title: WT.37C.0|prp18-1.37C.0

description: see PMID: 17388687

value: matched WT for prp18-1


title: WT.37C.20|prp18-1.37C.20

status: Public on Apr 04 2007

type: RNA

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

state: VA

address: 204 West Washington St

department: Biology

country: USA

institute: Washington and Lee Unversity

description: see PMID: 17388687

hyb_protocol: Competitive hybridization at 65oC for 12h

scan_protocol: images were acquired using an Axon Instruments GenePix 4000B scanner, reading at wavelengths of 635nm and 532nm (Axon Instruments, http://www.axon.com). Image analysis was performed using Axon Instruments GenePix Pro version 4.0.

data_processing: Spot ratio data were log2 transformed and normalized within each array using global loess regression implemented in the Bioconductor marray package

molecule: total RNA

organism: Saccharomyces cerevisiae

label_protocol: aa-dUTP incorporation during cDNA synthesis

extract_protocol: Acid phenol

tag: Genotype

tag: Temperature (C)

tag: Time (min)


title: snu114-60.37C.10|WT.37C.10

description: see PMID: 17388687

value: matched WT for snu114-60


title: WT.37C.30|prp18-1.37C.30

description: see PMID: 17388687


title: Transcript Mapping for Human HeLa Total RNA Sample 1

status: Public on Apr 06 2007

city: New Haven

first: Guoneng

last: Zhong

state: CT

address: 300 George St

institute: Yale Med

description:
Total RNA for HeLa S3 cells was obtained from Ambion (Austin, TX). All RNA samples had an agilent ratio greate than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of several different individuals.
First-strand cDNA synthesis was achieved using SuperScript II reverse transcriptase (Invitrogen) in the reaction volume of 105 ul for 15 of starting RNA material or scaled accordingly using the following protocol. RNA was mixed with random hexamers (83.3 ng/ g of mRNA; Invitrogen) and the bacterial control transcripts (see below) and subjected to the following cycling conditions in PE GeneAmp9600 PCR System: 70?C- 10 min and 20min ramp to 15C after which the 5x Superscript II First Strand buffer (Life Technologies), DTT and four dNTPs were added to the following final concentrations of 1x, 10mM and 0.5mM, respectively, followed by a 30 min incubation at 15C. At this point, Superscript II RTase was added (200Units/ g of mRNA; Life Technologies) followed by a 20 min ramp to 42C and 60 min incubation at 42C. At this point the SuperScript II was inactivated by 15 min incubation at 75C.
The first strand cDNA synthesis reaction was used for the second-strand cDNA synthesis in the presence of 50U of E. coli DNA Ligase, 200U of E. coli DNA polymerase I, and 10U of E. coli RNAse H supplemented with 0.2mM dNTPs in the final volume of 750 ul at 16oC (all reagents were from Invitrogen) based on 15ug of starting RNA or scaled appropriately. Upon treatment with RNAse H (Epicentre) and RNAse A/T1 (Ambion), double-stranded cDNA was extracted using QIAquick PCR purification kit (Qiagen) and subjected to further fragmentation to 50-100 bp by DNAse I (1U/ul; Epicentre) treatment in 1X One-Phor-All buffer (Pharmacia).Following DNAse I inactivation at 99C for 10 min, the size ditsribution of fragmented DNA was verified on a 1% agarose gel. The fragmented cDNA was then end-labeled with 70nM of bio-ddATP (Perkin Elmer) using 6-10U of terminal transferase (TdT, Roche) per 1ug of fragmented DNA in 1X TdT buffer (Roche) and 5mM CoCl2 (Roche) for 2 hours at 37C. The labeled DNA material was subsequently hybridized to the chips (previously prehybridized for 1 hour in 1X MES-triton at 45C) for 18 hours at 45C in a 3 M TMAC/1X MES-based solution.

scan_protocol: Scanned according to manufacturers procedures (http://www.affymetrix.com/).

data_processing: The value determined calculated from log (max [1, PM-MM] ) for each biological replicate separately.

label: biotin

organism: Homo sapiens

source_name: Human HeLa S3 Cells

extract_protocol: First-strand cDNA synthesis was achieved using SuperScript II reverse transcriptase (Invitrogen) in the reaction volume of 105 ul for 15 of starting RNA material or scaled accordingly using the following protocol. RNA was mixed with random hexamers (83.3 ng/ g of mRNA; Invitrogen) and the bacterial control transcripts (see below) and subjected to the following cycling conditions in PE GeneAmp9600 PCR System: 70?C- 10 min and 20min ramp to 15C after which the 5x Superscript II First Strand buffer (Life Technologies), DTT and four dNTPs were added to the following final concentrations of 1x, 10mM and 0.5mM, respectively, followed by a 30 min incubation at 15C. At this point, Superscript II RTase was added (200Units/ g of mRNA; Life Technologies) followed by a 20 min ramp to 42C and 60 min incubation at 42C. At this point the SuperScript II was inactivated by 15 min incubation at 75C. The first strand cDNA synthesis reaction was used for the second-strand cDNA synthesis in the presence of 50U of E. coli DNA Ligase, 200U of E. coli DNA polymerase I, and 10U of E. coli RNAse H supplemented with 0.2mM dNTPs in the final volume of 750 ul at 16oC (all reagents were from Invitrogen) based on 15ug of starting RNA or scaled appropriately. Upon treatment with RNAse H (Epicentre) and RNAse A/T1 (Ambion), double-stranded cDNA was extracted using QIAquick PCR purification kit (Qiagen) and subjected to further fragmentation to 50-100 bp by DNAse I (1U/ul; Epicentre) treatment in 1X One-Phor-All buffer (Pharmacia). Following DNAse I inactivation at 99C for 10 min, the size ditsribution of fragmented DNA was verified on a 1% agarose gel.

tag: Total RNA from Human HeLa S3 Cells.  All RNA samples had an agilent ratio greate than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of several different individuals.


title: WT.37C.40|prp18-1.37C.40

description: see PMID: 17388687


title: WT.37C.10|prp18-1.37C.10

description: see PMID: 17388687


title: prp18-1.37C.20|WT.37C.20

description: see PMID: 17388687


title: prp18-1.37C.0|WT.37C.0

description: see PMID: 17388687


title: prp18-1.37C.10|WT.37C.10

description: see PMID: 17388687


title: snu114-60.37C.90|WT.37C.90

description: see PMID: 17388687


title: Transcript Mapping for Human HeLa Total RNA Sample 3

hyb_protocol: The labeled DNA material was subsequently hybridized to the chips (previously prehybridized for 1 hour in 1X MES-triton at 45C) for 18 hours at 45C in a 3 M TMAC/1X MES-based solution.

label_protocol: The fragmented cDNA was then end-labeled with 70nM of bio-ddATP (Perkin Elmer) using 6-10U of terminal transferase (TdT, Roche) per 1ug of fragmented DNA in 1X TdT buffer (Roche) and 5mM CoCl2 (Roche) for 2 hours at 37C.


title: Transcript Mapping for Human HeLa Poly(A)+ RNA Sample 1

description:
PolyA RNA for HeLa S3 cells was obtained from Ambion (Austin, TX). All RNA samples had an agilent ratio greate than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of several different individuals.
First-strand cDNA synthesis was achieved using SuperScript II reverse transcriptase (Invitrogen) in the reaction volume of 105 ul for 15 of starting RNA material or scaled accordingly using the following protocol. RNA was mixed with random hexamers (83.3 ng/ g of mRNA; Invitrogen) and the bacterial control transcripts (see below) and subjected to the following cycling conditions in PE GeneAmp9600 PCR System: 70?C- 10 min and 20min ramp to 15C after which the 5x Superscript II First Strand buffer (Life Technologies), DTT and four dNTPs were added to the following final concentrations of 1x, 10mM and 0.5mM, respectively, followed by a 30 min incubation at 15C. At this point, Superscript II RTase was added (200Units/ g of mRNA; Life Technologies) followed by a 20 min ramp to 42C and 60 min incubation at 42C. At this point the SuperScript II was inactivated by 15 min incubation at 75C.
The first strand cDNA synthesis reaction was used for the second-strand cDNA synthesis in the presence of 50U of E. coli DNA Ligase, 200U of E. coli DNA polymerase I, and 10U of E. coli RNAse H supplemented with 0.2mM dNTPs in the final volume of 750 ul at 16oC (all reagents were from Invitrogen) based on 15ug of starting RNA or scaled appropriately. Upon treatment with RNAse H (Epicentre) and RNAse A/T1 (Ambion), double-stranded cDNA was extracted using QIAquick PCR purification kit (Qiagen) and subjected to further fragmentation to 50-100 bp by DNAse I (1U/ul; Epicentre) treatment in 1X One-Phor-All buffer (Pharmacia).Following DNAse I inactivation at 99C for 10 min, the size ditsribution of fragmented DNA was verified on a 1% agarose gel. The fragmented cDNA was then end-labeled with 70nM of bio-ddATP (Perkin Elmer) using 6-10U of terminal transferase (TdT, Roche) per 1ug of fragmented DNA in 1X TdT buffer (Roche) and 5mM CoCl2 (Roche) for 2 hours at 37C. The labeled DNA material was subsequently hybridized to the chips (previously prehybridized for 1 hour in 1X MES-triton at 45C) for 18 hours at 45C in a 3 M TMAC/1X MES-based solution.

molecule: polyA RNA

tag: Triple selected Poly(A)+ RNA from Human HeLa S3 Cells.  All RNA samples had an agilent ratio greate than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of several different individuals.


title: prp18-1.37C.40|WT.37C.40

description: see PMID: 17388687


title: prp18-1.37C.30|WT.37C.30

description: see PMID: 17388687


title: WT.16C.0|brr2-1.16C.0

description: see PMID: 17388687

value: matched WT for brr2-1


title: WT.16C.60|brr2-1.16C.60

description: see PMID: 17388687


title: WT.16C.180|brr2-1.16C.180

description: see PMID: 17388687


title: WT.16C.40|brr2-1.16C.40

description: see PMID: 17388687


title: WT.16C.20|brr2-1.16C.20

description: see PMID: 17388687


title: prp18-1.37C.5|WT.37C.5

description: see PMID: 17388687


title: WT.16C.120|brr2-1.16C.120

description: see PMID: 17388687


title: Germfree-2  (GF2) villi cells cy5-cy3

status: Public on Mar 04 2008

city: Urbana

first: H

middle: Rex

last: Gaskins

state: IL

address: 1207 W Gregory Dr

department: Animal Sciences

institute: UIUC

description: The hybridization chamber was disassembled and the LifterSlip™ was removed by immersing the array in 2X SSC, 0.1% SDS (at 42 °C) until the LifterSlip™ moved freely away from the slide. The arrays were placed in 2X SSC, 0.1% SDS for 5 min at 42 °C. Subsequently the arrays were placed in 0.1X SSC, 0.1% SDS for 10 min at room temperature followed by 0.1X SSC for 1 min at room temperature. The arrays were then rinsed in 0.01X SSC for 10 sec or less and dried by centrifugation.

hyb_protocol: Porcine oligonucleotide set represents 13,297 porcine cDNAs and ESTs. A reference design was used in which each of the experimental samples was cohybridized with the reference sample that contained equal amounts of all the RNA samples used in the experiment, which allowed the treatment of fluorescence ratios as measurements of relative expression. Single-spotted oligos were printed on GAPS II slides (Corning, Corning, NY) at the W. M. Keck Center for Comparative and Functional Genomics, University of Illinois. Before hybridization, the arrays were plunged in 0.2% SDS water and immediately agitated vigorously for 2 min, washed three times in successive jars of distilled water and rinse in 100% ethanol. The arrays were then incubated in 5X SSC, 0.1% SDS, 1% BSA in a Coplin jar for 45 to 60 min at 42 °C, washed by immersing in 5 successive Coplin jars of deionized distilled water (RICCA Chemical Company, Arlington, TX), rinsed in 100% isopropanol, to ensure that the SDS is completely removed from the arrays and subsequently dried by centrifugation. An array was placed into a Corning Hybridization Chamber (Sigma) and 80 μl of the leveled solution was applied to a slide and covered with a LifterSlip™ (Erie Scientific, Portsmouth, NH). The chamber was then assembled and submerged in a 42 °C water bath for 48 h.

