title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep7 on 2A array on 16-sample beadchip

description: Gene expression data from arctic ground squirrel skeletal muscle at post-reproductive during hibernation

source_name: Arctic ground squirrel skeletal muscle at post-reproductive (non-hibernation control) during hibernation

tag: post-reproductive skeletal muscle


title: Arctic ground squirrel skeletal muscle of torpor animal rep6 on 2A array on 16-sample beadchip

status: Public on Aug 03 2006

type: RNA

city: Fairbanks

first: Jun

last: Yan

state: AK

address: 311 Irving Building

department: Institute of Arctic Biology

country: USA

institute: University of Alaska Fairbanks

description: Gene expression data from arctic ground squirrel skeletal muscle of torpor animal sampled by saw-dust method during hibernation

data_processing: The data were analyzed with Illumina Inc. BeadStudio version 1.5.1.3 and normalized by rank invariant method.

label: Biotin Streptavidin-Cy3

molecule: total RNA

organism: Urocitellus parryii

source_name: Arctic ground squirrel skeletal muscle of torpor animal sampled by saw-dust method during hibernation

tag: torpor skeletal muscle


title: Transit amplifying cell sample 1 (A)

status: Public on Aug 04 2006

city: London

first: Kim

middle: B.

last: Jensen

address: 44 Lincoln's Inn Fields

department: London Research Institute

country: United Kingdom

institute: Cancer Research UK

description: Gene expression data from single cultured human epidermal keratinocytes

hyb_protocol: Following fragmentation, 10 microg of cDNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array HU133. GeneChips were washed and stained using an Affymetrix GeneChip Instrument System.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

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

label: biotin

organism: Homo sapiens

source_name: Cultured human keratinocytes at passage 3

label_protocol:
amplified mRNA from single cultured epidermal keratinocytes
Biotinylated cDNA were prepared according to Tietjen et al. 2003, Neuron.

growth_protocol: Keratinocytes were cultured on a feeder layer of J2-3T3 cells in FAD medium (1 part HAM’S F12, 3 parts Dulbecco’s modified Eagle’s medium, 1.8x10-4 M adenine), supplemented with 10% fetal calf serum (FCS), 0.5 µg/ml hydrocort

extract_protocol: Single cells were seeded in amplification buffer

treatment_protocol: Keratinocyte were picked upon putting them in suspension and seeded in single cell amplification buffer

tag: Human epidermal keratinocyte from healthy donor


title: Arctic ground squirrel skeletal muscle of torpor animal rep7 on 2A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep5 on 2A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle of torpor animal rep5 on 2A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle of torpor animal rep8 on 2A array on 16-sample beadchip


title: Transit amplifying cell sample 4 (A)


title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep6 on 2A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep4 on 2A array on 16-sample beadchip


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 4

city: Boston

first: Julja

last: Burchard

state: MA

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

description:
For details please see: Dianne S. Schwarz, Hongliu Ding, Lori Kennington,
Jessica T. Moore, Janell Schelter, Julja Burchard, Peter S. Linsley,
Neil Aronin, Zuoshang Xu and Phillip D. Zamore  (2006) PLoS Genetics.

data_processing: custom

label: Cy3/Cy5 (fluor-reversed pair)

source_name: HeLa cells

tag: Cells transfected with siRNA to SOD1, SNP at position 4

label: Cy5/Cy3 (fluor-reversed pair)

source_name: HeLa cells,

tag: Cells mock-transfected


title: Arctic ground squirrel skeletal muscle of torpor animal rep3 on 2A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle of torpor animal rep2 on 2A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep1 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep9 on 2A array on 16-sample beadchip

description: Gene expression data from arctic ground squirrel brown adipose tissue of torpor animal sampled by saw-dust method during hibernation

source_name: Arctic ground squirrel brown adipose tissue of torpor animal sampled by saw-dust method during hibernation

tag: torpor brown adipose tissue


title: Arctic ground squirrel skeletal muscle of torpor animal rep4 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep7 on 2A array on 16-sample beadchip

description: Gene expression data from arctic ground squirrel brown adipose tissue at post-reproductive during hibernation

source_name: Arctic ground squirrel brown adipose tissue at post-reproductive (non-hibernation control) during hibernation

tag: post-reproductive brown adipose tissue


title: Transit amplifying cell sample 2 (A)


title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep3 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep7 on 2A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle of torpor animal rep1 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep6 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep6 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep8 on 2A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep2 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep5 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep5 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep4 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep3 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep3 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep4 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep2 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep2 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep1 on 2A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep9 on 2A array on 16-sample beadchip

description: Gene expression data from arctic ground squirrel liver of torpor animal sampled by saw-dust method during hibernation

source_name: Arctic ground squirrel liver of torpor animal sampled by saw-dust method during hibernation

tag: torpor liver


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep7 on 2A array on 16-sample beadchip

description: Gene expression data from arctic ground squirrel liver at post-reproductive during hibernation

source_name: Arctic ground squirrel liver at post-reproductive (non-hibernation control) during hibernation

tag: post-reproductive liver


title: Arctic ground squirrel liver of torpor animal rep8 on 2A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep7 on 2A array on 16-sample beadchip


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep5 on 2A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep1 on 2A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep5 on 2A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep4 on 2A array on 16-sample beadchip


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep6 on 2A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep3 on 2A array on 16-sample beadchip


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep3 on 2A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep2 on 2A array on 16-sample beadchip


title: Arctic ground squirrel hypothalamus at late torpor (LT) animal rep5 on 2A array

description: Gene expression data from arctic ground squirrel hypothalamus at late torpor during hibernation

source_name: Arctic ground squirrel hypothalamus at late torpor (80-90% of torpid episode) during hibernation

tag: late torpor hypothalamus


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep1 on 2A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep1 on 2A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep6 on 2A array on 16-sample beadchip


title: Arctic ground squirrel hypothalamus at late torpor (LT) animal rep4 on 2A array


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep4 on 2A array on 16-sample beadchip


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep7 on 2A array

description: Gene expression data from arctic ground squirrel hypothalamus at post-reproductive during hibernation

source_name: Arctic ground squirrel hypothalamus at post-reproductive (non-hibernation control) during hibernation

tag: post-reproductive hypothalamus


title: Arctic ground squirrel hypothalamus at late arousal (LA) animal rep4 on 2A array

description: Gene expression data from arctic ground squirrel hypothalamus at late arousal during hibernation

source_name: Arctic ground squirrel hypothalamus at late arousal (body temperature >30C for 7~8 hours) during hibernation

tag: late arousal hypothalamus


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep6 on 2A array


title: Arctic ground squirrel hypothalamus at late arousal (LA) animal rep3 on 2A array


title: Arctic ground squirrel hypothalamus at late torpor (LT) animal rep2 on 2A array


title: Total RNA from Drosophila Embryo at 2-4 hrs: pipe_rm9

city: Berkeley

first: Frederic

last: Biemar

state: CA

address: 142 LSA

department: Molecular & Cell Biology

institute: UC Berkeley

description:
To generate pipe-/pipe- females, pipe664/TM3 Sb females were mated with males of the genotype pipe386/TM3 Sb. Non-Sb females of the genotype pipe386/pipe664 were selected. To generate Tollrm9/Tollrm10 females, females of the genotype Tollrm10/TM3 Sb were mated with males of the genotype Tollrm9/TM3 Ser. Non-Sb, non-Ser females of the genotype Tollrm9/Tollrm10 were selected. Females of the genotype Toll10B/+ were obtained directly from the balanced stock (Toll10b/TM3Sb Ser and Toll10b/OR60). Two hour embryo collections were collected from females of the selected genotypes, either pipe386/pipe664, Tollrm9/Tollrm10,or Toll10B/+, on apple juice/yeast plates at 25 degrees celcius. The embryos were placed for an additional 2 hrs at 25 degrees celcius to obtain samples of embryos aged 2-4 hrs. Embryos were collected for five different days, dechorionated, and frozen in liquid nitrogen for storage at -80 degrees celcius until RNA was to be isolated. The different collections were pooled for each sample in order to better normalize the age of these embryo populations.
Once sufficient amounts of embryos had been collected (~500 embryos), total RNA was extracted from them using Trizol Reagent (GIBCO-BRL) according to the manufacturer's protocol. For each sample, 100 ug of total RNA was further purified using the RNeasy Mini Kit (Qiagen) following the Rneasy Mini Protocol for RNA cleanup. Total RNA was prepared independently three times from embryos of each genetic background.
First-strand cDNA synthesis was performed by using SuperScript II reverse transcriptase in the reaction volume of 105 ul for 15 ug of starting RNA material. The RNA was mixed with random hexamers (83.3 ng/g mRNA), heated to 70 degrees celcius for 10 min, and cooled to 15 degrees celcius after which 5x SuperScript II First Strand buffer, DTT (10 mM), and dNTPs (0.5 mM) were added. SuperScript II was added after a 20-min incubation (200 units/ug RNA) followed by a 20-min ramp to 42 degrees celcius and 60-min incubation at 42 degrees celcius. SuperScript II was inactivated at 75 degrees celcius for 15 min.
The second-strand cDNA was synthesized by addition of 50 units of Escherichia coli DNA ligase, 200 units of E. coli DNA polymerase I, 10 units of E. coli RNase H, and 0.2 mM dNTPs to the first-strand synthesis reaction at 16 degrees celcius for 2 hrs.
Double-stranded cDNA was treated with RNase H (Epicentre Technologies) and RNases A/T1 (Ambion), extracted by using a QIAquick PCR purification kit (Qiagen), and subjected to further fragmentation to 50-100 bp by DNase I (1 unit/ul; Epicentre Technologies; size distribution of fragmented DNA was verified on a 2% agarose gel).
The fragmented cDNA was then end-labeled with 70 nM bio-dideoxy ATP (PerkinElmer) by using 6-10 units of terminal deoxynucleotidyltransferase (TdT; Roche Diagnostics) per ug of fragmented DNA in 1x TdT buffer (Roche Diagnostics) and 5 mM CoCl2 (Roche Diagnostics) for 2 hrs at 37 degrees celcius. The labeled DNA material was subsequently hybridized to Affymetrix Drosophila-tiled genomic microarrays for 18 hrs at 45 degrees celcius in a 3 M tetramethyl ammonium chlorate/1x Mes-based solution. All reagents were from Invitrogen, except where noted otherwise.

