title: Rosuvastatin 24h donor 269 [Steroltalk]

description: Human liver cells treated with rosuvastatin for 24h, donor d269.


title: control sample 41

status: Public on Sep 05 2011

type: RNA

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

description: control

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: summarizing of technical replica by median and quantile normalization.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: RNA from blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of patients and volunteers without known disease was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). For each blood donor, 5 ml of peripheral blood were obtained. The content of blood sampling tubes of each patient and healthy donor was centrifuged at 5000 g for 10 min at room temperature. The supernatant was discarded while the pellet was resuspended in 10 ml RNase free water by vortex. The suspension is again centrifuged at 5000 g for 10 min at RT. Subsequently, the total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden). Therefore the pellet was resuspended in 700 μl QIAzol lysis reagent and incubated for 5 min at RT. Then, 140 μl chloroform were added, vortexed for 15 sec, and incubated for 2-3 min at RT. This was followed by a centrifugation at 14000 rpm and 4°C for 15 min. The upper, watery phase was removed and 1,5 times of its volume added in 100% ethanol (ca. 900 μl). Each 700 μl of this mixture were placed on a column and centrifuged at 13000 rpm at RT for 15 sec. After the mixture had completely passed the column, 700 μl of Buffer RWT were added to each column, and again centrifuged at 13000 rpm at RT for 15 sec. Following this, 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 15 sec. After this, another 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 2 min. The column was then centrifuged at 13000 rpm and RT for 1 min to dry it. The following was the elution step with 40 μl RNase free water, centrifuging at 13000 rpm at RT for 1 min. The eluted RNA was stored at -70°C.

treatment_protocol: stored at -20 degree

tag: disease state

value: control

tag: tissue

value: blood


title: control sample 40

description: control


title: Rosuvastatin 24h donor 129 [Steroltalk]

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: Human liver cells treated with rosuvastatin for 24h, donor d129.

hyb_protocol: Channel 1 sample was mixed with channel 2 sample hybridization buffer was added (final concentration was 3xSSC, 0.2% SDS) and samples were denatured. Using LifterSlip cover glasses (Erie Scientific Company, Portsmouth, NH, USA) samples were hybridized for 16h at 65ºC in a water bath using humidified hybridization chambers (HybChambers, GeneMachines, San Carlos, CA, USA). Prior hybridizations Steroltalk v2 slides were pre-hybridized for 1 hour at 42ºC in 5xSSC, 0.1%SDS and 1%BSA, then washed at room temperature for 5 min in 2xSSC and 0.1%SDS, 3 min in 0.2xSSC and 2 min in MilliQ water and dried by centrifugation. After hybridization slides were washed at room temperature for 5 min in 2xSSC and 0.5%SDS, 5 min in 0.5xSSC, 5 min in 0.05xSSC, and then dried using vacuum centrifuge.

scan_protocol: Arrays scanned on an Tecan LS200 scanner; images analyzed using MediaCybernetics Array-Pro Analyzer software.

data_processing:
Raw data deposited to BASE (BioArray Software Environment). Normalization is achieved through expression of selected spike-in controls using OWNormalize widget from Orange (a component based machine learning library for Python developed at Laboratory of Artificial Intelligence, Faculty of Computer and Information Science, University of Ljubljana, Slovenia).
Since Steroltalk arrays are small-scale, containing about 300 genes which were selected from specific pathways, it is expected that their median expression varies across the experimental conditions.

source_name: Cells treated with rosuvastatin for 24h

label_protocol: To 20 μg of sample total RNA we added spike in RNA: 250 pg of Firefly Luciferase mRNA (Promega, Madison, WI, USA), and 0.5 μL of test spike mix from Lucidea Universal ScoreCard kit. We reverse-transcribed mRNA to amino-allyl cDNA using 2.5 μg of Oligo dT (Invitrogen, Carlsbad, CA, USA), 400U of SuperScriptTM III Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and 1μL of 10mM amino-allyl dUTP (Sigma, St Louis, MI, USA) according to the manufacturer’s protocol. Reaction was stopped after 2 hours by adding 10 μL of 0.5 M EDTA and of 1M NaOH and incubation at 65ºC for 15 min. 10 μL of 1 M HCl was added and cDNA was purified using MinElute PCR Purification Kit (Qiagen GmBH, Hilden, D) according to manufacturer’s protocol with exception of using a phosphate buffer (5mM KPO4 pH 8.5 in 80% ethanol) for washing step and MilliQ water for elution. Purified amino-allyl cDNA was dried and resuspended in 4.5 μL of 0.2 M Na2CO3 (pH 9.0) and 4.5 μL of cyanin dye in DMSO (Amersham Biosciences, GE Healthcare UK limited, Little Chalfont, UK). Labeling reaction was incubated at room temperature for two hours. Next we added 35 μL of 0.1 M Na acetate (pH 5.2) and purified reaction using MinElute PCR Purification Kit (Qiagen GmBH, Hilden, D) according to manufacturer’s protocol. Labeled cDNA was eluted in water and 1 μL was used for analyses using ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, Delaware, USA).

growth_protocol: Human livers from donors 089, 114, 129, 269, 270, 271 and 272 were obtained from kidney transplant donors or  from lobectomy segments resected from adult patients. Liver cells were isolated by the method of Bayliss and Skett (1996). Hepatocytes having viability better than 90% as determined by trypan blue exclusion, were used in the experiments. The cells were plated at a density of 1.7x105 cells/cm2 in plastic dishes precoated with collagen in medium described by Ferrini et al. (1998).

extract_protocol: Total RNA was isolated from human hepatocytes using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. The RNA was precipitated using ethanol.

treatment_protocol: After overnight culture, the medium was replaced by serum-free medium. Forty-eight hours after serum deprivation, cells were cultured in the presence or absence of inducers for 12, 24 or 48 hours. Hepatocytes were treated with rifampicin (5 µM), atorvastatin (10 µM) or rosuvastatin (10 µM).

value: Liver

tag: cell type

value: hepatocyte

tag: agent

value: Rosuvastatin

tag: time

tag: donor

source_name: Mix of untreated cells from all donors and other human liver RNA samples [reference]

value: Untreated


title: Rosuvastatin 24h donor 114 [Steroltalk]

description: Human liver cells treated with rosuvastatin for 24h, donor d114.


title: multiple sclerosis sample 39

description: multiple sclerosis

value: multiple sclerosis


title: multiple sclerosis sample 38

description: multiple sclerosis


title: Rosuvastatin 12h donor 272 [Steroltalk]

description: Human liver cells treated with rosuvastatin for 12h, donor d272.

source_name: Cells treated with rosuvastatin for 12h


title: multiple sclerosis sample 37

description: multiple sclerosis


title: Untreated donor 270 [Affy]

description: Gene expression data from untreated human liver cells, donor 270.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GHuman Genome U133 Plus 2.0 GeneChip Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner GCS 3000 7G .

data_processing: Data were normalized using GCRMA algorithm from R/Bioconductor package.

source_name: Untreated cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human livers from donors 089, 114, 129, 269, 270 and 271 were obtained from kidney transplant donors or  from lobectomy segments resected from adult patients. Liver cells were isolated by the method of Bayliss and Skett (1996). Hepatocytes having viability better than 90% as determined by trypan blue exclusion, were used in the experiments. The cells were plated at a density of 1.7x105 cells/cm2 in plastic dishes precoated with collagen in medium described by Ferrini et al. (1998).


title: multiple sclerosis sample 36

description: multiple sclerosis


title: multiple sclerosis sample 35

description: multiple sclerosis


title: Untreated donor 114 [Affy]

description: Gene expression data from untreated human liver cells, donor 114.


title: Untreated donor 269 [Affy]

description: Gene expression data from untreated human liver cells, donor 269.


title: Untreated donor 271 [Affy]

description: Gene expression data from untreated human liver cells, donor 271.


title: Untreated donor 089 [Affy]

description: Gene expression data from untreated human liver cells, donor 089.


title: Rosuvastatin 12h donor 271 [Steroltalk]

description: Human liver cells treated with rosuvastatin for 12h, donor d271.


title: Rosuvastatin 48h donor 269 [Affy]

description: Gene expression data from human liver cells treated with rosuvastatin for 48h, donor 269.

source_name: Cells treated with rosuvastatin for 48h


title: Rosuvastatin 48h donor 271 [Affy]

description: Gene expression data from human liver cells treated with rosuvastatin for 48h, donor 271.


title: Rosuvastatin 24h donor 114 [Affy]

description: Gene expression data from human liver cells treated with rosuvastatin for 24h, donor 114.


title: Rosuvastatin 24h donor 271 [Affy]

description: Gene expression data from human liver cells treated with rosuvastatin for 24h, donor 271.


title: Rosuvastatin 48h donor 114 [Affy]

description: Gene expression data from human liver cells treated with rosuvastatin for 48h, donor 114.


title: Rosuvastatin 24h donor 269 [Affy]

description: Gene expression data from human liver cells treated with rosuvastatin for 24h, donor 269.


title: Untreated donor 129 [Affy]

description: Gene expression data from untreated human liver cells, donor 129.


title: Rosuvastatin 24h donor 089 [Steroltalk]

description: Human liver cells treated with rosuvastatin for 24h, donor d089.


title: Rosuvastatin 48h donor 270 [Affy]

description: Gene expression data from human liver cells treated with rosuvastatin for 48h, donor 270.


title: Rosuvastatin 24h donor 129 [Affy]

description: Gene expression data from human liver cells treated with rosuvastatin for 24h, donor 129.


title: Rosuvastatin 24h donor 089 [Affy]

description: Gene expression data from human liver cells treated with rosuvastatin for 24h, donor 089.


title: Rosuvastatin 24h donor 270 [Affy]

description: Gene expression data from human liver cells treated with rosuvastatin for 24h, donor 270.


title: Rosuvastatin 12h donor 089 [Steroltalk]

description: Human liver cells treated with rosuvastatin for 12h, donor d089.


title: Rifampicin 48h donor 270 [Affy]

description: Gene expression data from human liver cells treated with rifampicin for 48h, donor 270.

source_name: Cells treated with rifampicin for 48h

value: Rifampicin


title: Rifampicin 48h donor 272 [Steroltalk]

description: Human liver cells treated with rifampicin for 48h, donor d272.

value: Rifmapicin


title: multiple sclerosis sample 34

description: multiple sclerosis


title: Rifampicin 48h donor 271 [Steroltalk]

description: Human liver cells treated with rifampicin for 48h, donor d271.


title: Rosuvastatin 12h donor 270 [Steroltalk]

description: Human liver cells treated with rosuvastatin for 12h, donor d270.


title: multiple sclerosis sample 32

description: multiple sclerosis


title: Rifampicin 48h donor 114 [Affy]

description: Gene expression data from human liver cells treated with rifampicin for 48h, donor 114.


title: multiple sclerosis sample 31

description: multiple sclerosis


title: Rifampicin 48h donor 269 [Steroltalk]

description: Human liver cells treated with rifampicin for 48h, donor d269.


title: multiple sclerosis sample 33

description: multiple sclerosis


title: Rifampicin 48h donor 271 [Affy]

description: Gene expression data from human liver cells treated with rifampicin for 48h, donor 271.


title: multiple sclerosis sample 29

description: multiple sclerosis


title: Rifampicin 48h donor 129 [Steroltalk]

description: Human liver cells treated with rifampicin for 48h, donor d129.


title: Rifampicin 48h donor 129 [Affy]

description: Gene expression data from human liver cells treated with rifampicin for 48h, donor 129.


title: Rifampicin 24h donor 270 [Affy]

description: Gene expression data from human liver cells treated with rifampicin for 24h, donor 270.

source_name: Cells treated with rifampicin for 24h


title: multiple sclerosis sample 27

description: multiple sclerosis


title: Rifampicin 24h donor 271 [Affy]

description: Gene expression data from human liver cells treated with rifampicin for 24h, donor 271.


title: Rifampicin 24h donor 114 [Affy]

description: Gene expression data from human liver cells treated with rifampicin for 24h, donor 114.


title: Rifampicin 24h donor 129 [Affy]

description: Gene expression data from human liver cells treated with rifampicin for 24h, donor 129.


