells were treated with RNAprotect reagent (Qiagen) and total RNA was extracted using Trizol reagent. Extracted total RNA was further cleaned up using Qiagen RNeasy columns, including the additional on-column DNaseI digestion.

treatment_protocol: After the cultures reached mid-log phase (OD600 ~1.4), one culture was induced by adding 0.01% (w/v) final concentration of glyphosate and continued shaking for 30 minutes.

value: wildtype strain E264

tag: treatment

source_name: Induced

value: induced by addition of 0.01%(w/v) glyphosate for 30 minutes


title: Bt_glyphosate induction_rep1


source_name: pathogen Efaecalis 25dC 24hr exposure post-adulthood N2 tiling array extraction2_array1 channel_1


title: Bt_glyphosate induction_rep2


source_name: pathogen Efaecalis 25dC 24hr exposure post-adulthood N2 tiling array extraction1_array1 channel_1


source_name: gonad from young adult 20dC 42hrs post-L1 N2 tiling array extraction3_array1 channel_1

growth_protocol:
Animals were synchronized by treating a mixed stage hermaphrodite population with bleach to collect embryos.   The embryos surviving bleach treatment were incubated without food, causing the larvae to arrest at the L1 stage upon hatching.  Starved L1 larvae were plated in the presence of food and raised at 20/25 degrees Celsius (as specified).
The embryos were incubated without food, causing the larvae to arrest at the L1 stage upon hatching. Starved L1 larvae were plated on standard NGM plates in the presence of food (OP50) and raised at 25 degrees Celsius. Staging was determined by examining a subset of animals under Nomarski optics at intervals for vulval and germline development. Animals were collected at the mid-L2, mid-L3, mid-L4, and young adult (pre-gravid) stages and washed in S basal buffer. Exact times for growth after plating of starved L1s (all at 25 degrees C) were as follows: (1) L1 worms were grown for 4 hours (2) L2 worms were grown for 17.75 hours (Pn.p cells visible but not divided, gonad just starting to proliferate); (3) L3 for 26.75 hours (Pn.p cells divided once or twice; gonad just starting to turn up); (4) L4 for 34.25 hours (vulvae are in Christmas tree stage gonad has passed bend, sperm are present); and (5) Young Adult for 46 hours (vulvae fully formed and oocytes present in gonad, but no embryos). The worms were centrifuged on a sucrose cushion to remove debris and recovered in several washes of S basal.
These gonads were dissected from adult N2 hermaphrodites at 1 day of adulthood in 1x egg salts using small gauge needles.  (From Chi and Reinke, 2006) Adult worms were placed in dissection buffer (M9 with 0.1% levamisole and 0.001% Tween 20) on a coverslip. For each strain, a pair of 30 1/2-gauge needles was used to extrude approximately 50 gonad arms, excising each just proximal to the spermatheca. Dissected gonads were carefully isolated from carcasses and transferred into an Eppendorf tube.

extract_protocol:
Add 300ul of TRIzol to dissected gonads and vortex for 10 second (Can be stored at -80 at this point)  - Thaw the samples on ice.   - Pre-spin the Phase Lock Gel-Heavy 2ml tubes (Brinkmann Instruments, INC.  Catalog No. 955-15-404-5) at 12,000g for 1 min. - Add 5ug linear polyacrylamide (GeneClute LPA from Sigma) to the samples. - Vortex for 10 sec. - Transfer the sample to the pre-spun Phase Lock Gel-Heavy 2ml tubes. - Add 60ul chloroform. Close the top and shake vigorously for 15 seconds by hands. DO NOT VORTEX! - Centrifuge samples at 12,000g (no more than 12,000g) for 10 minutes at 4°C. Examine phasing. Clear, aqueous phase should be on top of the Phase Lock Gel. The phenol-chloroform phase with TRIzol reagent (pink phase) should be at the bottom.  - Transfer the aqueous phase to a clean (RNase ? free) tube. I usually get about 180ul. - Add 0.7 - 0.8 volume of isopropanol (~120ul). - Precipitate overnight at -20°C - Next day, spin the sample at full speed (~14K g) for 25min at 4°C. The pellet should be a small transparent dot and it is barely visible.   - Carefully remove the supernatant by pipette. You do not need to remove them completely.  - Wash once with 500ul 75% ethanol. The pellet should be visible (opaque) after the addition of ethanol.  - Spin at full speed for 5 minutes. - Carefully remove the supernatant by pipette. Give a quick spin to collect all residual ethanol at the bottom and completely remove them by pipette. - Allow the pellet to air dry for 1 minute. Do not overdry the pellet. - Dissolve the pellet with 4ul RNase ? free water. Incubate at 55°C for 5 minutes to facilitate dissolution.  * If you want to quantify the yield of RNA isolation, dissolve the pellet in 5ul of water and take 1ul for spectrometer measurement.  - Freeze the total RNA samples at -80°C.
RNA is DNase treated as follows:  using the Ambion DNA-free kit, add 5ul of 10x DNAse I buffer and 1ul of DNAse I to 10ug total RNA in 50ul volume.  Incubate at 37deg C for 30'.  Add 5ul DNase inactivation reagent and mix well.  Incubate 2-3' at RT.  Spin 1.5' at 10K.  Put supernatant in clean RNAase-free tube.  Measure concentration by spectrophotometer. We follow the standard Affymetrix protocol for cDNA synthesis, using the GeneChip® WT Double-Stranded cDNA Synthesis Kit (#900813).  Everything is according to manufacturer.