data_processing: Processing of the microarray data was performed in three basic steps using TiMAT (http://bdtnp.lbl.gov/TiMAT/): data normalization, sliding window summary statistics, and enriched region identification. To normalize the data, all cel files were grouped together and the perfect match intensities(PM) were quantile-normalized and median-scaled to 100. Mismatch intensities were discarded. To identify regions enriched relative to each other, all pair-wise comparisons were made between pipe, Tollrm9/Tollrm10, and Toll10B data (i.e. pipe vs. rm9/rm10, pipe vs. 10B, rm9/rm10 vs. 10B, rm9/rm10 vs. pipe, 10B vs. rm9/rm10, and 10B vs. pipe). Cel files for a particular pairing were divided into treatment and control. Their intensities were mapped to the genome and a ratio score was calculated for each oligo by dividing the average treatment by the average control. To minimize noise, a sliding window of 675bp, containing approximately 19 oligos, was advanced, one oligo at a time across each chromosome (similar results were obtained using a window of 250bp containing 7 oligos). A trimmed mean of the grouped oligo ratios was used to score each window. To collapse overlapping windows into enriched regions, windows that (i) intersect by greater than 100bp, (ii) exceed a low threshold of 1.25x, and (iii) contain more than 5 oligos were joined.

label: bio-dideoxy ATP

organism: Drosophila melanogaster

source_name: pipe386/pipe664  Whole Embryo at 2-4 hrs

source_name: Tollrm9/Tollrm10  Whole Embryo at 2-4 hrs


title: Arctic ground squirrel hypothalamus at late torpor (LT) animal rep3 on 2A array


title: Arctic ground squirrel hypothalamus at late arousal (LA) animal rep1 on 2A array


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep5 on 2A array


title: Arctic ground squirrel hypothalamus at early arousal (EA) animal rep4 on 2A array

description: Gene expression data from arctic ground squirrel hypothalamus at early arousal during hibernation

source_name: Arctic ground squirrel hypothalamus at early arousal (body temperature >30C for 1~2 hours) during hibernation

tag: early arousal hypothalamus


title: Arctic ground squirrel hypothalamus at early torpor (ET) animal rep4 on 2A array

description: Gene expression data from arctic ground squirrel hypothalamus at early torpor during hibernation

source_name: Arctic ground squirrel hypothalamus at early torpor (10-20% of torpid episode) during hibernation

tag: early torpor hypothalamus


title: Total RNA from Drosophila Embryo at 2-4 hrs: pipe_10B

tag: To generate pipe-/pipe- females, pipe664/TM3 Sb females were mated with males of the genotype  pipe386/TM3 Sb. Non-Sb females of the genotype pipe386/pipe664 were selected.

source_name: Toll10B/+  Whole Embryo at 2-4 hrs

tag: Females of the genotype Toll10B/+ were obtained directly from the balanced stock (Toll10b/TM3Sb Ser and Toll10b/OR60).


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep3 on 2A array


title: Arctic ground squirrel hypothalamus at early arousal (EA) animal rep3 on 2A array


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep2 on 2A array


title: Arctic ground squirrel hypothalamus at early arousal (EA) animal rep2 on 2A array


title: Arctic ground squirrel hypothalamus at early torpor (ET) animal rep2 on 2A array


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep1 on 2A array


title: Total RNA from Drosophila Embryo at 2-4 hrs: rm9_pipe

tag: To generate Tollrm9/Tollrm10 females, females of the genotype Tollrm10/TM3 Sb were mated with males of the genotype Tollrm9/TM3 Ser. Non-Sb, non-Ser females of the genotype Tollrm9/Tollrm10 were selected.


title: Arctic ground squirrel hypothalamus at early torpor (ET) animal rep3 on 2A array


title: Total RNA from Drosophila Embryo at 2-4 hrs: rm9_10B


title: Arctic ground squirrel hypothalamus at late arousal (LA) animal rep2 on 2A array


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep4 on 2A array


title: Arctic ground squirrel heart at late torpor (LT) animal rep4 on 2A array

description: Gene expression data from arctic ground squirrel heart at late torpor during hibernation

source_name: Arctic ground squirrel heart at late torpor (80-90% of torpid episode) during hibernation

tag: late torpor heart


title: Arctic ground squirrel hypothalamus at early arousal (EA) animal rep1 on 2A array


title: Arctic ground squirrel heart at late arousal (LA) animal rep4 on 2A array

description: Gene expression data from arctic ground squirrel heart at late arousal during hibernation

source_name: Arctic ground squirrel heart at late arousal (body temperature >30C for 7~8 hours) during hibernation

tag: late arousal heart


title: Arctic ground squirrel heart at late torpor (LT) animal rep5 on 2A array


title: Arctic ground squirrel heart at late torpor (LT) animal rep3 on 2A array


title: Total RNA from Drosophila Embryo at 2-4 hrs: 10B_pipe

tag: To generate pipe-/pipe- females, pipe664/TM3 Sb females were mated with males of the genotype pipe386/TM3 Sb. Non-Sb females of the genotype pipe386/pipe664 were selected


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep7 on 2A array

description: Gene expression data from arctic ground squirrel heart at post-reproductive during hibernation

source_name: Arctic ground squirrel heart at post-reproductive (non-hibernation control) during hibernation

tag: post-reproductive heart


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep6 on 2A array


title: Arctic ground squirrel heart at late arousal (LA) animal rep3 on 2A array


title: Arctic ground squirrel hypothalamus at late torpor (LT) animal rep1 on 2A array


title: Arctic ground squirrel hypothalamus at early torpor (ET) animal rep1 on 2A array


title: Arctic ground squirrel heart at late arousal (LA) animal rep2 on 2A array


title: Total RNA from Drosophila Embryo at 2-4 hrs: 10B_rm9


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep5 on 2A array


title: Arctic ground squirrel heart at late arousal (LA) animal rep1 on 2A array


title: Arctic ground squirrel heart at late torpor (LT) animal rep1 on 2A array


title: Arctic ground squirrel heart at early torpor (ET) animal rep4 on 2A array

description: Gene expression data from arctic ground squirrel heart at early torpor during hibernation

source_name: Arctic ground squirrel heart at early torpor (10-20% of torpid episode) during hibernation

tag: early torpor heart


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep3 on 2A array


title: Arctic ground squirrel heart at early arousal (EA) animal rep4 on 2A array

description: Gene expression data from arctic ground squirrel heart at early arousal during hibernation

source_name: Arctic ground squirrel heart at early arousal (body temperature >30C for 1~2 hours) during hibernation

tag: early arousal heart


title: Arctic ground squirrel heart at early torpor (ET) animal rep3 on 2A array


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep2 on 2A array


title: Arctic ground squirrel heart at early torpor (ET) animal rep2 on 2A array


title: Arctic ground squirrel heart at early arousal (EA) animal rep2 on 2A array


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep1 on 2A array


title: Arctic ground squirrel heart at early arousal (EA) animal rep1 on 2A array


title: Arctic ground squirrel heart at early torpor (ET) animal rep1 on 2A array


title: Arctic ground squirrel brown adipose tissue at late torpor (LT) animal rep5 on 2A array

description: Gene expression data from arctic ground squirrel brown adipose tissue at late torpor during hibernation

source_name: Arctic ground squirrel brown adipose tissue at late torpor (80-90% of torpid episode) during hibernation

tag: late torpor brown adipose tissue


title: Arctic ground squirrel brown adipose tissue at late torpor (LT) animal rep4 on 2A array


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep7 on 2A array

source_name: Arctic ground squirrel brown adipose tissue at post-reproductive (non-hibernation control) during hibernation

tag: post-reproductive brown adipose tissue


title: Arctic ground squirrel brown adipose tissue at late torpor (LT) animal rep3 on 2A array


title: Arctic ground squirrel brown adipose tissue at late arousal (LA) animal rep3 on 2A array

description: Gene expression data from arctic ground squirrel brown adipose tissue at late arousal during hibernation

source_name: Arctic ground squirrel brown adipose tissue at late arousal (body temperature >30C for 7~8 hours) during hibernation

tag: late arousal brown adipose tissue


title: Arctic ground squirrel heart at late torpor (LT) animal rep2 on 2A array


title: Arctic ground squirrel brown adipose tissue at late torpor (LT) animal rep2 on 2A array