title: Rifampicin 24h donor 089 [Affy]

description: Gene expression data from human liver cells treated with rifampicin for 24h, donor 089.


title: Rifampicin 48h donor 270 [Steroltalk]

description: Human liver cells treated with rifampicin for 48h, donor d270.


title: Atorvastatin 48h donor 270 [Affy]

description: Gene expression data from human liver cells treated with atorvastatin for 48h, donor 270.

source_name: Cells treated with atorvastatin for 48h

value: Atorvastatin


title: multiple sclerosis sample 26

description: multiple sclerosis


title: multiple sclerosis sample 28

description: multiple sclerosis


title: Rifampicin 48h donor 089 [Steroltalk]

description: Human liver cells treated with rifampicin for 48h, donor d089.


title: Rifampicin 24h donor 272 [Steroltalk]

description: Human liver cells treated with rifampicin for 24h, donor d272.


title: Atorvastatin 48h donor 269 [Affy]

description: Gene expression data from human liver cells treated with atorvastatin for 48h, donor 269.


title: Rifampicin 24h donor 269 [Affy]

description: Gene expression data from human liver cells treated with rifampicin for 24h, donor 269.


title: Atorvastatin 48h donor 271 [Affy]

description: Gene expression data from human liver cells treated with atorvastatin for 48h, donor 271.


title: Rifampicin 24h donor 271 [Steroltalk]

description: Human liver cells treated with rifampicin for 24h, donor d271.


title: Rifampicin 48h donor 114 [Steroltalk]

description: Human liver cells treated with rifampicin for 48h, donor d114.


title: Rifampicin 48h donor 269 [Affy]

description: Gene expression data from human liver cells treated with rifampicin for 48h, donor 269.


title: multiple sclerosis sample 24

description: multiple sclerosis


title: Rifampicin 48h donor 089 [Affy]

description: Gene expression data from human liver cells treated with rifampicin for 48h, donor 089.


title: Atorvastatin 48h donor 129 [Affy]

description: Gene expression data from human liver cells treated with atorvastatin for 48h, donor 129.


title: Atorvastatin 48h donor 114 [Affy]

description: Gene expression data from human liver cells treated with atorvastatin for 48h, donor 114.


title: Atorvastatin 24h donor 271 [Affy]

description: Gene expression data from human liver cells treated with atorvastatin for 24h, donor 271.

source_name: Cells treated with atorvastatin for 24h


title: Atorvastatin 24h donor 270 [Affy]

description: Gene expression data from human liver cells treated with atorvastatin for 24h, donor 270.


title: multiple sclerosis sample 25

description: multiple sclerosis


title: multiple sclerosis sample 23

description: multiple sclerosis


title: Rifampicin 24h donor 269 [Steroltalk]

description: Human liver cells treated with rifampicin for 24h, donor d269.


title: Atorvastatin 24h donor 129 [Affy]

description: Gene expression data from human liver cells treated with atorvastatin for 24h, donor 129.


title: multiple sclerosis sample 22

description: multiple sclerosis


title: multiple sclerosis sample 21

description: multiple sclerosis


title: Atorvastatin 24h donor 269 [Affy]

description: Gene expression data from human liver cells treated with atorvastatin for 24h, donor 269.


title: Atorvastatin 24h donor 114 [Affy]

description: Gene expression data from human liver cells treated with atorvastatin for 24h, donor 114.


title: Atorvastatin 48h donor 089 [Affy]

description: Gene expression data from human liver cells treated with atorvastatin for 48h, donor 089.


title: multiple sclerosis sample 20

description: multiple sclerosis


title: Atorvastatin 24h donor 089 [Affy]

description: Gene expression data from human liver cells treated with atorvastatin for 24h, donor 089.


title: Rifampicin 24h donor 129 [Steroltalk]

description: Human liver cells treated with rifampicin for 24h, donor d129.


title: Rifampicin 24h donor 114 [Steroltalk]

description: Human liver cells treated with rifampicin for 24h, donor d114.


title: Rifampicin 24h donor 089 [Steroltalk]

description: Human liver cells treated with rifampicin for 24h, donor d089.


title: Rifampicin 24h donor 270 [Steroltalk]

description: Human liver cells treated with rifampicin for 24h, donor d270.


title: Rifampicin 12h donor 272 [Steroltalk]

description: Human liver cells treated with rifampicin for 12h, donor d272.

source_name: Cells treated with rifampicin for 12h


title: multiple sclerosis sample 19

description: multiple sclerosis


title: control sample 17

description: control


title: Rifampicin 12h donor 270 [Steroltalk]

description: Human liver cells treated with rifampicin for 12h, donor d270.


title: Rifampicin 12h donor 269 [Steroltalk]

description: Human liver cells treated with rifampicin for 12h, donor d269.


title: Rifampicin 12h donor 271 [Steroltalk]

description: Human liver cells treated with rifampicin for 12h, donor d271.


title: control sample 14

description: control


title: lung cancer sample 16

description: lung cancer

value: lung cancer


title: control sample 15

description: control


title: Rosuvastatin 12h donor 269 [Steroltalk]

description: Human liver cells treated with rosuvastatin for 12h, donor d269.


title: Atorvastatin 48h donor 272 [Steroltalk]

description: Human liver cells treated with atorvastatin for 48h, donor d272.


title: Rifampicin 12h donor 089 [Steroltalk]

description: Human liver cells treated with rifampicin for 12h, donor d089.


title: CRC4 Cold-Fixed Replicate B

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: Colorectal Cancer Sample #4, Cold-Fixed

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were summarized with the Illumina GenomeStudio software, without normalization and without background subtraction. The particular design of the experiment, aimed at technical assessments, requires that data are not normalized.

label: biotin-SA Cy3

source_name: Colorectal Cancer Sample #4

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to the manufacturer’s recommendations

growth_protocol: No growth - the samples are tissue specimens from human cancers

extract_protocol: For each sample, five sections for paraffin blocks (10-µm thick) or ten or more sections (20-µm thick) for frozen ones were serial sectioned and collected in a 1.5 ml sterile Eppendorf tube. RNA isolation from the SF and CF samples was performed using the MasterPure Purification kit (Epicentre, Madison, WI, USA). Sections were deparaffinized by incubations in xylene followed by incubations in 100% ethanol. The ethanol was discarded, and the pellet was air-dried for several minutes at room temperature before Proteinase K treatment. RNA extraction from FF sections was performed with 1 ml of Trizol® reagent (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s instructions.

treatment_protocol: Tumor specimens were under-vacuum sealed in plastic bags using a semi-professional machine (Mod. VAC 10, by Milestone, Bergamo, Italy; see http://www.milestonemedsrl.com) inside the surgical theatre immediately after surgery, and kept at 4°C until transfer to the pathology laboratory. Once in the pathology lab the surgical specimens were processed without delay. From each specimen, three samples were taken and processed as follows: (a) Standard fixation procedure(SF): the sample (4 mm. thick) was fixed for 24 hours in 4% neutral-buffered formalin (NBF) (Histo-Line Laboratories, Milan, Italy) at room temperature (RT), routinely processed and embedded in paraffin wax. (b) Cold fixation procedure (CF): the sample was immersed in pre-cooled 4% NBF (Histo-Line Laboratories, Milan, Italy) at 4°C for 24 hours. Thereafter, the specimens were transferred in ethanol 95% at 4°C for 4 hours in order to keep nucleases inhibited during the time of ethanol penetration. The already dehydrated tissues were routinely processed to paraffin embedding with an automatic processor (Leica ASP 300, Leica Microsystems, Wetzlar, Germany). (c) Fresh-Freezing procedure (FF): the sample was frozen in liquid nitrogen immediately after dissection and stored at - 80°C.

value: Colorectal Cancer

tag: preservation

value: Cold-Fixed


title: CRC3 Cold-Fixed Replicate B

description: Colorectal Cancer Sample #3, Cold-Fixed

source_name: Colorectal Cancer Sample #3


title: CRC3 Fresh-Frozen

description: Colorectal Cancer Sample #3, Fresh-Frozen

value: Fresh-Frozen


title: CRC4 Fresh-Frozen

description: Colorectal Cancer Sample #4, Fresh-Frozen


title: CRC4 Cold-Fixed Replicate A

description: Colorectal Cancer Sample #4, Cold-Fixed


title: control sample 12

description: control


title: Atorvastatin 48h donor 270 [Steroltalk]

description: Human liver cells treated with atorvastatin for 48h, donor d270.


title: CRC2 Cold-Fixed Replicate A

description: Colorectal Cancer Sample #2, Cold-Fixed

source_name: Colorectal Cancer Sample #2


title: CRC3 Cold-Fixed Replicate A

description: Colorectal Cancer Sample #3, Cold-Fixed


title: control sample 13

description: control


title: Atorvastatin 48h donor 129 [Steroltalk]

description: Human liver cells treated with atorvastatin for 48h, donor d129.


title: Atorvastatin 48h donor 114 [Steroltalk]

description: Human liver cells treated with atorvastatin for 48h, donor d114.


title: control sample 11

description: control


title: control sample 9

description: control


title: control sample 10

description: control


title: CRC1 Fresh-Frozen

description: Colorectal Cancer Sample #1, Fresh-Frozen

source_name: Colorectal Cancer Sample #1


title: multiple sclerosis sample 30

description: multiple sclerosis


title: CRC1 Cold-Fixed Replicate B

description: Colorectal Cancer Sample #1, Cold-Fixed


title: 25Ca2

city: shanghai

first: shu-han

last: sun

address: 800 Xiang-Yin Road

country: China

institute: Second Military Medical University

description: this sample is HCC tissue from a patient with following characteristics: sex, male; age, 56; HBV, HBsAg+++；HBsAb-；HBeAg-；HBeAb-；HBcAb+；HBV-DNA 1.0 ×103;AFP,971.9.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Raw data were extracted as pair files by NimbleScan software (version 2.5). NimbleScan software’s implementation of RMA offers quantile normalization and background correction. The Probe level (*_norm_RMA.pair) files and Gene summary (*_RMA.calls) files were produced. The 10 gene summary files were imported into Agilent GeneSpring Software (version11.0) for further analysis.

source_name: HCC tissues

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step.

value: liver

tag: cancer status

value: ca-caner

tag: Sex

value: male

tag: age

tag: hbv status

value: HBsAg+++; HBsAb-; HBeAg-; HBeAb-; HBcAb+; HBV-DNA 1.0 ×103

tag: alpha-fetoprotein (afp)


title: 35Ca4

description: this sample is HCC tissue from a patient with following characteristics: sex, male age,53; HBV, HBsAg+；HBsAb-；HBeAg-；HBeAb+；HBcAb+；HBV-DNA1.6×103; AFP,876.5

value: HBsAg+; HBsAb-; HBeAg-; HBeAb+; HBcAb+; HBV-DNA1.6×103


title: BrCa4 Fresh-Frozen

description: Breast Cancer Sample #4, Fresh-Frozen

source_name: Breast Cancer Sample #4

value: Breast Cancer


title: Atorvastatin 48h donor 089 [Steroltalk]

description: Human liver cells treated with atorvastatin for 48h, donor d089.

value: Liver

value: hepatocyte


title: control sample 8

description: control

source_name: RNA from blood

value: control

value: blood


title: Gastric Ca Fresh-Frozen

description: Gastric Cancer Sample, Fresh-Frozen

source_name: Gastric Cancer Sample

value: Gastric Cancer


title: BrCa2 Fresh-Frozen

description: Breast Cancer Sample #2, Fresh-Frozen

source_name: Breast Cancer Sample #2


title: CRC2 Cold-Fixed Replicate B

description: Colorectal Cancer Sample #2, Cold-Fixed


title: 28Ca4

description: this sample is HCC tissue from a patient with following characteristics: sex, male age,55; HBV, HBsAg+；HBsAb+；HBeAg+；HBeAb-；HBcAb+, AFP,8.6

value: HBsAg+; HBsAb+; HBeAg+; HBeAb-; HBcAb+


title: 35P2

description: this sample is paired non-tumor tissue from a patient with following characteristics: sex, male age,53; HBV, HBsAg+；HBsAb-；HBeAg-；HBeAb+；HBcAb+；HBV-DNA1.6×103; AFP,876.5

source_name: paired non-tumor samples

value: p-paired non-tumor samples


title: CRC2 Fresh-Frozen

description: Colorectal Cancer Sample #2, Fresh-Frozen


title: Pancreatic Ca Fresh-Frozen

description: Pancreatic Cancer Sample, Fresh-Frozen

source_name: Pancreatic Cancer Sample

value: Pancreatic Cancer


title: Atorvastatin 24h donor 270 [Steroltalk]

description: Human liver cells treated with atorvastatin for 24h, donor d270.

