title: WT vs. 5A sample 1

city: Greenville

last: Stiller

address: East 5th Street

institute: East Carolina University

description: Array ID YO06N from Operon Yeast Genome Oligo Set version 1.1.2 was used for the hybridization. The direct labeling protocol was performed for sample RNA, which included steps of first strand synthesis, slide preparation, hydrolysis, cDNA purification, hybridization and array washing. Cy3 and Cy5 were used for labeling the samples. Maui hybridization and TIGR washing system were used in this protocol for array hybridization and washing respectively. The protocol can be found in Duke University microarray center website as http://www.genome.duke.edu/cores/microarray/services/spotted-arrays/protocols/.

hyb_protocol: http://www.genome.duke.edu/cores/microarray/documents/spotted/protocols/maui_hyb_sys.doc Maui Hybridization Protocol: For AC 50 Mixers (double adhesive) •	Sidenote:  SL mixers will use 40-42 uls to fill and will fill on the bench instead of in the clamp… AC mixers should be used with all Human, Mouse, CNWash, and Rat arrays.  SL mixers can be used with Yeast, Drosphila, Songbird. 1)	For direct labeling: resuspend your dried down probes in 88 uls hyb buffer. For amplified samples:  you will have 20 uls after fragmentation (if you use LL’s amp protocol) so add 68 uls hyb buffer. 2)	Check microarray nanodrop as usual. 3)	Go ahead and open the clamps in the Maui and place slides in the holders for the slides to get to 42 degrees (no reason to heat the slides in the 80 degree oven anymore).  Do not heat the slides hotter than 42. 4)	Add appropriate COT-1 and Poly dA (1.9 uls each) to samples, quick vortex and spin and let samples sit away in the dark while you prepare mixers to slides. 5)	Do not open the airtight packs for the mixers until the last minute and do not heat mixers (they should be at RT).  Open the appropriate number of mixers and affix one at the time with the AC jig and brayer to each slide.  Make sure the air holes on the mixer line up in the center of the little redish 0-ring holes on the Maui system, so mixing will occur properly!  Then you can go ahead and clamp the slide with mixer in place in the Maui system. 6)	Now you can denature your sample tubes for 2 mins at 95 degrees.  Then spin for 20 secs or so to cool samples down and move them to the tube holders in the maui behind each appropriate slide.  Also heat the extra hyb buffer in an extra space in the Maui. 7)	Ready to LOAD:  Open the tube top for your 1st sample and the extra hyb buffer tube.  Get a new tip on the pipette and have it set to draw up 82-83 uls. 8)	First pipette up and down a small amt in the tip from the extra hyb buffer tube (you will see it clearing bubbles as it wets the end of the tip), then keep the plunger depressed as you move to pick up your full 82-83 uls of sample.   IF for some reason you do not have enough in the sample tube, than either lower your vol to pick up or add a few more uls from the extra hyb buffer and start again. 9)	Put the tip firmly on the loading port in the mixer and wiggle slightly to confirm its well on the hole.  Then inject the sample.  You should be able to watch it come back up the side channels in the mixeronce it gets over halfway back toward the hole, you can pull the tip away and then let go of the plunger.  IF for some reason the vol does not make it back up the channels you can touch slightly on the top of the mixer and it will come the rest of the way. 10)	  Load 4 at a time (or all if you prefer) and then go back and wipe away excess and affix the round or retangular sticker over all 3 little holes at the exit port.  To dry the excess, you can use q-tips to get the majority, then go back over with a kimwipe a few times.  Then can go on to the next 4 with loadinguntil all are done. 11)	 Close the lid on the Maui system and press on for the mixing portion.  Use mixing speed B.  It will default to B if you forget to press the B button… For Washes the next morning: Set up all washing jars and wash buffers as usual. Turn off mixing and open clamps on Maui System. Carry jig and slides with mixers over to the washing area. Pour 42 degree 1st wash buffer into the first wash jar and into a second (extra) wash jar. Put 1st slide into jig and immerse it in the extra jar of 1st wash buffer.  Hold the jig down with one hand and pull up on the free end of the mixer firmly and gently until it peels away (twist a little as you pull the mixer up).  Now take slide out and move it to 1st wash jar with rack. Do this quickly will all and then start 1st 1 minute rinse when all slides are in the 1st wash jar rack. Continue as usual… NEW SC Mixers!    					6-1-06 Will dry probe down completely and resuspend in 50 uls hyb buffer. Heat arrays on Maui at 42 as usual for 5-10 mins before adhearing mixers. SC mixers will still use AC jig, but will use SL clamp.  Will need to load sample and put port seals on before clamping mixer into Maui slot. There will be two port seals needed. The “fill port” is now within the adhesive at the fill end, so there will be not port seal required on the back side of the mixer (one less thing that can go wrong). The “exit port” is at the far end of the mixer like in the SL mixers. You will need to dry each port with a kimwipe simultaneously with equal pressure.  Then gently lay port seal stickers over each seal and push down on both at the same time with equal pressure to seal. Now you can clamp the mixer in and start Maui as usual. Make sure the air bladder holes match up over the red o-rings that control the air bladders during mixing. Don’t forget to put your wash buffer #1 in the waterbath overnight!!

scan_protocol: Fluorescent DNA bound to the microarray was detected with a GenePix 4000B scanner (Axon Instruments, Foster city, CA), using the GenePix 4000 software package to locate signal from spots. Normalization and statistical analysis were performed using Duke Univerisity BASE web server (https://base-server.duhs.duke.edu/). GO annotation was used for gene ontology.

data_processing: Data processing was performed using Duke University BASE web server (https://base-server.duhs.duke.edu/). The data file folder (WT vs. 5A final Submit) includes the complete original dense ratios for all probed genes of the four samples. Since many analysis programs use log2 values we converted into log2ratio. Value of the table in GSE14342, is the average of the log2ratio of the four samples. A value greater than 1 represented up regulation and a value of less than -1 represented a down regulation. Genes that did not have a signal from all four samples were not used in further analysis.

extract_protocol: RNA was extracted from fresh pellets of yeast cultures at log phase, grown to an optical density of 0.8 at 600nm in 100 ml of YPD medium (1% yeast extract, 2% peptone, and 2% dextrose) at 30 ºC in a shaker at 225 rpm. Total RNA was extracted using Qiagen’s RNeasy Kit (Valencia, CA). Four replicates for each sample yeast strain (5A and wild-type CTD control) were prepared, and 10ug total RNA for every replicates were sent to Duke university DNA microarray center for further analyses.

tag: Yeast cells were transformed with mutated CTD sequences containing 5 alanine insertions between diheptad units via the plasmid shuffle, as described in detail previously (West and Corden 1995; Stiller and Cook 2004).

source_name: WT

tag: Yeast cells containing nonmutated CTD sequences as described in detail previously (West and Corden 1995; Stiller and Cook 2004).


title: WT vs. 5A sample 3

status: Public on Jan 30 2009

type: RNA

first: John

state: NC

department: Biology

country: USA

molecule: total RNA

organism: Saccharomyces cerevisiae

label_protocol:
http://www.genome.duke.edu/cores/microarray/documents/spotted/protocols/maui_hyb_sys.doc
Maui Hybridization Protocol:
For AC 50 Mixers (double adhesive)
•	Sidenote:  SL mixers will use 40-42 uls to fill and will fill on the bench instead of in the clamp…
AC mixers should be used with all Human, Mouse, CNWash, and Rat arrays.  SL mixers can be used with Yeast, Drosphila, Songbird.
1)	For direct labeling: resuspend your dried down probes in 88 uls hyb buffer.
For amplified samples:  you will have 20 uls after fragmentation (if you use LL’s amp protocol) so add 68 uls hyb buffer.
2)	Check microarray nanodrop as usual.
3)	Go ahead and open the clamps in the Maui and place slides in the holders for the slides to get to 42 degrees (no reason to heat the slides in the 80 degree oven anymore).  Do not heat the slides hotter than 42.
4)	Add appropriate COT-1 and Poly dA (1.9 uls each) to samples, quick vortex and spin and let samples sit away in the dark while you prepare mixers to slides.
5)	Do not open the airtight packs for the mixers until the last minute and do not heat mixers (they should be at RT).  Open the appropriate number of mixers and affix one at the time with the AC jig and brayer to each slide.  Make sure the air holes on the mixer line up in the center of the little redish 0-ring holes on the Maui system, so mixing will occur properly!  Then you can go ahead and clamp the slide with mixer in place in the Maui system.
6)	Now you can denature your sample tubes for 2 mins at 95 degrees.  Then spin for 20 secs or so to cool samples down and move them to the tube holders in the maui behind each appropriate slide.  Also heat the extra hyb buffer in an extra space in the Maui.
7)	Ready to LOAD:  Open the tube top for your 1st sample and the extra hyb buffer tube.  Get a new tip on the pipette and have it set to draw up 82-83 uls.
8)	First pipette up and down a small amt in the tip from the extra hyb buffer tube (you will see it clearing bubbles as it wets the end of the tip), then keep the plunger depressed as you move to pick up your full 82-83 uls of sample.   IF for some reason you do not have enough in the sample tube, than either lower your vol to pick up or add a few more uls from the extra hyb buffer and start again.
9)	Put the tip firmly on the loading port in the mixer and wiggle slightly to confirm its well on the hole.  Then inject the sample.  You should be able to watch it come back up the side channels in the mixeronce it gets over halfway back toward the hole, you can pull the tip away and then let go of the plunger.  IF for some reason the vol does not make it back up the channels you can touch slightly on the top of the mixer and it will come the rest of the way.
10)	  Load 4 at a time (or all if you prefer) and then go back and wipe away excess and affix the round or retangular sticker over all 3 little holes at the exit port.  To dry the excess, you can use q-tips to get the majority, then go back over with a kimwipe a few times.  Then can go on to the next 4 with loadinguntil all are done.
11)	 Close the lid on the Maui system and press on for the mixing portion.  Use mixing speed B.  It will default to B if you forget to press the B button…
For Washes the next morning:
Set up all washing jars and wash buffers as usual.
Turn off mixing and open clamps on Maui System.
Carry jig and slides with mixers over to the washing area.
Pour 42 degree 1st wash buffer into the first wash jar and into a second (extra) wash jar.
Put 1st slide into jig and immerse it in the extra jar of 1st wash buffer.  Hold the jig down with one hand and pull up on the free end of the mixer firmly and gently until it peels away (twist a little as you pull the mixer up).  Now take slide out and move it to 1st wash jar with rack.
Do this quickly will all and then start 1st 1 minute rinse when all slides are in the 1st wash jar rack.
Continue as usual…