scan_protocol: Following hybridization and washing, slides were scanned immediately for both dye channels with an Axon 4000B (Molecular Devices, Union City, CA) dual-laser confocal scanner and images were processed using GenePix v6.0 software (Molecular Devices).

data_processing: Median foreground intensities (F) and median background intensities (B) were generated to construct the data matrix. Data were filtered out when the following criteria were satisfied: (I) removal of low intensity spots when F-B < M + 2 MAD, where M is the median of the negative control spots (blank or buffer spots); MAD is the median absolute deviation, (II) removal of saturated spots with very high intensity, and (III) removal of spots flagged by GenePix.  Data were normalized using the regional lowess normalization (rlowess) method from the MAANOVA package and analyzed by Proc GLM in SAS (version 8.2).  To avoid type I error of least square means, Proc multtest was conducted to generate a false discovery rate value (FDR). FDR adjustments balance type I and type II error rates. Genes were considered to be differentially expressed when P ≤ 0.05.

organism: Sus scrofa

source_name: Germfree-2  villi cells cy5

label_protocol: The amplified anti-sense (aRNA) was labeled with Cy3 or Cy5 dyes. Each of the 16 cell populations was reversed labeled with Cy3 and Cy5 to account for dye labeling bias, resulting in 32 target samples for microarray hybridization. Cy3 and Cy5 dyes were resuspended in 45 μl dimethyl sulfoxide (DMSO, Sigma) and stored at – 80 °C in a light protected area. For the labeling reaction, 5-7 μg of amino-allyl tagged aRNA was dried in a SpeedVac and 5 μl of 0.1 M Na2CO3 (pH, 9.0) and 5 μl of dye (Cy3 or Cy5) dissolved in DMSO were added to the dried sample. The mixture was then incubated in the dark for 75 min and unincorporated dye was removed with a modified protocol based on the Qiagen Mini Elute Kit (Qiagen, Valencia, CA) with a total elution volume of 50 µl for each sample.  The sample was then dried in a SpeedVac for 50 min to dryness followed by adding 10 µl of RNase free water.  To decrease the fragment size to 60-200 bases, 1 µL of fragmentation buffer (Ambion) was added to the sample and heated to 70 °C for 15 min. Stop solution (1 µl) was added to terminate the reaction. A blocking mixture containing 2 µl of poly d(A) and 20 µl of Porcine HyblocTM (Applied Genetics Laboratories, Inc, Melbourne, FL) were added to 12 µl probe and incubated at 100 °C for 1 min then snap cool on ice for 2 min. Subsequently, the mixture was centrifuged to dryness in a SpeedVac and 80 µl of the hybridization buffer (20% formamide, 5X Denhardts, 6x SSC, 0.1 % SDS, 25 µg/ml tRNA, and RNase free water) was added to each dried sample. The probe was warmed to 42 °C for 5 min and maintained at this temperature until hybridization.

extract_protocol: Total RNA was isolated from laser captured villus and crypt cells using the PicoPureTM RNA isolation Kit (Arcturus) according to manufacturer’s recommendations. Briefly, 20 μl of extraction buffer was placed into the LCM assembly microcentrifuge tube and incubated for 30 min at 42 °C. After incubation, the assembly was briefly centrifuged to collect the extraction fluid into the microcentrifuge tube. The fluid was then loaded onto a spin column, washed several times, and the total cellular RNA was eluted as 10 μl volume. RNA from each sample was subjected to 2 rounds of amplification using the RiboAmpTM RNA linear amplification kit (Arcturus). Subsequently, RNA was reverse-transcribed into cDNA incorporating a T7 promoter. The cDNA was eluted with 16 μl of elution buffer and in vitro transcribed into amplified anti-sense RNA with a T7 RNA polymerase incorporating amino-allyl-UTP (Ambion, Austin, TX).