value: Atorvastatin

source_name: Mix of untreated cells from all donors and other human liver RNA samples [reference]

value: Untreated


title: 25P2

description: this sample is paired non-tumor tissue from a patient with following characteristics: sex, male; age, 56; HBV, HBsAg+++；HBsAb-；HBeAg-；HBeAb-；HBcAb+；HBV-DNA 1.0 ×103;AFP,971.9.


title: Atorvastatin 24h donor 272 [Steroltalk]

description: Human liver cells treated with atorvastatin for 24h, donor d272.


title: CRC1 Cold-Fixed Replicate A

description: Colorectal Cancer Sample #1, Cold-Fixed

value: Colorectal Cancer

value: Cold-Fixed


title: BrCa3 Fresh-Frozen

description: Breast Cancer Sample #3, Fresh-Frozen

source_name: Breast Cancer Sample #3

value: Fresh-Frozen


title: Gastric Ca Cold-Fixed

description: Gastric Cancer Sample, Cold-Fixed


title: control sample 5

description: control


title: multiple sclerosis sample 18

description: multiple sclerosis

value: multiple sclerosis


title: control sample 7

description: control


title: lung cancer sample 4

description: lung cancer

value: lung cancer


title: Atorvastatin 24h donor 129 [Steroltalk]

description: Human liver cells treated with atorvastatin for 24h, donor d129.


title: Atorvastatin 24h donor 114 [Steroltalk]

description: Human liver cells treated with atorvastatin for 24h, donor d114.


title: Atorvastatin 24h donor 089 [Steroltalk]

description: Human liver cells treated with atorvastatin for 24h, donor d089.


title: BrCa3 Cold-Fixed

description: Breast Cancer Sample #3, Cold-Fixed


title: BrCa4 Cold-Fixed

description: Breast Cancer Sample #4, Cold-Fixed


title: Atorvastatin 12h donor 272 [Steroltalk]

description: Human liver cells treated with atorvastatin for 12h, donor d272.

source_name: Cells treated with atorvastatin for 12h


title: control sample 6

description: control


title: BrCa2 Cold-Fixed

description: Breast Cancer Sample #2, Cold-Fixed


title: BrCa1 Cold-Fixed

description: Breast Cancer Sample #1, Cold-Fixed

source_name: Breast Cancer Sample #1


title: Atorvastatin 12h donor 089 [Steroltalk]

description: Human liver cells treated with atorvastatin for 12h, donor d089.


title: 24P3

description: this sample is paired non-tumor tissue from a patient with following characteristics: sex, male; age, 52; HBV, HBsAg+++；HBsAb-；HBeAg-；HBeAb+；HBcAb+；HBV-DNA1.0 ×103; AFP, 1210.0

value: liver

value: male

value: HBsAg+++; HBsAb-; HBeAg-; HBeAb+; HBcAb+; HBV-DNA1.0 ×103


title: BrCa1 Fresh-Frozen

description: Breast Cancer Sample #1, Fresh-Frozen

value: Breast Cancer


title: Atorvastatin 12h donor 270 [Steroltalk]

description: Human liver cells treated with atorvastatin for 12h, donor d270.

value: Liver

value: hepatocyte


title: BRCa Cold-Fixed

description: Breast Cancer Sample a, Cold-Fixed

source_name: Breast Cancer Sample a


title: lung cancer sample 2

description: lung cancer

value: blood


title: lung cancer sample 3

description: lung cancer


title: 073126Ca

description: this sample is HCC tissue from a patient with following characteristics: sex, male; age, 50; HBV, HBsAg+++；HBsAb-；HBeAg-；HBeAb+；HBcAb+；HBV-DNA; AFP, ﹤103 142.7

value: ca-caner

value: HBsAg+++; HBsAb-; HBeAg-; HBeAb+; HBcAb+; HBV-DNA<103


title: 24Ca3

description: this sample is HCC tissue from a patient with following characteristics: sex, male; age, 52; HBV, HBsAg+++；HBsAb-；HBeAg-；HBeAb+；HBcAb+；HBV-DNA1.0 ×103; AFP, 1210.0


title: BRCa Fresh-Frozen

description: Breast Cancer Sample a, Fresh-Frozen


title: BRCa Standard Fixed

description: Breast Cancer Sample a, Formalin-fixed at room temperature

value: Formalin-fixed at room temperature


title: Pancreatic Ca Cold-Fixed

description: Pancreatic Cancer Sample, Cold-Fixed

value: Pancreatic Cancer


title: 073126P

description: this sample is  paired non-tumor tissue from a patient with following characteristics: sex, male; age, 50; HBV, HBsAg+++；HBsAb-；HBeAg-；HBeAb+；HBcAb+；HBV-DNA; AFP, ﹤103 142.7

value: p-paired non-tumor samples


title: lung cancer sample 1

description: lung cancer


title: 28P3

description: this sample is paired non-tumor tissue from a patient with following characteristics: sex, male age,55; HBV, HBsAg+；HBsAb+；HBeAg+；HBeAb-；HBcAb+, AFP,8.6

value: HBsAg+; HBsAb+; HBeAg+; HBeAb-; HBcAb+


title: testis gene expression data from Akt1 homozygous mice at postnatal day 15, sample 3

status: Public on Sep 04 2011

city: Providence

first: Mary

last: Hixon

state: RI

address: 70 Ship St

country: USA

institute: Brown University

hyb_protocol: All GeneChip microarrays (Mouse Genome MoGene-1_1-st-v1 Array) were hybridized, washed, stained, and scanned using the Complete Gene Chip Instrument System according to the Affymetrix Technical Manual.

data_processing: RMA in R Bioconductor

organism: Mus musculus

source_name: control testes at postnatal day 15

label_protocol: Equal amounts of purified cDNA per sample were used as the template for subsequent in vitro transcription reactions for complementary RNA (cRNA) amplification and biotin labeling using an Affymetrix RNA Transcript Labeling Kit. cRNA was purified and fragmented according to the protocol provided with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA).

extract_protocol: RNA isolation was performed according to the TriReagent manufacturer’s instructions.

tag: genotype

value: Akt1 homozygous

tag: treatment

value: unexposed

tag: developmental stage

value: postnatal day 15

tag: sample number

value: sample 3

tag: gender

tag: strain


title: testis gene expression data from Akt1 heterozygous mice at postnatal day 15, sample 2

scan_protocol: scanned using the Complete Gene Chip Instrument System according to the Affymetrix Technical Manual.

value: Akt1 heterozygous

value: sample 2


title: testis gene expression data from Akt1 homozygous, PTU-exposed mice at postnatal day 15, sample 1

source_name: PTU-exposed testes at postnatal day 15

value: PTU-exposed

value: sample 1

value: male


title: testis gene expression data from Akt1 heterozygous mice at postnatal day 15, sample 1


title: testis gene expression data from Akt1 wildtype mice at postnatal day 15, sample 1

value: Akt1 wildtype


title: CRCa Fresh-Frozen

description: Colorectal Cancer Sample a, Fresh-Frozen

source_name: Colorectal Cancer Sample a

tag: tissue

value: Colorectal Cancer

value: Fresh-Frozen


title: testis gene expression data from Akt1 homozygous, PTU-exposed mice at postnatal day 15, sample 2


title: testis gene expression data from Akt1 homozygous mice at postnatal day 15, sample 2


title: testis gene expression data from Akt1 wildtype, PTU-exposed mice at postnatal day 15, sample 2


title: CRCa Standard Fixed

description: Colorectal Cancer Sample a, Formalin-fixed at room temperature


title: testis gene expression data from Akt1 homozygous, PTU-exposed mice at postnatal day 15, sample 3


title: testis gene expression data from Akt1 wildtype, PTU-exposed mice at postnatal day 15, sample 3


title: testis gene expression data from Akt1 heterozygous, PTU-exposed mice at postnatal day 15, sample 2


title: testis gene expression data from Akt1 wildtype mice at postnatal day 15, sample 2


title: testis gene expression data from Akt1 heterozygous, PTU-exposed mice at postnatal day 15, sample 1


title: testis gene expression data from Akt1 heterozygous mice at postnatal day 15, sample 3


title: long-lived sib L2008

city: Leiden

first: Willemijn

middle: M

last: Passtoors

state: Zuid-Holland

department: Molecular Epidemiology

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Hybridisation was performed according to the manufacturer’s instructions.

scan_protocol: The slides were scanned with a MicroArray Scanner G2505B scanner (Agilent Technologies) and the image was quantified with CodeLink Expression software (version 4.2).

data_processing: Raw intensities were background subtracted, set on 0.5 when result was negative and normalized with the Cyclic Loess method using the Codelink package in the Bioconductor R software. After normalization, we used log2-transformed expression intensities for all subsequent analyses.

source_name: non-fasted whole blood

label_protocol: cDNA synthesis, amplification and biotin labeling were performed according to the manufacturer’s instructions using the Codelink iExpress reagent kit (cat. No. 67601000).

extract_protocol: Peripheral blood of the 150 non-fasted individuals was harvested using PAXgeneTM tubes (Qiagen). The tubes were frozen and kept at -20°C for ~3-5 years. After thawing at room temperature for at least 2 hours, total RNA was extracted from the approximately 2.5 ml of peripheral blood in each tube following the manufacturer’s recommended protocol (PaxGene Blood RNA Kit Handbook, Qiagen). The quality and integrity of the total RNA was evaluated on the 2100 Bioanalyzer (Agilent Technologies) and the concentration was measured using a NanoDrop spectrophotometer (NanoDrop Technologies). Quality criteria included a 28S/18S ratio as measured by the Bioanalyzer of at least 1.2, and a total RNA yield of at least 3 µg.

tag: group

value: long-lived sib

value: female

value: 92.69 years

tag: family

value: Family 324

tag: hybridization day

value: Day 14


title: long-lived sib L988

value: 97.14 years

value: Family 171


title: testis gene expression data from Akt1 wildtype, PTU-exposed mice at postnatal day 15, sample 1

value: postnatal day 15


title: long-lived sib L62

value: 94.95 years

value: Family 016


title: testis gene expression data from Akt1 homozygous mice at postnatal day 15, sample 1

value: Akt1 homozygous

value: unexposed


title: offspring L211

value: offspring

value: 66.85 years

value: Family 029


title: long-lived sib L376

value: male

value: 91.62 years

value: Family 055


title: testis gene expression data from Akt1 wildtype mice at postnatal day 15, sample 3

value: Akt1 wildtype

value: sample 3


title: control L877

value: control

value: 68.17 years

value: Family 136


title: control L2639

value: 63.92 years

value: Family 414

value: Day 14


title: testis gene expression data from Akt1 heterozygous, PTU-exposed mice at postnatal day 15, sample 3