title: WT vs. 5A sample 2


title: WT vs. 5A sample 4


title: D_fresh_Method 1

city: Portland

first: Christina

middle: A

last: Harrington

state: OR

address: 3303 SW Bond Ave

department: Gene Microarray Shared Resource

institute: Oregon Health and Science University

hyb_protocol: [see characteristics field for details]

scan_protocol: The distribution of fluorescent material on the processed array was determined using the Affymetrix 3000 GeneArray laser scanner with the 7G upgrade.  Image inspection was performed manually immediately following each scan.  The array image scan was processed with Affymetrix Microarray Suite, version 5.0, (MAS 5.0) software.

data_processing: Low-level analysis (background correction, normalization, and gene summarization) of microarray data was performed with both Affymetrix Microarray Suite 5.0 (MAS 5.0) and Robust Multi-Array Average (RMA). Individual arrays were analyzed and scaled with MAS 5.0 using manufacturer’s default thresholds for detection calls and with target scaling factor set as 275.  For RMA analysis, arrays were normalized in four separate groups based on target labeling method using RMA implemented in Affymetrix Expression Console (version 1.1).

label: biotin

organism: Homo sapiens

source_name: Whole blood, fresh, no depletion_Affymetrix

label_protocol: Amplifications and labelings were performed for each donor using one of the following four methods with RNA extracted from fresh and frozen blood samples:  Method 1 - Affymetrix one-cycle cDNA synthesis/Affymetrix in vitro-transcription (IVT) on whole blood RNA; Method 2 - Affymetrix one-cycle cDNA/Affymetrix IVT with globin peptide nucleic acids (PNAs) inclusion during cDNA synthesis; and Method 3- RNA pre-treated with Ambion GLOBINclear beads to reduce globin transcripts prior to labeling with the Affymetrix one-cycle cDNA synthesis/Affymetrix IVT.  In Method 4- cDNA target was synthesized from whole blood RNA using the NuGEN Ovation Biotin RNA Amplification and Labeling System. See individual sample annotation for protocol details.

extract_protocol: [see characteristics field for details]

treatment_protocol: Unfractionated whole blood collection and RNA isolation were performed using the PAXgene Blood RNA Isolation System (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA).  With the approval of the OHSU Institutional Review Board, blood was collected from healthy donors using eight PAXGene tubes per individual (donor).  Four tubes per donor were frozen for subsequent processing and four tubes per donor were processed fresh (see individual sample annotation for storage state details).  Following RNA isolation, DNase-treatment was performed as per PAXGene manufacturer’s recommendation.  Samples were then pooled within donor and within RNA storage state (fresh/frozen) resulting in two tubes per donor (fresh/frozen).  RNA recovery and quality was then assessed by examining UV 260/280 absorbance ratios and RNA size distribution on RNA Nano LabChips (Agilent Technologies, Santa Clara, CA, USA) processed on the Agilent 2100 Bioanalyzer.  For inclusion in this study, the RNA mass per donor had to be greater than 12 µg for both fresh and frozen blood aliquots.  Samples from three of the four donors (Donors A, C, D) met the quantitative and qualitative criteria and were used in the microarray analysis.

tag: Gender

value: M

tag: Age

value: 24, Normal

tag: Biosource

value: Peripheral whole blood

tag: Donor ID

value: Donor D

tag: Sample storage state

value: fresh

tag: Sample protocol

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then RNA was isolated from the fresh sample.

tag: Treatment protocol

value: Affymetrix one-cycle cDNA synthesis/Affymetrix IVT (no depletion_Affymetrix):No modifications of sample made prior to target synthesis.

tag: Label protocol

value: Affymetrix One-Cycle:Target synthesis was performed following the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Using 1 µg of total RNA as input, messenger RNA was amplified and labeled in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix, Santa Clara, CA, USA).  Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation.  In the second step, amplified and labeled cRNA (the target) was produced by a transcription reaction using T7 RNA polymerase and biotin-CTP (Affymetrix).  Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen) followed by an ethanol precipitation of the labeled target.

tag: Target molecule

value: cRNA

tag: Hyb protocol

value: Labeled cRNA targets were chemically fragmented at 95C for 35 min as per Affymetrix’s recommendations.  The fragmented material was combined with Affymetrix hybridization controls:biotinylated control oligomer (B2) and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Following the manufacturer’s recommendations, 6.5 µg of target were hybridized with the GeneChip Human Genome Focus array (Affymetrix) for 16 hours at 45C.  Post-hybridization array processing was performed on the Fluidics Station 450 (Affymetrix); array staining and signal amplification were performed according to manufacturer’s recommendations.


title: NHMEC 98040 - replicate 9 - mAdbID:47676

city: Bethesda

first: Ofelia

middle: Ana

last: Olivero

state: MD

address: 37 Convent Dr-MSC 4255

department: CDI

institute: NCI-CCR-

description: mAdb experiment ID: 47676

hyb_protocol: NCI Oligo Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.4962;; 3.72662 Temperature: 28.0969

data_processing:
mAdb Data Processing Protocol (v. 1)
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: NHMEC 98040 (untreated) - Cy3

label_protocol:
Cy3 Labeling Protocol
Other: Labeled with Cy3 by indirect coupling.

extract_protocol:
Trizol Extraction Protocol
Other: For isolation of RNA the cells were lysed with 1.0 mL of Trizol Reagent (Invitrogen Corp., Carlsbad, CA) and RNA was extracted according to manufacturer’s protocol.

value: female

tag: Tissue

value: mammary gland

tag: Cell line

value: NHMEC 98040

tag: Cell type

value: Normal Human Mammary Epithelial

source_name: NHMEC 98040 - TAM - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: Labeled with Cy5 by indirect coupling.

treatment_protocol:
Treatment type: compound
Agent: Tamoxifen
Treatment dose: 10 uM
Treatment time: 48 hours
Treatment temperature: 37C
Other: Cells at passage 13 were plated at 1 x10^6 cells/15 cm plate or T-175 flask for DNA preparation, and at 1x10^6 cells/6-well plate for RNA preparation and survival, and grown for 48 hours prior to treatment with 10 uM TAM in vehicle (DMSO) for an additional 48 hours.


title: NHMEC 99005 - dye swap - replicate 4 - mAdbID:53692

description: mAdb experiment ID: 53692

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.37474;; 3.72723 Temperature: 25.9606

source_name: NHMEC 99005 (untreated) - Cy5

value: NHMEC 99005

source_name: NHMEC 99005 - TAM - Cy3


title: NHMEC 98016 - dye swap - replicate 1 - mAdbID:53662

description: mAdb experiment ID: 53662

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.37077;; 4.073 Temperature: 24.7093

source_name: NHMEC 98016 (untreated) - Cy5

value: NHMEC 98016

source_name: NHMEC 98016 - TAM - Cy3


title: NHMEC 98040 - replicate 7 - mAdbID:47619

description: mAdb experiment ID: 47619

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.64574;; 3.8081 Temperature: 30.4468


title: NHMEC 98016 - replicate 2 - mAdbID:53664

description: mAdb experiment ID: 53664

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.42448;; 3.67443 Temperature: 27.1508

source_name: NHMEC 98016 (untreated) - Cy3

source_name: NHMEC 98016 - TAM - Cy5


title: NHMEC 99005 - replicate 5 - mAdbID:53409

description: mAdb experiment ID: 53409

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.39091;; 3.92041 Temperature: 24.6788

source_name: NHMEC 99005 (untreated) - Cy3

source_name: NHMEC 99005 - TAM - Cy5


title: NHMEC 98040 - dye swap - replicate 8 - mAdbID:47620

description: mAdb experiment ID: 47620

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.64635;; 3.6668 Temperature: 29.5923

source_name: NHMEC 98040 (untreated) - Cy5

source_name: NHMEC 98040 - TAM - Cy3


title: NHMEC 98040 - dye swap - replicate 10 - mAdbID:47677

description: mAdb experiment ID: 47677

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.55052;; 3.84411 Temperature: 29.3481


title: NHMEC 98040 - replicate 11 - mAdbID:47762

description: mAdb experiment ID: 47762

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.3903;; 3.74218 Temperature: 23.5191


title: NHMEC 99005 - replicate 15 - mAdbID:47110

description: mAdb experiment ID: 47110

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.661;; 3.96619 Temperature: 30.5078


title: NHMEC 98016 - replicate 3 - mAdbID:53405

description: mAdb experiment ID: 53405

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.38725;; 3.8847 Temperature: 26.3878


title: NHMEC 99005 - replicate 13 - mAdbID:47088

description: mAdb experiment ID: 47088

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.46812;; 3.71258 Temperature: 24.0989


title: NHMEC 99005 - dye swap - replicate 16 - mAdbID:47111

description: mAdb experiment ID: 47111

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.66863;; 3.90179 Temperature: 30.813