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep5 on 2A array


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep6 on 2A array


title: Arctic ground squirrel brown adipose tissue at late arousal (LA) animal rep2 on 2A array


title: Arctic ground squirrel brown adipose tissue at late torpor (LT) animal rep1 on 2A array


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep4 on 2A array


title: Arctic ground squirrel brown adipose tissue at late arousal (LA) animal rep1 on 2A array


title: Arctic ground squirrel brown adipose tissue at early torpor (ET) animal rep4 on 2A array

description: Gene expression data from arctic ground squirrel brown adipose tissue at early torpor during hibernation

source_name: Arctic ground squirrel brown adipose tissue at early torpor (10-20% of torpid episode) during hibernation

tag: early torpor brown adipose tissue


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep3 on 2A array

description: Gene expression data from arctic ground squirrel brown adipose tissue at post-reproductive during hibernation


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep4 on 2A array


title: Arctic ground squirrel brown adipose tissue at early arousal (EA) animal rep4 on 2A array

description: Gene expression data from arctic ground squirrel brown adipose tissue at early arousal during hibernation

source_name: Arctic ground squirrel brown adipose tissue at early arousal (body temperature >30C for 1~2 hours) during hibernation

tag: early arousal brown adipose tissue


title: Arctic ground squirrel brown adipose tissue at early torpor (ET) animal rep3 on 2A array


title: Arctic ground squirrel brown adipose tissue at early arousal (EA) animal rep3 on 2A array


title: Arctic ground squirrel brown adipose tissue at early torpor (ET) animal rep2 on 2A array


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep2 on 2A array


title: Arctic ground squirrel brown adipose tissue at early torpor (ET) animal rep1 on 2A array


title: Arctic ground squirrel brown adipose tissue at early arousal (EA) animal rep1 on 2A array


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep1 on 2A array


title: Arctic ground squirrel brown adipose tissue at late arousal (LA) animal rep4 on 2A array


title: Arctic ground squirrel liver at late torpor (LT) animal rep5 on 2A array

description: Gene expression data from arctic ground squirrel liver at late torpor during hibernation

source_name: Arctic ground squirrel liver at late torpor (80-90% of torpid episode) during hibernation

tag: late torpor liver


title: Arctic ground squirrel liver at late torpor (LT) animal rep4 on 2A array


title: Arctic ground squirrel liver at late arousal (LA) animal rep4 on 2A array

description: Gene expression data from arctic ground squirrel liver at late arousal during hibernation

source_name: Arctic ground squirrel liver at late arousal (body temperature >30C for 7~8 hours) during hibernation

tag: late arousal liver


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep7 on 2A array

description: Gene expression data from arctic ground squirrel liver at post-reproductive during hibernation

source_name: Arctic ground squirrel liver at post-reproductive (non-hibernation control) during hibernation

tag: post-reproductive liver


title: Arctic ground squirrel liver at late torpor (LT) animal rep3 on 2A array


title: Arctic ground squirrel liver at late torpor (LT) animal rep2 on 2A array


title: Arctic ground squirrel liver at late arousal (LA) animal rep2 on 2A array


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep6 on 2A array


title: Arctic ground squirrel liver at late arousal (LA) animal rep3 on 2A array


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep2 on 2A array on 16-sample beadchip


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep5 on 2A array


title: Arctic ground squirrel liver at late torpor (LT) animal rep1 on 2A array


title: Arctic ground squirrel liver at early torpor (ET) animal rep4 on 2A array

description: Gene expression data from arctic ground squirrel liver at early torpor during hibernation

source_name: Arctic ground squirrel liver at early torpor (10-20% of torpid episode) during hibernation

tag: early torpor liver


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep4 on 2A array


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep3 on 2A array


title: Arctic ground squirrel liver at early torpor (ET) animal rep3 on 2A array


title: Arctic ground squirrel liver at early arousal (EA) animal rep4 on 2A array

description: Gene expression data from arctic ground squirrel liver at early arousal during hibernation

source_name: Arctic ground squirrel liver at early arousal (body temperature >30C for 1~2 hours) during hibernation

tag: early arousal liver


title: Arctic ground squirrel heart at early arousal (EA) animal rep3 on 2A array


title: Arctic ground squirrel liver at early arousal (EA) animal rep3 on 2A array


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep2 on 2A array


title: Arctic ground squirrel liver at early torpor (ET) animal rep2 on 2A array


title: Arctic ground squirrel brown adipose tissue at early arousal (EA) animal rep2 on 2A array


title: Arctic ground squirrel liver at early arousal (EA) animal rep2 on 2A array


title: Arctic ground squirrel liver at early torpor (ET) animal rep1 on 2A array


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep1 on 2A array


title: Arctic ground squirrel liver at early arousal (EA) animal rep1 on 2A array


title: Arctic ground squirrel skeletal muscle of torpor animal rep9 on 1A array on 16-sample beadchip

description: Gene expression data from arctic ground squirrel skeletal muscle of torpor animal sampled by saw-dust method during hibernation

source_name: Arctic ground squirrel skeletal muscle of torpor animal sampled by saw-dust method during hibernation

tag: torpor skeletal muscle


title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep7 on 1A array on 16-sample beadchip

description: Gene expression data from arctic ground squirrel skeletal muscle at post-reproductive during hibernation

source_name: Arctic ground squirrel skeletal muscle at post-reproductive (non-hibernation control) during hibernation

tag: post-reproductive skeletal muscle


title: Arctic ground squirrel skeletal muscle of torpor animal rep8 on 1A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle of torpor animal rep7 on 1A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle of torpor animal rep5 on 1A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep6 on 1A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep4 on 1A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle of torpor animal rep4 on 1A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle of torpor animal rep6 on 1A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep3 on 1A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle of torpor animal rep3 on 1A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep2 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver at late arousal (LA) animal rep1 on 2A array


title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep1 on 1A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle of torpor animal rep1 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep9 on 1A array on 16-sample beadchip

description: Gene expression data from arctic ground squirrel brown adipose tissue of torpor animal sampled by saw-dust method during hibernation

source_name: Arctic ground squirrel brown adipose tissue of torpor animal sampled by saw-dust method during hibernation

tag: torpor brown adipose tissue


title: Arctic ground squirrel brown adipose tissue of torpor animal rep8 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep7 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep6 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep6 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep5 on 1A array on 16-sample beadchip


title: Arctic ground squirrel skeletal muscle of torpor animal rep2 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep4 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep5 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep3 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep2 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep2 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue of torpor animal rep1 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep1 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep8 on 1A array on 16-sample beadchip

description: Gene expression data from arctic ground squirrel liver of torpor animal sampled by saw-dust method during hibernation

source_name: Arctic ground squirrel liver of torpor animal sampled by saw-dust method during hibernation

tag: torpor liver


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep7 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep7 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep4 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep9 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep6 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep6 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep5 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep5 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep4 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep4 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep3 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep3 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep2 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver of torpor animal rep2 on 1A array on 16-sample beadchip


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep1 on 1A array on 16-sample beadchip


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep3 on 1A array on 16-sample beadchip


title: Arctic ground squirrel hypothalamus at late torpor (LT) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel hypothalamus at late torpor during hibernation

source_name: Arctic ground squirrel hypothalamus at late torpor (80-90% of torpid episode) during hibernation

tag: late torpor hypothalamus


title: Arctic ground squirrel brown adipose tissue of torpor animal rep7 on 1A array on 16-sample beadchip


title: Arctic ground squirrel hypothalamus at late torpor (LT) animal rep5 on 1A array


title: Arctic ground squirrel hypothalamus at late arousal (LA) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel hypothalamus at late arousal during hibernation

source_name: Arctic ground squirrel hypothalamus at late arousal (body temperature >30C for 7~8 hours) during hibernation

tag: late arousal hypothalamus


title: Arctic ground squirrel hypothalamus at late torpor (LT) animal rep2 on 1A array


title: Arctic ground squirrel hypothalamus at late arousal (LA) animal rep3 on 1A array


title: Arctic ground squirrel skeletal muscle at post-reproductive (PR) animal rep5 on 1A array on 16-sample beadchip


title: Arctic ground squirrel hypothalamus at late arousal (LA) animal rep1 on 1A array


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep6 on 1A array

description: Gene expression data from arctic ground squirrel hypothalamus at post-reproductive during hibernation

source_name: Arctic ground squirrel hypothalamus at post-reproductive (non-hibernation control) during hibernation

tag: post-reproductive hypothalamus


title: Arctic ground squirrel hypothalamus at early torpor (ET) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel hypothalamus at early torpor during hibernation

source_name: Arctic ground squirrel hypothalamus at early torpor (10-20% of torpid episode) during hibernation

tag: early torpor hypothalamus


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep4 on 1A array


title: Arctic ground squirrel hypothalamus at early arousal (EA) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel hypothalamus at early arousal during hibernation

source_name: Arctic ground squirrel hypothalamus at early arousal (body temperature >30C for 1~2 hours) during hibernation

tag: early arousal hypothalamus


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep3 on 1A array


title: Arctic ground squirrel hypothalamus at early torpor (ET) animal rep3 on 1A array


title: Arctic ground squirrel hypothalamus at early torpor (ET) animal rep2 on 1A array