value: Akt1 heterozygous

value: PTU-exposed

value: postnatal day 15


title: offspring L470

value: offspring

value: 42.79 years

value: Family 056


title: offspring L605

value: male

value: 66.62 years

value: Family 098


title: offspring L916

value: 48.6 years

value: Family 146

value: Day 13


title: offspring L1915

value: 66.29 years

value: Family 311


title: long-lived sib L1136

value: long-lived sib

value: 96.16 years

value: Family 181


title: control L1654

value: control

value: female

value: 56.53 years

value: Family 264


title: offspring L2009

value: offspring

value: 66.12 years

value: Family 324


title: offspring L676

value: male

value: 62.86 years

value: Family 129


title: offspring L1862

value: 59.25 years

value: Family 301

value: Day 12


title: long-lived sib L913

value: 91.26 years

value: Family 146


title: control L469

value: 43.71 years

value: Family 056

value: Day 14


title: long-lived sib L49

value: long-lived sib

value: 94.03 years

value: Family 013


title: long-lived sib L509

value: 89.27 years

value: Family 072


title: long-lived sib L628

value: 89.91 years

value: Family 092


title: offspring L630

value: offspring

value: male

value: 51.48 years

value: Day 13


title: long-lived sib L602

value: female

value: 95.3 years

value: Family 098


title: control L340

value: control

value: 60.84 years

value: Family 049

value: Day 11


title: offspring L337

value: 64.32 years


title: CRCa Cold-Fixed

description: Colorectal Cancer Sample a, Cold-Fixed

value: Colorectal Cancer

value: Cold-Fixed


title: control L744

value: 78.76 years

value: Family 123

value: Day 12


title: long-lived sib L183

value: long-lived sib

value: 92.18 years

value: Family 025


title: control L854

value: male

value: 63.7 years

value: Family 156


title: offspring L678

value: offspring

value: 57.46 years

value: Family 118


title: offspring L1892

value: female

value: 55.94 years

value: Family 305


title: offspring L1516

value: 69.37 years

value: Family 238

value: Day 11


title: offspring L696

value: 74.83 years

value: Family 112


title: offspring L935

value: 54.78 years

value: Family 168


title: control L1073

value: control

value: 57.36 years

value: Family 188


title: offspring L1816

value: male

value: 58.43 years

value: Family 295

value: Day 12


title: control L1863

value: 61.78 years

value: Family 301


title: long-lived sib L961

value: long-lived sib

value: 92.5 years

value: Family 172


title: long-lived sib L1914

value: female

value: 93.34 years

value: Family 311

value: Day 11


title: offspring L51

value: offspring

value: 57.8 years

value: Family 013


title: control L915

value: control

value: 47.67 years

value: Family 146

value: Day 10


title: control L2297

value: male

value: 72.33 years

value: Family 245


title: long-lived sib L2296

value: long-lived sib

value: 93.93 years


title: long-lived sib L231

value: 91.72 years

value: Family 039


title: control L2448

value: female

value: 65.25 years

value: Family 380

value: Day 09


title: control L934

value: 61.19 years

value: Family 168


title: long-lived sib L1861

value: 90.81 years

value: Family 301


title: long-lived sib L586

value: 91.43 years

value: Family 085


title: control L52

value: control

value: 49.7 years

value: Family 013

value: Day 10


title: long-lived sib L562

value: long-lived sib

value: 97.88 years

value: Family 103


title: long-lived sib L1334

value: female

value: 92.21 years

value: Family 228


title: control L233

value: 61.85 years

value: Family 039


title: control L2666

value: male

value: 61.78 years

value: Family 420

value: Day 09


title: control L106

value: 51.88 years

value: Family 008


title: long-lived sib L1770

value: 96.03 years

value: Family 291


title: control L976

value: control

value: 66.98 years

value: Family 176

value: Day 08


title: long-lived sib L1513

value: long-lived sib

value: female

value: 92.33 years

value: Family 238


title: offspring L561

value: offspring

value: 60.41 years

value: Family 103


title: control L606

value: 65.17 years

value: Family 098


title: offspring L234

value: male

value: 61.48 years

value: Family 039


title: control L697

value: 71.32 years

value: Family 112

value: Day 09


title: long-lived sib L973

value: 91.16 years

value: Family 176


title: control L212

value: control

value: 61.12 years

value: Family 029

value: Day 08


title: offspring L2597

value: offspring

value: female

value: 60.49 years

value: Family 371


title: long-lived sib L92

value: long-lived sib

value: 94.43 years

value: Family 015

value: Day 07


title: long-lived sib L2637

value: male

value: 91.93 years

value: Family 414


title: control L563

value: 63.98 years

value: Family 103


title: offspring L161

value: 54.25 years

value: Family 016


title: control L2010

value: control

value: 65.11 years

value: Family 324


title: control L458

value: 65.57 years

value: Family 055


title: long-lived sib L936

value: female

value: 92.03 years

value: Family 168


title: offspring L656

value: offspring

value: 57.54 years

value: Family 108

value: Day 06


title: control L91

value: male

value: 62.08 years

value: Family 015

value: Day 07


title: offspring L459

value: 62.65 years


title: long-lived sib L853

value: long-lived sib

value: 90.09 years

value: Family 156


title: offspring L975

value: 62.41 years

value: Family 176


title: offspring L1623

value: female

value: 61.76 years

value: Family 257


title: control L1773

value: control

value: 70.46 years

value: Family 291


title: control L962

value: 62.43 years

value: Family 172


title: offspring L745

value: offspring

value: 73.41 years

value: Family 123

value: Day 06


title: long-lived sib L210

value: long-lived sib

value: 92.81 years

value: Family 029


title: offspring L2298

value: 68.5 years

value: Family 245


title: control L1916

value: female

value: 60.87 years

value: Family 311


title: offspring L444

value: male

value: 61.08 years

value: Family 063


title: offspring L175

value: 55.78 years

value: Family 014

value: Day 03


title: offspring L1093

value: offspring

value: 62.37 years

value: Family 189


title: control L1517

value: control

value: 73.6 years

value: Family 238

value: Day 05


title: control L629

value: 61.05 years

value: Family 092

value: Day 06


title: offspring L1336

value: 56.17 years

value: Family 228


title: offspring L2640

value: female

value: 62.53 years

value: Family 414


title: offspring L2669

value: 59.56 years

value: Family 420


title: control L159

value: 70.11 years

value: Family 016

value: Day 04


title: offspring L987

value: offspring

value: 60.54 years

value: Family 171


title: offspring L585

value: 56.27 years

value: Family 085


title: control L675

value: control

value: 61.53 years

value: Family 129


title: offspring L700

value: male

value: 58.41 years

value: Family 072

value: Day 05


title: long-lived sib L1170

value: long-lived sib

value: female

value: 91.97 years

value: Family 196


title: offspring L1772

value: 72.25 years

value: Family 291


title: long-lived sib L1651

value: 93.68 years

value: Family 264

value: Day 04


title: control L1092

value: 64.13 years

value: Family 189


title: offspring L1655

value: offspring

value: 60.29 years


title: long-lived sib L695

value: male

value: Family 112

value: Day 06


title: long-lived sib L2594

value: 91.4 years

value: Family 371

value: Day 05


title: offspring L776

value: 59.02 years

value: Family 142


title: long-lived sib L446

value: long-lived sib

value: 92.67 years

value: Family 066


title: offspring L2447

value: 68.44 years

value: Family 380


title: long-lived sib L1812

value: female

value: 98.52 years

value: Family 295


title: long-lived sib L2662

value: 96.05 years

value: Family 420

value: Day 04


title: control L184

value: control

value: male

value: 54.97 years

value: Family 025


title: long-lived sib L330

value: 99.16 years

value: Family 049


title: offspring L447

value: offspring

value: 66 years


title: control L1815

value: 56.82 years


title: offspring L855

value: 63.67 years

value: Family 156

value: Day 03


title: offspring L964

value: female

value: 58.71 years

value: Family 172

value: Day 08


title: control L1171

value: 64.89 years

value: Family 196


title: control L174

value: control

value: 54.95 years

value: Family 014

value: Day 06


title: control L1893

value: male

value: 64.62 years

value: Family 305


title: control L699

value: 58.7 years

value: Family 072

value: Day 09


title: testis gene expression data from Akt1 wildtype, PTU-exposed mice at postnatal day 25, sample 3

hyb_protocol: All GeneChip microarrays (Mouse Genome 430 2.0 Array) were hybridized, washed, stained, and scanned using the Complete Gene Chip Instrument System according to the Affymetrix Technical Manual.

source_name: PTU-exposed testes at postnatal day 25

value: Akt1 wildtype

value: PTU-exposed

value: postnatal day 25

value: sample 3


title: offspring L1137

value: offspring

value: female

value: 60.31 years

value: Family 181

value: Day 03


title: long-lived sib L1620

value: long-lived sib

value: 89.71 years

value: Family 257


title: control L2596

value: control

value: male

value: 63.11 years

value: Family 371


title: long-lived sib L105

value: 90.37 years

value: Family 008


title: control L655

value: 63.1 years

value: Family 108


title: testis gene expression data from Akt1 wildtype mice at postnatal day 25, sample 3

source_name: control testes at postnatal day 25

value: Akt1 wildtype

value: unexposed

value: postnatal day 25

value: sample 3


title: long-lived sib L443

value: female

value: 94.33 years

value: Family 063


title: control L1622

value: 69.31 years

value: Day 02


title: long-lived sib L44

value: long-lived sib

value: 91.74 years

value: Family 014

value: Day 03


title: long-lived sib L773

value: male

value: 89.52 years

value: Family 142


title: long-lived sib L1894

value: 90.22 years

value: Family 305


title: testis gene expression data from Akt1 wildtype, PTU-exposed mice at postnatal day 25, sample 2

value: Akt1 wildtype

value: PTU-exposed

value: sample 2


title: control L445

value: control

value: female

value: 56.93 years


title: testis gene expression data from Akt1 homozygous, PTU-exposed mice at postnatal day 25, sample 2

value: Akt1 homozygous

value: postnatal day 25


title: control L989

value: 60.73 years

value: Family 171

value: Day 02


title: control L448

value: 62.88 years

value: Family 066


title: testis gene expression data from Akt1 wildtype mice at postnatal day 25, sample 1

value: unexposed

value: sample 1

value: male


title: testis gene expression data from Akt1 wildtype mice at postnatal day 25, sample 2


title: long-lived sib L1064

value: long-lived sib

value: 92.76 years

value: Family 188


title: offspring L90

value: offspring

value: 61.53 years

value: Family 015

value: Day 06


title: testis gene expression data from Akt1 homozygous mice at postnatal day 25, sample 2

value: Akt1 homozygous

value: sample 2


title: control L677

value: control

value: female

value: 59.93 years

value: Family 118


title: testis gene expression data from Akt1 homozygous mice at postnatal day 25, sample 3

value: postnatal day 25

value: sample 3


title: testis gene expression data from Akt1 wildtype, PTU-exposed mice at postnatal day 25, sample 1

value: Akt1 wildtype

value: PTU-exposed

value: sample 1


title: testis gene expression data from Akt1 homozygous, PTU-exposed mice at postnatal day 25, sample 1

value: male


title: offspring L1172

value: 58.01 years

value: Family 196

value: Day 02


title: testis gene expression data from Akt1 heterozygous, PTU-exposed mice at postnatal day 25, sample 2

value: Akt1 heterozygous


title: testis gene expression data from Akt1 heterozygous mice at postnatal day 25, sample 3

value: unexposed


title: testis gene expression data from Akt1 homozygous mice at postnatal day 25, sample 1

value: Akt1 homozygous


title: long-lived sib L2446

value: long-lived sib

value: Family 380


title: control L1335

value: control

value: female

value: 54.37 years

value: Family 228


title: testis gene expression data from Akt1 heterozygous mice at postnatal day 25, sample 2

value: postnatal day 25

value: sample 2


title: testis gene expression data from Akt1 heterozygous, PTU-exposed mice at postnatal day 25, sample 3

value: PTU-exposed

value: sample 3


title: long-lived sib L743

value: 96.75 years

value: Family 123


title: control L587

value: male

value: 59.75 years

value: Family 085

value: Day 01


title: offspring L109

value: offspring

value: 52.83 years

value: Family 008


title: offspring L185

value: 53.4 years

value: Family 025


title: control L1138

value: control

value: 64.27 years

value: Family 181


title: long-lived sib L763

value: long-lived sib

value: 90.79 years

value: Family 136


title: testis gene expression data from Akt1 heterozygous mice at postnatal day 25, sample 1

value: Akt1 heterozygous

value: unexposed

value: postnatal day 25

value: sample 1


title: long-lived sib L392

value: male

value: 93.19 years

value: Family 056


title: long-lived sib L653

value: female

value: 93.4 years

value: Family 108

value: Day 01


title: offspring L1072

value: offspring

value: 61.47 years

value: Family 188


title: control L777

value: control

value: 56.1 years

value: Family 142


title: long-lived sib L674

value: long-lived sib

value: 91.52 years

value: Family 129


title: long-lived sib L679

value: 91.53 years

value: Family 118


title: Human Foreskin Fibroblast (BJ) [gene expr]

status: Public on Sep 03 2011

city: London

first: Jonathan

middle: H

last: Teichroeb

state: Ontario

address: 1151 Richmond St.