title: NHMEC 99005 - dye swap - replicate 14 - mAdbID:47089

description: mAdb experiment ID: 47089

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.53526;; 3.92132 Temperature: 25.9911


title: NHMEC 98040 - dye swap - replicate 6 - mAdbID:47618

description: mAdb experiment ID: 47618

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.68;; 3.87 Temperature: 30.9


title: NHMEC 98040 - replicate 5 - mAdbID:47616

description: mAdb experiment ID: 47616

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.68;; 3.82 Temperature: 31.12


title: NHMEC 99005 - dye swap - replicate 10 - mAdbID:46949

description: mAdb experiment ID: 46949

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.55388;; 3.88165 Temperature: 24.2821


title: NHMEC 98040 - dye swap - replicate 12 - mAdbID:47763

description: mAdb experiment ID: 47763

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.41746;; 3.63903 Temperature: 25.0755


title: NHMEC 98040 - dye swap - replicate 4 - mAdbID:53658

description: mAdb experiment ID: 53658

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.36222;; 3.85937 Temperature: 26.2047


title: NHMEC 99005 - replicate 9 - mAdbID:46947

description: mAdb experiment ID: 46947

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.59416;; 3.81603 Temperature: 25.8385


title: NHMEC 99005 - replicate 11 - mAdbID:47072

description: mAdb experiment ID: 47072

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.53038;; 3.914 Temperature: 25.5943


title: JAY270 Chr6 long band array

status: Public on Jan 29 2009

type: mixed

city: Durham

first: Juan Lucas

last: Argueso

state: SP

address: 371 CARL Building, Box 3054

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

description: This is a Band-array experiment in which Cy5-labeled DNA from JAY270 Chr6 long was mixed to Cy3-labeled total genomic S288c DNA and hybridized to microarrays containing probes for the entire S288c genome. This experiment allows the determination of chromosomal rearrangements between the JAY270 and S288c yeast strain backgrounds.

hyb_protocol: Described in Argueso et al PNAS (2008) 105:11845

scan_protocol: Array scanned in Genepix 4000b scanner.

data_processing: The log2 R/G ratio for all probes in the arrays were collapsed to a single value in the case of repeated probes and normalized according to the median value for the entire array.

molecule: other

source_name: JAY270 Chr6 long DNA labeled with Cy5

label_protocol: Direct incorporation with klenow polymerase and random priming.

extract_protocol: DNA specific to JAY270 Chr6-short, which was separated in Pulse-Field gel electrophoresis and labeled with Cy5

tag: PFGE-purified Chrmosomal DNA from strain JAY270 Chr6 long.

molecule: genomic DNA

source_name: S288c genomic DNA

extract_protocol: Genomic DNA prepared using standard yeast DNA extraction protocol.

tag: Total genomic DNA from S288c isogenic strain.


title: JAY270xS288c CGH-array

type: genomic

description: This is a Comparative Genome Hybridization between the bioethanol diploid strain JAY270 and the reference laboratory strain FY86 which is isogenic to S288c. Note that the arrays used were designed based on the S288c genome.

source_name: JAY270 genomic DNA labeled with Cy5

tag: S. cerevisiae strain JAY270 total genomic DNA.

tag: S. cerevisiae strain FY86 (S288c) total genomic DNA.


title: C_fresh_Method 1

scan_protocol: The distribution of fluorescent material on the processed array was determined using the Affymetrix 3000 GeneArray laser scanner with the 7G upgrade.  Image inspection was performed manually immediately following each scan.  The array image scan was processed with Affymetrix Microarray Suite, version 5.0, (MAS 5.0) software.

tag: Gender

value: 25, Normal

value: Donor C


title: C23 (COG study 8704)

city: Albuquerque

first: Stuart

middle: S.

last: Winter

state: NM

department: Pediatrics

institute: University of New Mexico Health Sciences Center

description: C= Complete Continous Remission

hyb_protocol: 15 ug aliquots of fragmented, labelled cRNA were hybridized to the U133A chip (Affymetrix)

scan_protocol: Affymerix microarray scanner (Hewlett Packard), gene fluorescence was captured using GeneChip software.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and the RMA normalization method.

label: Biotin

source_name: Primary T-ALL cells; newly diagnosed patient; Complete Continous Remission

label_protocol: Biotin-labed cRNA from 2.5 micrgrams of tissue using a two-step method usng Affymetrix technical approach

growth_protocol: Derived from bone marrow in newly diagnosed patients

extract_protocol: RNeasyMini Kit (Qiagen)

treatment_protocol: COG study 8704

tag: Newly diagnosed patient


title: NHMEC 99005 - replicate 1 - mAdbID:46845

description: mAdb experiment ID: 46845

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.57097;; 3.79162 Temperature: 24.0989


title: NHMEC 99005 - replicate 7 - mAdbID:46868

description: mAdb experiment ID: 46868

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.549;; 3.85052 Temperature: 23.7632


title: NHMEC 99005 - dye swap - replicate 12 - mAdbID:47074

description: mAdb experiment ID: 47074

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.48399;; 3.93475 Temperature: 24.0684


title: mutant_with_amp vs wild_type_sibling_with_amp

city: Neuherberg

first: Katharine

last: Webb

address: Ingolstaedterlandstr. 1

department: Institute for developmental genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: No additional information

hyb_protocol: Hybridization and washing was performed using the standard Agilent protocol.

scan_protocol: Scanning of the microarray slides was performed using the Agilent dual laser DNA microarray scanner. The microarray data were processed from raw data image files with Feature Extraction Software v9.1 software, protocol GE1-v1_91(Agilent Technologies, Palo Alto, CA).

data_processing: Processed data were subsequently imported into Rosetta Resolver 7.1 (Rosetta Biosoftware, Seattle, Washington) and subjected to default intensity error modeling. Results from triplicate experiments were combined using the default intensity experiment builder. Ratio experiments were built from the intensity data using the Agilent/Intensity-pair wise ratio builder with the control group (wild type) as baseline. Data were analyzed at the level of UniGene clusters (UniGene build #105).

label: cyanine 3-CTP

organism: Danio rerio

source_name: nad/+ mutant with amphetamine

label_protocol: 500 ng total RNA in an 8.3 microlitre volume was mixed with 1.2 microlitre of T7 promoter primer.  Primer and template were denatured by incubating at 65 degrees Celsius for 10 minutes and annealed by placing the reaction on ice.  The First Strand Reaction was performed by adding a master mix containing 5x First Strand Buffer, DTT, 10 mM dNTP mix, RNaseOUT, and Moloney murine leukemia virus reverse transcriptase, and incubated at 40 degrees Celsius for 2 hours.  MMLV-RT enzyme was inactivated by incubation at 65 degrees Celsius for 15 minutes and the samples were directly transferred to ice.  Samples were labeled by adding 2.4 microlitre cyanine 3-CTP. In vitro transcription was initiated by addition of the IVT Mastermix containing 4x transcription buffer, DTT, NTP mix, 50% PEG, RNaseOUT, Inorganic Pyrophosphates, T7 RNA polymerase and incubated at 40 degrees Celsius for 2 hours.

growth_protocol: Kept in zebrafish facility.

extract_protocol: Total RNA was extracted from whole brains using RNeasy mini kit (Qiagen), following the protocol “Purification of Total RNA from Animal Tissues”.  For the disruption and homogenization step, brains were dissected and immediately frozen in liquid nitrogen.  Then, 600 microlitre buffer RLT was added to each brain and the tissue was homogenized using a needle and syringe.  The samples were individually controlled for RNA quality and genomic contamination using 2100 Bioanalyzer (Agilent technologies), according to the manufacturer’s instructions.  Samples from 4-5 brains were then pooled to generate a single replicate.

treatment_protocol: Amphetamine was administered on days 1, 3 and 5, as part of our conditioned place preference assay.  On day 6 it was determined whether or not the fish had a mutant phenotype (i.e. whether or not the fish had failed to change place preference in response to amphetamine).  Subsequently, the fish received a last amphetamine administration 30 minutes before death.

tag: Strain

value: nad/+ mutants and their wildtype siblings, Gender:female, Age:6 months, Tissue:whole brain,

source_name: wild type sibling with amphetamine


title: NHMEC 99005 - dye swap - replicate 2 - mAdbID:46846

description: mAdb experiment ID: 46846

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.62194;; 3.79437 Temperature: 25.9606


title: NHMEC 98016 - dye swap - replicate 7 - mAdbID:46081

description: mAdb experiment ID: 46081

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.50108;; 3.5258 Temperature: 29.4702


title: C21 (COG study 8704)

description: C= Complete Continous Remission


title: C24 (COG study 8704)

description: C= Complete Continous Remission


title: NHMEC 99005 - dye swap - replicate 8 - mAdbID:46869

description: mAdb experiment ID: 46869

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.60363;; 3.81298 Temperature: 25.869


title: wildtype_with_amphetamine vs wildtype_without_amphetamine

description: No additional information.

source_name: wildtype; amphetamine-treated

label_protocol: 500 ng total RNA in an 8.3 microlitre volume was mixed with 1.2 microlitre of T7 promoter primer. Primer and template were denatured by incubating at 65 degrees Celsius for 10 minutes and annealed by placing the reaction on ice. The First Strand Reaction was performed by adding a master mix containing 5x First Strand Buffer, DTT, 10 mM dNTP mix, RNaseOUT, and Moloney murine leukemia virus reverse transcriptase, and incubated at 40 degrees Celsius for 2 hours. MMLV-RT enzyme was inactivated by incubation at 65 degrees Celsius for 15 minutes and the samples were directly transferred to ice. Samples were labeled by adding 2.4 microlitre cyanine 3-CTP. In vitro transcription was initiated by addition of the IVT Mastermix containing 4x transcription buffer, DTT, NTP mix, 50% PEG, RNaseOUT, Inorganic Pyrophosphates, T7 RNA polymerase and incubated at 40 degrees Celsius for 2 hours.