tag: aRNA labeled with cy5

source_name: reference sample

tag: aRNA labeled with cy3


title: brr2-1.16C.40|WT.16C.40

description: see PMID: 17388687


title: brr2-1.16C.20|WT.16C.20

description: see PMID: 17388687


title: brr2-1.16C.60|WT.16C.60

description: see PMID: 17388687


title: WT.16C.40|brr5-1.16C.40

description: see PMID: 17388687

value: matched WT for brr5-1


title: brr2-1.16C.0|WT.16C.0

description: see PMID: 17388687


title: WT.16C.120|brr5-1.16C.120

description: see PMID: 17388687


title: WT.16C.0|brr5-1.16C.0

description: see PMID: 17388687


title: brr2-1.16C.180|WT.16C.180

description: see PMID: 17388687


title: WT.16C.20|brr5-1.16C.20

description: see PMID: 17388687


title: WT.16C.60|brr5-1.16C.60

description: see PMID: 17388687


title: WT.16C.180|brr5-1.16C.180

description: see PMID: 17388687


title: brr5-1.16C.0|WT.16C.0

description: see PMID: 17388687


title: brr5-1.16C.20|WT.16C.20

description: see PMID: 17388687


title: brr5-1.16C.180|WT.16C.180

description: see PMID: 17388687


title: WT.16C.60|brr1-1.16C.60

description: see PMID: 17388687

value: matched WT for brr1-1


title: WT.16C.20|brr1-1.16C.20

description: see PMID: 17388687


title: WT.16C.0|brr1-1.16C.0

description: see PMID: 17388687


title: brr5-1.16C.120|WT.16C.120

description: see PMID: 17388687


title: WT.16C.120|brr1-1.16C.120

description: see PMID: 17388687


title: WT.16C.40|brr1-1.16C.40

description: see PMID: 17388687


title: brr5-1.16C.60|WT.16C.60

description: see PMID: 17388687


title: Transcript Mapping for Human HeLa Poly(A)+ RNA Sample 3


title: WT.16C.180|brr1-1.16C.180

description: see PMID: 17388687


title: brr1-1.16C.20|WT.16C.20

description: see PMID: 17388687


title: brr1-1.16C.0|WT.16C.0

description: see PMID: 17388687


title: brr1-1.16C.40|WT.16C.40

description: see PMID: 17388687


title: brr1-1.16C.60|WT.16C.60

description: see PMID: 17388687


title: prp28-1.16C.0|WT.16C.0

description: see PMID: 17388687

value: matched WT for prp28-1


title: brr1-1.16C.180|WT.16C.180

description: see PMID: 17388687


title: WT.16C.10|prp28-1.16C.10

description: see PMID: 17388687


title: brr1-1.16C.120|WT.16C.120

description: see PMID: 17388687


title: WT.16C.30|prp28-1.16C.30

description: see PMID: 17388687


title: WT.16C.40|prp28-1.16C.40

description: see PMID: 17388687


title: WT.16C.20|prp28-1.16C.20

description: see PMID: 17388687


title: WT.16C.0|prp28-1.16C.0

description: see PMID: 17388687


title: WT.16C.60|prp28-1.16C.60

description: see PMID: 17388687


title: prp28-1.16C.10|WT.16C.10

description: see PMID: 17388687


title: prp28-1.16C.20|WT.16C.20

description: see PMID: 17388687


title: brr5-1.16C.40|WT.16C.40

description: see PMID: 17388687


title: prp17-1.37C.0|WT.37C.0

description: see PMID: 17388687

value: matched WT for prp17-1


title: WT.37C.10|prp17-1.37C.10

description: see PMID: 17388687


title: prp17-1.37C.10|WT.37C.10

description: see PMID: 17388687


title: WT.37C.50|prp17-1.37C.50

description: see PMID: 17388687


title: prp28-1.16C.60|WT.16C.60

description: see PMID: 17388687


title: WT.37C.10|prp21-1.37C.10

description: see PMID: 17388687

value: matched WT for prp21-1


title: WT.37C.30|prp17-1.37C.30

description: see PMID: 17388687


title: prp17-1.37C.50|WT.37C.50

description: see PMID: 17388687


title: WT.37C.20|prp17-1.37C.20

description: see PMID: 17388687


title: WT.37C.0|prp21-1.37C.0

description: see PMID: 17388687


title: prp17-1.37C.20|WT.37C.20

description: see PMID: 17388687


title: prp21-1.37C.0|WT.37C.0

description: see PMID: 17388687


title: prp28-1.16C.30|WT.16C.30

description: see PMID: 17388687


title: WT.37C.20|prp21-1.37C.20

description: see PMID: 17388687


title: WT.37C.60|prp21-1.37C.60

description: see PMID: 17388687


title: prp28-1.16C.40|WT.16C.40

description: see PMID: 17388687


title: prp21-1.37C.10|WT.37C.10

description: see PMID: 17388687


title: WT.37C.40|prp17-1.37C.40

description: see PMID: 17388687


title: WT.37C.90|prp21-1.37C.90

description: see PMID: 17388687


title: brr2-1.16C.120|WT.16C.120

description: see PMID: 17388687


title: WT.37C.0|prp17-1.37C.0

description: see PMID: 17388687


title: prp17-1.37C.30|WT.37C.30

description: see PMID: 17388687


title: prp21-1.37C.20|WT.37C.20

description: see PMID: 17388687


title: prp17-1.37C.40|WT.37C.40

description: see PMID: 17388687


title: WT.37C.30|prp21-1.37C.30

description: see PMID: 17388687


title: prp21-1.37C.60|WT.37C.60

description: see PMID: 17388687


title: WT.37C.60|prp24-1.37C.60

description: see PMID: 17388687

value: matched WT for prp24-1


title: WT.37C.30|prp24-1.37C.30

description: see PMID: 17388687


title: WT.37C.20|prp24-1.37C.20

description: see PMID: 17388687


title: WT.37C.90|prp24-1.37C.90

description: see PMID: 17388687


title: prp24-1.37C.60|WT.37C.60

description: see PMID: 17388687


title: prp21-1.37C.30|WT.37C.30

description: see PMID: 17388687


title: prp21-1.37C.90|WT.37C.90

description: see PMID: 17388687


title: WT.37C.10|prp6-1.37C.10

description: see PMID: 17388687

value: matched WT for prp6-1


title: prp24-1.37C.0|WT.37C.0

description: see PMID: 17388687


title: WT.37C.0|prp6-1.37C.0

description: see PMID: 17388687


title: WT.37C.0|prp24-1.37C.0

description: see PMID: 17388687


title: prp24-1.37C.90|WT.37C.90

description: see PMID: 17388687


title: prp24-1.37C.10|WT.37C.10

description: see PMID: 17388687


title: prp24-1.37C.30|WT.37C.30

description: see PMID: 17388687


title: WT.37C.90|prp6-1.37C.90

description: see PMID: 17388687


title: WT.37C.20|prp6-1.37C.20

description: see PMID: 17388687


title: WT.37C.60|prp6-1.37C.60

description: see PMID: 17388687


title: prp6-1.37C.10|WT.37C.10

description: see PMID: 17388687


title: prp6-1.37C.20|WT.37C.20

description: see PMID: 17388687


title: WT.37C.10|prp24-1.37C.10

description: see PMID: 17388687


title: prp6-1.37C.0|WT.37C.0

description: see PMID: 17388687


title: prp6-1.37C.60|WT.37C.60

description: see PMID: 17388687


title: prp24-1.37C.20|WT.37C.20

description: see PMID: 17388687


title: prp6-1.37C.30|WT.37C.30

description: see PMID: 17388687


title: WT.37C.0|prp9-1.37C.0

description: see PMID: 17388687

value: matched WT for prp9-1


title: WT.37C.40|prp9-1.37C.40

description: see PMID: 17388687


title: WT.37C.30|prp9-1.37C.30

description: see PMID: 17388687


title: WT.37C.20|prp9-1.37C.20

description: see PMID: 17388687


title: prp9-1.37C.0|WT.37C.0

description: see PMID: 17388687


title: WT.37C.10|prp9-1.37C.10

description: see PMID: 17388687


title: prp9-1.37C.5|WT.37C.5

description: see PMID: 17388687


title: WT.37C.0|prp4-1.37C.0

description: see PMID: 17388687

value: matched WT for prp4-1


title: WT.37C.20|prp4-1.37C.20

description: see PMID: 17388687


title: WT.37C.5|prp4-1.37C.5

description: see PMID: 17388687


title: prp9-1.37C.30|WT.37C.30

description: see PMID: 17388687


title: prp9-1.37C.20|WT.37C.20

description: see PMID: 17388687


title: WT.37C.30|prp4-1.37C.30

description: see PMID: 17388687


title: prp9-1.37C.10|WT.37C.10

description: see PMID: 17388687


title: WT.37C.10|prp4-1.37C.10

description: see PMID: 17388687


title: prp9-1.37C.40|WT.37C.40

description: see PMID: 17388687


title: WT.37C.40|prp4-1.37C.40

description: see PMID: 17388687


title: prp4-1.37C.0|WT.37C.0

description: see PMID: 17388687


title: prp4-1.37C.10|WT.37C.10

description: see PMID: 17388687


title: WT.37C.5|prp9-1.37C.5

description: see PMID: 17388687


title: prp4-1.37C.5|WT.37C.5

description: see PMID: 17388687


title: prp4-1.37C.40|WT.37C.40

description: see PMID: 17388687


title: prp4-1.37C.30|WT.37C.30

description: see PMID: 17388687


title: WT.16C.0|prp43-Q423E.16C.0

description: see PMID: 17388687

value: matched WT for prp43-Q423E


title: prp43-Q423E.16C.20|WT.16C.20

description: see PMID: 17388687


title: WT.16C.20|prp43-Q423E.16C.20

description: see PMID: 17388687


title: prp43-Q423E.16C.180|WT.16C.180

description: see PMID: 17388687


title: WT.16C.50|prp16-302.16C.50

description: see PMID: 17388687

value: matched WT for prp16-302


title: WT.16C.40|prp43-Q423E.16C.40

description: see PMID: 17388687


title: prp43-Q423E.16C.0|WT.16C.0

description: see PMID: 17388687


title: prp6-1.37C.90|WT.37C.90

description: see PMID: 17388687


title: WT.16C.60|prp43-Q423E.16C.60

description: see PMID: 17388687


title: WT.16C.120|prp43-Q423E.16C.120

description: see PMID: 17388687


title: prp4-1.37C.20|WT.37C.20

description: see PMID: 17388687


title: prp43-Q423E.16C.40|WT.16C.40

description: see PMID: 17388687


title: prp43-Q423E.16C.120|WT.16C.120

description: see PMID: 17388687


title: WT.16C.20|prp16-302.16C.20

description: see PMID: 17388687


title: WT.16C.10|prp16-302.16C.10

description: see PMID: 17388687


title: WT.16C.5|prp16-302.16C.5

description: see PMID: 17388687


title: WT.16C.30|prp16-302.16C.30

description: see PMID: 17388687


title: prp43-Q423E.16C.60|WT.16C.60

description: see PMID: 17388687


title: prp16-302.16C.20|WT.16C.20

description: see PMID: 17388687


title: prp16-302.16C.30|WT.16C.30

description: see PMID: 17388687


title: BS21110006_01 (tagD-mutant, 0%xyl, c2-A0.5)

status: Public on Mar 01 2008

city: Martinsried

first: Christoph

last: Schaab

address: Fraunhoferstrasse 20

country: Germany

institute: GPC Biotech AG

description: Second time point depleted cells.

hyb_protocol: We used three arrays with duplicate features for each hybridisation. These arrays contained the same clones but had differences in batch preparation, e.g. different robot runs or different PCR aliquots. Arrays were initially prehybridised for at least 2 h and then hybridised for 20 h at 50°C in a buffer containing 50% formamide, 63SSC, 7% SDS and 50mMNaphosphate, pH 7.5. The typical hybridisation volume was 50 ml. After hybridisation, arrays were washed twice for 15 min in Washing buffer I (23 SSC, 0.5% SDS) and then twice for 15 min in Washing buffer II (0.13 SSC, 0.5% SDS). Before wrapping with SaranWrap, excess liquid was removed by placing membranes on Whatman paper for a few seconds.

scan_protocol: Arrays were exposed for 100 h to Fuji BAS-IP MS 2025 plates and scanned at 25 mm resolution on a Fuji BAS-5000 phosphorimager (Raytest, Germany) (13,14). The acquired images were then analysed with a publicly available image analysis package VisualGrid. The diameter of the circular area used to quantify the spots, the node mask, was 27 pixels, which corresponds to 675 mm. The VisualGrid generates a text-file format output that was further used for data processing and analysis.

data_processing:
Data processing included the following steps: subtraction of
local background, correction for the neighbourhood effect
(when required) and normalisation. Calculation of the background
was based on the empty dots present in each block. The
local background of a block was taken as a mean value of the
empty dots located in the block and in the neighbouring
blocks. Normalisation was important to compensate for differences
caused by different labelling efficiencies of RNA samples. The mean
signal intensity of all features was set to `one' for all
experiments. In addition, the normalised signals from the six
replicas (three replica arrays times two duplicates) were used
to calculate the mean and standard error for every clone.

organism: Bacillus subtilis

source_name: tagD - mutant - 0 (control) - cycle 2, A600=0.5

label_protocol:
Four aliquots of the RNA sample each containing 2 µg of total RNA were prepared. Each aliquot
was handled as independently as possible. They were mixed
with 0.6 mg of random hexamers (dN)6 heated at 70°C for
3 min and chilled on ice. The volume was adjusted to 20 ml
with buffer according the SuperScript II manufacturer's
protocol (Life Technologies, UK). The labelling reaction
contained a final concentration of 1 mM each dATP, dGTP,
dTTP, 50 mCi 33P-dCTP (corresponding to ~0.5 mM) and
100 U SuperScript II. After 1 h incubation at 42°C, probes
were purified on mini Quick Spin DNA columns (Roche,
Germany) followed by denaturation in 0.5 M NaOH at 65°C
for 20 min, neutralisation with 1 M Na-phosphate buffer at
pH 7.5 and pooling of all four aliquots. The typical incorporation
rate was ~70% and we estimate that the amount of
synthesised cDNA is ~30 ng.

growth_protocol: pre culture grown with 2% xylose, then cells were washed and diluted to an A600 of 0.05; cells were then grown to an A600 of 0.5 without any xylose; then celle were again diluted to an A600 of 0.05 and grown yet again to an A600 of 0.5.

extract_protocol:
For RNA preparation, 10 ml of the culture was harvested by
centrifugation at 3,000 x g. After cells were harvested, cell pellets
were immediately resuspended in 450 µl of lysis buffer
(1% [vol/vol] beta-mercaptoethanol and 1 mM EDTA in RLT buffer
[Qiagen, Hilden, Germany]). This suspension was transferred to a
FastPrep tube (Qbiogene, Carlsbad, Calif.) prefilled with 400 µl
of glass beads (diameter, 106 µm; acid washed; Sigma), 500 µl of
citric acid-saturated phenol, and 200 µl of chloroform. The tube was
processed in a FP120 FastPrep cell disrupter (Qbiogene) for 45 s at
6.5 m/s. The slurry was then transferred to a Phase-Lock tube (2 ml,
heavy; Eppendorf, Hamburg, Germany) and spun for 10 min in a
microcentrifuge. Ethanol (250 µl) was added to the supernatant,
and the RNA was purified from this mixture on an RNeasy column
(Qiagen), according to the instructions of the manufacturer. At this
stage three replicates of each sample in equal amounts were pooled
to give a total RNA amount of 100 µg. The prepurified and pooled
RNAs were digested with RNase-free DNase I (Roche, Basel,
Switzerland), and cleanup was performed with RNeasy columns
(Qiagen). Quality control of each RNA sample included
spectrophotometric analysis and formaldehyde gel
electrophoresis. Furthermore, each RNA was subjected to reverse
transcription-PCR. Amplification of the transcript in the presence of
reverse transcriptase served as an indicator of the integrity of the
RNA, while reverse transcription-PCR without the addition of reverse
transcriptase was performed to verify the absence of any genomic DNA.