department: Physiology and Pharmacology

country: Canada

institute: University of Western Ontario

data_processing: Raw data exported from Beadstudio and subsequently quantile normalized and analyzed in Genespring GX 11

source_name: Human Foreskin

label_protocol: cRNA was prepared using Ambion - Illumina TotalPrep-96 RNA Amplification Kit (cat# 4393543), according to the manufacturers protocol, and hybridized using standard Illumina protocol.

growth_protocol: See Spontaneous reversal of the developmental aging of normal human cells following transcriptional reprogramming, H Vaziri, KB Chapman, A Guigova, J Teichroeb, et al., Regenerative Medicine 2010 5:3, 345-363. Also see:  Suppression of the imprinted gene NNAT and X-chromosome gene activation in isogenic human iPS cells, J.H. Teichroeb, D.H. Betts, H. Vaziri., Plos ONE

extract_protocol: RNA was extracted using TRIzol and an RNeasy Mini Kit (Qiagen) was used to purify RNA from all samples at once using the standard protocol with standard modifications for purification of total RNA, including small RNA, and for TRIzol suspensions. On column DNase treatment was performed. RNA was standardized to 100ng/µl and frozen for use with Illumina arrays.

tag: passage

tag: cell line

value: non-isogenic mortal


title: EN13 iPSC Line (B2) [gene expr]

source_name: reprogrammed from EN13, Isogenic with H9

value: isogenic hiPSC


title: EN13 iPSC Line (EH6A) [gene expr]


title: Mortal Splanchnopleuric Mesoderm (EN13) [gene expr]

source_name: Differentiated from H9, Isogenic with H9

value: isogenic mortal H9


title: EN13 iPSC Line (EH1) [gene expr]


title: IMR90-4 iPSC Line [gene expr]

source_name: reprogrammed from IMR90-4

value: non-isogenic hiPSC


title: Human Embryonic Stem Cell Line (H9) [gene expr]

source_name: Human Embryo ICM

value: hESC


title: EN13 iPSC Line (EH3) [gene expr]


title: Shift_worker_10

type: genomic

city: New Haven

first: Alan

last: Fu

state: CT

address: 60 College St.

institute: Yale University

description: Sample 20

data_processing: GenomeStudio software

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Periperhal blood lymphocytes

label_protocol: Standard Illumina labeling protocol

extract_protocol: Genomic DNA was extracted and purified from whole blood using Qiagen DNeasy Kit according to standard instructions.  Extracted DNA were bisulfite treated using the Zymo EZ DNA Methylation Kit according to manufacturer's protocol.

value: Female

tag: shift work status

value: Shift worker

value: Peripheral blood lymphocytes


title: Shift_worker_7

description: Sample 17


title: Shift_worker_6

description: Sample 16


title: EN13 iPSC Line (EH6) [gene expr]


title: Shift_worker_9

description: Sample 19


title: Shift_worker_8

description: Sample 18


title: Shift_worker_4

description: Sample 14


title: Shift_worker_5

description: Sample 15


title: Shift_worker_1

description: Sample 11


title: Day_worker_10

description: Sample 10

value: Day worker


title: Shift_worker_2

description: Sample 12


title: Shift_worker_3

description: Sample 13


title: EN13 iPSC Line (EH2) [gene expr]


title: offspring L875

value: offspring

value: female

value: 64.11 years

value: Family 136

value: Day 01


title: Day_worker_6

description: Sample 6


title: Day_worker_5

description: Sample 5


title: Day_worker_4

description: Sample 4


title: Day_worker_8

description: Sample 8


title: Day_worker_9

description: Sample 9


title: Day_worker_3

description: Sample 3


title: Day_worker_7

description: Sample 7


title: Day_worker_2

description: Sample 2


title: S33073_1_HP

city: Lund

first: Morten

last: Krogh

address: Skrivarevagen 9

country: Sweden

institute: Amber Biosciences

hyb_protocol: Prior to hybridization, slides were UV-cross linked at 800 mJ/cm2 and pre-treated using the Pronto Plus System 6 (Corning, Inc., Corning, NY), according to the manufacturer's instructions.

scan_protocol: Arrays were scanned at two wavelengths using an Agilent G2505A DNA microarray scanner (Agilent Technologies, Santa Clara, CA), with 10 Î¼m resolution. Gene Pix Pro 4.0 software (Axon Instruments, Inc., Union City, CA), was used for image analysis.

data_processing: Background correction of Cy3 and Cy5 intensities were calculated as the median foreground intensity value minus the median local background intensity. The corrected intensities were Lowess corrected, spots flagged as bad were set to missing values, and the log2 ratio was calculated for each spot. Spots representing the same reporter were averaged. The data processing was done in the BioArray Software Environment (BASE 2). The normalization and averaging differs a bit from the data used in the reference above.

source_name: breast tumor

label_protocol: Five micrograms of tumor RNA was labeled with Cy3 dCTP (Amersham Biosciences, Piscataway, NJ), and 5 ug of reference RNA (Stratagene, La Jolla, CA), consisting of a pool of ten different tumor cell lines, was labeled with Cy5 dCTP (Amersham Biosciences, Piscataway, NJ), according to the manufacturer's instructions using the reagents in the ChipShot labeling system kit (Corning Inc., Corning, NY).

extract_protocol: The samples were pulverized with a Micro-dismembrator II (B. Braun Biotech Int., Germany), and RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA), and purified with Qiagen RNeasy Midi columns (Qiagen, Chatsworth, CA). The RNA concentration was determined using a Nanodrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE). The RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) together with the reagents in the RNA 6000 Nano LabChip kit.

treatment_protocol: Frozen tumor samples were collected from patients representing the following four groups: (a) LR+RT+ (local recurrence developed after radiotherapy), (b) LR-RT+ (no local recurrence after radiotherapy), (c) LR+RT- (local recurrence developed, no radiotherapy given), and (d) LR-RT- (no local recurrence, no radiotherapy given). All patients were operated on with breast-conservation surgery and axillary clearance with no lymph node involvement, tumor size of less than or equal to 30 mm (two patients had tumors measuring 32 and 40 mm, respectively, and one was T2 without any further information on size), tumor-free margins (>1 mm), no multicentricity, and with frozen tumor tissue with good RNA quality available. Local recurrence was defined as the appearance of a new breast tumor in the ipsilateral residual breast parenchyma in the overlying skin or in the scar. Patients with recurrence in the contralateral breast or with distant metastases prior or simultaneous to local recurrence were excluded. In the first inclusion, 102 patients from a randomized clinical trial in the South and West health care regions in Sweden and 19 patients from a population-based cohort study with a nested case-control study (Stockholm and South Sweden) were included (Tables 1 and 2). To perform gene expression profiling in a more homogenous material with regard to ER status and yet with a sufficient number of cases in all four subgroups, 22 additional ER+ tumors from the South-East and South health care regions were included in a second inclusion (Tables 1 and 2). The study was approved by the Ethics Committee at Lund University (Lund, Sweden). Patient and primary tumor characteristics and follow-up information were collected from the patients' medical records.

value: alive

value: ok

tag: characteristics

value: s_found_by_screening_0no_1yes:_ch1 1

value: Tubular

value: Pre

value: Stockholm

tag: opdat

tag: extrdat

tag: sample type

value: reference


title: S33038_1_HP

value: s_found_by_screening_0no_1yes:_ch1 0

value: Post

source_name: reference RNA (Stratagene, La Jolla, CA), consisting of a pool of ten different tumor cell lines


title: S33105_1_HP


title: S32121_1_HP


title: S33107_1_HP

value: other


title: Day_worker_1

description: Sample 1

value: Female

value: Peripheral blood lymphocytes


title: S33060_1_HP


title: S32053_1_HP


title: S33067_1_HP


title: S32087_1_HP


title: S31130_1_HP

value: brca


title: long-lived sib L1091

value: long-lived sib

value: female

tag: age

value: 98.26 years

value: Family 189

value: Day 02


title: S32146_1_HP

value: alive

value: ok

value: Lobular


title: S31086_2_HP

value: Pre


title: S31075_2_HP_agilent

value: Stockholm


title: S31035_1_HP

value: reference


title: S31029_1_HP

value: s_found_by_screening_0no_1yes:_ch1 0


title: S31072_2_HP


title: S31093_2_HP_agilent


title: S31068_1_HP

value: Post


title: S31041_2_HP_Cy3 #2


title: L97164_1_HP

value: Linkoping


title: L94536_2_HP_agilent_2

value: pre


title: L93112_1_HP


title: L90675_1_HP_agilent


title: L92191_2_HP


title: L97458_2_HP_agilent_2


title: L87379_87_2_HP


title: L03272_2_HP


title: G71_8843_1_HP

value: Goteborg


title: G66_11237_1_HP


title: G32_8095_2_HP_agilent

value: s_found_by_screening_0no_1yes:_ch1 1


title: testis gene expression data from Akt1 heterozygous, PTU-exposed mice at postnatal day 25, sample 1

tag: genotype

value: Akt1 heterozygous

tag: treatment

value: PTU-exposed

value: postnatal day 25

value: sample 1

value: male


title: G61_5551_1_HP

value: alive


title: G311_8402_1_HP

value: brca


title: G62_5552_1_HP

value: ok


title: G319_8462_1_HP


title: G65_11757_1_HP


title: G84_11241_1_HP


title: G35_5038_1_HP


title: L86191_1_HP_agilent


title: G376_9004_1_HP


title: G270_7695_1_HP

value: Lobular


title: G251_7454_1_HP

value: Pre


title: G227_7174_2_HP

value: reference


title: G202_6877_1_HP

value: s_found_by_screening_0no_1yes:_ch1 0


title: G215_7046_1_HP

value: Post


title: G263_7615_1_HP


title: G252_7418_1_HP


title: G249_7474_2_HP


title: G191_6749_1_HP

value: Tubular


title: G250_7473_1_HP

value: Tubulolobular


title: G185_7434_2_HP

value: Goteborg


title: G178_6720_1_HP

value: s_found_by_screening_0no_1yes:_ch1 1


title: G169_7944_2_HP


title: G195_6528_1_HP


title: G143_6316_1_HP


title: G141_8535_1_HP


title: G146_6330_2_HP


title: G139_6255_1_HP

value: unreadable


title: G182_6710_1_HP


title: Ca9952_1_HP


title: Ca9865_1_HP


title: Ca9879_1_HP

value: Tubuloductal


title: Ca9878_1_HP

value: pre


title: G183_9454_1_HP


title: G11_5029_1_HP


title: Ca9383_1_HP


title: Ca9893_1_HP


title: Ca9866_1_HP


title: Ca9426_1_HP


title: G115_6106_1_HP


title: Ca9612_1_HP


title: Ca9546_1_HP


title: Ca9913_1_HP


title: Ca9598_1_HP


title: Ca9745_1_HP


title: G128_6107_1_HP


title: Ca9367_2_HP


title: Ca9665_1_HP


title: Ca9447_1_HP


title: Ca9689_1_HP


title: Ca9340_1_HP


title: Ca9362_1_HP


title: Ca9189_1_HP


title: Ca9222_2_HP


title: Ca9916_1_HP


title: Ca9212_1_HP


title: Ca9397_1_HP


title: Ca9152_1_HP


title: Ca9254_1_HP


title: Ca8967_1_HP


title: Ca9047_1_HP


title: Ca9107_1_HP


title: Ca8854_1_HP


title: Ca8962_1_HP


title: Ca8835_1_HP


title: Ca8888_1_HP


title: Ca9114_1_HP


title: Ca8825_1_HP


title: Ca9019_1_HP


title: Ca8883_1_HP


title: Ca6524_1_HP

value: Margareta


title: Ca8837_1_HP


title: Ca6513_2_HP


title: Ca8532_1_HP


title: Ca8798_1_HP


title: Ca8706_1_HP


title: Ca8950_1_HP


title: Ca8869_1_HP


title: Ca6858_1_HP


title: Ca14113_2_HP


title: Ca13833_1_HP


title: Ca8732_1_HP


title: Ca13335_1_HP_agilent


title: Ca8731_1_HP


title: Ca13327_2_HP

value: post


title: Ca8767_1_HP

value: alive


title: Ca7478_1_HP


title: Ca13880_2_HP_agilent


title: Ca13943_1_HP


title: C CD34+ VSEL

city: Leipzig

last: Heider

state: Bayern

address: Semmelweisstr. 14

department: Biologie

institute: Universität Leipzig

hyb_protocol: RNA hybridisation and microarray analysis was conducted by AROS Applied Biotechnology AS (Aarhus, Denmark) using Affymetrix GeneTitan Human Genome U219 microarray (Affymetrix, Santa Clara, USA)

data_processing: The data was preprocessed and analysed using R/Bioconductor and Tigr MeV Suite.