extract_protocol: Total RNA was extracted from whole brains using RNeasy mini kit (Qiagen), following the protocol “Purification of Total RNA from Animal Tissues”. For the disruption and homogenization step, brains were dissected and immediately frozen in liquid nitrogen. Then, 600 microlitre buffer RLT was added to each brain and the tissue was homogenized using a needle and syringe. The samples were individually controlled for RNA quality and genomic contamination using 2100 Bioanalyzer (Agilent technologies), according to the manufacturer’s instructions. Samples from 4-5 brains were then pooled to generate a single replicate.

treatment_protocol: Amphetamine was administered on days 1, 3 and 5.  On day 6 the fish received a last amphetamine administration 30 minutes before death.

value: wildtype AB/Tue zebrafish, Gender:female, Age:6 months, Tissue:whole brain

source_name: wild type; untreated


title: NHMEC 98016 - dye swap - replicate 6 - mAdbID:46072

description: mAdb experiment ID: 46072

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.57;; 3.53 Temperature: 24.62


title: nad/+ no treatment vs. wildtype sibling no treatment

description: No additional information.

source_name: nad/+ mutant; no treatment

extract_protocol: otal RNA was extracted from whole brains using RNeasy mini kit (Qiagen), following the protocol “Purification of Total RNA from Animal Tissues”. For the disruption and homogenization step, brains were dissected and immediately frozen in liquid nitrogen. Then, 600 microlitre buffer RLT was added to each brain and the tissue was homogenized using a needle and syringe. The samples were individually controlled for RNA quality and genomic contamination using 2100 Bioanalyzer (Agilent technologies), according to the manufacturer’s instructions. Samples from 4-5 brains were then pooled to generate a single replicate.

treatment_protocol: This fish were not treated (in this case we are looking at basal differences between two different genotypes).

source_name: wildtype sibling; no treatment


title: NHMEC 98016 - replicate 5 - mAdbID:46071

description: mAdb experiment ID: 46071

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.56;; 3.59 Temperature: 26.08


title: NHMEC 98016 - replicate 8 - mAdbID:45997

description: mAdb experiment ID: 45997

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.58;; 3.57 Temperature: 26.42


title: NHMEC 98016 - dye swap - replicate 9 - mAdbID:46000

description: mAdb experiment ID: 46000

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.56;; 3.64 Temperature: 25.69

source_name: NHMEC 98016 (untreated) - Cy5

source_name: NHMEC 98016 - TAM - Cy3


title: JAY270 Chr6 short band array

description: This is a Band-array experiment in which Cy5-labeled DNA from JAY270 Chr6 short was mixed to Cy3-labeled total genomic S288c DNA and hybridized to microarrays containing probes for the entire S288c genome. This experiment allows the determination of chromosomal rearrangements between the JAY270 and S288c yeast strain backgrounds.

source_name: JAY270 Chr6 short DNA labeled with Cy5

tag: JAY270 PFGE-purified Chr6 short band DNA.

tag: Total genomic DNA from FY86 strain, isogenic to S288c.


title: C22 (COG study 8704)

description: C= Complete Continous Remission


title: Patient_529_Never_Smoker

city: Gaithersburg

first: Sriram

last: Sridhar

address: 1 MedImmune Way

department: Translational Medicine

institute: MedImmune

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient529.gpr

hyb_protocol: 5uL of 10% BSA and 28.5uL of 2X enhanced hybridization buffer (Genisphere, Hatfield, PA) were added to the sample to make the hybridization mix. This was applied to Invitrogen NCode miRNA microarrays containing 1053 miRNAs from 6 species (467 human miRNAs) printed in triplicate.  The arrays incubated overnight (18 hours) in a humidified chamber at 52oC and the following morning, serial 15 minute washes were done with 2x SSC/0.2% SDS at 52oC, 2x SSC at room temperature and 0.2X SSC at room temperature.

scan_protocol: After drying, the arrays were scanned on a GenePix 4000 scanner (Axon/Molecular Devices, Sunnyvale CA).

data_processing: Raw data was extracted using GenePix Pro 4.0 (Molecular Devices Corporation, Sunnyvale, CA), quantile normalized and log transformed using the limma package for R (http://www.r-project.org/). Principle Component Analysis (PCA) was performed across all samples using all miRNAs to assess the relative homogeneity of the expression values between samples. Based on PCA, one non-smoker sample was removed from further analysis. In addition to our sample filter, only miRNA replicates that were detected at levels two standard deviations above the average background in at least 6 samples were considered for further analysis. The median of the remaining replicates for each miRNA was then taken to obtain a single expression value for each miRNA, leaving a total of 232 distinct miRNAs that were analyzed further.

label: fluorescent dendrimer with approximately 15 molecules of Oyster®-550 dye

source_name: epithelial cells from right mainstem bronchus

label_protocol: Three hundred nanograms of LMW RNA were labeled using the FlashTag labeling kit (Genisphere, Inc., Hatfield, PA). MicroRNA were first poly-A tailed and then directly ligated to a fluorescent dendrimer (a branched DNA structure carrying approximately 15 molecules of Oyster®-550 dye (DeNovo Biolabels GmBH, Munster, Germany)).

extract_protocol: Epithelial cells were obtained from brushing the right mainstem bronchus of current and never smoker volunteers at bronchoscopy. Epithelial cell content yields were generally approximately 90%. RNA was size fractionated, and low molecular weight RNA ( < 200 nucleotides) was obtained from each sample for microRNA microarray analysis.

tag: Sex

value: Female

tag: Race

value: African American

tag: Age

tag: PKYRS

tag: Never smoker


title: Patient_525_Never_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient525.gpr

value: Caucasian


title: Patient_142_Never_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient142.gpr

value: Hispanic


title: Patient_128_Never_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient128.gpr


title: Patient_527_Never_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient527.gpr

value: Male


title: C19 (COG study 8704)

description: C= Complete Continous Remission


title: C18 (COG study 8704)

description: C= Complete Continous Remission


title: Patient_539_Current_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient539.gpr

tag: Current smoker


title: C12 (COG study 8704)

description: C= Complete Continous Remission


title: C15 (COG study 8704)

description: C= Complete Continous Remission


title: Patient_534_Current_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient534.gpr


title: Patient_532_Current_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient532.gpr


title: Patient_533_Current_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient533.gpr


title: C13 (COG study 8704)

description: C= Complete Continous Remission


title: C16 (COG study 8704)

description: C= Complete Continous Remission


title: C17 (COG study 8704)

description: C= Complete Continous Remission


title: C9 (COG study 8704)

description: C= Complete Continous Remission


title: Patient_530_Current_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient530.gpr


title: C8 (COG study 8704)

description: C= Complete Continous Remission


title: Patient_526_Current_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient526.gpr


title: C10 (COG study 8704)

description: C= Complete Continous Remission


title: C11 (COG study 8704)

description: C= Complete Continous Remission


title: Patient_528_Current_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient528.gpr


title: Patient_524_Current_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient524.gpr


title: C14 (COG study 8704)

description: C= Complete Continous Remission


title: Clostridium_acetobutylicum_rDNA_butyrate_stress_0.6%_15min_dyeswap

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

description: No additional information.

hyb_protocol: Arrays were hybridized according to Agilent’s “Hybridization Procedure for 22k microarrays (cDNA labeled Targets)” (Agilent 60-mer Oligo Microarray Processing Protocol v. 4.1, Agilent); however, the 17 hr incubation was performed at 65 degrees C. Washing of the arrays was performed according to Agilent’s “Wash Procedure with Stabilization and Drying Solution” (Two-Color Microarray-Based Gene Expression Analysis v. 4.0.1, Agilent). Removal of microarrays from the final Stabilization and Drying Solution wash was immediately repeated for slides that were not completely dry.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 micrometers resolution using Agilent’s eXtended Dynamic Range technique. Each array was scanned twice: once at photomultiplier tube gain of 100%, and again at a 10% gain.

data_processing: Microarrays were scanned using a G2565BA Agilent Microarray Scanner (Agilent) at 10 microm resolution. Scans were performed using Agilent’s eXtended Dynamic Range technique. Each array was scanned twice: once at photomultiplier tube gain of 100%, and again at a 10% gain. Information from both scans was processed by Agilent Feature Extraction software (v. 9.1), used to assess spot quality and obtain feature intensity statistics; duplicate spots were averaged. Background-subtracted data were normalized using a segmental nearest neighbor logarithmic expression ratio-of-the mean (SNN-LERM) approach (Yang et al., PNAS 2003; 100:1122-1127).

organism: Clostridium acetobutylicum

source_name: C. acetobutylicum (rDNA7) stressed with 0.6% v/v butyrate 15 min

label_protocol: An indirect labeling approach was followed where cDNA was first made in the presence of nucleotides and aminoallyl dUTP, purified, and then the aminoallyl dUTP groups were coupled to a monoreactive dye (Cy3 or Cy5) as described previously (Alsaker et al. 2005. Biotechnology and Bioprocess Engineering 10: 432-443).

growth_protocol: Colonies of C. acetobutylicum ATCC 824 (pSOS95del) (American Type Culture Collection, Manassas, VA, USA) were grown on agar-solidifed 2xYTG plates (YTG is 8 g/liter tryptone, 5 g/liter yeast extract, 2 g/liter NaCl, 2.5 g/liter glucose, and 7.5 g/l agar, pH 5.8) containing 40 micrograms/mL of erythromycin. Liquid cultures were inoculated with single colonies from plates at least 4 days old and heat shocked at 70 to 80°C for 10 min. Cultures were grown in an anaerobic chamber (Forma Scientific, Marietta, OH) in Clostridial Growth Medium (CGM, Wiesenborn, D. P., et al. 1988. Appl. Environ. Microbiol. 54:2717–2722) supplemented with 80 g/liter glucose and 100 micrograms/mL erythromycin until they reached an A600 ca. 1.0 (corresponding to midexponential growth).  Butyric acid, adjusted to pH 6.7 with 10M sodium hydroxide, was then added to 0.6%v/v final concentration.