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep1 on 1A array


title: Arctic ground squirrel hypothalamus at early arousal (EA) animal rep2 on 1A array


title: Arctic ground squirrel liver of torpor animal rep1 on 1A array on 16-sample beadchip


title: Arctic ground squirrel hypothalamus at early arousal (EA) animal rep1 on 1A array


title: Arctic ground squirrel heart at late torpor (LT) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel heart at late torpor during hibernation

source_name: Arctic ground squirrel heart at late torpor (80-90% of torpid episode) during hibernation

tag: late torpor heart


title: Arctic ground squirrel heart at late arousal (LA) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel heart at late arousal during hibernation

source_name: Arctic ground squirrel heart at late arousal (body temperature >30C for 7~8 hours) during hibernation

tag: late arousal heart


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep7 on 1A array


title: Arctic ground squirrel hypothalamus at late torpor (LT) animal rep3 on 1A array


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep7 on 1A array

description: Gene expression data from arctic ground squirrel heart at post-reproductive during hibernation

source_name: Arctic ground squirrel heart at post-reproductive (non-hibernation control) during hibernation

tag: post-reproductive heart


title: Arctic ground squirrel heart at late torpor (LT) animal rep3 on 1A array


title: Arctic ground squirrel hypothalamus at late torpor (LT) animal rep1 on 1A array


title: Arctic ground squirrel hypothalamus at late arousal (LA) animal rep2 on 1A array


title: Arctic ground squirrel heart at late arousal (LA) animal rep3 on 1A array


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep5 on 1A array


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep6 on 1A array


title: Arctic ground squirrel heart at late torpor (LT) animal rep2 on 1A array


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep5 on 1A array


title: Arctic ground squirrel heart at late arousal (LA) animal rep1 on 1A array


title: Arctic ground squirrel heart at late arousal (LA) animal rep2 on 1A array


title: Arctic ground squirrel heart at late torpor (LT) animal rep1 on 1A array


title: Arctic ground squirrel hypothalamus at post-reproductive (PR) animal rep2 on 1A array


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep4 on 1A array


title: Arctic ground squirrel hypothalamus at early arousal (EA) animal rep3 on 1A array


title: Arctic ground squirrel heart at early torpor (ET) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel heart at early torpor during hibernation

source_name: Arctic ground squirrel heart at early torpor (10-20% of torpid episode) during hibernation

tag: early torpor heart


title: Arctic ground squirrel heart at early arousal (EA) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel heart at early arousal during hibernation

source_name: Arctic ground squirrel heart at early arousal (body temperature >30C for 1~2 hours) during hibernation

tag: early arousal heart


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep3 on 1A array


title: Arctic ground squirrel hypothalamus at early torpor (ET) animal rep1 on 1A array


title: Arctic ground squirrel heart at early torpor (ET) animal rep3 on 1A array


title: Arctic ground squirrel heart at early arousal (EA) animal rep3 on 1A array


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep2 on 1A array


title: Arctic ground squirrel heart at early torpor (ET) animal rep2 on 1A array


title: Arctic ground squirrel heart at post-reproductive (PR) animal rep1 on 1A array


title: Arctic ground squirrel heart at early torpor (ET) animal rep1 on 1A array


title: Arctic ground squirrel heart at early arousal (EA) animal rep1 on 1A array


title: Arctic ground squirrel heart at early arousal (EA) animal rep2 on 1A array


title: Arctic ground squirrel brown adipose tissue at late torpor (LT) animal rep5 on 1A array

description: Gene expression data from arctic ground squirrel brown adipose tissue at late torpor during hibernation

source_name: Arctic ground squirrel brown adipose tissue at late torpor (80-90% of torpid episode) during hibernation

tag: late torpor brown adipose tissue


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep7 on 1A array

description: Gene expression data from arctic ground squirrel brown adipose tissue at post-reproductive during hibernation

source_name: Arctic ground squirrel brown adipose tissue at post-reproductive (non-hibernation control) during hibernation

tag: post-reproductive brown adipose tissue


title: Arctic ground squirrel brown adipose tissue at late arousal (LA) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel brown adipose tissue at late arousal during hibernation

source_name: Arctic ground squirrel brown adipose tissue at late arousal (body temperature >30C for 7~8 hours) during hibernation

tag: late arousal brown adipose tissue


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep6 on 1A array


title: Arctic ground squirrel brown adipose tissue at late arousal (LA) animal rep3 on 1A array


title: Arctic ground squirrel brown adipose tissue at late torpor (LT) animal rep2 on 1A array


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep5 on 1A array


title: Arctic ground squirrel brown adipose tissue at early torpor (ET) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel brown adipose tissue at early torpor during hibernation

source_name: Arctic ground squirrel brown adipose tissue at early torpor (10-20% of torpid episode) during hibernation

tag: early torpor brown adipose tissue


title: Arctic ground squirrel brown adipose tissue at late arousal (LA) animal rep2 on 1A array


title: Arctic ground squirrel brown adipose tissue at late arousal (LA) animal rep1 on 1A array


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep4 on 1A array


title: Arctic ground squirrel brown adipose tissue at late torpor (LT) animal rep3 on 1A array


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep3 on 1A array


title: Arctic ground squirrel brown adipose tissue at early torpor (ET) animal rep3 on 1A array


title: Arctic ground squirrel brown adipose tissue at early arousal (EA) animal rep3 on 1A array

description: Gene expression data from arctic ground squirrel brown adipose tissue at early arousal during hibernation

source_name: Arctic ground squirrel brown adipose tissue at early arousal (body temperature >30C for 1~2 hours) during hibernation

tag: early arousal brown adipose tissue


title: Arctic ground squirrel brown adipose tissue at early torpor (ET) animal rep2 on 1A array


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep2 on 1A array


title: Arctic ground squirrel brown adipose tissue at early arousal (EA) animal rep2 on 1A array


title: Arctic ground squirrel brown adipose tissue at late torpor (LT) animal rep1 on 1A array


title: Arctic ground squirrel brown adipose tissue at early torpor (ET) animal rep1 on 1A array


title: Arctic ground squirrel brown adipose tissue at early arousal (EA) animal rep1 on 1A array


title: Arctic ground squirrel liver at late torpor (LT) animal rep5 on 1A array

description: Gene expression data from arctic ground squirrel liver at late torpor during hibernation

source_name: Arctic ground squirrel liver at late torpor (80-90% of torpid episode) during hibernation

tag: late torpor liver


title: Arctic ground squirrel liver at late arousal (LA) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel liver at late arousal during hibernation

source_name: Arctic ground squirrel liver at late arousal (body temperature >30C for 7~8 hours) during hibernation

tag: late arousal liver


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep7 on 1A array

description: Gene expression data from arctic ground squirrel liver at post-reproductive during hibernation

source_name: Arctic ground squirrel liver at post-reproductive (non-hibernation control) during hibernation

tag: post-reproductive liver


title: Arctic ground squirrel liver at late torpor (LT) animal rep3 on 1A array


title: Arctic ground squirrel liver at late arousal (LA) animal rep3 on 1A array


title: Arctic ground squirrel liver at late torpor (LT) animal rep2 on 1A array


title: Arctic ground squirrel liver at late arousal (LA) animal rep2 on 1A array


title: Arctic ground squirrel brown adipose tissue at early arousal (EA) animal rep4 on 1A array


title: Arctic ground squirrel liver at late torpor (LT) animal rep1 on 1A array


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep5 on 1A array


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep4 on 1A array


title: Arctic ground squirrel liver at late arousal (LA) animal rep1 on 1A array


title: Arctic ground squirrel liver at early torpor (ET) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel liver at early torpor during hibernation

source_name: Arctic ground squirrel liver at early torpor (10-20% of torpid episode) during hibernation

tag: early torpor liver


title: Arctic ground squirrel liver at early torpor (ET) animal rep3 on 1A array


title: Arctic ground squirrel liver at early arousal (EA) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel liver at early arousal during hibernation

source_name: Arctic ground squirrel liver at early arousal (body temperature >30C for 1~2 hours) during hibernation

tag: early arousal liver


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep3 on 1A array


title: Arctic ground squirrel liver at early torpor (ET) animal rep2 on 1A array


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep2 on 1A array


title: Arctic ground squirrel brown adipose tissue at post-reproductive (PR) animal rep1 on 1A array


title: Arctic ground squirrel liver at early arousal (EA) animal rep2 on 1A array


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep1 on 1A array


title: Arctic ground squirrel liver at early torpor (ET) animal rep1 on 1A array


title: Root_2xR3_vs_1x_Rep5

status: Public on Aug 02 2006

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

description: A synthetic autopolyploidy plant series O37 was developed from chromosome doublings of a monoploid (12 chromosome) plant derived from a Solanum phureja background.  Monoploid (1x), diploid (2xR3 and 2xR5) and tetraploid (4x) plants were used for gene expression profiling.  Total RNA was isolated from growing leaflets of six plants of each genotype at 20 day after planting.  Microarrays were performed in a loop design for three biological replicates.  Total RNA was isolated and amplified from growing root tips of each genotype at 7 days after planting.  Microarrays were performed in a loop design for two biological replicates (according to Bioreps 1 and 2 in the Design Diagram).