source_name: CD34+ VSEL

label_protocol: RNA labelling was conducted by AROS Applied Biotechnology AS (Aarhus, Denmark) using NuGen Pico labelling kit (NuGen, San Carlos, USA)

growth_protocol: primary FACS sorted cells; not cultured

extract_protocol: RNA extraction was conducted by AROS Applied Biotechnology AS (Aarhus, Denmark) using Rneasy kit (Qiagen, Hilden, Germany)

treatment_protocol: hVSEL were FACS sorted (BD Vantage SE) from lineage-depleted (MACS) total nucleated human umbilical cord blood cells after NH4Cl lysis. Two populations of hVSEL cells were sorted: Lin-CD45-CXCR4+CD34- and Lin-CD45-CXCR4+CD34+. Dead cells and non-nucleated cells were excluded through Hoechst 33342 and propidium iodid staining.

tag: isolation source

value: umbilical cord blood

tag: cell type

value: very small embryonic-like (VSEL) cells

tag: surface markers

value: Lin- CD45- CXCR4+ CD34+


title: C VSEL

scan_protocol: RNA hybridisation and microarray analysis was conducted by AROS Applied Biotechnology AS (Aarhus, Denmark) using Affymetrix GeneTitan Human Genome U219 microarray (Affymetrix, Santa Clara, USA)

source_name: VSEL

value: Lin- CD45- CXCR4+


title: B CD34+ VSEL


title: Ca12455_1_HP

value: ok

value: reference


title: Ca12545_2_HP


title: Ca12873_2_HP_agilent

value: brca

value: Post


title: Ca11014_1_HP

value: degraded

value: Lobular


title: A CD34+ VSEL


title: Ca12984_1_HP

value: s_found_by_screening_0no_1yes:_ch1 0

value: Pre


title: A VSEL


title: Ca11370_1_HP

value: s_found_by_screening_0no_1yes:_ch1 1

value: Tubular


title: B VSEL


title: Ca11336_1_HP

value: pre


title: Ca11305_1_HP_agilent

value: post


title: Ca10742_1_HP

value: alive


title: Ca12078_2_HP


title: S. gordonii amylase treated Rep2

city: Buffalo

first: Anna

last: Nikitkova

state: NY

address: 3435 Main St.

institute: University at Buffalo

hyb_protocol: Cy-dye-labeled cDNA probes were hybridized to S. gordonii microarray slides according to the Nexterion Slide E DNA application protocol (Schott). Briefly, slides were pre-washed sequentially in 0.1% Triton X-100 solution, 1 mM HCl solution and 100 mM KCl solution before blocking with Nexterion Blocking Solution (Schott). The Cy-dye-labeled cDNA from both samples were mixed, dried and re-suspended in Nexterion Hyb solution. The probe mixture was heated to 95o C and pipetted onto a dried microarray slide. A coverslip (Lifter Slip from Erie Scientific Co., Portsmouth, NH) was placed over the slide which was then sealed in a hybridization chamber (Corning Inc., Lowell, MA) and incubated in a 42°C water bath for 16 hours. After hybridization, the slides were washed sequentially with 2X SSC 0.2% SDS, then 2X SSC, and 0.2X SSC solutions, dried briefly by centrifugation, and kept in a desiccator in a light tight container until scanned.

scan_protocol: The fluorescent spots on the microarray were scanned using the Axon 4000A laser scanner (Axon Instruments, Foster City, CA) and Genepix® software was used to extract the raw data, which was analyzed using the TM4 Microarray Software Suite (www.jcvi.org/cms/research/software).

data_processing: The TIGR TM4 Microarray Software Suite (http://www.tigr.org) was used for all analyses, including analysis of TIF files using TIGR Spotfinder and normalization using Microarray Data Analysis System (MIDAS). Normalization included LocFit, a low intensity filter, and in-slide replicate analysis which calculated geometric means for in-slide replicates. Geometric means were then calculated for flip dye pairs using flip dye pair consistency checking in MIDAS. Statistical analyses were conducted using Multiexperiment Viewer (MEV).

organism: Streptococcus gordonii str. Challis

source_name: S. gordonii, denatured-amylase treated

label_protocol: S. gordonii total RNA was reverse transcribed to amino-allyl-cDNA and indirectly labeled with Cy dyes according the standard operating protocol from Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute http://pfgrc.jcvi.org/index.php/microarray.html.  Briefly, 4 µg of total RNA was reverse transcribed using Superscript II or III (Invitrogen, Carlsbad, CA) reverse transcriptase in a deoxynucleotide mixture containing aminoallyl-dUTP (Ambion). After alkaline hydrolysis to remove the RNA template, aminoallyl-cDNA was purified with QIAquick PCR columns (Qiagen), and dried in a SpeedVacTM. The cDNA was labeled with the appropriate Cy3 or Cy5 NHS-dye (GE Healthcare Bio-Sciences Corp., Piscataway, NJ), and unbound Cy dyes were removed from the probe using the QIAquick PCR column (Qiagen). The quality of the probes and their specific activity were confirmed by a spectrophotometric scan from 200 to 700 nm on a Nanodrop 2000 spectrophotometer. Only labeled cDNA with >200 pmol of dye incorporation per sample and a ratio of less than 50 nucleotides/dye molecules were used for hybridizations. The Cy dye-labeled cDNA from the amylase-treated aliquot of the culture was mixed with Cy dye-labeled cDNA from the denatured amylase-treated control aliquot, and used to probe the S. gordonii microarray slides. cDNA from cells exposed to denatured amylase was labeled with Cy5.

growth_protocol: Bacteria from frozen stocks were streaked onto Todd Hewitt (TH) (Difco, Detroit, MI) agar plates and grown overnight at 37°C in microaerophilic conditions in a candle jar. Several colonies were inoculated into chemically-defined medium (CDM) of Jenkinson, as modified by Loo {Loo, 2000; Jenkinson, 1986}. Bacterial culture was grown statically in 40 ml CDM at 37°C in a candle jar to mid-log phase corresponding to an optical density at 600 nm of 0.5 to 0.6. At this point bacterial culture was divided into two aliquots and treated either with salivary amylase or with denatured salivary amylase.

extract_protocol: otal RNA was isolated by the hot acid phenol method as described previously {Vickerman et al. 2007}, briefly four milliliters of cells were mixed with hot acid phenol (95C), incubated for 10 minutes at 95C, chilled on ice and 0.2 volumes of chloroform was added. After vigorous shaking the mixture was centrifuged at 10 000 x g to separate the aqueous and organic layers. The aqueous layer (containing the RNA) was re-extracted with 1 volume of acid phenol-chloroform and centrifuged. The supernatant was adjusted to 0.3 M sodium acetate, mixed with one volume of isopropanol and centrifuged to precipitate the RNA. The RNA pellet was resuspended in DEPC treated water containing 150 U/ml of RNase inhibitor (RNaseOUT, Invitrogen, Carlsbad, CA) followed by treatment with TurboDNase (Applied Biosystems/Ambion, Austin, TX) according to manufacturer’s protocol. Remaining contaminants were removed using the RNeasy minikit column (Qiagen, Valencia, CA) with the cleanup protocol. Total RNA was quantified using the Nanodrop 2000 spectrophotometer and RNA integrity determined by agarose gel electrophoresis. Total RNA was used immediately for cDNA synthesis.

treatment_protocol: The mid-log phase bacterial culture was divided into two aliquots of equal volume. Bacterial cells from aliquots were pelleted by centrifugation at 6,000 x g in a Sorvall RC6 centrifuge at 20°C, and washed once with simulated salivary buffer preconditioned to 37°C. To one of the aliquots was added simulated salivary buffer (4ml) containing 0.4 mg/ml salivary amylase denatured by heating to 100°C and cooled to 37°C , and was incubated statically for 15 min at 37°C in a candle jar.

tag: sample

value: Streptococcus gordonii str. Challis CH1

tag: growth stage

value: mid-log

value: denatured salivary amylase

tag: treatment time

value: 15 min

source_name: S. gordonii, amylase treated

label_protocol: S. gordonii total RNA was reverse transcribed to amino-allyl-cDNA and indirectly labeled with Cy dyes according the standard operating protocol from Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute http://pfgrc.jcvi.org/index.php/microarray.html.  Briefly, 4 µg of total RNA was reverse transcribed using Superscript II or III (Invitrogen, Carlsbad, CA) reverse transcriptase in a deoxynucleotide mixture containing aminoallyl-dUTP (Ambion). After alkaline hydrolysis to remove the RNA template, aminoallyl-cDNA was purified with QIAquick PCR columns (Qiagen), and dried in a SpeedVacTM. The cDNA was labeled with the appropriate Cy3 or Cy5 NHS-dye (GE Healthcare Bio-Sciences Corp., Piscataway, NJ), and unbound Cy dyes were removed from the probe using the QIAquick PCR column (Qiagen). The quality of the probes and their specific activity were confirmed by a spectrophotometric scan from 200 to 700 nm on a Nanodrop 2000 spectrophotometer. Only labeled cDNA with >200 pmol of dye incorporation per sample and a ratio of less than 50 nucleotides/dye molecules were used for hybridizations. The Cy dye-labeled cDNA from the amylase-treated aliquot of the culture was mixed with Cy dye-labeled cDNA from the denatured amylase-treated control aliquot, and used to probe the S. gordonii microarray slides. cDNA from cells exposed to native amylase was labeled with Cy3.

extract_protocol: Total RNA was immediately isolated by the hot acid phenol method as described previously {Vickerman et al. 2007}, briefly four milliliters of cells were mixed with hot acid phenol (95C), incubated for 10 minutes at 95C, chilled on ice and 0.2 volumes of chloroform was added. After vigorous shaking the mixture was centrifuged at 10 000 x g to separate the aqueous and organic layers. The aqueous layer (containing the RNA) was re-extracted with 1 volume of acid phenol-chloroform and centrifuged. The supernatant was adjusted to 0.3 M sodium acetate, mixed with one volume of isopropanol and centrifuged to precipitate the RNA. The RNA pellet was resuspended in DEPC treated water containing 150 U/ml of RNase inhibitor (RNaseOUT, Invitrogen, Carlsbad, CA) followed by treatment with TurboDNase (Applied Biosystems/Ambion, Austin, TX) according to manufacturer’s protocol. Remaining contaminants were removed using the RNeasy minikit column (Qiagen, Valencia, CA) with the cleanup protocol. Total RNA was quantified using the Nanodrop 2000 spectrophotometer and RNA integrity determined by agarose gel electrophoresis. Total RNA was used immediately for cDNA synthesis.

treatment_protocol: The mid-log phase bacterial culture was divided into two aliquots of equal volume. Bacterial cells from aliquots were pelleted by centrifugation at 6,000 x g in a Sorvall RC6 centrifuge at 20°C, and washed once with simulated salivary buffer preconditioned to 37°C. To one of the aliquots was added simulated salivary buffer (4ml) containing 0.4 mg/ml native salivary amylase preconditioned to 37°C , and was incubated statically for 15 min at 37°C in a candle jar.