extract_protocol: Cell pellets were collected by centrifuging 3 to 10 mL of cultures at 5,000xg for 10 min, 4 degrees C. Cells were then lysed by resuspending in 200 microL SET buffer (25% sucrose, 50 mM EDTA [pH 8.0], 50 mM Tris [pH 8.0]) with 20 mg/mL lysozyme (Sigma) and incubation at 37 degrees C for 4 min. One milliliter of ice cold TRIzol (Invitrogen, Carlsbad, CA, USA) was added and the sample was vortexed. Samples were immediately stored at -85 degrees C and used within one month to minimize RNA degradation. To isolate and purify the RNA, samples were thawed at room temperature; 500 microL of sample was diluted with an equal amount of ice cold TRIzol and then purified following manufacturer’s instructions. The RNA was resuspended in 20-30 microL RNase-free water and quantitated in a spectrophotometer by measuring absorbance at 260 and 280 nm. Samples were only used if the A260/A280 ratio was greater than 1.8. RNA integrity was also verified by running 0.5 microL of sample on a 1.0% agarose gel. Purified RNA were stored at -85 degree C and used within one week of purification.

treatment_protocol: This culture is the experimental strain.  The culture was challenged with 0.6% butyrate at an OD of 1.0 (mid-exponential growth).  Before challenging, the butyrate was adjusted to pH 6.7 (the approximate pH of the growing culture). This sample was taken 15 min after addition of butyrate.

tag: Clostridium acetobutylicum ATCC 824 (pSOS95del)

source_name: C. acetobutylicum (pSOS95del) plasmid control stressed with 0.6% v/v butyrate 15 min

label_protocol: Same as channel 1

growth_protocol: Same as channel 1

extract_protocol: Same as channel 1

treatment_protocol: This culture is the control strain for this experiment.  The culture was challenged with 0.6% butyrate at an OD of 1.0 (mid-exponential growth).  Before challenging, the butyrate was adjusted to pH 6.7 (the approximate pH of the growing culture).  This sample was taken 15 min after addition of butyrate.

tag: Clostridium acetobutylicum ATCC 824 (pRDNA7)


title: C7 (COG study 8704)

description: C= Complete Continous Remission


title: Patient_462_Current_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient462.gpr


title: C6 (COG study 8704)

description: C= Complete Continous Remission


title: Clostridium_acetobutylicum_rDNA_butyrate_stress_0.6%_15min

description: No additional information.


title: Patient_459_Current_Smoker_temp_replicate

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient459-2.gpr


title: Clostridium_acetobutylicum_rDNA_butyrate_stress_0.6%_0min_dyeswap

description: No additional information.

source_name: C. acetobutylicum (rDNA7) not stressed 0 min

treatment_protocol: This culture is the experimental strain.  The culture was challenged with 0.6% butyrate at an OD of 1.0 (mid-exponential growth).  Before challenging, the butyrate was adjusted to pH 6.7 (the approximate pH of the growing culture). This sample was taken immediately prior to addition of butyrate.

source_name: C. acetobutylicum (pSOS95del) plasmid control not stressed 0 min

treatment_protocol: This culture is the control strain for this experiment.  The culture was challenged with 0.6% butyrate at an OD of 1.0 (mid-exponential growth).  Before challenging, the butyrate was adjusted to pH 6.7 (the approximate pH of the growing culture).  This sample was taken immediately prior to addition of butyrate.


title: input DNA

city: Kansas City

first: Steven

last: Hart

state: KS

address: 3901 Rainbow Blvd

department: Pharmacology, Toxicology & Therapeutics

institute: University of Kansas Medical Center

description: input DNA

hyb_protocol: Labeled products (12 µg) were hybridized to the Affymetrix mouse tiling 2.0R array. DNA without immunoprecipitation was used as control (input) for background hybridization.

scan_protocol: Arrays were washed and scanned by GeneChip ® HT Array Plate Scanner according to standard procedures.

data_processing: Standard Affymetrix protocol

organism: Mus musculus

source_name: control

label_protocol: Amplified DNAs were fragmented, labeled using the DNA Terminal Labeling Kit according to the standard Affymetrix protocol. (http://www.affymetrix.com/products/arrays/specific/mouse_tiling_2.affx).

growth_protocol: C57 BL/6 breeding pairs were purchased from Charles River Laboratories (Wilmington, MA). Mice were housed according to the American Animal Association Laboratory Animal Care guidelines, and were bred under standard conditions in Lab Animal Resources building in the University of Kansas Medical Center. Body weights of the female mice were recorded every day to monitor pregnancy status. Tissues from male offspring were collected at day -2 (17-days gestation), 1, 5, and 45 after birth. Tissues were frozen immediately in liquid nitrogen after harvest, and stored at -80℃ for further analysis.

extract_protocol: To determine DNA and histone methylation, a combination of immunoprecipitation of methylated DNA fragments with an antibody against 5-methyl-cytosine (ab51552; Abcam Inc. Cambridge, MA) anti-H3K4me2 (Millipore 07-030) and anti-H3k27me3 (Millipore 07-449) and hybridization of the precipitated DNA fragments to the GeneChip array were used. Genomic DNA from the liver tissues was isolated by a ChargeSwitch gDNA Mini Tissue Kit (Invitrogen, Carlsbad, CA), following the manufacturer’s protocol. The purified ChIP-enriched fragments were amplified by random priming. A fixed sequence of 17 bases containing 9 random bases at the 3' end was first used in four linear amplification reactions with Sequenase (USB, Cleveland, OH). Following purification, the randomly primed ChIP DNA was amplified for 30 cycles using a fixed sequence primer. The resulting amplified DNA was purified, quantified, and tested by Q-PCR at the same genomic regions as the original immunoprecipitated DNA to assess quality of the amplification reactions

treatment_protocol: No treatments


title: Patient_459_Current_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient459-1.gpr


title: meDNA Day 45

description: ChIP

source_name: liver, Day 45


title: Clostridium_acetobutylicum_rDNA_butyrate_stress_0.6%_0min

description: No additional information.

extract_protocol: Cell pellets were collected by centrifuging 3 to 10 mL of cultures at 5,000xg for 10 min, 4 degrees C. Cells were then lysed by resuspending in 200 microL SET buffer (25% sucrose, 50 mM EDTA [pH 8.0], 50 mM Tris [pH 8.0]) with 20 mg/mL lysozyme (Sigma) and incubation at 37 degrees C for 4 min. One milliliter of ice cold TRIzol (Invitrogen, Carlsbad, CA, USA) was added and the sample was vortexed. Samples were immediately stored at -85 degrees C and used within one month to minimize RNA degradation. To isolate and purify the RNA, samples were thawed at room temperature; 500 microL of sample was diluted with an equal amount of ice cold TRIzol and then purified following manufacturer’s instructions. The RNA was resuspended in 20 microL RNase-free water and quantitated in a spectrophotometer by measuring absorbance at 260 and 280 nm. Samples were only used if the A260/A280 ratio was greater than 1.8. RNA integrity was also verified by running 0.5 microL of sample on a 1.0% agarose gel. Purified RNA were stored at -85 degree C and used within one week of purification.

source_name: C. acetobutylicum (RDNA7) not stressed 0 min


title: C5 (COG study 8704)

description: C= Complete Continous Remission

source_name: Primary T-ALL cells; newly diagnosed patient; Complete Continous Remission


title: C3 (COG study 8704)

description: C= Complete Continous Remission


title: Clostridium_acetobutylicum_rDNA_butyrate_stress_0.6%_240min

description: No additional information.

source_name: C. acetobutylicum (pSOS95del) plasmid control stressed with 0.6% v/v butyrate 240 min

treatment_protocol: This culture is the control strain for this experiment.  The culture was challenged with 0.6% butyrate at an OD of 1.0 (mid-exponential growth).  Before challenging, the butyrate was adjusted to pH 6.7 (the approximate pH of the growing culture).  This sample was taken 240 min after addition of butyrate.

source_name: C. acetobutylicum (rDNA7) stressed with 0.6% v/v butyrate 240 min

treatment_protocol: This culture is the experimental strain.  The culture was challenged with 0.6% butyrate at an OD of 1.0 (mid-exponential growth).  Before challenging, the butyrate was adjusted to pH 6.7 (the approximate pH of the growing culture). This sample was taken 240 min after addition of butyrate.


title: C4 (COG study 8704)

description: C= Complete Continous Remission


title: Clostridium_acetobutylicum_rDNA_butyrate_stress_0.6%_360min

description: No additional information.

source_name: C. acetobutylicum (pSOS95del) plasmid control stressed with 0.6% v/v butyrate 360 min

treatment_protocol: This culture is the control strain for this experiment.  The culture was challenged with 0.6% butyrate at an OD of 1.0 (mid-exponential growth).  Before challenging, the butyrate was adjusted to pH 6.7 (the approximate pH of the growing culture).  This sample was taken 360 min after addition of butyrate.

source_name: C. acetobutylicum (rDNA7) stressed with 0.6% v/v butyrate 360 min

treatment_protocol: This culture is the experimental strain.  The culture was challenged with 0.6% butyrate at an OD of 1.0 (mid-exponential growth).  Before challenging, the butyrate was adjusted to pH 6.7 (the approximate pH of the growing culture). This sample was taken 360 min after addition of butyrate.