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

organism: Solanum phureja

growth_protocol: 7 days in growth chamber (Fafard 2 potting mix; 15h/9h light/dark; 23.5C day, 15.5C dark; 50% Rel. humidity)

treatment_protocol: Genotype

tag: Solanum phureja, Root_tips, Other


title: Arctic ground squirrel liver at post-reproductive (PR) animal rep6 on 1A array


title: Root_2xR5_vs_4x_Rep5


title: Root_4x_vs_2xR3_Rep5


title: Arctic ground squirrel liver at early arousal (EA) animal rep3 on 1A array


title: Leaf_2xR3_vs_2xR5_Rp3

growth_protocol: 20 days in growth chamber (Fafard 2 potting mix; 15h/9h light/dark; 23.5C day, 15.5C dark; 50% Rel. humidity; daily treatments of 0.5x Hoagland solution)

tag: Solanum phureja, Leaflets, Other


title: Root_4x_vs_2xR5_Rep4


title: Root_1x_vs_2xR5_Rep5


title: Leaf_4x_vs_1x_Rep3


title: Leaf_1x_vs_4x_Rep3


title: Leaf_2xR5_vs_2xR3_Rp3


title: Leaf_1x_vs_2xR5_Rep2


title: Leaf_2xR5_vs_4x_Rep2


title: Arctic ground squirrel liver at late torpor (LT) animal rep4 on 1A array


title: Leaf_4x_vs_2xR3_Rep2


title: Leaf_2xR3_vs_1x_Rep2


title: Leaf_4x_vs_2xR5_Rep1


title: Root_2xR3_vs_4x_Rep4


title: Arctic ground squirrel liver at early arousal (EA) animal rep1 on 1A array


title: Spinal Cord SC_REP 3

city: Memphis

first: Ramin

last: Homayouni

state: TN

address: 3774 Walker avenue

department: Bioinformatics

institute: University of memphis

description: Total RNA was extracted from pooled left and right lumbar (L1-L6) SC isolated from male, 3 month-old C57BL/6J mice

data_processing: Data were obtained using the Affymetrix Microarray Suite version 5.0 (MAS 5.0) with default analysis settings and global scaling. Expression values were further normalized to the median expression for each chip and each gene across all samples.

organism: Mus musculus

source_name: Spinal Cord (SC)

tag: Pooled SC from 4 male, 3 month-old C57BL/6J mice


title: Leaf_2xR3_vs_4x_Rep1


title: Leaf_2xR5_vs_1x_Rep1


title: Leaf_1x_vs_2xR3_Rep1


title: Arctic ground squirrel heart at late torpor (LT) animal rep5 on 1A array

description: Gene expression data from arctic ground squirrel heart at late torpor during hibernation

tag: late torpor heart


title: Spinal Cord SC_REP 2


title: Spinal Cord SC_REP 1


title: Dorsal Root Ganglion DRG_REP 2

description: Total RNA was extracted from pooled left and right lumbar (L1-L6) DRG isolated from male, 3 month-old C57BL/6J mice

source_name: Dorsal Root Ganglion (DRG)

tag: Pooled DRG from 4 male, 3 month-old C57BL/6J mice


title: Root_2xR5_vs_1x_Rep4


title: Root_1x_vs_2xR3_Rep4


title: Dorsal Root Ganglion DRG_REP 3


title: Mjannaschii_mtlimited_rep1

status: Public on Aug 01 2006

first: Boonchai

last: Boonyaratanakornkit

address: 201 Gilman Hall #1462

department: Chemical Engineering

description: Effect of gas substrate limitation on barophilic growth at 500 atm.

hyb_protocol: Slides were pre-hybridized in filter-sterilized buffer (5X SSC, 0.1% SDS, 1% BSA) at 42C for at least 1 h. Slides were then washed in Milli-Q (Millipore) ultrapure H2O for 10 min, then in isopropanol for 6 min, and spun dry. Dried, labeled cDNA targets were resuspended in at least 10 ul of hybridization buffer (50% formamide, 5X SSC, 0.1% SDS, 1 ug/ul salmon sperm DNA) for 15 min at RT so that the dye concentrations in samples hybridized on the same slide were approximately the same. Cy5 and Cy3 labeled targets were combined, and targets were heated for 10 min at 95C and cooled on ice for 30 sec.

scan_protocol: Slides were scanned on a GenePix 4000 dual-color confocal laser scanner (Axon). Images were collected in the Cy3 and Cy5 channels (532 nm and 635 nm, respectively) and stored as paired TIFF images.

data_processing: VALUES were quantified using Spot (http://experimental.act.cmis.csiro.au/Spot/index.php).

organism: Methanocaldococcus jannaschii

source_name: Methanocaldococcus jannaschii, 7.8 atm, 600 ml medium

label_protocol: Two ug of total RNA and 6 ug of random hexamers (Invitrogen) were combined, incubated at 70C for 10 min, and snap frozen in a dry-ice/ethanol bath for 30 s. First-strand cDNA synthesis was carried out at 42C overnight with 400 U of SuperScript II (Invitrogen), 1X first-strand buffer (Invitrogen SuperScript II), 0.01 M DTT (Invitrogen SuperScript II), 12.5 mM dATP (Invitrogen), 12.5 mM dCTP (Invitrogen), 12.5 mM dGTP (Invitrogen), 4.16 mM dTTP (Invitrogen), and 8.33 mM aa-dUTP (Ambion). The reaction was quenched by adding 10 ul 0.5 M EDTA, and the RNA template was hydrolyzed with the addition of 10 ul 1 M NaOH followed by incubation at 65C for 15 min. The reaction was neutralized by adding 25 ul 1M Tris-HCl, pH 7.0 (Ambion). cDNA was separated from reaction reagents using a Microcon 30 spin column (Millipore) and lyophilized to dryness with a Speed Vac (Savant). For NHS-Cy dye coupling, sample was re-suspended in 4.5 ul 0.1 M sodium carbonate, pH 9.0, and 4.5 ul of either NHS-Cy3 or NHS-Cy5 (Amersham Pharmacia) and allowed to couple to the cDNA for 1 h at room temperature in the dark. The coupling reaction was quenched with 4.5 ul 4 M hydroxylamine and incubated in the dark for 15 min at room temperature. 35 ul 100 mM sodium acetate pH 5.2 was added and unincorporated dye was removed using QIAquick columns (Qiagen). The whole undiluted sample was analyzed using a spectrophotometer (Beckman) to determine dye incorporation and nucleotides per dye; targets with dye incorporation of over 10 pmol and nucleotides-per-dye ratios below 60 were used in hybridizations. The Cy3 and Cy5 labeled cDNA targets were lyophilized to dryness in a Speed Vac (Savant).

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) at a temperature of 88C. An unbaffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm. The system was operated with 600 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463).

extract_protocol: Samples were withdrawn from the high T-P bioreactor through a micrometer control valve (High Pressure Equipment, Co.), passed through a 0.45 um nitrocellulose filter (Millipore) to collect cells. This filter was placed in cold phenol with 1% SDS and 0.1 M sodium acetate and homogenized using a beadbeater (BioSpec Products, Inc.) for 5 min at the highest setting. The aqueous layer was removed and re-extracted with cold phenol. Total RNA was precipitated overnight at -20C with 3M sodium acetate and isopropanol, treated with DNase (Invitrogen), and cleaned with RNeasy columns (Qiagen).

tag: Methanocaldococcus jannaschii (DSM 2661) pressure

value: 7.8 atm

tag: temperature

tag: volume

value: 600 ml medium

source_name: Methanocaldococcus jannaschii, 500 atm, 600 ml medium

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) at a temperature of 88C. An unbaffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm. Further increases in pressure to 500 atm were obtained by addition of He. The system was operated with 600 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463).

value: 500 atm


title: Mjannaschii_500atm_rep2

source_name: Methanocaldococcus jannaschii, 500 atm, 200 ml medium

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) at a temperature of 88C. An unbaffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm. Further increases in pressure to 500 atm were obtained by addition of He. The system was operated with 200 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463).

value: 200 ml medium

source_name: Methanocaldococcus jannaschii, 7.8 atm, 200 ml medium

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) at a temperature of 88C. An unbaffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm. The system was operated with 200 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463).


title: Mjannaschii_500atm_rep4


title: Dorsal Root Ganglion DRG_REP 1


title: Mjannaschii_mtlimited_7.8atm_rep1

hyb_protocol: Slides were pre-hybridized in filter-sterilized buffer (5X SSC, 0.1% SDS, 1% BSA) at 42C for at least 1 h. Slides were then washed in Milli-Q (Millipore) ultrapure H2O for 10 min, then in isopropanol for 6 min, and spun dry. Dried, labeled cDNA targets were resuspended in at least 10 ul of hybridization buffer (50% formamide, 5X SSC, 0.1% SDS, 1 ug/ul salmon sperm DNA) for 15 min at RT so that the dye concentrations in samples hybridized on the same slide were approximately the same. Cy5 and Cy3 labeled targets were combined, and targets were heated for 10 min at 95C and cooled on ice for 30 sec. A clean 25 mm X 60 mm glass lifterslip (Erie Scientific) was placed onto the pre-hybridized slide and target was applied using capillary action. Slides were placed in hybridization chambers (Corning) and hybridized at 42C in the dark for 16 to 20 hours. All post-hybridization washes were performed in aluminum-foil wrapped glass dishes (VWR) on an orbital shaker. The first wash was performed in 1X SSC, 0.1% SDS at 42C for 5 min. The second wash was performed in 0.1X SSC, 0.1% SDS for 5 min and the final three washes were performed in 0.1X SSC for 5 min, all at room temperature. Slides were blow-dried with filtered house air.