value: salivary amylase


title: S. gordonii amylase treated Rep3

label_protocol: S. gordonii total RNA was reverse transcribed to amino-allyl-cDNA and indirectly labeled with Cy dyes according the standard operating protocol from Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute http://pfgrc.jcvi.org/index.php/microarray.html.  Briefly, 4 µg of total RNA was reverse transcribed using Superscript II or III (Invitrogen, Carlsbad, CA) reverse transcriptase in a deoxynucleotide mixture containing aminoallyl-dUTP (Ambion). After alkaline hydrolysis to remove the RNA template, aminoallyl-cDNA was purified with QIAquick PCR columns (Qiagen), and dried in a SpeedVacTM. The cDNA was labeled with the appropriate Cy3 or Cy5 NHS-dye (GE Healthcare Bio-Sciences Corp., Piscataway, NJ), and unbound Cy dyes were removed from the probe using the QIAquick PCR column (Qiagen). The quality of the probes and their specific activity were confirmed by a spectrophotometric scan from 200 to 700 nm on a Nanodrop 2000 spectrophotometer. Only labeled cDNA with >200 pmol of dye incorporation per sample and a ratio of less than 50 nucleotides/dye molecules were used for hybridizations. The Cy dye-labeled cDNA from the amylase-treated aliquot of the culture was mixed with Cy dye-labeled cDNA from the denatured amylase-treated control aliquot, and used to probe the S. gordonii microarray slides. cDNA from cells exposed to native salivary amylase was labeled with Cy3.


title: S. gordonii amylase treated Rep4


title: Ca10692_2_HP

value: ok

value: reference


title: Male Uninjured Fin

city: Durham

first: Michael

last: Czerwinski

state: North Carolina

address: 4034 GSRBII Research Drive

department: Cell Biology

institute: Duke University

description: Unamputated pectoral fin total RNA of adult male Danio rerio, 1 of 3 biological replicates

hyb_protocol: standard NimbleGen protcol by Mogene (St. Louis, MO)

data_processing: Chips were read using Nimblegen NimbleScan Software then further processed with bioconductor

organism: Danio rerio

source_name: Male Danio rerio EK Strain

growth_protocol: Fish were grown under standard conditions

extract_protocol: Standard Trizol extraction

treatment_protocol: Amputation was made with scissors at the middle of the pectoral fin P/D axis, fins were allowed to recover 4 days and tissue samples were then collected

value: unamputated

tag: strain

value: EK

tag: gender

value: male

tag: tissue

value: fin


title: S. gordonii amylase treated Rep1

label_protocol: protocol S. gordonii total RNA was reverse transcribed to amino-allyl-cDNA and indirectly labeled with Cy dyes according the standard operating protocol from Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute http://pfgrc.jcvi.org/index.php/microarray.html.  Briefly, 4 µg of total RNA was reverse transcribed using Superscript II or III (Invitrogen, Carlsbad, CA) reverse transcriptase in a deoxynucleotide mixture containing aminoallyl-dUTP (Ambion).  After alkaline hydrolysis to remove the RNA template, aminoallyl-cDNA was purified with QIAquick PCR columns (Qiagen), and dried in a SpeedVacTM. The cDNA was labeled with the appropriate Cy3 or Cy5 NHS-dye (GE Healthcare Bio-Sciences Corp., Piscataway, NJ), and unbound Cy dyes were removed from the probe using the QIAquick PCR column (Qiagen). The quality of the probes and their specific activity were confirmed by a spectrophotometric scan from 200 to 700 nm on a Nanodrop 2000 spectrophotometer. Only labeled cDNA with >200 pmol of dye incorporation per sample and a ratio of less than 50 nucleotides/dye molecules were used for hybridizations. The Cy dye-labeled cDNA from the amylase-treated aliquot of the culture was mixed with Cy dye-labeled cDNA from the denatured amylase-treated control aliquot, and used to probe the S. gordonii microarray slides. Initially, cDNA from cells exposed to native amylase was labeled with Cy5, and cDNA from cells exposed to denatured amylase was labeled with Cy3. Each amylase-exposure experiment was repeated from four biological replicates. To confirm microarray results the cDNA from each strain was labeled with the opposite Cy dye and hybridized to similar arrays for the flip-dye comparison.

growth_protocol: Bacteria from frozen stocks were streaked onto Todd Hewitt (TH) (Difco, Detroit, MI) agar plates and grown overnight at 37°C in microaerophilic conditions in a candle jar. Several colonies were inoculated into chemically-defined medium (CDM) of Jenkinson, as modified by Loo {Loo, 2000; Jenkinson, 1986}. Bacterial culture was grown statically in 40 ml CDM at 37°C in a candle jar to mid-log phase corresponding to an optical density at 600 nm of 0.5 to 0.6. At this point bacterial culture was divided into two aliquots and treated either with salivary  amylase or with denatured salivary amylase.

extract_protocol: Total RNA was isolated by the hot acid phenol method as described previously {Vickerman et al. 2007}, briefly four milliliters of cells were mixed with hot acid phenol (95C), incubated for 10 minutes at 95C, chilled on ice and 0.2 volumes of chloroform was added. After vigorous shaking the mixture was centrifuged at 10 000 x g to separate the aqueous and organic layers. The aqueous layer (containing the RNA) was re-extracted with 1 volume of acid phenol-chloroform and centrifuged. The supernatant was adjusted to 0.3 M sodium acetate, mixed with one volume of isopropanol and centrifuged to precipitate the RNA. The RNA pellet was resuspended in DEPC treated water containing 150 U/ml of RNase inhibitor (RNaseOUT, Invitrogen, Carlsbad, CA) followed by treatment with TurboDNase (Applied Biosystems/Ambion, Austin, TX) according to manufacturer’s protocol. Remaining contaminants were removed using the RNeasy minikit column (Qiagen, Valencia, CA) with the cleanup protocol. Total RNA was quantified using the Nanodrop 2000 spectrophotometer and RNA integrity determined by agarose gel electrophoresis. Total RNA was used immediately for cDNA synthesis.

treatment_protocol: The  mid-log phase bacterial culture was divided into two aliquots of equal volume. Bacterial cells from aliquots were pelleted by centrifugation at 6,000 x g in a Sorvall RC6 centrifuge at 20°C, and washed once with simulated salivary buffer preconditioned to 37°C. To one of the aliquots was added simulated salivary buffer (4ml) containing 0.4 mg/ml salivary amylase denatured by heating to 100°C and cooled to 37°C , and was incubated statically for 15 min at 37°C in a candle jar.

treatment_protocol: The  mid-log phase bacterial culture was divided into two aliquots of equal volume. Bacterial cells from aliquots were pelleted by centrifugation at 6,000 x g in a Sorvall RC6 centrifuge at 20°C, and washed once with simulated salivary buffer preconditioned to 37°C. To one of the aliquots was added simulated salivary buffer (4ml) containing 0.4 mg/ml native salivary amylase preconditioned to 37°C , and was incubated statically for 15 min at 37°C in a candle jar.


title: Ca10959_1_HP

value: s_found_by_screening_0no_1yes:_ch1 0

value: Post


title: Male Injured Fin

description: 4 days post amputation pectoral fin total RNA of adult male Danio rerio, 1 of 3 biological replicates

scan_protocol: standard NimbleGen protcol by Mogene (St. Louis, MO)

value: distal 50% of pectoral fin amputated, 4 days post amputation


title: Ca10624_1_HP

value: pre


title: Female Uninjured Fin

description: Unamputated pectoral fin total RNA of adult female Danio rerio, 1 of 3 biological replicates

source_name: Female Danio rerio EK Strain

label_protocol: standard NimbleGen protcol by Mogene (St. Louis, MO)

value: female


title: Ca11338_1_HP

value: alive

value: s_found_by_screening_0no_1yes:_ch1 1

value: Pre


title: Female Injured Fin

description: 4 days post amputation pectoral fin total RNA of adult female Danio rerio, 1 of 3 biological replicates

value: distal 50% of pectoral fin amputated , 4 days post amputation


title: Ca10533_1_HP


title: Ca10844_1_HP

value: Tubular


title: Ca10430_1_HP


title: Mutant # 4

city: Salt Lake city

first: Nadja

last: Makki

address: 15 North ,2030 East

institute: University of Utah

description: Gene expression in Hoxa1 null compared to wildtype embryos

hyb_protocol: Agilent One-color Heterologous GE Hybridization and Wash Protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing: Array images were processed with Agilent Feature Extraction software version 10.5.1.1. Array data files were filtered to remove positive and negative control features and any features flagged as non-uniform outliers or population outliers, as recommended by Agilent. The remaining features for each unique probe were averaged and finally log transformed (log base 2) to yield a single log 2 intensity for each unique probe sequence.

source_name: Hoxa1 null

label_protocol: Agilent One-Color Quick Amp Labeling Protocol

extract_protocol: RNA was isoltaed using the RNAqueous Micro kit in combination with the Qiagen RLT buffer and on-column DNase treatment. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The rhomobere 3-5 from 24 wildtype and 24 Hoxa1Δ/Δ embryos was used.  Tissue from each embryo was homogenized and stored at    -80° C in RLT buffer and finally pooled into four wildtype and four mutant samples, containing tissue from 1-6 somite embryos (one embryo of each somite stage per pool).

value: rhombomere 3-5 region of embryo including neuroectoderm, mesoderm, otic ectoderm


title: Ca10656_1_HP

value: ok


title: Ca10227_1_HP

value: reference


title: Wildtype # 3

source_name: wildtype


title: Wildtype # 4


title: Ca10372_1_HP

value: Tubuloductal


title: Ca10152_1_HP


title: Ca10389_1_HP


title: Mutant # 1


title: Mutant # 3


title: ISP794_exponential_rep1

status: Public on Sep 02 2011

city: Rochester

first: Paul

last: Dunman

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

hyb_protocol: 1.5 micrograms of biotinylated cDNA was hybridized for 16 hr at 45oC in Affymetrix hybridization oven.  GeneChips were washed and stained in Affymetrix fluidics station 400.

scan_protocol: GeneChips were scanned in an Affymetrix GeneChip scanner 7N

data_processing: The data were analyzed using Affymetrix microarray suite 5.0 using default settings and global scaling as normalization method.

organism: Staphylococcus aureus

source_name: wild type exponential phase cells replicate 1

label_protocol: 10 micrograms of total bacterial RNA from each sample was biotinylated following Affymetrix recommendations for labeling prokaryotic RNA.

growth_protocol: S. aureus strains were grown to mid-exponential phase (Optical Density of 0.5) in BHI at 37oC on an orbital shaker (250 rpm); flask to volume ratio of 5:1

extract_protocol: Approximately 1 x 10^9 colony forming units of cell suspenseions were removed from culture flask and added to an equal vol (10 ml) of acetone:ethanol (1:1).  Cells were pelleted by centrifugation at 1600 x g, the pellet was washed twice in TE buffer (10 mM Tris, 1 mM EDTA, pH 7.6) and resuspended in a final vol of 750 ul TE buffer.  The cell suspension was mechanically disrupted in a Savant FastPrep 120 instrument.  Total bacterial RNA was purified using Qiagen RNeasy mini-columns following the manufacturer's recommendations for prokaryotic RNA purification.

treatment_protocol: The experimental variable, or treatment, was the presence vs. absence of a functional norG gene.  ISP794 contains a wild type copy of the norG gene, whereas QTII is an isogenic strain harboring a cat^R cassette

value: ISP794 (wild type)

tag: cell phase

value: exponential

tag: replicate


title: Ca10388_1_HP

tag: characteristics

tag: opdat


title: Ca10017_1_HP

tag: extrdat

tag: sample type


title: Ca10015_1_HP


title: Wildtype # 2


title: Mutant # 2


title: QT11_exponential_rep 2

source_name: norG exponential phase cells replicate 2

value: QT11 (like ISP749 but norG)


title: ISP794_exponential_rep2

source_name: wild type exponential phase cells replicate 2


title: ISP794_exponential_rep3

source_name: wild type exponential phase cells replicate 3


title: QT11_exponential_rep 1

source_name: QT11 (norG) exponential phase cells replicate 1


title: Wildtype # 1


title: QT11_exponential_rep 3

source_name: norG exponential phase cells replicate 3


title: shoot base lower at 0.5h, biological rep3

first: Mei

last: Zhiling

address: 300 Fenglin Road

institute: Institute of Plant Physiology and Ecology

description: Gene expression data from lower parts of rice shoot base at 0.5 after gravisimulation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Oryza sativa Japonica Group