value: Gonad

value: Young Adult 20dC 42 hrs post-L1


source_name: L1 20dC 0hrs post-L1 N2 tiling array extraction1_array1 channel_1

growth_protocol:
Animals were synchronized by treating a mixed stage hermaphrodite population with bleach to collect embryos.   The embryos surviving bleach treatment were incubated without food, causing the larvae to arrest at the L1 stage upon hatching.  Starved L1 larvae were plated in the presence of food and raised at 20/25 degrees Celsius (as specified).
The embryos were incubated without food, causing the larvae to arrest at the L1 stage upon hatching. Starved L1 larvae were plated on standard NGM plates in the presence of food (OP50) and raised at 25 degrees Celsius. Staging was determined by examining a subset of animals under Nomarski optics at intervals for vulval and germline development. Animals were collected at the mid-L2, mid-L3, mid-L4, and young adult (pre-gravid) stages and washed in S basal buffer. Exact times for growth after plating of starved L1s (all at 25 degrees C) were as follows: (1) L1 worms were grown for 4 hours (2) L2 worms were grown for 17.75 hours (Pn.p cells visible but not divided, gonad just starting to proliferate); (3) L3 for 26.75 hours (Pn.p cells divided once or twice; gonad just starting to turn up); (4) L4 for 34.25 hours (vulvae are in Christmas tree stage gonad has passed bend, sperm are present); and (5) Young Adult for 46 hours (vulvae fully formed and oocytes present in gonad, but no embryos). The worms were centrifuged on a sucrose cushion to remove debris and recovered in several washes of S basal.

extract_protocol:
RNA isolation from medium- to large-scale preparations of staged C. elegans nematodes. The worms were centrifuged on a sucrose cushion to remove debris and recovered in several washes of S basal.  Total RNA isolation was performed by adding 4 volumes of Trizol (Gibco) per volume of packed worms.  After two rounds of freeze/thaw and vortexing, the slurry was extracted with 2 volumes of chloroform. The aqueous layer was precipitated with one volume of isopropanol and the pellet washed with 70% ethanol.  The pellet was resuspended in water and the concentration determined by UV spectrometry.  RNA quality was assessed by examining an aliquot run on an ethidium bromide stained gel for discrete ribosomal and transfer RNA bands, as well as an mRNA "smear".
We follow the standard Affymetrix protocol for cDNA synthesis, using the GeneChip® WT Double-Stranded cDNA Synthesis Kit (#900813).  Everything is according to manufacturer.

value: larva mid-L1 25dC 4.0 hrs post-L1


source_name: pathogen Pluminscens 25dC 24hr exposure post-adulthood N2 tiling array extraction3_array1 channel_1


source_name: L1 20dC 0hrs post-L1 N2 tiling array extraction2_array1 channel_1


source_name: gonad from young adult 20dC 42hrs post-L1 N2 tiling array extraction2_array1 channel_1


source_name: soma-only mid-L4 25dC 36hrs post-L1 JK1107 tiling array extraction1_array1 channel_1

value: larva mid-L4 25dC 34.25 hrs post-L1

value: glp-1(q224) III


source_name: L1 20dC 0hrs post-L1 N2 tiling array extraction3_array1 channel_1


source_name: pathogen Pluminscens 25dC 24hr exposure post-adulthood N2 tiling array extraction1_array1 channel_1

value: Hermaphrodite


source_name: soma-only mid-L4 25dC 36hrs post-L1 JK1107 tiling array extraction3_array1 channel_1


source_name: pathogen Pluminscens 25dC 24hr exposure post-adulthood N2 tiling array extraction2_array1 channel_1


source_name: late embryo 20dC 6-12hrs post-fertilization N2 tiling array extraction1_array1 channel_1

value: late embryo 20dC 4.5 hrs post-early embryo


source_name: late embryo 20dC 6-12hrs post-fertilization N2 tiling array extraction2_array1 channel_1


source_name: late embryo 20dC 6-12hrs post-fertilization N2 tiling array extraction3_array1 channel_1


source_name: gonad from young adult 20dC 42hrs post-L1 N2 tiling array extraction1_array1 channel_1


source_name: soma-only mid-L4 25dC 36hrs post-L1 JK1107 tiling array extraction2_array1 channel_1


source_name: male L4 25dC 36hrs post-L1 CB4689 tiling array extraction1_array1 channel_1

value: Male larva mid-L4 25dC 30 hrs post-L1

value: Male


source_name: male L4 25dC 36hrs post-L1 CB4689 tiling array extraction3_array1 channel_1


source_name: male L4 25dC 36hrs post-L1 CB4689 tiling array extraction2_array1 channel_1


source_name: L2 polyA enriched 20dC 14hrs post-L1 N2 tiling array extraction2_array1 channel_1

extract_protocol: For each library, a 10µg aliquot of DNaseI treated total RNA was separated into polyA+ and polyA- fractions using the MACSTM mRNA Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany).  Double-stranded cDNAs were made from the polyA+ fractions using the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, California, USA) and random hexamer primers (Invitrogen, 25 µM).  The quality and quantity of the resulting double-stranded cDNAs was assessed using an Agilent DNA 1000 series II assay (Agilent Technologies, Santa Clara, CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA). Aliquots containing ~200 ng amplified cDNA were each diluted with water to 100uL and sonicated for 5 minutes. Sonication was performed in an ice water bath using a Sonic DismembratorTM 550 (Fisher, Ottawa, Ontario, Canada) with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling. Total sonication times refer to active sonication time only and do not include the rest periods in between each pulse.

value: larva mid-L2 25dC 17.75 hrs post-L1


source_name: early embryo 20dC 0-4hrs post-fertilization N2 tiling array extraction1_array1 channel_1

value: early embryo


source_name: early embryo 20dC 0-4hrs post-fertilization N2 tiling array extraction2_array1 channel_1


source_name: early embryo 20dC 0-4hrs post-fertilization N2 tiling array extraction3_array1 channel_1


source_name: young adult 25dC 42hrs post-L1 N2 tiling array extraction3_array1 channel_1

value: Young Adult (pre-gravid) 25dC 46 hrs post-L1


source_name: young adult 25dC 42hrs post-L1 N2 tiling array extraction2_array1 channel_1

value: wild type


source_name: young adult 25dC 42hrs post-L1 N2 tiling array extraction1_array1 channel_1


source_name: L2 polyA enriched 20dC 14hrs post-L1 N2 tiling array extraction1_array1 channel_1


source_name: L3 25dC 25hrs post-L1 N2 tiling array extraction3_array1 channel_1

value: larva mid-L3 25dC 26.75 hrs post-L1


source_name: L3 25dC 25hrs post-L1 N2 tiling array extraction2_array1 channel_1


source_name: L4 25dC 36hrs post-L1 N2 tiling array extraction1_array1 channel_1


source_name: L3 25dC 25hrs post-L1 N2 tiling array extraction1_array1 channel_1


source_name: L4 25dC 36hrs post-L1 N2 tiling array extraction2_array1 channel_1


source_name: L4 25dC 36hrs post-L1 N2 tiling array extraction3_array1 channel_1


source_name: embryo body wall muscle tiling array (v2) extraction1_array1 channel_1