tag: Strain

tag: xylose inducible conditional tagD mutant


title: WT.37C.30|prp6-1.37C.30

description: see PMID: 17388687


title: prp16-302.16C.50|WT.16C.50

description: see PMID: 17388687


title: WT.16C.0|prp16-302.16C.0

description: see PMID: 17388687


title: prp16-302.16C.10|WT.16C.10

description: see PMID: 17388687


title: prp16-302.16C.0|WT.16C.0

description: see PMID: 17388687


title: prp16-302.16C.5|WT.16C.5

description: see PMID: 17388687


title: WT.37C.0|prp19-1.37C.0

description: see PMID: 17388687

value: matched WT for prp19-1


title: WT.16C.180|prp43-Q423E.16C.180

description: see PMID: 17388687


title: WT.37C.10|prp19-1.37C.10

description: see PMID: 17388687


title: prp19-1.37C.60|WT.37C.60

description: see PMID: 17388687


title: WT.37C.90|prp19-1.37C.90

description: see PMID: 17388687


title: prp19-1.37C.90|WT.37C.90

description: see PMID: 17388687


title: prp8-1.37C.10|prp2-1.37C.10

description: see PMID: 17388687


title: prp8-1.37C.30|prp2-1.37C.30

description: see PMID: 17388687


title: WT.37C.20|prp19-1.37C.20

description: see PMID: 17388687


title: WT.37C.60|prp19-1.37C.60

description: see PMID: 17388687


title: prp2-1.37C.10|prp8-1.37C.10

description: see PMID: 17388687


title: prp19-1.37C.10|WT.37C.10

description: see PMID: 17388687


title: prp19-1.37C.0|WT.37C.0

description: see PMID: 17388687


title: prp8-1.37C.20|prp2-1.37C.20

description: see PMID: 17388687


title: prp19-1.37C.30|WT.37C.30

description: see PMID: 17388687


title: prp19-1.37C.20|WT.37C.20

description: see PMID: 17388687


title: prp2-1.37C.30|prp8-1.37C.30

description: see PMID: 17388687


title: WT.37C.30|prp19-1.37C.30

description: see PMID: 17388687


title: prp8-1.37C.5|prp2-1.37C.5

description: see PMID: 17388687


title: prp8-1.37C.0|prp2-1.37C.0

description: see PMID: 17388687


title: prp2-1.37C.0|prp8-1.37C.0

description: see PMID: 17388687


title: prp2-1.37C.5|prp8-1.37C.5

description: see PMID: 17388687


title: prp2-1.37C.20|prp5-1.37C.20

description: see PMID: 17388687


title: prp2-1.37C.0|prp5-1.37C.0

description: see PMID: 17388687


title: prp2-1.37C.5|prp5-1.37C.5

description: see PMID: 17388687


title: prp5-1.37C.0|prp2-1.37C.0

description: see PMID: 17388687


title: prp2-1.37C.30|prp5-1.37C.30

description: see PMID: 17388687


title: prp2-1.37C.10|prp5-1.37C.10

description: see PMID: 17388687


title: prp5-1.37C.10|prp2-1.37C.10

description: see PMID: 17388687


title: prp5-1.37C.20|prp2-1.37C.20

description: see PMID: 17388687


title: prp5-1.37C.30|prp2-1.37C.30

description: see PMID: 17388687


title: prp5-1.37C.0|prp8-1.37C.0

description: see PMID: 17388687


title: prp5-1.37C.5|prp8-1.37C.5

description: see PMID: 17388687


title: prp5-1.37C.10|prp8-1.37C.10

description: see PMID: 17388687


title: prp5-1.37C.30|prp8-1.37C.30

description: see PMID: 17388687


title: prp8-1.37C.20|prp5-1.37C.20

description: see PMID: 17388687


title: prp5-1.37C.5|prp2-1.37C.5

description: see PMID: 17388687


title: prp8-1.37C.30|prp5-1.37C.30

description: see PMID: 17388687


title: prp5-1.37C.20|prp8-1.37C.20

description: see PMID: 17388687


title: prp8-1.37C.0|prp5-1.37C.0

description: see PMID: 17388687


title: prp8-1.37C.5|prp5-1.37C.5

description: see PMID: 17388687


title: WT.37C.5|prp5-1.37C.5

description: see PMID: 17388687

value: matched WT for prp5-1


title: WT.37C.20|prp5-1.37C.20

description: see PMID: 17388687


title: WT.37C.30|prp5-1.37C.30

description: see PMID: 17388687


title: prp5-1.37C.30|WT.37C.30

description: see PMID: 17388687


title: WT.37C.10|prp5-1.37C.10

description: see PMID: 17388687


title: WT.37C.5|prp8-1.37C.5

description: see PMID: 17388687

value: matched WT for prp8-1


title: prp5-1.37C.0|WT.37C.0

description: see PMID: 17388687


title: WT.37C.30|prp8-1.37C.30

description: see PMID: 17388687


title: prp8-1.37C.30|WT.37C.30

description: see PMID: 17388687


title: prp8-1.37C.20|WT.37C.20

description: see PMID: 17388687


title: prp8-1.37C.10|WT.37C.10

description: see PMID: 17388687


title: WT.37C.0|prp5-1.37C.0

description: see PMID: 17388687


title: prp8-1.37C.5|WT.37C.5

description: see PMID: 17388687


title: WT.37C.10|prp8-1.37C.10

description: see PMID: 17388687


title: WT.37C.0|prp2-1.37C.0

description: see PMID: 17388687

value: matched WT for prp2-1


title: WT.37C.20|prp8-1.37C.20

description: see PMID: 17388687


title: prp2-1.37C.30|WT.37C.30

description: see PMID: 17388687


title: prp5-1.37C.10|WT.37C.10

description: see PMID: 17388687


title: prp5-1.37C.5|WT.37C.5

description: see PMID: 17388687


title: prp2-1.37C.20|WT.37C.20

description: see PMID: 17388687


title: prp5-1.37C.20|WT.37C.20

description: see PMID: 17388687


title: WT.37C.10|prp2-1.37C.10

description: see PMID: 17388687


title: prp8-1.37C.10|prp5-1.37C.10

description: see PMID: 17388687


title: prp2-1.37C.10|WT.37C.10

description: see PMID: 17388687


title: WT.37C.5|prp2-1.37C.5

description: see PMID: 17388687


title: prp2-1.37C.0|WT.37C.0

description: see PMID: 17388687


title: WT.37C.0|prp8-1.37C.0

description: see PMID: 17388687


title: WT.37C.20|prp2-1.37C.20

description: see PMID: 17388687


title: Salt Susceptible2 root 48hpt

status: Public on Apr 03 2007

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Bldg 223, Level 1, Plenty Road

department: Biotechnology & Environmental Biology

country: Australia

institute: RMIT University

description: The data submitted represents the mean data from three biological replications that inlcuded dye swaps between control and treatment samples

hyb_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666

data_processing: Data transformations consisted of a local background correction (mean intensity of background was subtracted from mean signal intensity for each spot), omitting flagged spots, Lowess normalisation of the entire population, creating a Cy5/Cy3 mean signal ratio, taking a shifted log (base 2), and combination of duplicated spot data. To identify differentially expressed (DE) genes, expression ratio results were filtered to eliminate genes whose 95% confidence interval for mean fold change (FC) did not extend to 2-fold up or down, followed by Students t test with False Discovery Rate (FDR) multiple testing correction to retain only genes in which expression changes versus untreated control were significant at P < 0.05.

organism: Cicer arietinum

source_name: Treatment

growth_protocol: The treatment plants were cultivated in a hydroponic system using 50 L plastic crates. Forty holes (8 x 5 grid) of 5 cm diameter were drilled in the crates’ lid and rock wool plugs were placed in them. The germinated seeds were transplanted in alternate plugs within the crate. The seedlings were watered normally from above for four days. The following day, the crates were filled with 0.5 X modified Hoagland’s nutrient medium (pH 6.5; Taiz and Zeiger 2002). The medium was aerated using two aquarium pumps. The nutrient medium was subsequently replaced with 1.0 X Hoagland’s solution (pH 6.5) after a further seven days.

treatment_protocol: At day 18, the nutrient medium for the treatment plants was replaced with 1.0 X modified Hoagland’s with 150 mM Sodium Chloride (NaCl) (pH 6.5), which represented a salinity concentration known to be toxic to chickpea (unpublished data; Munns 2002). Root tissues were collected from five treatment plants at 48 h post-treatment (hpt).

tag: Age

value: 18 days

tag: Tissue type

value: roots

source_name: Control

growth_protocol: The control plants were cultivated in a hydroponic system using 50 L plastic crates. Forty holes (8 x 5 grid) of 5 cm diameter were drilled in the crates’ lid and rock wool plugs were placed in them. The germinated seeds were transplanted in alternate plugs within the crate. The seedlings were watered normally from above for four days. The following day, the crates were filled with 0.5 X modified Hoagland’s nutrient medium (pH 6.5; Taiz and Zeiger 2002). The medium was aerated using two aquarium pumps. The nutrient medium was subsequently replaced with 1.0 X Hoagland’s solution (pH 6.5) after a further seven days.

treatment_protocol: At day 18, the nutrient medium for the control plants was replaced with just 1.0 X modified Hoagland’s medium (pH 6.5). Root tissues were collected from five control plants at 48 h post medium change.


title: prp2-1.37C.20|prp8-1.37C.20

description: see PMID: 17388687


title: prp2-1.37C.5|WT.37C.5

description: see PMID: 17388687


title: WT.37C.30|prp2-1.37C.30

description: see PMID: 17388687


title: prp8-1.37C.0|WT.37C.0

description: see PMID: 17388687


title: Salt Tolerant2 root 24hpt

scan_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666

treatment_protocol: At day 18, the nutrient medium for the treatment plants was replaced with 1.0 X modified Hoagland’s with 150 mM Sodium Chloride (NaCl) (pH 6.5), which represented a salinity concentration known to be toxic to chickpea (unpublished data; Munns 2002). Root tissues were collected from five treatment plants at 24 h post-treatment (hpt).

treatment_protocol: At day 18, the nutrient medium for the control plants was replaced with just 1.0 X modified Hoagland’s medium (pH 6.5). Root tissues were collected from five control plants at 24 h post medium change.


title: Salt Susceptible1 root 48hpt

label_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666


title: TGF-beta treated lung carcinoma cells at 4hr_Exp2

city: Bangalore

first: Paturu

last: Kondaiah

address: C.N.R. Rao Circle

department: Molecular Reproduction, Development and Genetics

country: India

institute: Indian Institute of Science

description: no additional information is necessary

hyb_protocol: The hybridisation was carried out in the GeneTAC Hyb Station (Genomic solutions, UK) at 65 degree for 4 hours, 60 degree for 4 hours and 55 degree for 10 hours. The slides were then washed with medium stringency (2X SSC and 0.1% SDS), high stringency (0.1X SSC and 0.1% SDS) and post wash (0.1X SSC) buffers for 5 minutes each, dried and scanned using a Scanner (Scanarray Express, Perkin Elmer life Sciences, USA).

scan_protocol: Scanned using Scanarray Express (Perkin Elmer Life Sci), the software used for image aquisition was scanarray.

data_processing: All the image analyses have been done using the Quantarray software (Perkin Elmer Life Sciences, USA). Filtering and compilation of data have been done using Microsoft Excel and Microsoft Access. Spots of compromised quality and with low intensity were eliminated from the analysis. The data was normalized by LOWESS method (Avadis 3.1, Strand Life Sciences, India), Cy5:Cy3 ratios were established and log2 values were calculated.

source_name: lung carcinoma cells control

label_protocol: The labelling of the probe was done using the Micromax direct labelling kit (Perkin Elmer Life Sci.) according to the recommended protocol.

growth_protocol: Cells were plated in tissue culture dishes in DMEM with 10% Fetal Bovine Serum and other constituents, incubated at 37 degrees C in 5% CO2 and 90% humidity.

extract_protocol: RNA was Extracted using TRI reagent from Sigma Aldrich with an extra chloroform extraction and cleaned up using RNA easy mini columns.RNA was quantitated on a spectrophotometer and analyzed on a formaldehyde-agarose gel.

treatment_protocol: No treatment (Control for 5ng/ml TGF-beta1treatment), grown in recommended medium, washed with serum free medium and allowed to remain in serum free medium for 4hr before extraction of the sample.

tag: Lung carcinoma cell-line derived from caucasian male

source_name: lung carcinoma cells TGF beta treated

treatment_protocol: Cells grown in recommended medium, washed with serum free medium and treated with 5ng/ml TGF-beta1 in serum free medium, for 4hr before extraction of the sample.

tag: lung carcinoma cell-line derived from caucasian male


title: Salt Suceptible1 shoot 48hpt

extract_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666

treatment_protocol: At day 18, the nutrient medium for the treatment plants was replaced with 1.0 X modified Hoagland’s with 150 mM Sodium Chloride (NaCl) (pH 6.5), which represented a salinity concentration known to be toxic to chickpea (unpublished data; Munns 2002). Leaf/shoot tissues were collected from five treatment plants at 48 h post-treatment (hpt).

value: leaf/shoot

treatment_protocol: At day 18, the nutrient medium for the control plants was replaced with just 1.0 X modified Hoagland’s medium (pH 6.5). Leaf/shoot tissues were collected from five control plants at 48 h post medium change.


title: TGF-beta treated lung carcinoma cells at 12hr_Exp1

description: no additional information is necessary

treatment_protocol: No treatment (Control for 5ng/ml TGF-beta1treatment), grown in recommended medium, washed with serum free medium and allowed to remain in serum free medium for 12hr before extraction of the sample.

treatment_protocol: Cells grown in recommended medium, washed with serum free medium and treated with 5ng/ml TGF-beta1 in serum free medium, for 12hr before extraction of the sample.


title: Cold Susceptible1 flowers

growth_protocol: Five treatment plants were cultivated (one plant per 15 cm pot) in sterile potting mix in a glasshouse at 15-25oC. All plants were watered to keep the soil moist but excess watering was avoided. The plants were fertilized twice with urea during establishment and once with Nitrosol® (Amgrow, Australia) 10 days before flowering.

treatment_protocol: To simulate cold stress, the treatment plants were exposed to a 12h day/12h night temperature cycle of 15-25oC and 5oC (Dr. H. Clarke, 2005, pers comm.; Croser et al. 2003; Clarke and Siddique 2004). The flowers/buds/early pods were harvested after the seventh night at 5oC.

value: Amethyst (ATC 42331)

value: 2 weeks after flowering

value: flowers/buds/early pods

growth_protocol: Five control plants were cultivated (one plant per 15 cm pot) in sterile potting mix in a glasshouse at 15-25oC. All plants were watered to keep the soil moist but excess watering was avoided. The plants were fertilized twice with urea during establishment and once with Nitrosol® (Amgrow, Australia) 10 days before flowering.

treatment_protocol: The control plants were maintained in Glasshouse conditions at 15-25oC while the treatment plants were exposed to cold stress. The flowers/buds/early pods were harvested at the same time as treatment plants (after seventh night of cold stress to treatment plants)


title: TGF-beta treated lung epithelial cells at 4hr_Exp2

description: no additional information is necessary

scan_protocol: Scanned using Scanarray Express (Perkin Elmer Life Sci), the software used for image aquisition was scanarray

data_processing: All the image analyses have been done using the Quantarray software (Perkin Elmer Life Sciences, USA). Filtering and compilation of data have been done using Microsoft Excel and Microsoft Access. Spots of compromised quality and with low intensity  were eliminated from the analysis. The data was normalized by LOWESS method (Avadis 3.1, Strand Life Sciences, India), Cy5:Cy3 ratios were established and log2 values were calculated.