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rice plants (O. sativa sp. japonica) were germinated and grown in soil at a photon flux density of 350–400 µmol m-2 s-1, 60–80% relative humidity (RH) and 12/12 h day/night (D/N) cycle at 25°C in a phytotron

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

treatment_protocol: The lower side and upper side were marked before re-orientation. Seedlings were kept in the dark for 16 h prior to gravistimulation. Plants were subsequently gravistimulated by a 90° rotation to the horizontal position (controls were maintained vertically). The entire process was carried out in the absence of light

value: lower shoot base

tag: age

value: seedling of 21 day

value: after gravistimulation

tag: time


title: shoot base lower at 6h, biological rep2

description: Gene expression data from lower parts of rice shoot base at 6 after gravisimulation

tag: treatment

value: 6 h


title: shoot base upper at 6h, biological rep1

description: Gene expression data from upper parts of rice shoot base at 6 after gravisimulation

value: upper shoot base


title: shoot base upper at 0.5h, biological rep2

description: Gene expression data from upper parts of rice shoot base at 0.5 after gravisimulation


title: shoot base lower at 0.5h, biological rep2

source_name: lower parts of rice shoot base at 0.5 after gravisimulation


title: shoot base upper at 0.5h, biological rep3

source_name: upper parts of rice shoot base at 0.5 after gravisimulation


title: shoot base lower at 6h, biological rep3

source_name: lower parts of rice shoot base at 6 after gravisimulation


title: shoot base upper at 6h, biological rep2

source_name: upper parts of rice shoot base at 6 after gravisimulation


title: shoot base lower at 6h, biological rep1


title: shoot base at 0h, biological rep2

description: Gene expression data from rice shoot base before gravisimulation

source_name: rice shoot base before gravisimulation

value: shoot base

value: before gravistimulation

value: control


title: shoot base lower at 0.5h, biological rep1


title: shoot base at 0h, biological rep3


title: Patient 44

city: Vienna

first: Dietmar

last: Pils

address: Waehringer Guertel 18-20

department: Dept. of Surgery

country: Austria

institute: Medical University of Vienna

description: Human Genome Survey Microarray V2.0 (Applied Biosystems)

hyb_protocol: Applied Biosystems Chemiluminescence Detection Kit

scan_protocol: Expression Array System Software v1.1.1

data_processing: R Package ABarray 1.4.2 (Filtering flags > 5000, quantile normalization, log-2 transformation)

label: DIG

source_name: Blood fraction

label_protocol: Applied Biosystems Chemiluminescent RT-IVT Labeling Kit

extract_protocol: Total RNA from the blood fraction was isolated with the RNAesy kit (QIAGEN)

tag: disease

value: epithelial ovarian cancer


title: Patient 45


title: Patient 48


title: Patient 37


title: Patient 43


title: Patient 38


title: shoot base upper at 6h, biological rep3


title: Patient 47


title: shoot base upper at 0.5h, biological rep1


title: Patient 39


title: Patient 41


title: Patient 42


title: Patient 46


title: Patient 40


title: Patient 36


title: shoot base at 0h, biological rep1


title: Patient 35


title: Patient 31


title: Patient 33


title: Patient 32


title: Patient 24


title: Patient 26


title: Patient 25


title: Patient 28


title: Patient 30


title: Patient 18


title: Patient 21


title: Patient 27


title: Patient 19


title: Patient 20


title: Patient 23


title: Patient 11


title: Patient 13


title: Patient 29


title: Patient 22


title: Patient 16


title: Patient 15


title: Patient 10


title: Patient 14


title: Patient 8


title: Patient 9


title: Patient 7


title: Patient 6


title: Patient 12


title: Patient 17


title: Patient 3


title: Patient 5


title: Patient 34


title: Patient 2


title: Patient 1


title: Control 20


title: Control 18


title: Control 19


title: Control 16


title: Control 11


title: Control 9


title: Control 4


title: Control 12


title: Control 14


title: Control 7


title: Control 13


title: Control 6


title: Control 5


title: Control 1


title: Control 15


title: H413

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Affymetrix Standard protocol

data_processing: The scanned images of microarray chips were analyzed using the Affymetrix GenChip Operating Software (GCOS) and Expression Console with the default settings except that the target signal was set to 100.

source_name: oral squamous cell carcinoma-derived cell line

label_protocol: The cDNA was synthesized, in vitro transcribed and labeled using standard Affymetrix protocols.

growth_protocol: Tumour-derived cell line was cultured in DMEM/F12 (1:1) containing 10% fetal bovine serum, L-glutamine and hydrocortisone.

extract_protocol:
Total RNA was extracted from cells using the RNeasy Total
RNA Mini Kit (Qiagen, Crawley, West Sussex, UK).

treatment_protocol: Tumour-derived cell line was established by single cell suspension from fresh surgical biopies of untreated human oral squamous cell carcinoma.

tag: cell line

tag: disease state

value: Oral cancer


title: Patient 4


title: Control 2


title: H357


title: Control 17


title: Control 3


title: M9


title: H376


title: H314


title: H157


title: Control 10


title: H400


title: H103


title: NK1

source_name: culture of normal oral keratinocytes

growth_protocol: Keratinocytes were cultured in keratinocyte serum free medium (KSFM) containing bovine pituitary extract, epidermal growth factor and calcium chloride.

treatment_protocol: Normal oral keratinocyte culture were established by single cell suspension from excess tissue originating from routine oral surgical procedures.

value: Normal


title: Sarcoma tumor WD9370

city: New York

first: Brian

last: Denton

address: 307 E. 63rd Street

department: Epidemiology and Biostatistics

institute: Memorial Sloan-Kettering Cancer Center

description: Soft-tissue sarcoma

hyb_protocol: Per manufacturer's instructions.

scan_protocol: Fluorescence was measured by confocal scanner (Agilent, Palo Alto, CA).

data_processing: Signal intensity was generated with Affymetrix Microarray Suite v5 software, and expression was estimated with robust multi-array average (RMA).

label: Biotin

source_name: liposarcoma, well-differentiated

label_protocol: Per manufacturer's instructions.

growth_protocol: None.

extract_protocol: Total RNA was extracted from macro-dissected cryomolds and homogenized in QIAzol lysis reagent.

treatment_protocol: None.

value: primary liposarcoma

tag: subtype

value: well-differentiated

tag: sample id

tag: trainingtest

value: Test

tag: drfs

value: FALSE


title: Sarcoma tumor WD0429

description: Soft-tissue sarcoma

tag: tissue


title: Sarcoma tumor WD9343

description: Soft-tissue sarcoma

value: Training


title: Sarcoma tumor WD721

description: Soft-tissue sarcoma


title: Sarcoma tumor WD724

description: Soft-tissue sarcoma


title: Sarcoma tumor WD510

description: Soft-tissue sarcoma


title: Sarcoma tumor WD687

description: Soft-tissue sarcoma


title: Sarcoma tumor WD705

description: Soft-tissue sarcoma


title: Sarcoma tumor WD6233

description: Soft-tissue sarcoma


title: Sarcoma tumor WD589

description: Soft-tissue sarcoma


title: Sarcoma tumor WD419

description: Soft-tissue sarcoma


title: Sarcoma tumor WD4994

description: Soft-tissue sarcoma


title: Sarcoma tumor WD691

description: Soft-tissue sarcoma


title: Sarcoma tumor WD426

description: Soft-tissue sarcoma


title: Sarcoma tumor WD558

description: Soft-tissue sarcoma


title: Sarcoma tumor WD696

description: Soft-tissue sarcoma


title: Sarcoma tumor WD5700

description: Soft-tissue sarcoma


title: Sarcoma tumor WD725

description: Soft-tissue sarcoma


title: Sarcoma tumor WD706

description: Soft-tissue sarcoma


title: Sarcoma tumor WD472

description: Soft-tissue sarcoma


title: Sarcoma tumor WD688

description: Soft-tissue sarcoma


title: Sarcoma tumor WD468

description: Soft-tissue sarcoma


title: Sarcoma tumor WD60

description: Soft-tissue sarcoma


title: Sarcoma tumor WD463

description: Soft-tissue sarcoma


title: Sarcoma tumor WD701

description: Soft-tissue sarcoma


title: Sarcoma tumor WD418

description: Soft-tissue sarcoma


title: Sarcoma tumor WD356

description: Soft-tissue sarcoma


title: Sarcoma tumor WD0611

description: Soft-tissue sarcoma


title: Sarcoma tumor WD286

description: Soft-tissue sarcoma


title: Sarcoma tumor WD410

description: Soft-tissue sarcoma


title: Sarcoma tumor WD459

description: Soft-tissue sarcoma


title: Sarcoma tumor WD702

description: Soft-tissue sarcoma


title: Sarcoma tumor WD72

description: Soft-tissue sarcoma


title: Control 8


title: Sarcoma tumor WD450

description: Soft-tissue sarcoma

value: TRUE


title: Sarcoma tumor ALT479

description: Soft-tissue sarcoma


title: Sarcoma tumor WD200

description: Soft-tissue sarcoma


title: Sarcoma tumor WD375

description: Soft-tissue sarcoma


title: Sarcoma tumor ALT500

description: Soft-tissue sarcoma


title: Sarcoma tumor WD444

description: Soft-tissue sarcoma


title: Sarcoma tumor WD700

description: Soft-tissue sarcoma


title: Sarcoma tumor ALT486

description: Soft-tissue sarcoma


title: Sarcoma tumor WD602

description: Soft-tissue sarcoma


title: Sarcoma tumor WD401

description: Soft-tissue sarcoma


title: Sarcoma tumor WD194

description: Soft-tissue sarcoma


title: Sarcoma tumor WD199

description: Soft-tissue sarcoma


title: Sarcoma tumor ALT497

description: Soft-tissue sarcoma


title: Sarcoma tumor WD368

description: Soft-tissue sarcoma


title: Sarcoma tumor WD359

description: Soft-tissue sarcoma


title: Sarcoma tumor WD221

description: Soft-tissue sarcoma


title: Sarcoma tumor WD380

description: Soft-tissue sarcoma


title: Sarcoma tumor ALT476

description: Soft-tissue sarcoma


title: Sarcoma tumor PL9313

description:
Soft-tissue sarcoma

Re-analysis of GSM528913

source_name: liposarcoma, pleomorphic

value: pleomorphic


title: Sarcoma tumor PL640

description:
Soft-tissue sarcoma

Re-analysis of GSM528911


title: Sarcoma tumor PL634

description:
Soft-tissue sarcoma

Re-analysis of GSM528910


title: Sarcoma tumor PL278

description: Soft-tissue sarcoma


title: Sarcoma tumor PL617

description:
Soft-tissue sarcoma

Re-analysis of GSM528906


title: Sarcoma tumor PL4580

description:
Soft-tissue sarcoma

Re-analysis of GSM528905


title: Sarcoma tumor PL269

description:
Soft-tissue sarcoma

Re-analysis of GSM528897


title: Sarcoma tumor ML414

description: Soft-tissue sarcoma

source_name: liposarcoma, myxoid

value: myxoid


title: Sarcoma tumor PL128

description:
Soft-tissue sarcoma

Re-analysis of GSM528893


title: Sarcoma tumor PL625

description:
Soft-tissue sarcoma

Re-analysis of GSM528908


title: Sarcoma tumor PL619

description:
Soft-tissue sarcoma

Re-analysis of GSM528907


title: Sarcoma tumor PL268

description: Soft-tissue sarcoma


title: Sarcoma tumor ML169

description: Soft-tissue sarcoma


title: Sarcoma tumor ML618

description: Soft-tissue sarcoma


title: Sarcoma tumor PL627

description:
Soft-tissue sarcoma

Re-analysis of GSM528909


title: Sarcoma tumor PL130

description: Soft-tissue sarcoma


title: Sarcoma tumor PL289

description:
Soft-tissue sarcoma

Re-analysis of GSM528898


title: Sarcoma tumor ML708

description: Soft-tissue sarcoma


title: Sarcoma tumor PL126

description:
Soft-tissue sarcoma

Re-analysis of GSM528892


title: Sarcoma tumor PL295

description: Soft-tissue sarcoma