value: PD4251 (engineered, target gene myo-3 tagged by GFP)

value: body wall muscle

value: Mixed stage of embryos 20dC


source_name: embryo body wall muscle tiling array (v2) extraction2_array1 channel_1


source_name: L2 25dC 14hrs post-L1 N2 tiling array extraction2_array1 channel_1


source_name: L2 25dC 14hrs post-L1 N2 tiling array extraction3_array1 channel_1


source_name: L2 25dC 14hrs post-L1 N2 tiling array extraction1_array1 channel_1


source_name: embryo GABA motor neurons tiling array extraction2_array1 channel_1

value: CZ1200 (engineered, target gene unc-25 tagged by GFP)

value: GABA neurons (embryonic)


source_name: embryo GABA motor neurons tiling array extraction3_array1 channel_1


source_name: embryo dopaminergic neurons tiling array extraction3_array1 channel_1

value: BY200 (engineered, target gene dat-1 tagged by GFP)

value: dopaminergic neurons (embryonic)


source_name: embryo GABA motor neurons tiling array extraction1_array1 channel_1


source_name: embryo dopaminergic neurons tiling array extraction1_array1 channel_1


source_name: embryo dopaminergic neurons tiling array extraction2_array1 channel_1


source_name: embryo coelomocytes tiling array extraction2_array1 channel_1

value: TV1112 (engineered, target gene unc-122 tagged by RFP)

value: coelomocytes


source_name: embryo coelomocytes tiling array extraction3_array1 channel_1

value: Hermaphrodite


source_name: embryo AVA neurons tiling array extraction1_array1 channel_1

value: NC1749 (engineered, target gene rig-3 tagged by GFP)

value: embryo-AVA


source_name: embryo AVA neurons tiling array extraction3_array1 channel_1


source_name: embryo coelomocytes tiling array extraction1_array1 channel_1


source_name: embryo AVA neurons tiling array extraction2_array1 channel_1


source_name: adult male,eclosion + 30 days (Celniker/RNA:392) 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.
Protocol for staging adult flies for RNA isolation.

value: Y cn bw sp

value: Adult male, eclosion + 30 days

value: Male


source_name: embryo body wall muscle tiling array (v2) extraction3_array1 channel_1


source_name: embryo intestine tiling array extraction1_array1 channel_1

value: JR1130 (engineered, target gene elt-2 tagged by GFP)

value: intestinal cells

value: wIs84 [elt-2::GFP ]


source_name: embryo intestine tiling array extraction2_array1 channel_1


source_name: embryo intestine tiling array extraction3_array1 channel_1


source_name: embryo all cells reference tiling array extraction3_array1 channel_1

value: reference (embryo)

value: wild type


source_name: embryo all cells reference tiling array extraction1_array1 channel_1

value: Mixed stage of embryos 20dC


source_name: embryo panneural tiling array extraction3_array1 channel_1

value: NW1229 (engineered, target gene F25B3.3 tagged by GFP)

value: panneural


source_name: embryo panneural tiling array extraction2_array1 channel_1


source_name: embryo panneural tiling array extraction1_array1 channel_1


source_name: embryo all cells reference tiling array extraction2_array1 channel_1


title: IQE3866

type: genomic

city: La Jolla

first: Neekesh

middle: V

last: Dharia

state: CA

address: 10550 N Torrey Pines Road

institute: The Scripps Research Institute

description: Genomic DNA hybridization of Peruvian isolate

hyb_protocol: The samples were hybridized to the microarrays overnight at 45°C in Affymetrix buffers, washed, and scanned using a modified protocol with wash temperatures of 23°C to account for the high AT content of P. falciparum (Supplementary File 6 from this publication) (Dharia et al. 2009).

data_processing:
Briefly, for polymorphism detection, using a sliding window of three overlapping probes we scanned for sets probes that had significantly lower hybridization when compared to the reference indicative of a polymorphism as determined by z-test using a p-value cutoff of 1´10-5 and a reference 3D7 hybridization. Gene copy number variation scanning was performed by calculating the log2 ratio of the mean intensity for probes to a gene divided by the mean intensity of the probes for a reference 3D7 hybridization as previously described (Dharia et al. 2009).
The arrays were analyzed using our custom software available at http://www.scripps.edu/cb/winzeler/software and described in Dharia et al Genome Biology 2009, 10:R21.

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: Genomic DNA from Peruvian isolate

label_protocol: Fifteen micrograms of genomic DNA from each isolate and 2.5 ng each of Bio B, Bio C, Bio D, and Cre Affymetrix control plasmids (Affymetrix Inc., Santa Clara, CA, USA) were fragmented with DNaseI and end-labeled with biotin (Winzeler et al. 1998).

growth_protocol: 3D7 (MRA-151) was obtained from the Malaria Research and Reference Reagent Resource Center (MR4; American Type Culture Collection, Manassas, VA, USA). 3D7 and Peruvian P. falciparum patient isolates were propagated in human erythrocytes as previously described (Trager and Jenson 1978) with media for 3D7 containing 5% human serum and 1.2% GIBCO™ AlbuMAX II (Invitrogen) while the media for patient isolates contained 10% human serum.

extract_protocol: Genomic DNA was isolated by standard phenol-chloroform extraction.

value: Peruvian isolate


title: IQE4015

scan_protocol: The samples were hybridized to the microarrays overnight at 45°C in Affymetrix buffers, washed, and scanned using a modified protocol with wash temperatures of 23°C to account for the high AT content of P. falciparum (Supplementary File 6 from this publication) (Dharia et al. 2009).


title: IQE3648


title: IQE4081


title: IQE4006


title: IQE3848


title: IQE3785


title: IQE2980


title: IQE3466


title: TBI Blood_4h_1.25Gy_rep1_055

city: New York

first: Thomas

last: Templin

state: NY

address: 630 West 168th Street

institute: Columbia University Medical Center

description: Gene expression in patient blood at 4 h after TBI with 1.25 Gy

hyb_protocol: 1.65 µg Cy3-labeled cRNA (specific activity > 10.0 pmol Cy3/µg cRNA) was fragmented at 60° C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent, following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65° C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 min at room temperature with GE Wash Buffer 1 (Agilent) and for 1 minute with GE Wash buffer 2 at 37° C (Agilent).

