title: preCC mouse OR291m157

description: preCC mouse OR291m157

value: preCC  OR291


title: preCC mouse OR2075m59

status: Public on Nov 15 2013

type: RNA

city: Chapel Hill

first: Samir

last: Kelada

state: NC

address: 120 Mason Farm Road

department: Genetics

country: USA

institute: University of North Carolina

description: preCC mouse OR2075m59

hyb_protocol: 2 micrograms of labeled cRNAs were hybridized overnight to the Illumina MouseRef-8 plex using Illumina hybridization mixture and temperature.  The slides were washed and stained using standard Illumina's reagents and procedure.

scan_protocol: The Illumina BeadChips were scanned on the Illumina BeadArray scanner.

data_processing: The resulting data were initially processed using Illumina Genome Studio software and then imported into R (v2.9.2) for post-processing. Normalization was conducted using RMA with quantile normalization and log2 transformation.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse lung

label_protocol: 500 nanogram of total RNA was subjeceted to amplification and biotin labeling with the  Ambion Illumina® TotalPrep RNA Amplification Kit (Ambion kit cat# AMIL1791)

growth_protocol: The right lower lobe was inflated with OCT and then flash frozen in liquid nitrogen.

extract_protocol: Lung lobes were homogenized and then RNA was isolated using RNeasy Mini Kits (Qiagen), according to the manufacturer’s instructions. RNAs were DNAseI treated.

treatment_protocol: mice were  i.p. sensitized with 10 ug Der p 1 and then challenged with 50 ug Der p 1 on day 15.  All mice were harvested on day 18 (72 hours after challenge).

tag: strain

value: preCC  OR2075

tag: tissue

value: lung


title: preCC mouse OR5154m140

description: preCC mouse OR5154m140

value: preCC  OR5154


title: preCC mouse OR801m64

description: preCC mouse OR801m64

value: preCC  OR801


title: 200cGy-LPS6hr-m4 (2666_7848_33986)

city: durham

first: lingling

last: zheng

address: research dr

institute: duke university

hyb_protocol: Hybridization protocol was that of the manufacturer protocol by Affymertrix.

scan_protocol: Scanning protocol was that of the manufacturer protocol by Affymetrix.

data_processing: The data was analyzed using RMA from the affy package to pre-process Affymetrix arrays.

label: Biotin

label_protocol: 500ngs of total RNA was amplified according to the MessageAmp Premier protocol (Ambion).  Affymetrix GeneChip analysis was prepared according to the manufacturer’s instructions, and targets were hybridized to the Mouse 430A 2.0 GeneChip (Affymetrix, Santa Clara, CA).

extract_protocol: Blood was collected in PAXgene fluid and total RNA was extracted using the RNeasy Protect Animal Blood Kit.  RNA was beta globin reduced using Ambion Mouse/Rat GLOBINclear kit for the mouse studies.  RNA was purified using the Qiagen RNEasy Mini Kit.  All total RNA samples were assessed for quality using a NanoDrop ND8000 Spectrophotometer for absorbance ratios, and the Agilent Bioanalyzer 2100 for RIN scores.

treatment_protocol: Ten to 12 week old female and male C57Bl6 mice (Jackson Laboratory, Bar Harbor, ME) were housed in the Duke Cancer Center Isolation Facility and all protocols were approved by the Duke University Animal Care and Use Committee (Protocol Number A037-10-02).  Mice were exposed to 0, 100, 150, 200, 300, 450, 600, 800 or 1050 cGy total body irradiation (TBI) via a Cs137 irradiator at a dose rate of 480 cGy/min.  Peripheral blood samples were collected via terminal cardiac puncture at 6, 24, 48 and 72 hrs, as well as day +5 and +7 following TBI.