tag: Methanocaldococcus jannaschii (DSM 2661)

tag: pressure


title: Mjannaschii_mtlimited_500atm_rep2


title: Mjannaschii_mtlimited_500atm_rep3


title: Mjannaschii_mtlimited_500atm_rep1

hyb_protocol: Slides were pre-hybridized in filter-sterilized buffer (5X SSC, 0.1% SDS, 1% BSA) at 42C for at least 1 h. Slides were then washed in Milli-Q (Millipore) ultrapure H2O for 10 min, then in isopropanol for 6 min, and spun dry.  Dried, labeled cDNA targets were resuspended in at least 10 ul of hybridization buffer (50% formamide, 5X SSC, 0.1% SDS, 1 ug/ul salmon sperm DNA) for 15 min at RT so that the dye concentrations in samples hybridized on the same slide were approximately the same. Cy5 and Cy3 labeled targets were combined, and targets were heated for 10 min at 95C and cooled on ice for 30 sec. A clean 25 mm X 60 mm glass lifterslip (Erie Scientific) was placed onto the pre-hybridized slide and target was applied using capillary action. Slides were placed in hybridization chambers (Corning) and hybridized at 42C in the dark for 16 to 20 hours. All post-hybridization washes were performed in aluminum-foil wrapped glass dishes (VWR) on an orbital shaker. The first wash was performed in 1X SSC, 0.1% SDS at 42C for 5 min. The second wash was performed in 0.1X SSC, 0.1% SDS for 5 min and the final three washes were performed in 0.1X SSC for 5 min, all at room temperature. Slides were blow-dried with filtered house air.

label_protocol:
Two ug of total RNA and 6 ug of random hexamers (Invitrogen) were combined, incubated at 70C for 10 min, and snap frozen in a dry-ice/ethanol bath for 30 s. First-strand cDNA synthesis was carried out at 42C overnight with 400 U of SuperScript II (Invitrogen), 1X first-strand buffer (Invitrogen SuperScript II), 0.01 M DTT (Invitrogen SuperScript II), 12.5 mM dATP (Invitrogen), 12.5 mM dCTP (Invitrogen), 12.5 mM dGTP (Invitrogen), 4.16 mM dTTP (Invitrogen), and 8.33 mM aa-dUTP (Ambion). The reaction was quenched by adding 10 ul 0.5 M EDTA, and the RNA template was hydrolyzed with the addition of 10 ul 1 M NaOH followed by incubation at 65C for 15 min. The reaction was neutralized by adding 25 ul 1M Tris-HCl, pH 7.0 (Ambion). cDNA was separated from reaction reagents using a Microcon 30 spin column (Millipore) and lyophilized to dryness with a Speed Vac (Savant). For NHS-Cy dye coupling, sample was re-suspended in 4.5 ul 0.1 M sodium carbonate, pH 9.0, and 4.5 ul of either NHS-Cy3 or NHS-Cy5 (Amersham Pharmacia) and allowed to couple to the cDNA for 1 h at room temperature in the dark. The coupling reaction was quenched with 4.5 ul 4 M hydroxylamine and incubated in the dark for 15 min at room temperature. 35 ul 100 mM sodium acetate pH 5.2 was added and unincorporated dye was removed using QIAquick columns (Qiagen). The whole undiluted sample was analyzed using a spectrophotometer (Beckman) to determine dye incorporation and nucleotides per dye;
targets with dye incorporation of over 10 pmol and nucleotides-per-dye ratios below 60 were used in hybridizations. The Cy3 and Cy5 labeled cDNA targets were lyophilized to dryness in a Speed Vac (Savant).


title: Mjannaschii_mtlimited_rep3


title: Lasseter 06 hpi

city: Raleigh

first: Tristan

last: Coram

state: NC

address: 4118 Williams Hall, NC State University

institute: USDA-ARS, NC State University

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

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 1.8-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. See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Molecular Biology. Submitted

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105184/suppl/GSM105184_Lasseter 06h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105184/suppl/GSM105184_Lasseter 06h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105184/suppl/GSM105184_Lasseter 06h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105184/suppl/GSM105184_Lasseter 06h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105184/suppl/GSM105184_Lasseter 06h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105184/suppl/GSM105184_Lasseter 06h treated(cy5) rep3.TXT.txt.gz

organism: Cicer arietinum

source_name: Control

growth_protocol: Seeds surface sterilised, germinated, and grown in pots according to Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Molecular Biology. Submitted

treatment_protocol: Sprayed with water (~5 mL per plant) at 0 hours.  See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Molecular Biology. Submitted

tag: Genotype

value: Lasseter

tag: Age

value: 14 days (seedling)

tag: Tissue

value: Shoot (stem and leaf)

source_name: Treatment

treatment_protocol: Sprayed with A. rabie spores (~5 mL per plant) at 0 hours.  See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Molecular Biology. Submitted


title: Lasseter 24 hpi

hyb_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Molecular Biology. Submitted

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105186/suppl/GSM105186_Lasseter 24h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105186/suppl/GSM105186_Lasseter 24h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105186/suppl/GSM105186_Lasseter 24h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105186/suppl/GSM105186_Lasseter 24h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105186/suppl/GSM105186_Lasseter 24h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105186/suppl/GSM105186_Lasseter 24h treated(cy5) rep3.TXT.txt.gz


title: Lasseter 48 hpi

scan_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Molecular Biology. Submitted

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105187/suppl/GSM105187_Lasseter 48h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105187/suppl/GSM105187_Lasseter 48h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105187/suppl/GSM105187_Lasseter 48h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105187/suppl/GSM105187_Lasseter 48h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105187/suppl/GSM105187_Lasseter 48h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105187/suppl/GSM105187_Lasseter 48h treated(cy5) rep3.TXT.txt.gz


title: Lasseter 12 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105185/suppl/GSM105185_Lasseter 12h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105185/suppl/GSM105185_Lasseter 12h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105185/suppl/GSM105185_Lasseter 12h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105185/suppl/GSM105185_Lasseter 12h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105185/suppl/GSM105185_Lasseter 12h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105185/suppl/GSM105185_Lasseter 12h treated(cy5) rep3.TXT.txt.gz

label_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Molecular Biology. Submitted


title: ILWC245 24 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105181/suppl/GSM105181_ILWC245 24h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105181/suppl/GSM105181_ILWC245 24h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105181/suppl/GSM105181_ILWC245 24h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105181/suppl/GSM105181_ILWC245 24h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105181/suppl/GSM105181_ILWC245 24h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105181/suppl/GSM105181_ILWC245 24h treated(cy5) rep3.TXT.txt.gz

extract_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Molecular Biology. Submitted


title: ILWC245 12 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105180/suppl/GSM105180_ILWC245 12h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105180/suppl/GSM105180_ILWC245 12h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105180/suppl/GSM105180_ILWC245 12h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105180/suppl/GSM105180_ILWC245 12h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105180/suppl/GSM105180_ILWC245 12h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105180/suppl/GSM105180_ILWC245 12h treated(cy5) rep3.TXT.txt.gz


title: ILWC245 06 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105179/suppl/GSM105179_ILWC245 06h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105179/suppl/GSM105179_ILWC245 06h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105179/suppl/GSM105179_ILWC245 06h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105179/suppl/GSM105179_ILWC245 06h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105179/suppl/GSM105179_ILWC245 06h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105179/suppl/GSM105179_ILWC245 06h treated(cy5) rep3.TXT.txt.gz


title: Mjannaschii_mtlimited_rep2


title: ICC3996 72 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105178/suppl/GSM105178_ICC3996 72h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105178/suppl/GSM105178_ICC3996 72h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105178/suppl/GSM105178_ICC3996 72h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105178/suppl/GSM105178_ICC3996 72h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105178/suppl/GSM105178_ICC3996 72h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105178/suppl/GSM105178_ICC3996 72h treated(cy5) rep3.TXT.txt.gz


title: ICC3996 48 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105177/suppl/GSM105177_ICC3996 48h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105177/suppl/GSM105177_ICC3996 48h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105177/suppl/GSM105177_ICC3996 48h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105177/suppl/GSM105177_ICC3996 48h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105177/suppl/GSM105177_ICC3996 48h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105177/suppl/GSM105177_ICC3996 48h treated(cy5) rep3.TXT.txt.gz


title: Mjannaschii_mtlimited_7.8atm_rep3


title: ICC3996 24 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105176/suppl/GSM105176_ICC3996 24h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105176/suppl/GSM105176_ICC3996 24h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105176/suppl/GSM105176_ICC3996 24h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105176/suppl/GSM105176_ICC3996 24h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105176/suppl/GSM105176_ICC3996 24h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105176/suppl/GSM105176_ICC3996 24h treated(cy5) rep3.TXT.txt.gz