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505B) using the one-color scan setting for 4 x 44 k array slides (scan setting with extended dynamic range, scan area 61 x 21.6 mm, scan resolution 5 µm, dye channel is set to Green, and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v1_91 and grid 014850_D_20070207) to obtain background subtracted and spatially detrended green processed signal intensities.  Features flagged in Feature Extraction as non-uniform outliers or as not positive and significant were excluded.

organism: Homo sapiens

source_name: Peripheral Blood, 4 h, 1.25 Gy, replicate 1

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.5 µg RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND 1000 Spectrophotometer (Thermo Fisher Scientific).

extract_protocol: RNA was extracted using the PAXgene Blood RNA Kit (Qiagen/BD company, TX) according to manufacturer’s instructions, followed by removal of globin transcripts using the GLOBINclear kit (Ambion Inc., Austin, TX) to remove both α- and β-globin. RNA was quantified using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Peripheral blood was collected shortly before total body irradiation (TBI) and at 4 hr after TBI with 1.25-Gy. Blood was drawn into PAXgene blood RNA tubes (PreAnalytiX GmbH, Switzerland) and kept at room temperature for at least 6 h before RNA isolation.

value: whole blood

tag: gender

value: male


title: stimulated_24hr_donor_2

city: Tampa

first: Matthew

middle: Adams

last: Smith

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

description: Donor 2 Stim

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000

data_processing: 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.

source_name: 24hr stimulated, human natural killer cells

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

growth_protocol: NK cells were obtained from PBMC using EZSep Negative Selection kit.  Cells were >95% CD3-CD56+.  Stimulated NK cells were grown in RPMI, supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.  Cells were grown at density of 1.5 x 10^6 per mL

extract_protocol: Cells were harvested, washed 1X in PBS.  RNA extracted using Trizol, resuspended in RNAse-free H2O, then further purified using Qiagen column per manufacturer's instructions.

treatment_protocol: Recombinant human cytokines were added at start of culture: IL-2 (100U/mL), IL-12 (10ng/mL) and IL-18 (100ng/mL) from 2 male donors

tag: cell type

value: natural killer cells

tag: protocol

value: treated with cytokines IL-2, IL-12 and IL-18


title: Pre-TBI Blood_0Gy_rep1_057

description: Gene expression in non-irradiated patient blood

source_name: Peripheral Blood, 0 Gy, replicate 1


title: TBI Blood_4h_1.25Gy_rep1_057


title: Pre-TBI Blood_0Gy_rep1_091


title: TBI Blood_4h_1.25Gy_rep1_091


title: IQE3416


title: IQE3502


title: IQE3435


title: IQE3296


title: TBI Blood_4h_1.25Gy_rep1_051


title: Pre-TBI Blood_0Gy_rep1_053

value: female


title: Mouse retina_Control_ rep1

source_name: retina, no hyperoxia

value: Retina

value: Adult P80 - 120


title: unstimulated_freshly_isolated_donor_2

description: Donor 2 Resting

source_name: freshly isolated, human natural killer cells

value: control


title: Pre-TBI Blood_0Gy_rep1_055


title: stimulated_24hr_donor_1

description: Donor 1 Stim


title: TBI Blood_4h_1.25Gy_rep1_053


title: 3D7_2 REFERENCE

description: Genomic DNA hybridization of 3D8

source_name: Genomic DNA from 3D7 reference


title: 3D7_1 REFERENCE

description: Genomic DNA hybridization of 3D7


title: Low N2O west rep3

type: mixed

city: St Lucia

first: Regina

last: Sintrajaya

state: Queensland

address: Mansfield Pl, Blg 62 John Hines Lvl 3

department: School of Biological Science

institute: The University of Queensland

description:
cDNA was normalised with a 'blank' PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen) amplified under the same condition as the cDNA. The 'blank' PCR product was called nPCR. The nPCR fragment was labeled with 635 AlexaFlour dye (Invitrogen) before mixing with cDNA sample which had been labeled with 532 AlexaFlour. Both cDNA/nPCR was combined for hybridisation.
West chamber 2 rep 2

hyb_protocol: E-FGA array was pre-hybridised in a humidity chamber (55°C) for approximately 30 min before the labelled cDNA was incoperated. Microarray was then hybridised overnight (14-16 h) at 42°C, using the method outlined at http://ag.arizona.edu/microarray/methods.html

scan_protocol: The microarray was exposed for 1 hour and scanned using Axon Instrument at 20 micron resolution. Signal intensity was analysed with GenePix 6.0

data_processing: To account for variations in spot size and density across microarrays, a PCR product was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs. This product was homologous to the flanking regions that were amplified with each cDNA clone, and hence this sequence was present on each valid spot of the microarray hence the amount of hybridization of the nPCR fragment could be used to normalize variations in DNA deposition and spotting efficiencies when comparing data between arrays. Foreground fluorescence values for each channel and spot were used for the anaylsis. This foreground signal had to be greater than the average background plus two standard deviations for both channels to be consider valid (F532 > B532avg + 2SD AND F635 > B635avg + 2SD; 2, 28). For each valid spot, the ratio of the cDNA to the nPCR probe was calculated (F532/F635ratio), resulting in locally normalized data. Additionally, the average fluorescence levels across the entire microarray for each channel were determined and used to calculate a ‘scan bias’ ratio for each microarray (F532avg/F635avg). This value was multiplied across all individual data ratios, and then log10 transformed, to produce the globally-normalized log-data set used for the comparison between microarrays. Student’s t-test was performed between the normalized data sets for the duplicate spots on the three high and three low N2O-emitting soil samples using two-tailed, heteroscedastic parameters (Microsoft Excel).