tag: gender

value: male

tag: stress

value: ionizing radiation

tag: dose

tag: treatment

value: LPS

tag: time

value: peripheral blood


title: 200cGy-GCSF6hr-m4 (2666_7848_33985)

value: GCSF


title: preCC mouse OR477m143

description: preCC mouse OR477m143

value: preCC  OR477


title: preCC mouse OR1237m84

description: preCC mouse OR1237m84

value: preCC  OR1237


title: 300cGy-GCSF6hr-m4 (2666_7848_33988)


title: 0cGy-LPS6hr-m4 (2666_7848_33983)

value: control (no ionizing radiation)


title: preCC mouse OR779m146

description: preCC mouse OR779m146

value: preCC  OR779


title: 200cGy-NOTRT6hr-m4 (2666_7848_33987)

source_name: 200cGy,no treatment,6hr

value: no treatment


title: 0cGy-GCSF6hr-m4 (2666_7848_33982)


title: 0cGy-NOTRT6hr-m4 (2666_7848_33984)

source_name: 0cGy,no treatment,6hr


title: preCC mouse OR3168m50

description: preCC mouse OR3168m50

value: preCC  OR3168


title: preCC mouse OR3019m54

description: preCC mouse OR3019m54

value: preCC  OR3019


title: preCC mouse OR5118m137

description: preCC mouse OR5118m137

value: preCC  OR5118


title: preCC mouse OR3358m55

description: preCC mouse OR3358m55

value: preCC  OR3358


title: 600cGy-NOTRT24hr-m4 (2666_7848_33981)

source_name: 600cGy,no treatment,24hr

value: female


title: 600cGy-GCSF24hr-m4 (2666_7848_33979)


title: preCC mouse OR799m164

description: preCC mouse OR799m164

value: preCC  OR799

value: lung


title: preCC mouse OR4078m152

description: preCC mouse OR4078m152

value: preCC  OR4078


title: preCC mouse OR5049m130

description: preCC mouse OR5049m130

value: preCC  OR5049


title: 300cGy-NOTRT24hr-m4 (2666_7848_33978)

source_name: 300cGy,no treatment,24hr

value: ionizing radiation


title: preCC mouse OR5546m131

description: preCC mouse OR5546m131

value: preCC  OR5546


title: preCC mouse OR692m181

description: preCC mouse OR692m181

value: preCC  OR692


title: 200cGy-GCSF24hr-m4 (2666_7848_33975)

value: GCSF

value: peripheral blood


title: 200cGy-LPS24hr-m4 (2666_7848_33976)

value: LPS


title: preCC mouse OR4251m142

description: preCC mouse OR4251m142

value: preCC  OR4251


title: 600cGy-LPS24hr-m4 (2666_7848_33980)


title: preCC mouse OR5019m130

description: preCC mouse OR5019m130

value: preCC  OR5019


title: Rv0516c Tn 140 mM NaCl Rep 4

city: Berkeley, CA

first: Stavroula

last: Hatzios

address: B84 Hildebrand Hall #1460

institute: UC Berkeley

description: Biological replicate 4 of 4.

hyb_protocol: Slides were prehybridized for at least 1 hour in pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA), washed with water (2 x 1 min washes) and isopropanol (5-10 seconds), and dried with filtered air.  Probe pairs were hybridized to slides in sealed incubation chambers in a 42 °C water bath overnight.  Post-hybridization washes: 2X SSC, 0.1% SDS for 5 min at 42 °C; 0.1X SSC, 0.1% SDS for 10 min at rt; 0.1X SSC for 1 min at rt (4 times); 0.01X SSC for 10 sec at rt.  Slides dried with filtered air.

scan_protocol: Arrays scanned using GenePix 4000B scanner and GenePix 6.0 software.  Channels roughly normalized by adjusting gain during preview scan.

data_processing: Data analyzed with Acuity 4.1 software.  Spots flagged as not found were discarded from the dataset and remaining features were Lowess-normalized.

organism: Mycobacterium tuberculosis

source_name: Rv0516c transposon mutant, 0 mM NaCl for 0 h

label_protocol: Followed standard amino-allyl labeling protocol (TIGR).  Total RNA (5 ug per sample) was reverse-transcribed with Superscript III in the presence of aminoallyl dUTP, purified using a Qiaquick column (Qiagen), and covalently labeled with either Cy5 or Cy3 in sodium carbonate.  Excess dye was removed using a Qiaquick column.  Cy3- and Cy5-labeled cDNA samples were resuspended in hybridization buffer (50% formamide, 5X SSC, and 0.1% SDS).

growth_protocol: Bacteria were grown in 1-L roller bottles in a rolling-bottle incubator at 37 °C.  Cultures were prepared from frozen glycerol stocks and grown to mid-log phase in 7H9 medium.  Bacteria were washed and passaged once in Sauton’s medium, then grown for 2 days to early log phase in 60-mL Sauton's medium.