source_name: lung epithelial cells control

growth_protocol: Cells were plated in tissue culture dishes in Ham’s F-12 medium with 5% Fetal Bovine Serum and other constituents, incubated at 37 degrees C in 5% CO2 and 90% humidity.

tag: Lung epithelial cell-line immortalized with SV-40 large T antigen

source_name: lung epithelial cells TGF-beta treated


title: TGF-beta treated lung epithelial cells at 1hr_Exp1

description: no additional information is necessary

data_processing: All the image analyses have been done using the Quantarray software (Perkin Elmer Life Sciences, USA).  Filtering and compilation of data have been done using Microsoft Excel and Microsoft Access. Spots of compromised quality and with low intensity  were eliminated from the analysis. The data was normalized by LOWESS method (Avadis 3.1, Strand Life Sciences, India), Cy5:Cy3 ratios were established and log2 values were calculated.

treatment_protocol: No treatment  (Control for 5ng/ml TGF-beta1treatment), grown in recommended medium, washed with serum free medium and allowed to remain in serum free medium for 1hr before extraction of the sample.

treatment_protocol: Cells grown in recommended medium, washed with serum free medium and treated with 5ng/ml TGF-beta1 in serum free medium, for 1hr before extraction of the sample.


title: Salt Tolerant2 root 48hpt


title: TGF-beta treated lung carcinoma cells at 12hr_Exp2

description: no additional information is necessary

tag: Lung carcinoma cell-line derived from Caucasian male


title: Drought Tolerant2 leaves

treatment_protocol: The drought stress was imposed two weeks after flowering as follows: The pots were saturated with water late in the evening, and the following morning pots were bagged so that no water was allowed to evaporate. A 1.0 ml pipette tip was cut slightly at the tip and inserted in the pot to allow addition of water. The pots were then weighed and recorded as the initial pot weight. The amount of water (water content) in each pot was estimated to be 30% of the initial pot weight. From the subsequent day onwards, the pots were allowed to lose 5-10% of their water content per day and any extra water lost (>10%) was replenished. The leaf tissues were collected when the treatment pots reached 30% water content, indicative of a drought or high water deficit condition

value: two weeks after flowering

value: leaves

treatment_protocol: Two weeks after flowering as follows, the pots were saturated with water late in the evening, and the following morning pots were bagged so that no water was allowed to evaporate. A 1.0 ml pipette tip was cut slightly at the tip and inserted in the pot to allow addition of water. The pots were then weighed and recorded as the initial pot weight. The amount of water (water content) in each pot was estimated to be 30% of the initial pot weight. From the subsequent day onwards, the control pots were maintained at 80% water content and any extra water lost was replenished. The leaf tissues were collected at the time when the treatment pots reached 30% water content


title: TGF-beta treated lung carcinoma cells at 4hr_Exp1

description: no additional information is necessary


title: Rice MH63 Control2

city: Wuhan

first: Qianwen

last: Sun

state: Hubei

address: Luoshi Road

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agriculture University

description: Rice MH63 Control

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCOS 1.2

organism: Oryza sativa

source_name: Rice MH63 Control2

label_protocol: standard Affymetrix procedures

growth_protocol: Seedlings were grown in 1/2MS medium under a 16-h-light (2000 l×)/8-h-dark cycle at 25°C for 11 days.

extract_protocol: RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA, USA) as described by the manufacturer.

tag: Age:11 days


title: Rice MH63 Control1

description: Rice MH63 Control

source_name: Rice MH63 Control1


title: TGF-beta treated lung epithelial cells at 4 hr_Exp1

description: no additional information is necessary

hyb_protocol: The hybridisation was carried out in the GeneTAC Hyb Station (Genomic solutions, UK) at 650 for 4 hours, 600 for 4 hours and 550 for 10 hours. The slides were then washed with medium stringency (2X SSC and 0.1% SDS), high stringency (0.1X SSC and 0.1% SDS) and post wash (0.1X SSC) buffers for 5 minutes each, dried and scanned using a Scanner (Scanarray Express, Perkin Elmer life Sciences, USA).


title: TGF-beta treated lung carcinoma cells at 1hr Exp 1

description: no additional information is necessary

treatment_protocol: No treatment (Control for 5ng/ml TGF-beta1treatment), grown in recommended medium, washed with serum free medium and allowed to remain in serum free medium for 1hr before extraction of the sample.

tag: Lung carcinoma cells derived from caucasian male

source_name: lung carcinoma cells TGF-beta treated


title: TGF-beta treated lung epithelial cells at 12hr_Exp1

description: no additional information is necessary


title: TGF-beta treated lung epithelial cells at 12hr_Exp2

description: no additional information is necessary


title: TGF-beta treated lung epithelial cells at 1hr_Exp2

description: no additional information is necessary

data_processing: All the image analyses have been done using the Quantarray software (Perkin Elmer Life Sciences, USA).  Filtering and compilation of data have been done using Microsoft Excel and Microsoft Access. Spots of compromised quality and with low intensity were eliminated from the analysis. The data was normalized by LOWESS method (Avadis 3.1, Strand Life Sciences, India), Cy5:Cy3 ratios were established and log2 values were calculated.


title: Rice OsSRT1 RNAi transgenic line LM3

description: Rice OsSRT1 RNAi transgenic line

source_name: Rice OsSRT1 RNAi transgenic line LM3

tag: Rice OsSRT1 RNAi transgenic line


title: Rice OsSRT1 RNAi transgenic line LM1

description: Rice OsSRT1 RNAi transgenic line

source_name: Rice OsSRT1 RNAi transgenic line LM1

tag: OsSRT1 RNAi transgenic line


title: TGF-beta treated lung carcinoma cells at 1hr_Exp2

description: no additional information is necessary


title: Rice OsSRT1 RNAi transgenic line LM2

description: Rice OsSRT1 RNAi transgenic line

source_name: Rice OsSRT1 RNAi transgenic line LM2

tag: OsSRT1 RNAi transgenic line LM1


title: Rice MH63 Control3

description: Rice  MH63 Control

source_name: Rice MH63 Control3


title: Salt Susceptible1 root 24hpt

tag: Genotype


title: Salt Susceptible2 shoot 48hpt


title: Salt Susceptible2 shoot 24hpt

treatment_protocol: At day 18, the nutrient medium for the treatment plants was replaced with 1.0 X modified Hoagland’s with 150 mM Sodium Chloride (NaCl) (pH 6.5), which represented a salinity concentration known to be toxic to chickpea (unpublished data; Munns 2002). Leaf/shoot tissues were collected from five treatment plants at 24 h post-treatment (hpt).

tag: Genotype:ICC 08161 (ATC 40707)

treatment_protocol: At day 18, the nutrient medium for the control plants was replaced with just 1.0 X modified Hoagland’s medium (pH 6.5). Leaf/shoot tissues were collected from five control plants at 24 h post medium change.


title: Salt Susceptible2 root 24hpt

treatment_protocol: At day 18, the nutrient medium for the treatment plants was replaced with 1.0 X modified Hoagland’s with 150 mM Sodium Chloride (NaCl) (pH 6.5), which represented a salinity concentration known to be toxic to chickpea (unpublished data; Munns 2002). Root tissues were collected from five treatment plants at 24 h post-treatment (hpt).


title: Salt Tolerant2 shoot 48hpt


title: Salt Tolerant1 shoot 48hpt


title: Normal E Vessel

city: Chapel Hill

first: Nancy

last: DeMore

state: NC

address: 3010 Old Clinic Rd., CB 7213

department: Surgery

institute: UNC @ Chapel Hill

description: Array Reader

hyb_protocol: Agilent

scan_protocol: Axon

data_processing: Axon proprietary software & Genespring

source_name: reference rna

label_protocol: Agilent

extract_protocol: Agilent

tag: reference

source_name: Normal

tag: tissue from breast reduction


title: Normal E Vessel tech repeat

description: Array Reader


title: Cold Susceptible1 leaves

treatment_protocol: To simulate cold stress, the treatment plants were exposed to a 12h day/12h night temperature cycle of 15-25oC and 5oC (Dr. H. Clarke, 2005, pers comm.; Croser et al. 2003; Clarke and Siddique 2004). The leaf tissues were harvested after the seventh night at 5oC.

treatment_protocol: The control plants were maintained in Glasshouse conditions at 15-25oC while the treatment plants were exposed to cold stress. The leaf tissues were harvested at the same time as treatment plants (after seventh night of cold stress to treatment plants)


title: Normal C Vessel

description: Array Reader


title: Normal D Vessel

description: Array Reader


title: Normal C Vessel tech repeat

description: Array Reader


title: Cold Susceptible2 leaves

value: DOOEN (ATC 40874)


title: Salt Tolerant1 shoot 24hpt

treatment_protocol: At day 18, the nutrient medium for the treatment plants was replaced with 1.0 X modified Hoagland’s medium and 150 mM Sodium Chloride (NaCl) (pH 6.5), which represented a salinity concentration known to be toxic to chickpea (unpublished data; Munns 2002). Leaf/shoot tissues were collected from five treatment plants at 24 h post-treatment (hpt).

value: leaf/shoots


title: Salt Tolerant1 Root 24hpt

treatment_protocol: At day 18, the nutrient medium for the treatment plants was replaced with 1.0 X modified Hoagland’s medium and 150 mM Sodium Chloride (NaCl) (pH 6.5), which represented a salinity concentration known to be toxic to chickpea (unpublished data; Munns 2002). Root tissues were collected from five treatment plants at 24 h post-treatment (hpt).

treatment_protocol: At day 18, the nutrient medium for the control plants was replaced with just 1.0 X modified Hoagland’s medium (pH 6.5). Root tissues were collected from five control plants at 24 h post medium change.


title: Normal B Vessel tech repeat

description: Array Reader


title: TCRab CD8aa 2

city: La Jolla

first: Steve

middle: W.

last: Granger

state: CA

address: 9420 Atherna Circle

department: Data Analysis

institute: The La Jolla Institute for Allergy and Immunology

description: Cell populations were isolated from a pool of 20 C57BL/6 mice less than 8wks of age by cell sorting.  RNA quality was assessed using an Agilent Bioanalyzer.

scan_protocol: HP GeneArray scanner

data_processing: Affymetrix GeneChip software (MAS5.0)

label: SA-PE

organism: Mus musculus

source_name: Small Intestine (TCRab CD8aa)

label_protocol: In vitro translation with biotinylated rNTPs performed using manufacturers specifications in the Affymetrix GeneChip Expression Analysis Manual.

extract_protocol: Qiagen RNAeasy

treatment_protocol: Untreated (freshly isolated)

tag: TCRab CD8aa sorted cell populations from pooled IEL preps from C57BL/6 mice


title: Salt Tolerant2 Shoot 24hpt


title: Cold Susceptible2 flowers


title: Cold Tolerant2 flowers


title: TCRgb CD8aa 2

source_name: Small Intestine (TCRgd CD8aa)

tag: TCRgd CD8aa sorted cell populations from pooled  IEL preps from C57BL/6 mice


title: Normal D Vessel tech repeat

description: Array Reader


title: TCRab CD8ab 2

source_name: Small Intestine (TCRab CD8ab)

tag: TCRab CD8ab sorted cell populations from pooled IEL preps from C57BL/6 mice


title: Normal A Vessel

description: Array Reader


title: Cold Tolerant2 leaves

source_name: Treatment

tag: Age

tag: Tissue type

source_name: Control


title: Cold Tolerant1 flowers

value: Sonali (ATC 48113)

value: Flowers/Buds/Early pods


title: Normal A Vessel tech rep

description: Array Reader


title: Luminal E Vessel tech rep

description: Array Reader

source_name: Breast tumor

tag: tumor


title: TCRgb CD8aa 1

tag: TCRgd CD8aa sorted cell populations from pooled IEL preps from C57BL/6


title: TCRab CD8ab 1

source_name: Small intestine (TCR ab CD8ab)

tag: TCR ab CD8ab sorted cell populations from pooled IEL preps from C57BL/6 mice


title: Salt Susceptible1 shoot 24hpt


title: TCRab CD8aa 1

source_name: Small Intestine (TCR ab CD8aa)

tag: TCR ab CD8aa sorted cell population from pooled IEL preps from C57BL/6 mice


title: Normal B Vessel

description: Array Reader


title: Cold Tolerant1 leaves


title: Luminal E Vessel

description: Array Reader


title: Primary Memory B cells #1

city: New York

first: Kathryn

last: Calame

state: NY

address: 701 W.168th Street, HHSC 1204

institute: Columbia University

description: mAdb experiment ID: 36178

hyb_protocol: protocol_name: NCI cDNA 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 µl 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), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to NCI Microarray Manual)