label: AlexaFlour 532

organism: uncultured microorganism

source_name: Sugarcane soil

label_protocol: 1-2μg of mRNA was converted into cDNA using the SuperScript Indirect cDNA Labelling Kit (Invitrogen) according to the manufacture instructions. However, the oligo dT nucleotides were omitted from the reaction, and twice the recommended amount of random hexamer was used. The cDNA was labeled with AlexaFluor 532 dye according to the manufacture instructions (Invitrogen)

extract_protocol: 500g of soil was sampled and mixed before 20g was immedietely collected for total RNA extraction. Soil samples were fully suspended in 20mL water for 20-30s, then left to settle for 10s to separate larger particles. The supernantant was discarded after 2 min (14,000 x g) of centrifuged, the pellet was snap-frozen in liquied nitrogen and stored at -80 degree Celcius. Total RNA from the soil microbes were extracted according to the RNA powersoil Total RNA isolation Kit (Mo Bio). mRNA was enriched by using gel-electrophoresis-based size separation.

treatment_protocol: Soil at sampling site consists of a non-calcic brown clay-loam that was either fertilised with 160 kg/ha of ammonium nitrate 8 days prior to collection, or unfertilised. The sites was sown with trash blanket of the previous sugarcane crop (100-130 cm high), where greenhouse gas (N2O) chamber measurements were being monitored. Three samples from each of the two high- and low- emitting N2O chambers from fertilised and non-fertilised soils, respectively, were taken at a depth of 5-20 cm.

tag: sample source

value: anonymous soil microbes

tag: soil site

value: West

tag: soil nitrogen composition

value: Low N2O content soil

label: AlexaFlour 635

molecule: other

organism: synthetic construct

source_name: nPCR

value: blank PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen)


title: IQE2924


title: Low N2O west rep2

description:
cDNA was normalised with a 'blank' PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen) amplified under the same condition as the cDNA. The 'blank' PCR product was called nPCR. The nPCR fragment was labeled with 635 AlexaFlour dye (Invitrogen) before mixing with cDNA sample which had been labeled with 532 AlexaFlour. Both cDNA/nPCR was combined for hybridisation.
West chamber 2 rep 1


title: Pre-TBI Blood_0Gy_rep1_051


title: Low N2O west rep1

description:
cDNA was normalised with a 'blank' PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen) amplified under the same condition as the cDNA. The 'blank' PCR product was called nPCR. The nPCR fragment was labeled with 635 AlexaFlour dye (Invitrogen) before mixing with cDNA sample which had been labeled with 532 AlexaFlour. Both cDNA/nPCR was combined for hybridisation.
West chamber 1 rep 1


title: TBI Blood_4h_1.25Gy_rep1_049


title: experimental2_Day4_repB

city: Athens

first: Shalabh

last: Sharma

state: GA

address: Department of Marine Science

department: Marine Science

institute: UGA

description:
Natural seawater Roseobacter community.
d4-E2b

hyb_protocol: CombiMatrix CustomArray manual.

scan_protocol: Axon GenePix 4000B microarray scanner, GenePix Pro 6.0 software.

data_processing: The background-subtracted median of pixel intensities were globally normalized among all microarrays hybridized for this experiment (20 arrays; 10 samples x 2 technical replicates) by calculating the sum of fluorescence values for all spots on each array and normalizing each array to the mean of the sums from all arrays. Bad spots were flagged according to criteria established in Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755 (PMID 17922758). For the remaining probes, a combined data set was generated by averaging fluorescence values for each probe among the technical and biological replicates. The results are interpreted based on the fluorescence ratio calculated for each probe by dividing the mean fluorescence of replicated probes from experimental arrays by the mean fluorescence of replicated probes from control arrays.

label: Alexa Fluor 647

organism: marine metagenome

source_name: natural seawater bacterial community, incubated in experimental microcosm 2 (amended with N and P) for four days

label_protocol: Dye in each single-use vial was dissolved in 11 µl DMSO, and added to the aa-aRNA, mixed, and incubated for 1 hour in the dark at room temperature.

growth_protocol: Microcosms were incubated at 27ºC in a temperature-controlled incubator on a 12 h light/dark cycle.

extract_protocol: Total RNA was extracted.

value: nutrients N and P

tag: incubation time

value: 4 days

tag: fraction size


title: ncRNA_NPC

city: Chapel Hill

first: Susan

middle: C

last: Wu

state: NC

address: 32-026 Lineberger Comprehensive Cancer Center

department: Biochemistry

institute: UNC Chapel Hill

hyb_protocol: Performed by the UNC Genomics and Bioinformatics Core Facility by the standard protocol.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: Data was quality filtered, and data for both channels were Lowess-normalized and then log(2) Cy5/Cy3 ratio was taken.

source_name: Universal Mouse Reference RNA

label_protocol: RNA was amplified using the Low RNA Linear Amplification Kit (Agilent Technologies) by the standard manufacturer's protocol.

extract_protocol: Total RNA isolated by Stratagene.

tag: sample type

value: reference

source_name: neuroprogenitors

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Kit. RNA quality was assessed via the Agilent Bioanlayzer.

value: neuroprogenitor cells


title: experimental1_Day4_repB

description:
Natural seawater Roseobacter community.
d4-E1b

source_name: natural seawater bacterial community, incubated in experimental microcosm 1 (amended with N and P) for four days


title: Pre-TBI Blood_0Gy_rep1_049


title: control2_Day4_repB

description:
Natural seawater Roseobacter community.
d4-C2b

source_name: natural seawater bacterial community, incubated in control microcosm 2 for four days

value: untreated


title: experimental1_Day4_repA

description:
Natural seawater Roseobacter community.
d4-E1a


title: Low N2O center rep2

description:
cDNA was normalised with a 'blank' PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen) amplified under the same condition as the cDNA. The 'blank' PCR product was called nPCR. The nPCR fragment was labeled with 635 AlexaFlour dye (Invitrogen) before mixing with cDNA sample which had been labeled with 532 AlexaFlour. Both cDNA/nPCR was combined for hybridisation.
Central chamber 2 rep 2

value: Central


title: control2_Day4_repA

description:
Natural seawater Roseobacter community.
d4-C2a


title: Low N2O center rep3

description:
cDNA was normalised with a 'blank' PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen) amplified under the same condition as the cDNA. The 'blank' PCR product was called nPCR. The nPCR fragment was labeled with 635 AlexaFlour dye (Invitrogen) before mixing with cDNA sample which had been labeled with 532 AlexaFlour. Both cDNA/nPCR was combined for hybridisation.
Central chamber 2 rep 3