title: meDNA Day 5

description: ChIP

source_name: liver, Day 5


title: Clostridium_acetobutylicum_rDNA_butyrate_stress_0.6%_240min_dyeswap

description: No additional information.


title: C1 (COG study 8704)

description: C= Complete Continous Remission


title: F21 (COG study 8704)

description: F= failure (relapse)

source_name: Primary T-ALL cells; newly diagnosed patient; failure (relapse)


title: Clostridium_acetobutylicum_rDNA_butyrate_stress_0.6%_120min

description: No additional information.

source_name: C. acetobutylicum (pSOS95del) plasmid control stressed with 0.6% v/v butyrate 120 min

treatment_protocol: This culture is the control strain for this experiment.  The culture was challenged with 0.6% butyrate at an OD of 1.0 (mid-exponential growth).  Before challenging, the butyrate was adjusted to pH 6.7 (the approximate pH of the growing culture).  This sample was taken 120 min after addition of butyrate.

source_name: C. acetobutylicum (rDNA7) stressed with 0.6% v/v butyrate 120 min

treatment_protocol: This culture is the experimental strain.  The culture was challenged with 0.6% butyrate at an OD of 1.0 (mid-exponential growth).  Before challenging, the butyrate was adjusted to pH 6.7 (the approximate pH of the growing culture). This sample was taken 120 min after addition of butyrate.


title: F20 (COG study 8704)

description: F= failure (relapse)


title: F18 (COG study 8704)

description: F= failure (relapse)


title: meDNA Day 2

description: ChIP

source_name: liver, Day -2


title: Clostridium_acetobutylicum_rDNA_butyrate_stress_0.6%_120min_dyeswap

description: No additional information.


title: F15 (COG study 8704)

description: F= failure (relapse)


title: Clostridium_acetobutylicum_rDNA_butyrate_stress_0.6%_40min_dyeswap

description: No additional information.

source_name: C. acetobutylicum (rDNA7) stressed with 0.6% v/v butyrate 40 min

treatment_protocol: This culture is the experimental strain.  The culture was challenged with 0.6% butyrate at an OD of 1.0 (mid-exponential growth).  Before challenging, the butyrate was adjusted to pH 6.7 (the approximate pH of the growing culture). This sample was taken 40 min after addition of butyrate.

source_name: C. acetobutylicum (pSOS95del) plasmid control stressed with 0.6% v/v butyrate 40 min

treatment_protocol: This culture is the control strain for this experiment.  The culture was challenged with 0.6% butyrate at an OD of 1.0 (mid-exponential growth).  Before challenging, the butyrate was adjusted to pH 6.7 (the approximate pH of the growing culture).  This sample was taken 40 min after addition of butyrate.


title: F16 (COG study 8704)

description: F= failure (relapse)

treatment_protocol: COG study 8704


title: F17 (COG study 8704)

description: F= failure (relapse)


title: Clostridium_acetobutylicum_rDNA_butyrate_stress_0.6%_360min_dyeswap

description: No additional information.


title: H3K27met3 Day 1

description: ChIP

source_name: liver, Day 1


title: F10 (COG study 8704)

description: F= failure (relapse)


title: H3K4met2 Day 45

description: ChIP


title: F14 (COG study 8704)

description: F= failure (relapse)


title: meDNA Day 1

description: ChIP


title: H3K27met3 Day 5

description: ChIP


title: H3K27met3 Day 2

description: ChIP


title: F11 (COG study 8704)

description: F= failure (relapse)


title: F6 (COG study 8704)

description: F= failure (relapse)


title: Clostridium_acetobutylicum_rDNA_butyrate_stress_0.6%_40min

description: No additional information.


title: H3K4met2 Day 2

description: ChIP


title: H3K4met2 Day 1

description: ChIP


title: H3K4met2 Day 5

description: ChIP


title: F7 (COG study 8704)

description: F= failure (relapse)


title: H3K27met3 Day 45

description: ChIP


title: F9 (COG study 8704)

description: F= failure (relapse)


title: C20 (COG study 8704)

description: C= Complete Continous Remission


title: F3 (COG study 8704)

description: F= failure (relapse)


title: F5 (COG study 8704)

description: F= failure (relapse)


title: F1 (COG study 8704)

description: F= failure (relapse)


title: F2 (COG study 8704)

description: F= failure (relapse)


title: NR4 (COG study 8704)

description: NR =no response (induction failure)

source_name: Primary T-ALL cells; newly diagnosed patient; no response (induction failure)


title: MCF7_CRY2KO_Rep1

city: New Haven

first: Aaron

middle: Ezra

last: Hoffman

state: CT

address: 60 College St.

department: LEPH

institute: Yale School of Medicine

description: All protocols performed by an Agilent-certified service provider

hyb_protocol: Agilent's Gene Expression Hybridization Kit followed by Agilent's Gene Expression Wash Buffer Kit

scan_protocol: Agilent’s Microarray Scanner with SureScan technology

data_processing: Agilent Feature Extraction Software, data were analyzed using the Rosetta Luminator gene expression data analysis system.  Value = log10(intensity2/intensity1).

source_name: MCF7 Negative Control siRNA

label_protocol: mRNA converted to Cyanine 3-labeled cRNA using Agilent's Quick Amp Labeling Kit

extract_protocol: Qiagen RNeasy mini kit with on-column DNAse digestion

tag: MCF7 cells transfected with a negative control siRNA

source_name: MCF7 CRY2 siRNA

label_protocol: mRNA converted to Cyanine 5-labeled cRNA using Agilent's Quick Amp Labeling Kit

tag: MCF7 cells transfected with a CRY2-targeting siRNA


title: Patient_537_Never_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient537.gpr

source_name: epithelial cells from right mainstem bronchus


title: Case-Control 7

city: London

first: James

last: Flanagan

address: Du Cane Rd

department: Dept of Oncology

country: United Kingdom

institute: Imperial College London

hyb_protocol: Arrays performed by Nimblegen Inc, using standard protocols (see http://www.nimblegen.com/)

data_processing: Data were analysed using MA2C (Song et al, Genome biology, 8, R178 (2007)).

source_name: case 7

extract_protocol: genomic DNA was extracted using commerical kits (typically Qiagen)

treatment_protocol: Enrichment of unmethylated DNA fraction using methylation sensitive enzymes (HpaII, Hin6I and AciI). For Full method see Schumacher et al, Nucleic Acids Res, 34, 528-42 (2006)

tag: female

source_name: control 7


title: Case-Control 12

scan_protocol: Arrays performed by Nimblegen Inc, using standard protocols (see http://www.nimblegen.com/)

source_name: case 12

source_name: control 12


title: Case-Control 11

source_name: case 11

label_protocol: Arrays performed by Nimblegen Inc, using standard protocols (see http://www.nimblegen.com/)

source_name: control 11


title: Case-Control 6

source_name: case 6

source_name: control 6


title: Clostridium_acetobutylicum_824pSOS95delvs824pHK654_C_rep2

description: Samples compare transcritptional differences between the CAC0654 asRNA strain 824pHK654 and the plasmid control strain 24pSOS95del

hyb_protocol: Oppositely labeled microarray probe pairs (1 microgram of each) were mixed together, dried in a rotary SpeedVac, and redissolved in Pronto Universal Hybridization Solution. The samples were incubated at 95 degrees C for 5 min and loaded on the microarray under a LifterSlip (Erie Scientific, Portsmouth, NH, USA). The microarrays were placed in a Corning hybridization chamber with 50 microL 10xSSC (1xSSC is 0.15 M NaCl and 0.015 M sodium citrate) to maintain humidity. Microarrays were hybridized for 14-16 h in a 42 degrees C water bath. Following hybridization, microarrays were washed in TeleChem (Sunnyvale, CA, USA) wash buffers A (42 degrees C, 5 min), B (room temperature, 5 min), and C (room temperature, 2 min) and water. Slides were then spun dry at 240xg for 10 min.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 micrometer resolution.

data_processing: Samples were quantitated using GenePix Pro software version 5.0 (Molecular Devices, Sunnyvale, CA).  Microarrays were normalized using a segmental nearest neighbor logarithmic expression ratio of the mean (Yang, Haddad et al. 2003) using 200 genes per interval, 25 intervals, and a gamma factor of 2.0.

label_protocol: Random hexamer primed reverse transcription reactions using Superscript II (Invitrogen) reverse transcriptase with aminoallyl dUTP were used as previously described (Alsaker, Paredes et al. 2005).  Reactions were purified using Millipore YM-30 columns and dried in a rotary SpeedVac.  cDNA samples were resuspended in 4.5 microliters of 0.1 M sodium bicarbonate buffer pH 9.0 and incubated at room temperature in the dark for one hour with Cy3 or Cy5 dye (Amersham).  Samples were purified on a Qiagen Qiaquick PCR purification column.  Samples were stored at -20°C.

growth_protocol: C. acetobutylicum was stored at -85 degrees C in clostridial growth media (CGM, Wiesenborn, D. P., et al. 1988. Appl. Environ. Microbiol. 54:2717–2722) containing 15% glycerol. Solid cultures were carried out on agar-solidified 2xYTG (YTG is 8 g/liter tryptone, 5 g/liter yeast extract, 2 g/liter NaCl, 2.5 g/liter glucose, and 7.5 g/l agar, pH 5.8) plates. Liquid cultures were inoculated with single colonies from plates at least 4 days old and heat shocked at 70 to 80°C for 10 min. Fermentations were carried out using a BioFlo 110 or BioFlo II (New Brunswick Scientific Co., Edison, NJ) bioreactor with 4.0 L working volumes.  Fermentations used a 10% v/v inoculum (A600 = 0.2).  CGM were supplemented with 0.10% (v/v) antifoam and 75 micrograms/mL clarithromycin.  Fermentations were maintained at pH 5.0 using 6 M NH4OH.  Anaerobic conditions were maintained through nitrogen sparging.  Temperature was maintained at 37°C and agitation was set at 200 rpm.  Glucose was restored to the initial concentration (440 mM) in fermentations if glucose levels fell below 200 mM.