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 620;; 670 ScanPower: 100;; 100 LaserPower: 1.25;; 2.41 Temperature: 38.36

data_processing:
mAdb Standard Data Processing Protocol
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: Lymphoma Cell Lines

label_protocol:
Lymphochip Labeling-cy3
Label amount: 4ul
Label method: reverse transcription
Nature. 2000 Feb 3;403(6769):503-11

extract_protocol: All cDNA microarray analyses were performed using poly-(A)+ mRNA (Fast Track, Invitrogen).

tag: Raji, Jurkat, L428, OCI-Ly3, OCI-Ly8, OCI-Ly1, SUDHL5, SUDHL6 and WSU1

source_name: Primary Memory B cells #1

label_protocol:
Lymphochip Labeling-cy5
Label amount: 4ul
Label method: reverse transcription
Nature. 2000 Feb 3;403(6769):503-11

extract_protocol:
Trizol Total RNA
Extraction method: Trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

tag: Ex vivo Memory B cells


title: Primary Centrocytes #1

description: mAdb experiment ID: 36170

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 650;; 700 ScanPower: 100;; 100 LaserPower: 1.25;; 2.38 Temperature: 38.55

source_name: Primary Centrocytes #1

tag: Ex vivo primary centrocytes


title: Drought Tolerant1 flowers

treatment_protocol: The drought stress was imposed two weeks after flowering as follows: The pots were saturated with water late in the evening, and the following morning pots were bagged so that no water was allowed to evaporate. A 1.0 ml pipette tip was cut slightly at the tip and inserted in the pot to allow addition of water. The pots were then weighed and recorded as the initial pot weight. The amount of water (water content) in each pot was estimated to be 30% of the initial pot weight. From the subsequent day onwards, the pots were allowed to lose 5-10% of their water content per day and any extra water lost (>10%) was replenished. The flowers/buds were collected when the treatment pots reached 30% water content, indicative of a drought or high water deficit condition

value: flowers/buds

treatment_protocol: Two weeks after flowering as follows, the pots were saturated with water late in the evening, and the following morning pots were bagged so that no water was allowed to evaporate. A 1.0 ml pipette tip was cut slightly at the tip and inserted in the pot to allow addition of water. The pots were then weighed and recorded as the initial pot weight. The amount of water (water content) in each pot was estimated to be 30% of the initial pot weight. From the subsequent day onwards, the control pots were maintained at 80% water content and any extra water lost was replenished. The flowers/buds were collected at the time when the treatment pots reached 30% water content


title: Drought Tolerant2 flowers


title: Primary Memory B cells #2

description: mAdb experiment ID: 36177

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 610;; 680 ScanPower: 100;; 100 LaserPower: 1.2;; 2.28 Temperature: 36.9

source_name: Primary Memory B cells #2

tag: Ex vivo memory B cells


title: In Vitro Cultured Memory B cells #2

description: mAdb experiment ID: 59444

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 670;; 710 ScanPower: 100;; 100 LaserPower: 2.98;; 5.78 Temperature: 40.09

source_name: In Vitro Cultured Memory B cells #2

tag: In vitro cultured tonsillar germinal center B cells treated with CD40L, IL-2, and IL-4 for 7 days.


title: Drought Susceptible1 flowers

tag: Genotype

value: Kaniva (ATC 40030)


title: Luminal D Vessel tech rep

description: Array Reader

tag: reference


title: In Vitro Cultured Plasma Cells#3

description: mAdb experiment ID: 65541

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 720;; 710 ScanPower: 100;; 100 LaserPower: 3.4;; 3.5 Temperature: 34.51

source_name: In Vitro Cultured Plasma Cells Sample #3

tag: In vitro cultured tonsillar germinal center B cells treated with CD40L, IL-2, and IL-10 for 7 days.


title: Luminal D Vessel

description: Array Reader


title: In Vitro Cultured Plasma Cells#2

description: mAdb experiment ID: 65542

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 730;; 700 ScanPower: 100;; 100 LaserPower: 3.45;; 3.48 Temperature: 34.6

source_name: In Vitro Culture Plasma Cells Sample #2


title: Drought Susceptible2 flowers

value: Genesis 508 (ATC 45226)


title: Primary Centrocytes #2

description: mAdb experiment ID: 36169

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 610;; 700 ScanPower: 100;; 100 LaserPower: 1.22;; 2.43 Temperature: 37.4

source_name: Primary Centrocytes #2

tag: Primary Ex vivo centrocytes


title: In Vitro Cultured Centrocytes #2

description: mAdb experiment ID: 65539

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 760;; 780 ScanPower: 100;; 100 LaserPower: 3.45;; 3.49 Temperature: 34.17

source_name: In Vitro Cultured Centrocytes Sample #2

tag: In vitro cultured tonsillar germinal center B cells treated with CD40L, and IL-2 for 3 days.


title: Luminal C Vessel

description: Array Reader

source_name: reference rna


title: Drought Susceptible2 leaves


title: Drought Susceptible1 leaves


title: Luminal B Vessel tech rep

description: Array Reader


title: Luminal C Vessel tech rep

description: Array Reader


title: In Vitro Cultured Memory B cells #1

description: mAdb experiment ID: 59441

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 650;; 730 ScanPower: 100;; 100 LaserPower: 3.1;; 5.71 Temperature: 39.66

source_name: IVT Memory

extract_protocol:
Trizol Total RNA
Extraction method: Trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions
(Invitrogen, Carlsbad, CA).

tag: In vitro culture of tonsillar germinal center B cells treated with CD40L, IL-2, and IL-4

tag: for 7 days.


title: Salt Tolerant1 root 48hpt

treatment_protocol: At day 18, the nutrient medium for the treatment plants was replaced with 1.0 X modified Hoagland’s with 150 mM Sodium Chloride (NaCl) (pH 6.5), which represented a salinity concentration known to be toxic to chickpea (unpublished data; Munns 2002). Root tissues were collected from five treatment plants at 48 h post-treatment (hpt).

tag: Age

tag: Tissue type

treatment_protocol: At day 18, the nutrient medium for the control plants was replaced with just 1.0 X modified Hoagland’s medium (pH 6.5). Root tissues were collected from five control plants at 48 h post medium change.


title: Luminal B Vessel

description: Array Reader

tag: tumor


title: Luminal A Vessel tech rep

description: Array Reader


title: In Vitro Cultured Plasma Cells#1

description: mAdb experiment ID: 60940

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 700;; 650 ScanPower: 100;; 100 LaserPower: 3.18;; 6 Temperature: 40.88

source_name: In Vitro Cultured Plasma Cells Sample #1


title: Patient 27 Follicular Lymphoma

status: Public on Apr 02 2007

type: genomic

city: London

first: Jude

last: Fitzgibbon

address: Charterhouse Square

department: Centre Medical Oncology

country: United Kingdom

institute: Barts and the London Medical School

description: SNP genotype data from FL patient

hyb_protocol: Affymetrix 10K mapping assay protocol

scan_protocol: Affymetrix GeneChip scanner 3000

data_processing: GCOS, GTYPE. Genotype calling algorithm MPAM

molecule: genomic DNA

source_name: follicular lymphoma/lymph node

label_protocol: Affymetrix 10K mapping assay protocol

extract_protocol: Phenol chloroform

treatment_protocol: FL / t-FL cells collected from lymph node biopsies. Solid biopsy cryopreserved in liquid nitrogen. Remission cells collected from bone marrow. Ficoll separation, and cryopreserved in liquid nitrogen.

tag: tissue

value: lymph node


title: Drought Tolerant1 leaves

scan_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666

source_name: Treatment

treatment_protocol: The drought stress was imposed two weeks after flowering as follows: The pots were saturated with water late in the evening, and the following morning pots were bagged so that no water was allowed to evaporate. A 1.0 ml pipette tip was cut slightly at the tip and inserted in the pot to allow addition of water. The pots were then weighed and recorded as the initial pot weight. The amount of water (water content) in each pot was estimated to be 30% of the initial pot weight. From the subsequent day onwards, the pots were allowed to lose 5-10% of their water content per day and any extra water lost (>10%) was replenished. The leaf tissues were collected when the treatment pots reached 30% water content, indicative of a drought or high water deficit condition

source_name: Control


title: Patient 27 Transfomed

description: SNP genotype data from t-FL patient

source_name: transformed follicular lymphoma/ lymph node


title: SCI-1 cell line

description: SNP genotype data from lymphoma derived cell line

source_name: lymphoma derived cell line

value: cell line


title: Patient 28 Follicular Lymphoma

description: SNP genotype data from FL patient


title: DoHH2 cell line


title: Patient 28 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 26 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 24 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 25 Follicular Lymphoma

description: SNP genotype data from FL patient


title: Patient 26 Follicular Lymphoma

description: SNP genotype data from FL patient


title: breast tumor-s1615

city: Novato

first: Christina

last: Yau

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

description: Gene expression data from ER+ N0 breast cancer from old cohort

hyb_protocol: Affymetrix Comm Hyb Setup 21 & Affymetrix Comm Wash Stain 21  (performed by  HTArray Genomics Core Facility of Lawrence Berkeley National Laboratory)

scan_protocol: GeneChip HT Scanner protocol v2.2.09  (performed by  HTArray Genomics Core Facility of Lawrence Berkeley National Laboratory)

data_processing: RMA normalization with affy package in Bioconductor R

source_name: TISSUE_ID s1615

label_protocol: Affymetrix Gene Expression TP 21 (performed by  HTArray Genomics Core Facility of Lawrence Berkeley National Laboratory)

extract_protocol: Qiagen RNAesy purification from formaide extracted samples

tag: ER+


title: Luminal A Vessel

description: Array Reader

source_name: Breast tumor


title: Patient 25 Transfomed

description: SNP genotype data from t-FL patient


title: breast tumor-s1545

description: Gene expression data from ER+ N0 breast cancer from young cohort

source_name: TISSUE_ID s1545


title: RL2261 cell line


title: breast tumor-s1521

source_name: TISSUE_ID s1521


title: Patient 23 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 22 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 24 Follicular Lymphoma

description: SNP genotype data from FL patient


title: breast tumor-s0278

source_name: TISSUE_ID s0278


title: Patient 23 Follicular Lymphoma

description: SNP genotype data from FL patient


title: breast tumor-s1518

source_name: TISSUE_ID s1518


title: breast tumor-s0367

source_name: TISSUE_ID s0367


title: breast tumor-s0320

source_name: TISSUE_ID s0320


title: Patient 22 Follicular Lymphoma

description: SNP genotype data from FL patient


title: breast tumor-s0248

source_name: TISSUE_ID s0248


title: Patient 21 Follicular Lymphoma

description: SNP genotype data from FL patient


title: Patient 20 Remission Bone Marrow

description: SNP genotype data from FL patient remission bone marrow

source_name: remission/bone marrow

value: remission bone marrow


title: breast tumor-s0202

source_name: TISSUE_ID s0202

tag: recurrence (1=event,_0=censored)