extract_protocol: Cell pellets were thawed on ice and resuspended in Trizol, disrupted by bead beating, and centrifuged to clarify cell lysates.  Following chloroform extraction with Heavy Phase Lock Gel, the aqueous layer was precipitated using a 50% isopropanol 50% high salt solution (0.8 M sodium citrate, 1.2 M NaCl).  RNA purification and DNAse treatment were performed with the RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Each 60-mL culture was divided into two 30-mL cultures.  One culture (t=0 sample) was centrifuged (10 min, 3500 rpm, rt), and the cell pellet was immediately frozen on dry ice and stored at -80 °C.  The second culture (t=1 h sample) was treated with 140 mM NaCl (~1.5 mL of Sauton’s medium containing 3 M NaCl) to increase the culture osmolarity by  ~280 mOsm/L and incubated for 1 h at 37 °C prior to harvesting and freezing the cells as before.

value: CDC1551 with a transposon insertion in Rv0516c

value: 0 mM NaCl for 0 h

source_name: Rv0516c transposon mutant, 140 mM NaCl for 1 h

value: 140 mM NaCl for 1 h


title: Rv0516c Tn 140 mM NaCl Rep 3

description: Biological replicate 3 of 4.


title: 0cGy-NOTRT24hr-m4 (2666_7848_33974)

source_name: 0cGy,no treatment,24hr

value: control (no ionizing radiation)

value: no treatment


title: Rv0516c Tn 140 mM NaCl Rep 1

description: Biological replicate 1 of 4.


title: Rv0516c Tn 140 mM NaCl Rep 2

description: Biological replicate 2 of 4.


title: 0cGy-GCSF24hr-m4 (2666_7848_33973)

value: female


title: preCC mouse OR3443m48

description: preCC mouse OR3443m48

value: preCC  OR3443

value: lung


title: 600cGy-NOTRT6hr-m4 (2666_7848_33972)

source_name: 600cGy,no treatment,6hr


title: preCC mouse OR5087m133

description: preCC mouse OR5087m133

value: preCC  OR5087


title: 600cGy-LPS6hr-m4 (2666_7848_33971)

value: ionizing radiation


title: ALL P11 dose2 CF

city: Stockholm

first: Ali

last: Moshfegh

department: Oncology & Pathology

country: Sweden

institute: Karolinska Institutet

description: Blood sample were collected 24 hours after first Cyclophsphamimde infusion

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: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Homo sapiens

source_name: blood

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

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

tag: Sex

value: Male

tag: sample type

value: Peripheral blood mononuclear cells

tag: patient

tag: tumor type

value: ALL

tag: collection time point


title: preCC mouse OR3515m67

description: preCC mouse OR3515m67

value: preCC  OR3515


title: preCC mouse OR900m153

description: preCC mouse OR900m153

value: preCC  OR900


title: 300cGy-NOTRT6hr-m4 (2666_7848_33969)

source_name: 300cGy,no treatment,6hr

value: peripheral blood


title: ALL P11 dose3 CF

description: Blood sample were collected 6 hours after second Cyclophsphamimde infusion


title: ALL P11_before CF

description: Blood sample were collected before the start of Cyclophsphamimde infusion


title: 300cGy-GCSF6hr-m4 (2666_7848_33967)

value: GCSF


title: T-Lymphoma P10 dose2 CF

value: Female

value: T-Lymphoma

value: collected 24 hours after first Cyclophsphamimde infusion


title: T-Lymphoma P10 dose3 CF

value: collected 6 hours after second Cyclophsphamimde infusion


title: T-Lymphoma P10 dose1 CF

description: Blood sample were collected 6 hours after first Cyclophsphamimde infusion


title: 200cGy-NOTRT6hr-m4 (2666_7848_33966)

value: no treatment


title: ALL P9 dose3 CF


title: ALL P9 dose1 CF

value: collected 6 hours after first Cyclophsphamimde infusion


title: ALL P9 dose2 CF


title: preCC mouse OR5454m136

description: preCC mouse OR5454m136

value: preCC  OR5454


title: T-Lymphoma P10_before CF

value: collected before the start of Cyclophsphamimde infusion


title: 300cGy-NOTRT24hr-m5 (2666_7848_34045)