extract_protocol: Cell pellets from 3 to 10 mL of culture were incubated at 37°C for 4 minutes in 200 microliters of SET buffer (25% sucrose, 50 mM EDTA pH 8.0, 50 mM Tris-HCl pH 8.0) with 20 mg/mL lysozyme.  1 mL trizol was added to each sample and stored at -85°C until purification.  0.5 mL Trizol and 0.2 mL chloroform were added to 0.5 mL RNA sample and centrifuged at 12,000 rpm for 15 minutes.  The aqueous phase was collected and added to an equal volume of isopropanol and RNA was precipitated at 12,000 rpm for 10 minutes.  1 mL ethanol was added to wash the pellet and centrifuged at 9,500 rpm for 4 minutes.  Samples were dried and resuspended in 20-100 microliters of RNase free water and stored at -85°C.

treatment_protocol: Culture was grown to an OD of 5.14 after 15 hours of growth.

tag: Clostridium acetobutylicum ATCC 824 containing plasmid pHK654

treatment_protocol: Culture was grown to an OD of 4.7 after 13.5 hours of growth.

tag: Clostridium acetobutylicum ATCC 824 containing plasmid pSOS95del


title: Clostridium_acetobutylicum_824pSOS95delvs824pHK654_D_rep1

treatment_protocol: Culture was grown to an OD of 4.9after  15 hours of growth.

treatment_protocol: Culture was grown to an OD of 6.08 after 16.5 hours of growth.


title: Clostridium_acetobutylicum_824pSOS95delvs824pHK654_D_rep2

treatment_protocol: Culture was grown to an OD of 4.9 after  15 hours of growth.


title: Clostridium_acetobutylicum_824pSOS95delvs824pHK654_A_rep1

treatment_protocol: Culture was grown to an OD of 1.23 after 9 hours of growth.

treatment_protocol: Culture was grown to an OD of 1.09 after 10.5 hours of growth.


title: Patient_538_Never_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient538.gpr


title: Clostridium_acetobutylicum_824pSOS95delvs824pHK654_A_rep2


title: Case-Control 10

source_name: case 10

source_name: control 10


title: Clostridium_acetobutylicum_824pSOS95delvs824pHK654_E_rep1

treatment_protocol: Culture was grown to an OD of 5.34 after 16.5 hours of growth.

treatment_protocol: Culture was grown to an OD of 6.58 after 18.5 hours of growth.


title: Clostridium_acetobutylicum_824pSOS95delvs824pHK654_C_rep1


title: Patient_536_Never_Smoker_tech_replicate

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient536-2.gpr


title: Case-Control 3

source_name: case 3

source_name: control 3


title: Case-Control 5

source_name: case 5

source_name: control 5


title: Clostridium_acetobutylicum_824pSOS95delvs824pHK654_B_rep1

treatment_protocol: Culture was grown to an OD of 3.74 after 12 hours of growth.

treatment_protocol: Culture was grown to an OD of 3.94 after 13.5 hours of growth.


title: Case-Control 2

source_name: case 2

source_name: control 2


title: Case-Control 1

source_name: case 1

source_name: control 1


title: Case-Control 9

source_name: case 9

source_name: control 9


title: Patient_536_Never_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient536-1.gpr

source_name: epithelial cells from right mainstem bronchus


title: Clostridium_acetobutylicum_824pSOS95delvs824pHK654_F_rep2

treatment_protocol: Culture was grown to an OD of 6.05 after 20.5 hours of growth.

treatment_protocol: Culture was grown to an OD of 5.88 after 19.5 hours of growth.


title: Patient_535_Never_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient535.gpr


title: Clostridium_acetobutylicum_824pSOS95delvs824pHK654_F_rep1


title: Patient_531_Never_Smoker

description:
Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background.
Patient531.gpr


title: Clostridium_acetobutylicum_824pSOS95delvs824pHK654_E_rep2


title: nla28 cells 12h replicate 1

status: Public on Jan 28 2009

city: Syracuse

first: Anthony

last: Garza

state: NY

address: 212 BRL,  130 College Place

institute: Syracuse University

description: Biological replicate 1

hyb_protocol: cDNA was resuspended in 9 µl of 0.1 M sodium bicarbonate (pH 9.0). The cDNA was labeled with Cy3 (Reference: mixed wild type cDNA) or Cy5 (mutant developmental cDNA) (Amersham Pharmacia) by the addition of 4.5 µl of dye dissolved in 73 µl of dimethyl sulfoxide, and incubated for 1 hour in the dark.

scan_protocol: Post-hybridized DNA microarrays were scanned using a GenePix 4100A microarray scanner and read using GenePix Pro 6.0 (Axon Inc. Union City, CA) Images were quantified using GenePix Pro 6.0 (Axon Inc). Data extracted from the images were transferred to the software package Acuity 4.0 (Axon Instruments) for normalization and statistical analysis

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Green signal/processed Red signal.

organism: Myxococcus xanthus

source_name: cells undergoing development for 12 hours

label_protocol: Fifty µg of total RNA were used to synthesize cDNA using 10 µg of pdN6 primers (Amersham Pharmacia) in the presence of 40 µg/µl RNase inhibitor (Promega)

growth_protocol: Strains were grown at 28° or 32 °C in flasks containing 350 ml of CTTYE broth [1.0% Casitone, 10 mM Tris-HCl (pH 8.0), 1 mM KH2PO4, 8 mM MgSO4, and 0.5% yeast extract] with vigorous swiriling.  CTTYE broth was supplemented with 40 mg/ml of kanamycin sulfate as needed.

extract_protocol: Total RNA was extracted using the Hot-Phenol-Chloroform method (Sambrook et al., 1989) and subsequently purified using Agilent Technologies Total RNA Purification Kit

treatment_protocol: After culutres reached a density of 5 X 108 cells/ml, 40 ml aliquts of the cells were pelleted by centrifugation, the supernatants were removed, the cells were quick-frozen in dry ice/ethanol mixure, and the cells were stored at -80 °C as the vegetative (0 hour) test samples.  The cells in the remaining 350 ml culture wre pelleded by centrifugatin, the supernatants were removed and cells were resuspended in MC7 starvation buffer (10 mM morpholinepropanesulfonic acid [pH 7.0], 1 mM Ca cl2) to a density of 5 X 109 cells/ml.  Four ml of the concentrated cells were added to 28 ml of MC7 buffer and the cells were allowed to develop in a petri dish at 32°C.  At certain time points (1, 2, 4, 6, 12, 24 hours post-starvation) in development, the cells were detatched from the bottoms of the petri dishes using a cell scraper, pelleted by centrifugation, and the supernatants were removed.  The cells were quick-frozen in dry ice/ethanol mixure, and the stored at -80° C as developmental samples.

source_name: Total RNA from pooled M. xanthus cells at developmental time points


title: Case-Control 13

source_name: case 13

source_name: control 13


title: nla28 cells 6h replicate 3

description: Biological replicate 3

source_name: cells undergoing development for 6 hours


title: Case-Control 14

source_name: case 14

source_name: control 14


title: nla28 cells 12h replicate 3

description: Biological replicate 3


title: Case-Control 4

source_name: case 4

source_name: control 4


title: nla28 cells 6h replicate 2

description: Biological replicate 2


title: nla28 cells 6h replicate 1

description: Biological replicate 1


title: nla28 cells 4h replicate 1

description: Biological replicate 1

source_name: cells undergoing development for 4 hours


title: nla28 cells 4h replicate 2

description: Biological replicate 2


title: nla28 cells 2h replicate 2

description: Biological replicate 2

source_name: cells undergoing development for 2 hours


title: nla28 cells 12h replicate 2

description: Biological replicate 2


title: nla28 cells 2h replicate 1

description: Biological replicate 1


title: nla28 cells 4h replicate 3

description: Biological replicate 3


title: nla28 cells 1h replicate 3

description: Biological replicate 3

source_name: cells undergoing development for 1 hour


title: nla28 cells 1h replicate 2

description: Biological replicate 2


title: nla28 cells 0h replicate 1

description: Biological replicate 1

source_name: actively growing cells - 0h


title: nla28 cells 0h replicate 3

description: Biological replicate 3


title: nla28 cells 2h replicate 3

description: Biological replicate 3


title: nla6 cells 12h replicate 3

description: Biological replicate 3


title: nla28 cells 0h replicate 2

description: Biological replicate 2


title: nla28 cells 1h replicate 1

description: Biological replicate 1


title: nla6 cells 12h replicate 2

description: Biological replicate 2


title: nla6 cells 12h replicate 1

description: Biological replicate 1


title: nla6 cells 6h replicate 3

description: Biological replicate 3


title: nla6 cells 4h replicate 3

description: Biological replicate 3


title: nla6 cells 2h replicate 3

description: Biological replicate 3


title: nla6 cells 4h replicate 1

description: Biological replicate 1


title: nla6 cells 6h replicate 1

description: Biological replicate 1


title: nla6 cells 2h replicate 1

description: Biological replicate 1


title: nla6 cells 4h replicate 2

description: Biological replicate 2


title: nla6 cells 6h replicate 2

description: Biological replicate 2


title: nla6 cells 1h replicate 3

description: Biological replicate 3


title: Non-smoker 3

city: Maastricht

first: Joost

last: Linschooten

address: Universiteitssingel 50

department: Health Risk Analysis & Toxicology

country: Netherlands

institute: Maastricht University

hyb_protocol: Hybridization according to Agilent instructions.