title: experimental2_Day4_repA

description:
Natural seawater Roseobacter community.
d4-E2a


title: TBI Blood_4h_1.25Gy_rep1_035

value: whole blood


title: ncRNA_TTF

source_name: tail tip fibroblasts

value: tail tip fibroblasts


title: Low N2O center rep1

description:
cDNA was normalised with a 'blank' PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen) amplified under the same condition as the cDNA. The 'blank' PCR product was called nPCR. The nPCR fragment was labeled with 635 AlexaFlour dye (Invitrogen) before mixing with cDNA sample which had been labeled with 532 AlexaFlour. Both cDNA/nPCR was combined for hybridisation.
Central chamber 2 rep 1


title: Pre-TBI Blood_0Gy_rep1_040

value: male


title: control1_Day4_repB

description:
Natural seawater Roseobacter community.
d4-C1b

source_name: natural seawater bacterial community, incubated in control microcosm 1 for four days


title: ncRNA_E14_EZH2_KD1

source_name: ES Ezh2 KD1

value: Ezh2-knockdown embryonic stem (ES) cells


title: unstimulated_freshly_isolated_donor_1

description: Donor 1 Resting

value: natural killer cells


title: experimental2_Day2_repB

description:
Natural seawater Roseobacter community.
d2-E2b

source_name: natural seawater bacterial community, incubated in experimental microcosm 2 (amended with N and P) for two days

value: 2 days


title: control1_Day4_repA

description:
Natural seawater Roseobacter community.
d4-C1a


title: experimental2_Day2_repA

description:
Natural seawater Roseobacter community.
d2-E2a


title: High N2O east rep1

description:
cDNA was normalised with a 'blank' PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen) amplified under the same condition as the cDNA. The 'blank' PCR product was called nPCR. The nPCR fragment was labeled with 635 AlexaFlour dye (Invitrogen) before mixing with cDNA sample which had been labeled with 532 AlexaFlour. Both cDNA/nPCR was combined for hybridisation.
East chamber 2 rep 1

value: East

value: High N2O content soil


title: High N2O east rep3

description:
cDNA was normalised with a 'blank' PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen) amplified under the same condition as the cDNA. The 'blank' PCR product was called nPCR. The nPCR fragment was labeled with 635 AlexaFlour dye (Invitrogen) before mixing with cDNA sample which had been labeled with 532 AlexaFlour. Both cDNA/nPCR was combined for hybridisation.
East chamber 2 rep 3

value: anonymous soil microbes


title: High N2O east rep2

description:
cDNA was normalised with a 'blank' PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen) amplified under the same condition as the cDNA. The 'blank' PCR product was called nPCR. The nPCR fragment was labeled with 635 AlexaFlour dye (Invitrogen) before mixing with cDNA sample which had been labeled with 532 AlexaFlour. Both cDNA/nPCR was combined for hybridisation.
East chamber 2 rep 2


title: experimental1_Day2_repA

description:
Natural seawater Roseobacter community.
d2-E1a

source_name: natural seawater bacterial community, incubated in experimental microcosm 1 (amended with N and P) for two days


title: ncRNA_E14_EZH2_KD2

source_name: ES Ezh2 KD2


title: High N2O center rep3

description:
cDNA was normalised with a 'blank' PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen) amplified under the same condition as the cDNA. The 'blank' PCR product was called nPCR. The nPCR fragment was labeled with 635 AlexaFlour dye (Invitrogen) before mixing with cDNA sample which had been labeled with 532 AlexaFlour. Both cDNA/nPCR was combined for hybridisation.
Central chamber 1 rep 3


title: ncRNA_E14ps

source_name: ES E14ps

value: embryonic stem (ES) cells


title: control2_Day2_repB

description:
Natural seawater Roseobacter community.
d2-C2b

source_name: natural seawater bacterial community, incubated in control microcosm 2 for two days


title: control2_Day2_repA

description:
Natural seawater Roseobacter community.
d2-C2a


title: experimental1_Day2_repB

description:
Natural seawater Roseobacter community.
d2-E1b


title: control1_Day2_repA

description:
Natural seawater Roseobacter community.
d2-C1a

source_name: natural seawater bacterial community, incubated in control microcosm 1 for two days


title: experimental_time0_repB

description:
Natural seawater Roseobacter community.
t0_E0b

source_name: natural seawater bacterial community, experimental microcosm (amended with N and P), time=0

value: 0 day


title: control1_Day2_repB

description:
Natural seawater Roseobacter community.
d2-C1b


title: High N2O center rep2

description:
cDNA was normalised with a 'blank' PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen) amplified under the same condition as the cDNA. The 'blank' PCR product was called nPCR. The nPCR fragment was labeled with 635 AlexaFlour dye (Invitrogen) before mixing with cDNA sample which had been labeled with 532 AlexaFlour. Both cDNA/nPCR was combined for hybridisation.
Central chamber 1 rep 2

source_name: Sugarcane soil

value: blank PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen)


title: High N2O center rep1

description:
cDNA was normalised with a 'blank' PCR product that was produced from an empty pCR-Blunt vector using M13 primers and amino-allyl dNTPs (Invitrogen) amplified under the same condition as the cDNA. The 'blank' PCR product was called nPCR. The nPCR fragment was labeled with 635 AlexaFlour dye (Invitrogen) before mixing with cDNA sample which had been labeled with 532 AlexaFlour. Both cDNA/nPCR was combined for hybridisation.
Central chamber 1 rep 1

source_name: nPCR


title: TBI Blood_4h_1.25Gy_rep1_040

description: Gene expression in patient blood at 4 h after TBI with 1.25 Gy

source_name: Peripheral Blood, 4 h, 1.25 Gy, replicate 1


title: experimental_time0_repA

description:
Natural seawater Roseobacter community.
t0_E0a

value: nutrients N and P


title: Pre-TBI Blood_0Gy_rep1_035

description: Gene expression in non-irradiated patient blood

source_name: Peripheral Blood, 0 Gy, replicate 1

value: female


title: control_time0_repB

description:
Natural seawater Roseobacter community.
t0_C0b

source_name: natural seawater bacterial community, control microcosm, time=0


title: control_time0_repA

description:
Natural seawater Roseobacter community.
t0_C0a


title: PP/5F1

city: Shanghai

first: Ling

last: Tian

address: Fenglin Road 300

department: Institute of Plant Physiology and Ecology

country: China

institute: Chinese Academy of Sciences

description: prepupal compared to 5th instar feeding 1, Biological replicate 1 of 3 PP compared to 5F

hyb_protocol: Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Bombyx mori

source_name: Bombyx 5th feeding stage fat body

label_protocol: 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 5 μL of 4×first-strand buffer, 2 μL of 0.1M DTT, and 1.5 μL CbcScript Ⅱ reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 μL. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 μL Klenow buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1.2 μL Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray

growth_protocol: Bombyx larvae (Nistari) were provided by The Sericultural Research Institute, Chinese Academy of Agricultural Sciences. They were reared with fresh mulberry leaves in the laboratory at 25oC under 14 hour light/10 hour dark cycles.