title: Mjannaschii_mtlimited_7.8atm_rep2


title: ICC3996 12 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105175/suppl/GSM105175_ICC3996 12h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105175/suppl/GSM105175_ICC3996 12h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105175/suppl/GSM105175_ICC3996 12h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105175/suppl/GSM105175_ICC3996 12h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105175/suppl/GSM105175_ICC3996 12h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105175/suppl/GSM105175_ICC3996 12h treated(cy5) rep3.TXT.txt.gz


title: ICC3996 06 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105174/suppl/GSM105174_ICC3996 06h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105174/suppl/GSM105174_ICC3996 06h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105174/suppl/GSM105174_ICC3996 06h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105174/suppl/GSM105174_ICC3996 06h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105174/suppl/GSM105174_ICC3996 06h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105174/suppl/GSM105174_ICC3996 06h treated(cy5) rep3.TXT.txt.gz


title: FLIP94-508C 72 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105173/suppl/GSM105173_FLIP94-508C 72h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105173/suppl/GSM105173_FLIP94-508C 72h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105173/suppl/GSM105173_FLIP94-508C 72h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105173/suppl/GSM105173_FLIP94-508C 72h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105173/suppl/GSM105173_FLIP94-508C 72h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105173/suppl/GSM105173_FLIP94-508C 72h treated(cy5) rep3.TXT.txt.gz


title: FLIP94-508C 48 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105172/suppl/GSM105172_FLIP94-508C 48h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105172/suppl/GSM105172_FLIP94-508C 48h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105172/suppl/GSM105172_FLIP94-508C 48h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105172/suppl/GSM105172_FLIP94-508C 48h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105172/suppl/GSM105172_FLIP94-508C 48h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105172/suppl/GSM105172_FLIP94-508C 48h treated(cy5) rep3.TXT.txt.gz


title: FLIP94-508C 24 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105171/suppl/GSM105171_FLIP94-508C 24h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105171/suppl/GSM105171_FLIP94-508C 24h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105171/suppl/GSM105171_FLIP94-508C 24h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105171/suppl/GSM105171_FLIP94-508C 24h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105171/suppl/GSM105171_FLIP94-508C 24h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105171/suppl/GSM105171_FLIP94-508C 24h treated(cy5) rep3.TXT.txt.gz


title: FLIP94-508C 06 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105169/suppl/GSM105169_FLIP94-508C 06h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105169/suppl/GSM105169_FLIP94-508C 06h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105169/suppl/GSM105169_FLIP94-508C 06h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105169/suppl/GSM105169_FLIP94-508C 06h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105169/suppl/GSM105169_FLIP94-508C 06h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105169/suppl/GSM105169_FLIP94-508C 06h treated(cy5) rep3.TXT.txt.gz

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. In press.


title: oral_squamous_cell_carcinoma_78_A

city: Zagreb

first: Maja

last: Herak Bosnar

address: Bijenicka 54

department: Div. Molecular Medicine

country: Croatia

institute: Rudjer Boskovic Institute

description:
Amount: 15µg fragmented cRNA
Amplification: cDNA (superscript II, Invitrogen), cRNA (ENZO, one cycle)

hyb_protocol: 1. Hybridization: 16 hours at 45°C and 60rpm, Affymetrix GeneChip Hybridization Oven 640, Affymetrix Fluidics Station 400 2. Washing and Staining: Post Hyb Wash #1: 10 cycles of of 2 mixes/cycle with Wash Buffer A at 25°C Post Hyb Wash #2:4 cycles of 15 mixes/cycle with Wash Buffer B at 50°C Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C Post Stain Wash:10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C 2nd Stain:Stain the probe array for 10 minutes in antibody solution at 25°C 3rd Stain:Stain the probe array for 10 minutes in SAPE solution at 25°C Final Wash:15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The holding temperature is 25°C 3. Buffers: Hybridization Buffer:100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20 Wash Buffer A: Nonstringent 6x SSPE, 0.01% Tween 20 Wash Buffer B: Stringent 100 mM MES, 0.1 M [Na+], 0.01% Tween 20 Stain Buffer:100 mM MES, 1 M [Na+], 0.05% Tween 20 SAPE Solution:100 mM MES, 1 M [Na+], 0.05% Tween 20, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin Antibody Solution:100 mM MES, 1 M [Na+], 0.05% Tween 20, 2 mg/ml acetylated BSA, 0.1 mg/ml Normal Goat IgG, 3 μg/ml biotinylated Anti-Streptavidin

scan_protocol: Pixel Size: 3µm Filters: 570nm Number of Scans: 2 Agilent GeneArray Scanner Affymetrix Microarray Suite 5.0

label: Biotinylated Oligonucleotides

source_name: oral squamous cell carcinoma

growth_protocol: The cells were cultured in Dulbecco's modified Eagle medium (DMEM, Life Technologies) supplemented with 10% fetal bovine serum (FBS, LifeTechnologies), XXX g/mL streptomycin in humidifiedm2 mM glutamine, 100 U/mL penicillin and 100 XXX chamber with 5% CO2, at 37C

extract_protocol:
* TRIzol Reagent (Life Technologies)
* RNeasy mini spin columns followed by on-column DNase digestion (Qiagen) according to manufacturer’s instructions

treatment_protocol: CAL 27 cells stable transfected with empty vector only (overexpressing GFP)

tag: Strain/Line

value: CAL 27 cells, empty vector transfected cells

tag: Cell line

value: oral squamous cell carcinoma

tag: Cell type

value: CAL 27 cells

tag: Disease state

value: poorly differentiated, G3 cells


title: ILWC245 72 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105183/suppl/GSM105183_ILWC245 72h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105183/suppl/GSM105183_ILWC245 72h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105183/suppl/GSM105183_ILWC245 72h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105183/suppl/GSM105183_ILWC245 72h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105183/suppl/GSM105183_ILWC245 72h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105183/suppl/GSM105183_ILWC245 72h treated(cy5) rep3.TXT.txt.gz


title: oral_squamous_cell_carcinoma_49_A

growth_protocol: The experiments were conducted on human cell line CAL 27 (poorly differentiated, G3, squamous cell carcinoma of the tongue), obtained by courtesy of Dr. Jeannine Gioanni, Centre Antoine Lacassagne, Nice France). The cells were cultured in Dulbecco’s modified Eagle medium (DMEM, Life Technologies) supplemented with 10% fetal bovine serum (FBS, LifeTechnologies), 2 mM glutamine, 100 U/mL penicillin and 100 ug/mL streptomycin in humidified chamber with 5% CO2, at 37oC.

treatment_protocol: CAL 27 cells stable transfected with pEGFP-nm23-H1 (overexpressing GFP-Nm23-H1)

value: CAL 27 cells,nm23-H1 transfected


title: TLR5KO LPC unstim

city: Suita

first: Satoshi

last: Uematsu

state: Osaka

address: 3-1, Yamada-oka

department: Host Defense

country: Japan

institute: Research Institue for Micrbial Diseases Osaka University

description: TLR5KO; CD11c+ LPC unstim.

data_processing: MAS5.0, scaled to 500

label: PE

source_name: TLR5KO CD11c+ lamina propria cells

tag: Strain

tag: Cell

value: CD11c+ lamina propria cells


title: FLIP94-508C 12 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105170/suppl/GSM105170_FLIP94-508C 12h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105170/suppl/GSM105170_FLIP94-508C 12h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105170/suppl/GSM105170_FLIP94-508C 12h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105170/suppl/GSM105170_FLIP94-508C 12h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105170/suppl/GSM105170_FLIP94-508C 12h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105170/suppl/GSM105170_FLIP94-508C 12h treated(cy5) rep3.TXT.txt.gz


title: wild LPC 4 h

description: wild-type; CD11c+ LPC flagellin 4 h stim.

source_name: CD11c+ lamina propria cells


title: ILWC245 48 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105182/suppl/GSM105182_ILWC245 48h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105182/suppl/GSM105182_ILWC245 48h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105182/suppl/GSM105182_ILWC245 48h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105182/suppl/GSM105182_ILWC245 48h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105182/suppl/GSM105182_ILWC245 48h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105182/suppl/GSM105182_ILWC245 48h treated(cy5) rep3.TXT.txt.gz


title: TLR5KO LPC 4 h

description: TLR5KO; CD11c+ LPC flagellin 4 h stim.


title: wild CD11c+ LPC unstim

description: wild-type; CD11c+ LPC unstim.

source_name: CD11c+ LPC


title: Wild_IEC_unstim

description: wild-type IEC unstim.

source_name: IEC

value: intestinal epithelial cells


title: TLR5KO IEC 4 h

description: TLR5KO IEC 4 h


title: Wild IECs 4h

description: wild-type 4 h stim.


title: TLR5KO IEC unstim

description: TLR5KO IEC unstim.


title: e18-10

city: Amsterdam

first: Jildau

last: Bouwman

address: de Boelelaan 1085

department: Functional genomics

country: Netherlands

institute: CNCR, Vrije Universiteit

description: Comparison of RNA levels in the neocortex of normal mice versus synaptically silent munc18-1 null mutants.