scan_protocol: Scanning on GenePix 4000B (Molecular Devices). All slides were scanned with set laser power at 100% and photomultiplier gain at 69,9% for Cy5 and 64,5% for Cy3 channel based on automatic establishment of ideal scan settings

data_processing: Data preparations were performed in GeneSight software (BioDiscovery) andf included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), LOWESS normalization, log (base=2) transformations, calculation of difference of Cy5 (test) with Cy3 (common reference) sample

source_name: Spermatozoa obtained from frozen pure ejaculate

label_protocol: Agilent Low RNA Input Linear Amplification system according to the manufacturer's instructions.

growth_protocol: No growth protocols were used as RNA was extracted from sperm without any ex vivo performances.

extract_protocol: Total RNA isolation with Qiagen RNA MinElute RNA Isolation Kit according to manufacturer's instructions, including an additional DNAse treatment.

treatment_protocol: Sperm collection into appropriate containers.

tag: Ejaculate collected by masturbation, pure ejaculate snap-frozen

source_name: common reference sample composed of spermatozoal total RNA isolated from one non-smoking subject


title: nla6 cells 0h replicate 2

description: Biological replicate 2

tag: Strain


title: Smoker 4


title: Non-smoker 2


title: Non-smoker 1


title: Non-smoker 4


title: Smoker 3


title: nla6 cells 1h replicate 2

description: Biological replicate 2


title: nla6 cells 1h replicate 1

description: Biological replicate 1


title: GCB-DLBCL SUDHL-6

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

country: Spain

institute: University of Navarra/ Clínica Universidad de Navarra

description: Biological replicate 3 of 3. SUDHL-6 GCB-DLBCL cell line, untreated

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a microcirculation pump. Hybridization solution consisted of 100 µL of 6× SSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C. After hybridization, the miRNAs were detected by fluorescence labeling using tag-specific Cy3 and Cy5 dyes

scan_protocol: Scanned on a GenePix 4000B (Molecular Device) laser scanner Images were quantified using Array-Pro image analysis software (Media Cybernetics)

data_processing: Median normalized, background subtracted data was used to calculate the ratio of processed Green signal/processed Red signal, and ratios were then log2 transformed. Probes hsa-miR-377 and hsa-miR-542-5p were excluded due to systematic dye bias, following manufacturer instructions.

source_name: GCB-DLBCL SUDHL-6 cell line

label_protocol: The assay started with 5 µg of total RNA sample. The RNA was size-fractionated using a YM-100 Microcon centrifugal filter (GE Millipore), and the 3′ ends of the small RNAs (<300 nt) were extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in the dual-sample experiments

growth_protocol: Cultured till exponential growth in IMDM (Cellgro) with 20% human plasma, 1% penicillin/streptomycin/L-glutamine (Cellgro) and 0,2% beta mercaptoethanol (Invitrogen)

extract_protocol: Total RNA extracted using mirVana™ miRNA Isolation Kit (Ambion) following manufacturer's instructions

tag: Lymphoma derived cell line

source_name: FirstChoice® Human Skeletal Muscle Total RNA (Ambion)

tag: Total RNA from healthy human skeletal muscle

tag: Tissue

value: skeletal muscle


title: ABC-DLBCL U2932

description: Biological replicate 4 of 5. U2932 ABC-DLBCL cell line, untreated

source_name: ABC-DLBCL U2932 cell line


title: nla6 cells 0h replicate 3

description: Biological replicate 3

source_name: Total RNA from pooled M. xanthus cells at developmental time points


title: ABC-DLBCL HBL-1

description: Biological replicate 5 of 5. HBL-1 ABC-DLBCL cell line, untreated

source_name: ABC-DLBCL HBL-1 cell line


title: Case-Control 8

source_name: case 8

source_name: control 8


title: nla6 cells 2h replicate 2

description: Biological replicate 2


title: nla6 cells 0h replicate 1

description: Biological replicate 1


title: ABC-DLBCL RIVA

description: Biological replicate 3 of 5. RIVA ABC-DLBCL cell line, untreated

source_name: ABC-DLBCL RIVA cell line


title: nla18 cells 12h replicate 2

description: Biological replicate 2

source_name: cells undergoing development for 12 hours


title: GCB-DLBCL Oci-Ly-19

description: Biological replicate 1 of 3. Oci-Ly-19 GCB-DLBCL cell line, untreated

source_name: GCB-DLBCL Oci-Ly-19 cell line


title: nla18 cells 12h replicate 1

description: Biological replicate 1


title: ABC-DLBCL Oci-Ly-10

description: Biological replicate 2 of 5. Oci-Ly-10 ABC-DLBCL cell line, untreated

source_name: ABC-DLBCL Oci-Ly-10 cell line


title: Smoker 1


title: Smoker 2


title: GCB-DLBCL Oci-Ly-7

description: Biological replicate 2 of 3. Oci-Ly-7 GCB-DLBCL cell line, untreated

source_name: GCB-DLBCL Oci-Ly-7 cell line


title: nla18 cells 6h replicate 3

description: Biological replicate 3

source_name: cells undergoing development for 6 hours


title: ABC-DLBCL Oci-Ly-3

description: Biological replicate 1 of 5. Oci-Ly-3 ABC-DLBCL cell line, untreated

source_name: ABC-DLBCL Oci-Ly-3 cell line


title: nla18 cells 4h replicate 3

description: Biological replicate 3

source_name: cells undergoing development for 4 hours


title: nla18 cells 12h replicate 3

description: Biological replicate 3


title: C2 (COG study 8704)

description: C= Complete Continous Remission

scan_protocol: Affymerix microarray scanner (Hewlett Packard), gene fluorescence was captured using GeneChip software.

source_name: Primary T-ALL cells; newly diagnosed patient; Complete Continous Remission

treatment_protocol: COG study 8704

tag: Newly diagnosed patient


title: nla18 cells 6h replicate 1

description: Biological replicate 1


title: nla18 cells 6h replicate 2

description: Biological replicate 2


title: nla18 cells 4h replicate 1

description: Biological replicate 1


title: nla18 cells 2h replicate 3

description: Biological replicate 3

source_name: cells undergoing development for 2 hours


title: nla18 cells 2h replicate 2

description: Biological replicate 2


title: nla18 cells 4h replicate 2

description: Biological replicate 2


title: nla18 cells 2h replicate 1

description: Biological replicate 1


title: nla18 cells 1h replicate 2

description: Biological replicate 2

source_name: cells undergoing development for 1 hour


title: Synchronized cells, 60 min, cell cycle CCA | array yofG_81B

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 60 minutes later, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

hyb_protocol: Labeled samples were combined, concentrated in Microcon YM-30 columns, and hybridized to the microarrays in 3.4X SSC and 0.3% SDS for 16 hours at 65 degrees.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 expression ratios (Cy5/Cy3) were calculated to produce the values given in the data table.

source_name: Mid-log mRNA (unsynchronized)

label_protocol: The mRNA was reverse-transcribed, incorporating amino-allyl dUTP and then coupled with Cy3 NHS ester, and cleaned up with the Qiagen MinElute kit.

extract_protocol: Cells were lysed in a buffered SDS solution and extracted twice with hot phenol and once with chloroform, and then precipiated with 0.1 volume sodium acetate and 2.5 volumes of 100% ethanol.  Total RNA pellets were washed and resuspended, and mRNA was purified using the Qiagen Oligotex kit following manuf. instructions.

source_name: 60 min

label_protocol: The mRNA was reverse-transcribed, incorporating amino-allyl dUTP and then coupled with Cy5 NHS ester, and cleaned up with the Qiagen MinElute kit.


title: Synchronized cells, 90 min, cell cycle CCA | array yofG_83T

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 90 minutes later, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 90 min


title: Synchronized cells, 80 min, cell cycle CCA | array yofG_83B

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 80 minutes later, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 80 min


title: Synchronized cells, 50 min, cell cycle CCA | array yofG_80T

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 50 minutes later, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 50 min


title: Synchronized cells, 70 min, cell cycle CCA | array yofG_81T

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 70 minutes later, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 70 min


title: Synchronized cells, 40 min, cell cycle CCA | array yofG_80B

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 40 minutes later, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 40 min


title: nla18 cells 1h replicate 3

description: Biological replicate 3

source_name: Total RNA from pooled M. xanthus cells at developmental time points


title: nla18 cells 0h replicate 3

description: Biological replicate 3

source_name: actively growing cells - 0h


title: nla18 cells 1h replicate 1

description: Biological replicate 1


title: nla18 cells 0h replicate 2

description: Biological replicate 2


title: Synchronized cells, 30 min, cell cycle CCA | array yofG_78T

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 30 minutes later, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 30 min


title: nla4 cells 12h replicate 3

description: Biological replicate 3

source_name: cells undergoing development for 12 hours

tag: Stain


title: nla18 cells 0h replicate 1

description: Biological replicate 1


title: Synchronized cells, 10 min, cell cycle CCA | array yofG_77B

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 10 minutes later, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 10 min


title: Synchronized cells, 0 min, cell cycle CCA | array yofG_75B

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were immediately harvested, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 0 min


title: Synchronized cells, 20 min, cell cycle CCA | array yofG_75T

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 20 minutes later, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 20 min


title: Synchronized cells, 15 min, cell cycle CCA | array yofG_77T

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 15 minutes later, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 15 min


title: Synchronized cells, 100 min, cell cycle CCA | array yofG_84B

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 100 minutes later, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 100 min


title: nla4 cells 12h replicate 2

description: Biological replicate 2


title: nla4 cells 12h replicate 1

description: Biological replicate 1


title: F13 (COG study 8704)

description: F= failure (relapse)

source_name: Primary T-ALL cells; newly diagnosed patient; failure (relapse)


title: nla4 cells 6h replicate 3

description: Biological replicate 3

source_name: cells undergoing development for 6 hours