extract_protocol: the different stages Bombyx fat bodys  were dissected and quickly frozen in liquid nitrogen, total RNA was extracted with Trizol Reagent (BD Biosciences Clontech, Palo Alto, CA) and ethanol precipitation

treatment_protocol: Fat body was vivisected in PBS and fat body quickly frozen in liquid nitrogen.

value: fat body

source_name: Bombyx prepupa fat body


title: 4M/5F1

description: 4th molting  compared to 5th instar feeding 1, Biological replicate 1 of 3 4M compared to 5F

source_name: Bombyx 4th molting fat body


title: 4M/5F3

description: 4th molting  compared to 5th instar feeding 3, Biological replicate 3 of 3 4M compared to 5F


title: PP/5F3

description: prepupal compared to 5th instar feeding 3, Biological replicate 3 of 3 PP compared to 5F


title: PP/5F2

description: prepupal compared to 5th instar feeding 2, Biological replicate 2 of 3 PP compared to 5F


title: plasma from healthy donor 1

status: Public on Aug 03 2010

type: other

first: Guokun

last: Wang

address: 168 Changhai Road

institute: Changhai Hospital

description:
microRNA profile in plasma from healthy people
CH_001

hyb_protocol: Cy3-labelled RNA was dried with vacuum concentrator for 1 hour at 45 ºC, and dissolved in a volume of 45 ul hybridization mixture contraining 1x GE Blocking Agent and 1x Hi-RPM Hybridization Buffer following the manufacturers instructions. On completion of the reaction, the mixture was hybridized to Agilent microRNA Oligo Microarrays (G4470B) for 20 hours at 55 ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute at 37 ºC with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Finally, data was normalized by quantile.

source_name: plasma from healthy donor 1

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 100 ng RNA using the miRNA Complete Labeling and Hyb Kit (Agilent p/n 5190-0456) according to the manufacturer's instructions.

extract_protocol: Small RNA  (<200nt) was prepared using the mirVana PARIS kit (Applied Biosystem p/n AM1556) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: Freshly peripheral blood from healthy volunteers were drawn into EDTA tubes, and were processed within 1 hour by two-step centrifugation. The plasma was transfered to RNasa/DNase-free tubes and stored at -80 ºC.

tag: donor

value: Male

value: plasma


title: wild type bldd3

status: Public on Aug 04 2010

city: Norwich

first: Chris

last: den Hengst

state: Norfolk

address: Colney

department: Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

hyb_protocol: DNA was hybridized to microarrays in an Agilent Technologies microarray chamber by using hybridisation buffer (1 M NaCl/50 mM Mes, pH 7/20% formamide/1% Triton X-100) and rotated at 55°C over 40 h. The arrays were then washed with Wash 1 [6× standard saline phosphate/EDTA (0.18 M NaCl/10 mM phosphate, pH 7.4/1 mM EDTA) (SSPE) containing 0.005% N-Lauroyl sarcosine] and Wash 2 (0.06% SSPE/0.18% polyethylene glycol 200), both for 5 min at room temperature.

scan_protocol: For data collection, an Agilent Technologies microarray scanner was used, and results were extracted by using Agilent Technologies feature extraction software.

data_processing:
Data was analyzed using a combination of bespoke Perl and R programs. Essentially, the following steps were carried out. Columns containing the positions of probes in the genome sequence, the green median signals and, the red median signals were extracted from the raw data files. Ratios of green median signals to the red median signals were calculated. For the bldD mutant control and for each of the three replicates of the wild-type, the signal ratios were read into a data frame in R and scaled to make the mean as well as the standard deviation for each fall within the range of 0 to 1. For each probe, the mean of the three (scaled) bldD ratios was calculated and from it the control ratio was subtracted to arrive at a vector of the differences between the bldD means and the control.  For each of the difference so calculated, a P value was calculated assuming a population mean equal to the mean of all differences and a population standard deviation equal to the standard deviation of all the differences. These P values were adjusted for multiple testing by the method of Benjamini and Hochberg to arrive at adjusted P values. Data were ordered by increasing (adjusted) P values and all probes having an adjusted P value < 5e-3 were manually inspected to determine whether they were a part of a signal peak or not.
The final processed data is available as a supplementary file on the Series record

organism: Streptomyces coelicolor

source_name: ChIP DNA cells harvested from log phase in YEME/TSB

label_protocol: Using the Bio-Prime kit (Invitrogen), 800 ng of the total and immuno-precipitated DNA was labelled with Cy5-dCTP and Cy3-dCTP

extract_protocol: S. coelicolor was grown in triplicate for in YEME/TSB liquid medium and was done in triplicate for the wild-type strain. Formaldehyde was added to cultures at a final concentration of 1% (v/v) and incubation was continued for 30 min

tag: strain

value: wild-type M600

tag: chip antibody

value: anti-BldD custom antibody

source_name: total DNA control


title: Dual speicies array test using RNA isolated from human cancer cell line MDA-MB-435 rep1

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: GenePix 4000B axon scanner Images were quantified using Agilent Feature Extraction Software version 9

data_processing: Background correction: local background subtracted mean expression values from FE software; Normalization: vsn (variance stabilization and normalization); glog scale to base 2

source_name: 1.5µg human total RNA

label_protocol: 1.5µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

extract_protocol: Mouse total RNA were purchased from ArrayIt (Sunnyvale, CA). Human total RNA were isolated from head and neck squamous carcinoma cell line.