title: Patient 21 Transfomed

description: SNP genotype data from t-FL patient


title: breast tumor-s0268

source_name: TISSUE_ID s0268


title: breast tumor-s0148

source_name: TISSUE_ID s0148


title: breast tumor-s0260

source_name: TISSUE_ID s0260


title: Patient 20 Follicular Lymphoma

description: SNP genotype data from FL patient

source_name: follicular lymphoma/lymph node


title: Patient 21 Remission Bone Marrow


title: breast tumor-s0141

source_name: TISSUE_ID s0141


title: Patient 19 Follicular Lymphoma

description: SNP genotype data from FL patient


title: breast tumor-s0117

source_name: TISSUE_ID s0117


title: Patient 19 Transfomed

description: SNP genotype data from t-FL patient

source_name: transformed follicular lymphoma/ lymph node


title: breast tumor-s0116

source_name: TISSUE_ID s0116


title: Patient 20 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 18 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 17 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 18 Follicular Lymphoma

description: SNP genotype data from FL patient


title: breast tumor-s0035

source_name: TISSUE_ID s0035


title: breast tumor-s0099

source_name: TISSUE_ID s0099


title: breast tumor-s0047

source_name: TISSUE_ID s0047


title: breast tumor-s0100

source_name: TISSUE_ID s0100


title: breast tumor-s0069

source_name: TISSUE_ID s0069


title: Patient 16 Remission Bone Marrow


title: breast tumor-s0021

source_name: TISSUE_ID s0021


title: Patient 17 Follicular Lymphoma

description: SNP genotype data from FL patient


title: Patient 15 Transfomed

description: SNP genotype data from t-FL patient


title: breast tumor-s0006

source_name: TISSUE_ID s0006


title: breast tumor-b1285

source_name: TISSUE_ID b1285


title: Patient 16 Follicular Lymphoma

description: SNP genotype data from FL patient


title: Patient 13 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 15 Follicular Lymphoma

description: SNP genotype data from FL patient


title: breast tumor-s0033

source_name: TISSUE_ID s0033


title: breast tumor-b1279

source_name: TISSUE_ID b1279


title: breast tumor-b1067

source_name: TISSUE_ID b1067


title: breast tumor-b1306

source_name: TISSUE_ID b1306


title: Patient 16 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 11 Transfomed

description: SNP genotype data from t-FL patient


title: breast tumor-b1148

source_name: TISSUE_ID b1148


title: Patient 13 Follicular Lymphoma

description: SNP genotype data from FL patient

source_name: follicular lymphoma/lymph node


title: Patient 12 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 12 Follicular Lymphoma

description: SNP genotype data from FL patient


title: breast tumor-b0668

source_name: TISSUE_ID b0668


title: breast tumor-b0729

source_name: TISSUE_ID b0729


title: breast tumor-b0493

source_name: TISSUE_ID b0493


title: breast tumor-b0592

source_name: TISSUE_ID b0592


title: Patient 10 Follicular Lymphoma

description: SNP genotype data from FL patient


title: breast tumor-b0491

source_name: TISSUE_ID b0491


title: Patient 8 Transfomed

description: SNP genotype data from t-FL patient

source_name: transformed follicular lymphoma/ lymph node


title: Patient 10 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 9 Transfomed

description: SNP genotype data from t-FL patient


title: breast tumor-b1144

source_name: TISSUE_ID b1144


title: breast tumor-b0513

source_name: TISSUE_ID b0513


title: breast tumor-b0862

source_name: TISSUE_ID b0862


title: Patient 8 Remission Bone Marrow

source_name: remission/bone marrow


title: breast tumor-b0468

source_name: TISSUE_ID b0468


title: breast tumor-b0524

source_name: TISSUE_ID b0524


title: breast tumor-b0639

source_name: TISSUE_ID b0639


title: Patient 7 Remission Bone Marrow

description: SNP genotype data from t-FL patient


title: Patient 11 Follicular Lymphoma

description: SNP genotype data from FL patient


title: breast tumor-b0414

source_name: TISSUE_ID b0414


title: Patient 18 Remission Bone Marrow


title: breast tumor-b0420

source_name: TISSUE_ID b0420


title: breast tumor-b0404

source_name: TISSUE_ID b0404


title: breast tumor-b0395

source_name: TISSUE_ID b0395


title: Patient 8 Follicular Lymphoma

description: SNP genotype data from FL patient

source_name: follicular lymphoma/lymph node


title: In Vitro Cultured Centrocytes #1

description: mAdb experiment ID: 59442

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 690;; 740 ScanPower: 100;; 100 LaserPower: 3;; 5.77 Temperature: 39.97

source_name: Lymphoma Cell Lines

tag: Raji, Jurkat, L428, OCI-Ly3, OCI-Ly8, OCI-Ly1, SUDHL5, SUDHL6 and WSU1

source_name: In Vitro Cultured Centrocytes Sample #1

tag: In vitro cultured tonsillar germinal center B cells with CD40L and IL-2 for 3 days.


title: breast tumor-b0442

source_name: TISSUE_ID b0442


title: breast tumor-b0341

source_name: TISSUE_ID b0341


title: Patient 7 Follicular Lymphoma


title: Patient 7 Transfomed

description: SNP genotype data from FL patient

source_name: transformed follicular lymphoma/ lymph node


title: breast tumor-b0337

source_name: TISSUE_ID b0337


title: Patient 9 Follicular Lymphoma

description: SNP genotype data from FL patient


title: breast tumor-b0370

source_name: TISSUE_ID b0370


title: Patient 6 Transfomed

description: SNP genotype data from t-FL patient


title: breast tumor-b0175

source_name: TISSUE_ID b0175


title: breast tumor-b0166

source_name: TISSUE_ID b0166


title: breast tumor-b0255

source_name: TISSUE_ID b0255


title: Patient 5 Transfomed

description: SNP genotype data from t-FL patient


title: breast tumor-b0296

source_name: TISSUE_ID b0296


title: breast tumor-b0317

source_name: TISSUE_ID b0317


title: Patient 5 Follicular Lymphoma

description: SNP genotype data from FL patient


title: breast tumor-b0243

source_name: TISSUE_ID b0243


title: Patient 4 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 6 Follicular Lymphoma

description: SNP genotype data from FL patient


title: Patient 2 Transfomed

description: SNP genotype data from t-FL patient


title: Patient 2 Follicular Lymphoma

description: SNP genotype data from FL patient


title: Patient 1 Transfomed

description: SNP genotype data from t-FL patient


title: Cervical cancer tissue (India: CaCx82)

status: Public on Mar 30 2007

city: Navi Mumbai

first: Chandan

last: Kumar

state: Maharashtra

address: Kharghar Node

department: ACTREC

institute: Tata Memorial Center

description: Pathology: Invasive Moderately differntiated Squamous Carcinoma

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

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

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

source_name: Cervical cancer tissue

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

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

tag: Lab ID

tag: Gender

value: Female

tag: Tissue

value: cervical cancer biopsy

tag: Tumor Stage

value: IIB

source_name: Human Universal Reference RNA

extract_protocol: Commercial RNA

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

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


title: Patient 4 Follicular Lymphoma

description: SNP genotype data from FL patient


title: Patient 1 Follicular Lymphoma

description: SNP genotype data from FL patient


title: Homocysteine experiment treated 3

status: Public on Jan 26 2007

city: Omaha

first: Greg

last: Bennett

state: NE

address: Nebraska Medical Center 985805

department: Genetics Cell Biology and Anatomy

institute: University of Nebraska Medical Center

description: Homocysteine Induced Alterations In Gene Expression In Neural Crest Cells

hyb_protocol: Standard Affymetrics Protocol

scan_protocol: Standard Affymetrics Protocol

data_processing: All analyses were conducted using the BRB ArrayTool software package (http://linus.nci.nih.gov/BRB-ArrayTools.html).  Pre-processing of the probe-level data was performed using the robust multiarray average (RMA) algorithm; a function of the Bioconductor Project (www.bioconductor.org/) using R-programming language (Bolstad et al, 2005; R-Development Core Team, 2004).  This function performs background correction, normalization, and summarization of probe-level data.  The background correction method uses the perfect match (PM) probe intensity model which is based on the assumption that the observed gene expression is the sum of both expression and background noise. Quantile-Normalization was used to normalize the PM probe intensities, and the summarization of the expression data were preformed using the Median Polish Method which fits a multichip linear model to the data and reports the expression as a log2 value (Irizarry et al., 2002).  Data from both control and treated arrays were normalized as one set.

organism: Gallus gallus

source_name: CHICKEN embryo treated

label_protocol: Standard Affymetrics Protocol

extract_protocol: RNA was isolated from these embryos using the RNAqueous kit from Ambion (Austin, TX) following the manufacture’s protocol.  Briefly, whole embryos or tissues were placed in a guanidinium salt solution which is diluted with ethanol and passed through a glass filter cartridge which specifically binds the RNA.  The RNA was then washed and recovered by a low ionic strength solution.  All reagents for this protocol are included in the kit.  The purity and concentration of the isolated RNA was determined by its UV-absorbance at 260 and 280 nm.

treatment_protocol: After 4 hours, the cultures were either exposed to media or homocyteine (100uM final concentration) which has previously been shown to be teratogenic and alter neural crest cell migration, for 6 hours.

tag: Neural tube explants were obtained from stage 9+ chicken embryos to generate neural crest cell cultures. After 4 hours in culture the cells were exposed to either media or homocysteine for 6 hours. The cultures were then processed for gene expression using the affymetrics chicken chip.


title: Homocysteine experiment control 3

source_name: CHICKEN embryo control


title: breast tumor-b0316

source_name: TISSUE_ID b0316


title: CLL#5 CD38- sub-clones

status: Public on Nov 23 2006

city: Cardiff

first: Chris

last: Pepper

state: Wales

address: Heath Park

department: Haematology

institute: Cardiff University

description: CD38- sub-clones derived from a CLL patient with bimodal expression of the CD38 antigen

hyb_protocol: The fragmentation buffer was made up as follows; 20ug cRNA, 6ul 5X fragmentation buffer, and the volume was made up to 40ul with RNase-free water. This solution was incubated for 35 minutes at 94oC, and then placed on ice. An aliquot was run on the Agilent Bioanalyzer to check the process had occurred Target hybridization The probe array (Affymetrix U133A gene chip) was equilibrated to room temperature immediately before it was used. Hybridization cocktail was made up of fragmented RNA (10ug), control oligonucleotide B2 (3nM) (3.3ul), 20X eukaryotic hybridization controls (bioB, bioC, bioD, cre) (10ul), Herring Sperm DNA (10mg/ml) (2ul), bovine serum albumin (BSA) (50mg/ml) (2ul) 2X hybridization buffer (100ul), dimethyl sulfoxide (DMSO) (20ul) and water to make the final volume 200ul. This was heated to 99oC for 5 minutes in a heat block. While the hybridization cocktail was heating, the 130ul of 1X Hybridization buffer was added to the array and it was incubated at 45oC for 10 minutes with rotation. The hybridization cocktail was transferred to a 45oC heat block for 5 minutes, and then was spun to remove any insoluble material. The buffer was removed from the array, and the hybridization cocktail (200ul) was added, and the array was placed in the Hybridization oven set to 45oC for 16 hours.

scan_protocol: The fluidics station was primed with Non-stringent wash buffer and Stringent wash buffer before use. After hybridization, the cocktail was removed from the probe array, and the array was filled with non-stringent wash buffer. Three staining solutions were made up and place onto the fluidics station. Staining solutions 1 and 3 were 600ul Streptavidin Phycoerythrin (SAPE) solution made up of 600ul 2X stain buffer, 48ul of 50mg/ml BSA, 12ul 1mg/ml SAPE, 540ul water. The 2nd stain solution is Antibody solution made up of 2X stain buffer (300ul), 50mg/ml BSA (24ul), 10mg/ml goat Immunoglobulin G (IgG) stock (6ul), 0.5mg/ml biotinylated antibody (3.6ul) and water (266.4ul). The fluidic protocol was as follows: Post hybridization wash #1 	10 cycles of 2 mixes/cycle with wash buffer A at 30oC Post hybridization wash #2	6 cycles of 15 mixes/cycle with wash buffer B at 50oC

data_processing: Analysis of the microarray data was carried out on GeneSpring software (Agilent Technology). Firstly, any genes that were not present in at least one of the samples were removed from the gene list. Then any genes that had less than a 2 fold change were also removed. Statistical analysis was carried out (ANOVA test and Student’s t test) and a gene list produced after comparing the gene lists from the two tests and finding the genes present in both. The gene list was exported into Pathway Assist (Stratagene), where pathways were produced with any genes that were directly connected. Pathway assist connects to Pubmed (http://www.ncbi.nlm.nih.gov) and searches for any associations between the genes input. It then uses this information to build the pathway.