data_processing: Log2 transformed and Normalized to total background

tag: Background:C57BL/6, Embryonic day

value: 18, Mutant:munc18-1 null mutant, brain region:neocortex

source_name: wt, e18

value: 18, brain region:neocortex


title: Mjannaschii_500atm_rep3


title: Arctic ground squirrel brown adipose tissue at late torpor (LT) animal rep4 on 1A array

description: Gene expression data from arctic ground squirrel brown adipose tissue at late torpor during hibernation

source_name: Arctic ground squirrel brown adipose tissue at late torpor (80-90% of torpid episode) during hibernation

tag: late torpor brown adipose tissue


title: e18-8


title: e18-9


title: e18-7


title: e18-5


title: e18-2


title: e18-1

value: 14, brain region:neocortex


title: e18-6


title: e18-4


title: e18-3


title: e16-4

source_name: wt, e16

value: 16, brain region:neocortex

value: 16, Mutant:munc18-1 null mutant, brain region:neocortex


title: e16-2


title: e16-1


title: e14-6

source_name: wt, e14

value: 14, Mutant:munc18-1 null mutant, brain region:neocortex


title: e14-5


title: e18-11


title: e14-3


title: e14-2


title: e14-1

data_processing: Log2 transformed and Normalized to total background,


title: Lasseter 72 hpi

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105188/suppl/GSM105188_Lasseter 72h control(cy3) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105188/suppl/GSM105188_Lasseter 72h control(cy3) rep3.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105188/suppl/GSM105188_Lasseter 72h control(cy5) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105188/suppl/GSM105188_Lasseter 72h treated(cy3) rep2.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105188/suppl/GSM105188_Lasseter 72h treated(cy5) rep1.TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105188/suppl/GSM105188_Lasseter 72h treated(cy5) rep3.TXT.txt.gz


title: N2

status: Public on Jul 28 2006

type: genomic

city: Tel-Aviv

first: Anat

last: Bar-Shira

address: 6 Weizmann St.

department: Genetic Institute

country: Israel

institute: Tel-Aviv Sourasky Medical Center

description: Total spots: 853, Mean CV: 1%, CorrC: 0.98, Ratio normalizer: 1.01, Modal mean: 1.01, SD: 0.06

hyb_protocol: Equal aliquots of labeled test and reference DNA were combined in a tube with hybridization buffer, were denatured at 80°C for 10 min, and were incubated for 1 h at 37°C to allow blocking of repetitive sequences. The solutions were then hybridized for 72 h at 37°C with a GenoSensor Array 300. This array contains 287 genomic clones, including those for each human telomere, as well as all of the known microdeletion syndromes and additional selected loci representing each chromosome arm. The GenoSensor CGH Array 300 clone list is available at http://www.vysis.com/PDF/GenoSensor300ClonesAndKey_July2004.pdf. After hybridization, the arrays were washed in 50% formamide/2ª SSC at 40°C and 1ª SSC at 25°C, and were counter-stained with 4`,6-diamidino-2-phenylindole (DAPI). Hybridization signal images in three colors, Cy3, Cy5 and DAPI blue were then analyzed by the GenoSensor reader system based on DAPI staining that identified target spots and their location on the grid.

data_processing: By analyzing the set of Cy3/Cy5 ratios (test-to-reference ratios) on all targets, the GenoSensor Array 300 Reader Software (version 1) calculates the ratio most representative of the modal DNA copy number of the sample DNA. For each target the normalized ratio, relative to the modal DNA copy number is calculated. This normalized ratio of the target indicates the degree of gain or loss of copy number, and for each clone the copy number changes are presented and a P value is calculated.

molecule: genomic DNA

source_name: Peripheral blood leukocytes

label_protocol: 100 ng of each test DNA and normal reference DNA (from an individual of the opposite sex of the test sample) was labeled by Random Priming Kit (Abbott Vysis) to incorporate Cy3 or Cy5 fluorophores (Perkin-Elmer, Boston, MA). DNA was denatured at 100°C for 10 min and was cooled to 4°C before the addition of Klenow fragments and nucleotide mix. After incubation at 37°C for 2 h, the samples were digested using a 1: 20 DNAse dilution for 1 h at 15°C. Unincorporated nucleotides were then removed using Sephadex G-50 spin columns (Amersham-Biosciences). Probes were precipitated with ethanol and resuspended in 10 mM Tris, pH 8.0.

extract_protocol: High-molecular weight genomic DNA was extracted from patient’s peripheral blood leukocytes using the PureGene DNA Isolation Kit (Gentra Systems, Minneapolis, MN, USA).

tag: Gender

value: female, normal control

value: female, normal reference DNA (commercial genomic DNA)


title: N1

description: Total spots: 847, Mean CV: 1%, CorrC: 0.98, Ratio normalizer: 0.82, Modal mean: 1, SD: 0.04

scan_protocol: GenoSensor Array 300 Reader Software (version 1)


title: Case7

description: Total spots: 856, Mean CV: 2%, CorrC: 0.97, Ratio normalizer: 0.88, Modal mean: 1, SD: 0.05

value: female Age:4 years

value: male, normal reference DNA (commercial genomic DNA)


title: Case8

description: Total spots: 849, Mean CV: 2%, CorrC: 0.98, Ratio normalizer: 0.85, Modal mean: 1, SD: 0.06

value: male Age:8 months


title: Case4

description: Total spots: 844, Mean CV: 2%, CorrC: 0.97, Ratio normalizer: 0.28, Modal mean: 1, SD: 0.06

value: male Age:newborn


title: N3

description: Total spots: 855, Mean CV: 1%, CorrC: 0.98, Ratio normalizer: 1.1, Modal mean: 1, SD: 0.05

value: male, normal control


title: Case2

description: Total spots: 858, Mean CV: 2%, CorrC: 0.99, Ratio normalizer: 0.77, Modal mean: 1.01, SD: 0.05

value: female Age:newborn


title: Case3

description: Total spots: 850, Mean CV: 1%, CorrC: 0.99, Ratio normalizer: 1.3, Modal mean: 1, SD: 0.06


title: N4

description: Total spots: 812, Mean CV: 2%, CorrC: 0.98, Ratio normalizer: 1.01, Modal mean: 1.01, SD: 0.06


title: Case6

description: Total spots: 859, Mean CV: 2%, CorrC: 0.98, Ratio normalizer: 1.1, Modal mean: 1, SD: 0.07

value: male Age:3 years


title: Case1

description: Total spots: 852, Mean CV: 3%, CorrC: 0.97, Ratio normalizer: 0.81, Modal mean: 1, SD: 0.07

value: female Age:15 years


title: MDS54

status: Public on Jul 01 2006

city: Oxford

first: Andrea

last: Pellagatti

address: John Radcliffe Hospital

department: NDCLS, RDM

institute: University of Oxford

description: Gene expression data from CD34+ cells isolated from bone marrow

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000

data_processing: Affymetrix CEL files were used for Robust MultiChip Analysis (RMA)

source_name: CD34+ cells isolated from the bone marrow of an MDs patient

label_protocol: Biotinylated cRNA were prepared according to the Two-cycle Affymetrix protocol from 50 nanograms total RNA

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

tag: Subtype

value: RARS

tag: Karyotype

value: normal


title: MDS55

source_name: CD34+ cells isolated from the bone marrow of an MDS patient

value: RA

value: other


title: e14-4

value: 14, brain region:neocortex


title: MDS52


title: MDS53


title: MDS49


title: MDS51


title: MDS48

hyb_protocol: Following fragmentation. 10 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450


title: MDS47


title: MDS46


title: MDS44


title: Case5

description: Total spots: 844, Mean CV: 2%, CorrC: 0.98, Ratio normalizer: 1.04, Modal mean: 1, SD: 0.08

value: male Age:8 years


title: MDS43


title: MDS39


title: MDS41


title: N9

source_name: CD34+ cells isolated from the bone marrow of a normal control


title: MDS40


title: MDS37


title: N11


title: MDS45


title: MDS50


title: e16-3

value: 16, brain region:neocortex

value: 16, Mutant:munc18-1 null mutant, brain region:neocortex


title: MDS38


title: MDS33


title: MDS32


title: MDS34


title: MDS42


title: MDS31


title: MDS28


title: MDS27


title: MDS30


title: MDS26


title: Mjannaschii_500atm_rep1

description: Effect of gas substrate limitation on barophilic growth at 500 atm.

source_name: Methanocaldococcus jannaschii, 500 atm, 200 ml medium

tag: Methanocaldococcus jannaschii (DSM 2661) pressure

value: 500 atm

tag: temperature

tag: volume

value: 200 ml medium

value: 7.8 atm


title: MDS23

hyb_protocol: Following fragmentation 10 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450


title: MDS36


title: MDS25


title: N7


title: MDS22


title: MDS20


title: MDS21


title: N8


title: MDS19


title: MDS29


title: MDS18


title: N4


title: N5


title: N6


title: MDS16


title: MDS17


title: MDS15


title: MDS14


title: MDS12


title: MDS11


title: MDS13


title: MDS10


title: MDS9


title: MDS6


title: MDS7


title: MDS8


title: MDS5


title: MDS4


title: MDS3


title: MDS1


title: MDS2


title: N2


title: N3


title: N1