value: Human reference RNA


title: Dual speicies array test using  mouse reference RNA rep2

source_name: 1.5µg mouse reference RNA

value: Mouse reference RNA


title: plasma from healthy donor 2

description:
microRNA profile in plasma from healthy people
CH_002

source_name: plasma from healthy donor 2

tag: age

tag: tissue


title: wild type bldd2


title: bldD null mutant

value: bldD null mutant


title: plasma from healthy donor 4

description:
microRNA profile in plasma from healthy people
CH_004

source_name: plasma from healthy donor 4


title: plasma from healthy donor 3

description:
microRNA profile in plasma from healthy people
CH_003

source_name: plasma from healthy donor 3


title: Dual speicies array test using  mouse reference RNA rep3


title: AH vs. AC R3

city: College Station

first: Huaijun

last: Zhou

state: TX

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

description: Four arrays are included in one slide

hyb_protocol: A 825 ng of labeled cRNA with specificity over 8 were used for the hybridization reaction using the in situ hybridization kit plus (Agilent Technologies). A 100 ul hybridization solution was loaded on each of array in Agilent 4x44K microarrays. Arrays were incubated at 65 ℃ for 17h in Agilent’s microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol.

scan_protocol: Slides were scanned at 5-μm resolution using GenePix Personal 4100A (Molecular Devices Corporation, Sunnyvale, CA) and were saved as TIFF images. Auto Photomultiplier tube (PMT) were selected and adjusted to get the ratio of the overall intensities between the two channels (Cy3 and Cy5) was 0.9~1.1. The intensities of the spots on each image were quantified by Genepix pro 6.0 software (Molecular Devices Corporation, Downingtown, PA), and data were saved as .txt files for further analyses.

data_processing: The signal intensity of each gene was globally normalized using LOWESS by R program

organism: Gallus gallus

source_name: Cecal tonsil

label_protocol: A 500 ng of aliquot of total RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The synthesized cDNA was transcribed into cRNA labeled with one of two cyanine-labeled nucleotides (Perkin Elmer, Wellesley, MA). Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity measured with ND-100 spectrophotometer (NanoDrop Technologies).

growth_protocol: Raised on the floor in isolated room

extract_protocol: Cecal tonsil was homogenized by tissue miser (Fisher Scientific, Houston, TX). Total RNA was isolated using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Orally inoculated with 10^5 cfu C. jejuni on one day after hatch

tag: Broiler

tag: one week

tag: high C. jejuni burden

treatment_protocol: Orally inoculated with PBS on one day after hatch

tag: control


title: BC vs. BL R3

description: Four arrays are included in one slide

tag: low C. jejuni burden


title: 4M/5F2

description: 4th molting  compared to 5th instar feeding 2, Biological replicate 2 of 3 4M compared to 5F


title: BH vs. BC R3

description: Four arrays are included in one slide

treatment_protocol: Orally inoculated with 10^5 C. jejuni on one day after hatch

tag: Control


title: BC vs. BL R4

description: Four arrays are included in one slide


title: Dual speicies array test using RNA isolated from human cancer cell line MDA-MB-435 rep2

tag: cell line


title: BL vs. BH R4

description: Four arrays are included in one slide


title: Dual speicies array test using RNA isolated from human cancer cell line MDA-MB-435 rep3


title: BH vs. BC R4

description: Four arrays are included in one slide


title: HFRs of embryo at stage HH4-4+, biological rep1

city: Gambelas

first: Margaret

middle: Carvalho

last: Bento

state: Faro

department: Biomedical and Medicine

country: Portugal

institute: University of Algarve

description:
gene expression data from embryos at HH4-4+
chick_T1-1.CEL

hyb_protocol: 15 µg of fragmented cRNA was used in a 300-µl hybridization containing added hybridization controls. 200 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (EukGE-WS2v5) were used on an Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000.

data_processing:
Scanned arrays were analyzed first with Affymetrix GCOS 1.3 software to obtain Absent/Present calls and for subsequent analysis with dChip 2006. Four GeneChip chicken arrays used for another study were added to the two arrays in this study to ensure a robust model for expression value computation (Note: The 4 samples chick_T2-1, chick_T2-2, chick_T2-3, chick_T2-4, were performed by another group and for a different array, and nothing has to do with our data.  They were only run at the same time and used for normalization. Raw data unavailable.). The arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method. Normalized CEL intensities of the six arrays were used to obtain model-based gene expression indices (MBEI) based on a PM (Perfect Match)-only model.
Processed data for all 6 samples can be found in supplementary file linked to Series GSE23389.

source_name: Heart Forming Regions of chick embryos at stage HH4-4+

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Chicken Genome Arrays, according to the manufacturer’s Two-Cycle Target Labeling Assay. Briefly, 45 ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction (Two-Cycle DNA synthesis kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA (MEGAscript T7 kit; Ambion, Austin, TX). The cRNA obtained was used for a second round of cDNA and cRNA synthesis, resulting in biotinylated cRNA (GeneChip Expression 3’-Amplification Reagents for IVT-Labeling; Affymetrix).

growth_protocol: Chick embryos were incubated at 37.5ºC for approximately 12 hours

extract_protocol: Heart Forming Regions (exhibiting EGFP) or the Posterior Part of the Primitive Streak  at HH4-4+ were excised, and Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Embryos were microinjected and electroporated at stage HH3 with the vector pCer2.5-EGFP, that contains a 2.5Kb fragment upstream the ATG from the Cerberus regulatory region.

value: Heart Forming Regions

value: embryo

tag: developmental stage


title: Dual speicies array test using  mouse reference RNA rep1


title: BL vs. BH R3

description: Four arrays are included in one slide


title: PPPs of embryo at stage HH4-4+, biological rep1

description:
gene expression data from embryos at HH4-4+
chick_T0-1.CEL

source_name: Posterior Part of the Primitive Streak of chick embryos at stage HH4-4+

value: Posterior Part of the Primitive Streak


title: wild type bldd1


title: BL vs. BH R2

description: Four arrays are included in one slide


title: BC vs. BL R2

description: Four arrays are included in one slide

tag: Low C. jejuni burden


title: BH vs. BC R2

description: Four arrays are included in one slide


title: BH vs. BC R1

description: Four arrays are included in one slide

tag: High C. jejuni burden