source_name: CLL#5 CD38- sub-clones

label_protocol:
The following solution was made up; 4ul 10X IVT labelling buffer, 12ul IVT (in vitro transcription) labelling NTP (nucleotide triphosphate) mix, 4ul IVT labelling enzyme mix, required amount of template cDNA and the volume made up to 40ul with RNase-free water. The mixture was incubated at 37oC overnight. The following day 60ul of RNase-free water, 350ul cRNA binding buffer and 250ul ethanol was added to the sample, which was applied to the IVT cRNA Cleanup Spin Column. This was spun at >8,000 x g for 15 seconds, and the flow through and collection tube was discarded. The spin column was placed in a new collection tube. 0.5ml IVT cRNA wash buffer was added to the column and was spun as before with the flow through being discarded. 80% ethanol (0.5ml) was added to the sample and was spun as before. The spin column’s cap was opened and it was spun at maximum speed for 5 minutes. The flow through and collection tube was discarded. After a new collection tube was added, 16ul of RNase-free water was added directly onto the membrane and the column was spun at maximum speed for 5 minutes. This step was then repeated. To quantify the cRNA the absorbance was read at 260nm and 280nm. The yield was determined using the following equation;
Adjusted cRNA yield = RNAm – (total RNAi)(y)
Where: RNAm = amount of cRNA measured after IVT (ug)
Total RNAi = starting amount of total RNA (ug)
y = fraction of cDNA reaction used in IVT

extract_protocol:
Trizol reagent was added the cell-sorted populations (1 x 107 cells), and this was placed in tubes containing Phase Lock Gel-Heavy and were incubated for 5 minutes at 37oC. 0.2ml of chloroform was added and the tubes were shaken. The samples were spun at 12,000 x g for 10 minutes at 2-8oC, to separate the phases (the clear aqueous phase was on top and cloudy chloroform phase was on the bottom). The aqueous phase was transferred to a clean tube, and to which 0.6ml of isopropyl alcohol was added. The tubes were shaken, and spun as before. The pellet of RNA was re-suspended in 75% ethanol and centrifuged at 7,500 x g for 5 minutes at 2-8oC. The supernatant was removed, and the pellet allowed to air dry. The pellet was re-suspended in RNase-free water, and incubated at 65oC for at least 30 minutes. The RNA was quantified using the Nanodrop 1000 (Nanodrop Technologies), and the purity was checked by running an Agilent chip on the Agilent bioanalyzer (Agilent Technologies).
One-cycle cDNA synthesis
A 1:20 dilution of Poly-A (poly-adenine) control stock was made in Poly-A Control Dilution Buffer from the commercially available kit (Affymetrix). From this solution, 2ul was added to Poly-A control dilution buffer to make a 1:50 dilution. Again, 2ul was taken from this solution and added to Poly-A control dilution buffer to make a 1:10 dilution. 2ul of this final dilution was added to the sample of RNA.
T7-Oligo(dT) Primer was added to the RNA and the volume was made up to 12ul with RNase-free water. The reaction was incubated at 70oC for 10 minutes and then cooled for at least 2 minutes. The First-Strand master mix was made up as follows: 4ul of 5X 1st strand master mix, 2ul 0.1M Dithiothreitol (DTT) and 1ul 10mM dNTP. This was added to the RNA/T7-oligo(dT) primer mix and incubated at 42oC for 2 minutes. The appropriate amount of SuperScript II was added to each RNA sample and incubated for 1 hour at 42oC. The sample was then cooled at 4oC for at least 2 minutes. The Second-Strand master mix was made up as follows: 91ul of RNase-free water, 30ul 5X 2nd strand reaction mix, 3ul 10mM dNTP, 1ul E. coli DNA ligase, 4ul of E.coli DNA polymerase I and 1ul RNase H. 130ul of this master mix was added to each RNA sample and it was incubated for 2 hours at 16oC.  T4 DNA Polymerase (2ul) was added to the sample and was incubated at 16oC for 2 minutes. 10ul of 0.5M ethylene diamine tetra-acetic acid (EDTA) was added to the sample. cDNA (compliment DNA) Binding Buffer (600ul) was added to the sample making the mixture yellow. The sample was applied to the cDNA Cleanup Spin Column and spun at ≥ 8,000 x g for 1 minute. The spin column was transferred into a new collection tube and cDNA Wash Buffer was added to the column. This was then spun at ≥ 8,000 x g for 1 minute and the flow through was discarded. The caps of the spin columns were opened, centrifuged for 5 minutes at maximum speed and the collection tube and flow-through were discarded. The column membranes were dried by centrifugation and the spin columns were placed in clean collection tubes. cDNA elution buffer was added directly onto the column membrane and incubated for 1 minute at room temperature. This was then spun at maximum speed for 1 minute to elute.


title: CLL#6 CD38+ sub-clones

source_name: CLL#6 CD38+ sub-clones

tag: CD38+ sub-clones derived from a CLL patient with bimodal expression of the CD38 antigen


title: Homocysteine experiment treated 1


title: Homocysteine experiment control 2


title: CLL#4 CD38- sub-clones

source_name: CLL#4 CD38- sub-clones

tag: CD38- sub-clones derived from a CLL patient with bimodal expression of the CD38 antigen


title: CLL#5 CD38+ sub-clones

source_name: CLL#5 CD38+ sub-clones


title: CLL#6 CD38- sub-clones

source_name: CLL#6 CD38- sub-clones


title: CLL#3 CD38- sub-clones

source_name: CLL#3 CD38- sub-clones


title: Homocysteine experiment treated 2


title: CLL#2 CD38+ sub-clones

source_name: CLL#2 CD38+ sub-clones


title: Myoblasts_rep3, chip 10K, after chipping with H4-acetylated chromatin

status: Public on Aug 29 2006

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description: The goal is to study the genome-wide mapping of histone modifications in differentiating human primary myoblasts.

data_processing: GeneChip DNA Analysis Software 2.0 (Affymetrix)

label: Biotin

source_name: Fetal skeletal myoblasts

growth_protocol: Cultured in SKGM-2 media

extract_protocol: Qiagen DNeasy Tissue Kit

tag: myoblasts


title: Myoblasts_rep2, chip 10K, after chipping with H4-acetylated chromatin


title: CLL#3 CD38+ sub-clones

source_name: CLL#3 CD38+ sub-clones


title: Myoblasts_rep1, chip 10K, after chipping with H4-acetylated chromatin


title: Myotubes_rep2, chip 10K, after chipping with H4-acetylated chromatin

tag: myotubes


title: CLL#1 CD38- sub-clones

source_name: CLL#1 CD38- subclones


title: Myotubes_rep1, chip 10K, after chipping with H4-acetylated chromatin


title: Myoblasts_rep3, chip 10K


title: CLL#1 CD38+ sub-clones

source_name: CLL#1 CD38+ sub-clones


title: Myotubes_rep3, chip 10K, after chipping with H4-acetylated chromatin


title: CLL#4 CD38+ sub-clones

source_name: CLL#4 CD38+ sub-clones


title: Myoblasts_rep1, chip 10K


title: Homocysteine experiment control 1


title: Myoblasts_rep2, chip 10K

source_name: Fetal dkeletal myoblasts


title: CLL#2 CD38- sub-clones

source_name: CLL#2 CD38- sub-clones


title: Medicago truncatula  72 hpi after Sinorhizobium meliloti inoculation, rep4

status: Public on Oct 27 2005

city: St Paul

middle: A

last: VandenBosch

state: MN

address: Room 250 BioSci 6022 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: Medicago truncatula  72  hour(s) post inoculation with Sinorhizobium meliloti  rep4

scan_protocol: Microarray slides were scanned using an GenePix4000B (Axon) two-laser scanner and image analysis was performed using GenePix 4.0 (Axon) software

data_processing: Background-subtracted mean intensities for both tissues were log2 transformed and normalized using lowess and ANOVA

organism: Medicago truncatula

source_name: Medicago truncatula  72 hpi after mock inoculation

label_protocol: 11 ug RNA from each of 3 biological replicates was pooled to make a total of 33 ug for cDNA synthesis with a RT Primer for labeling with either Cy3 or Cy5 dye molecules using a 3DNA Array 50 Expression Array Detection Kit for cDNA Microarrays (Genisophere, Inc., Hatfield, PA). cDNA was synthesized following instructions from 3DNA Array 50 Expression Array Detection Kit Appendix A (Genisphere Inc.).

extract_protocol: Root samples from 3 independent experimental replicates were collected for the experiment. RNA from frozen root samples was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) following the manufacturerés instructions.

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  72 hpi after mock inoculation

growth_protocol: Medicago truncatula genotype A17 was germinated and grown as previously described (Penmetsa and Cook, 2000).

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  72 hpi after inoculation with Sinorhizobium meliloti


title: Medicago truncatula  24 hpi after Sinorhizobium meliloti inoculation, rep3

description: Medicago truncatula  24  hour(s) post inoculation with Sinorhizobium meliloti  rep3

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  24 hpi after inoculation with Sinorhizobium meliloti

source_name: Medicago truncatula  24 hpi after mock inoculation

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  24 hpi after mock inoculation


title: Medicago truncatula  48 hpi after Sinorhizobium meliloti inoculation, rep6

description: Medicago truncatula  48  hour(s) post inoculation with Sinorhizobium meliloti  rep6

source_name: Medicago truncatula  48 hpi after mock inoculation

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  48 hpi after mock inoculation

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  48 hpi after inoculation with Sinorhizobium meliloti


title: Medicago truncatula  72 hpi after Sinorhizobium meliloti inoculation, rep3

description: Medicago truncatula  72  hour(s) post inoculation with Sinorhizobium meliloti  rep3


title: Medicago truncatula  72 hpi after Sinorhizobium meliloti inoculation, rep5

description: Medicago truncatula  72  hour(s) post inoculation with Sinorhizobium meliloti  rep5


title: Medicago truncatula  72 hpi after Sinorhizobium meliloti inoculation, rep2

description: Medicago truncatula  72  hour(s) post inoculation with Sinorhizobium meliloti  rep2


title: Medicago truncatula  48 hpi after Sinorhizobium meliloti inoculation, rep3

description: Medicago truncatula  48  hour(s) post inoculation with Sinorhizobium meliloti  rep3


title: Medicago truncatula  24 hpi after Sinorhizobium meliloti inoculation, rep5

description: Medicago truncatula  24  hour(s) post inoculation with Sinorhizobium meliloti  rep5


title: Medicago truncatula  48 hpi after Sinorhizobium meliloti inoculation, rep5

description: Medicago truncatula  48  hour(s) post inoculation with Sinorhizobium meliloti  rep5


title: Medicago truncatula  72 hpi after Sinorhizobium meliloti inoculation, rep1

description: Medicago truncatula  72  hour(s) post inoculation with Sinorhizobium meliloti  rep1


title: Medicago truncatula  48 hpi after Sinorhizobium meliloti inoculation, rep1

description: Medicago truncatula  48  hour(s) post inoculation with Sinorhizobium meliloti  rep1


title: Medicago truncatula  24 hpi after Sinorhizobium meliloti inoculation, rep4

description: Medicago truncatula  24  hour(s) post inoculation with Sinorhizobium meliloti  rep4


title: Medicago truncatula  24 hpi after Sinorhizobium meliloti inoculation, rep2

description: Medicago truncatula  24  hour(s) post inoculation with Sinorhizobium meliloti  rep2