value: male


title: 300cGy-LPS6hr-m4 (2666_7848_33968)

value: female

value: ionizing radiation

value: LPS


title: 200cGy-LPS6hr-m4 (2666_7848_33965)


title: 300cGy-LPS6hr-m5 (2666_7848_34033)


title: preCC mouse OR3066m50

description: preCC mouse OR3066m50

value: preCC  OR3066

value: lung


title: 0cGy-NOTRT6hr-m4 (2666_7848_33963)

value: control (no ionizing radiation)


title: preCC mouse OR5156m127

description: preCC mouse OR5156m127

value: preCC  OR5156


title: 200cGy-GCSF6hr-m4 (2666_7848_33964)

value: GCSF

value: peripheral blood


title: preCC mouse OR41m114

description: preCC mouse OR41m114

value: preCC  OR411


title: preCC mouse OR3081m35

description: preCC mouse OR3081m35

value: preCC  OR3081


title: preCC mouse OR5140m134

description: preCC mouse OR5140m134

value: preCC  OR5140


title: 0cGy-LPS6hr-m4 (2666_7848_33962)


title: preCC mouse OR3564m41

description: preCC mouse OR3564m41

value: preCC  OR3564


title: ALL P9_before CF

value: Male

value: Peripheral blood mononuclear cells

value: ALL


title: 0cGy-GCSF6hr-m4 (2666_7848_33961)


title: preB-ALL P8 dose3 CF

value: preB-ALL

value: collected 6 hours after second Cyclophsphamimde infusion


title: preB-ALL P8 dose1 CF

value: collected 6 hours after first Cyclophsphamimde infusion


title: het (+/-) kidney replicate 4

city: Seville

first: Jose

middle: I

last: Piruat

address: Hospital Virgen del Rocio-Edif IBiS. Av. Manuel Siurot sn

department: Hematology

country: Spain

institute: Institute of Biomedicine of Seville (IBIS)

description: array 121010b_2-4.mev

hyb_protocol: Labeled cRNA was mixed and hybridized against the oligonucleotide microarray slides Mouse GE 4x44k V2 (Agilent Technologies).

scan_protocol: The microarrays were scanned in a GenePix® reader, with data acquired at wavelengths of 635nm and 532nm for Cy3 and Cy5, respectively.

data_processing:
The raw data were generated with the GenePix(R) Pro v6.0 microarray acquisition and analysis software. This software automatically sets the PMT gain to minimize the variability due to different signal intensities of the two dyes. After adjusting the PMTs they are producing roughly the same response in both channels.
The obtained files (.gpr format) were transformed to .mev files with the ExpressConverter (Version 2.1) software. ExpressConverter is a file transformation tool that reads microarray data files in a variety of file formats and generates TIGR MultiExperiment Viewer files (.mev) as output so that the microarray data can be analyzed with the MultiExperiment Viewer v4.5 software.
In this software, samples from different hybrydizations were normalized. For this, the values were transformed by use of the mean and the standard deviation of each sample (column) of the matrix to which the value belongs, using the following formula: Value = [(Value) - Mean(column)]/[Standard deviation(column)].

source_name: kidney total RNA heterozygous (+/-) mice

label_protocol: 200 ng of kidney RNA were reverse-transcribed into cRNA and labeled with the Two-Color Microarray Low Input Quick Amp Labeling Kit (Agilent Technologies). Samples from 8 homozygous (+/+) individuals were pooled, labeled with cyanine 3-CTP (Cy3), and used as reference samples. Samples from 8 heterozygous (+/-) and 8 SDHD-ESR individuals were labeled with cyanine 5-CTP (Cy5) and used as test samples.

growth_protocol: Mice were housed under temperature-controlled conditions (22 ºC) in a 12 h light/dark cycle, and provided with food and water ad libitum.

extract_protocol: Tissues were dissected and stored frozen at -80° until processing. Total RNA was prepared from mouse tissues with TRIzol® reagent (Life Technologies), according to the manufacturer's directions for each type of sample. Total RNA was cleaned-up using the RNeasy® microkit (Qiagen).

treatment_protocol: 9-weeks old mice were injected with 100 ug/g tamoxifen i.p. daily for 4 days to induce deletion of SdhD gene and sacrificed 1 week after the first tamoxifen injection.

tag: strain background

tag: age

value: 10 weeks

tag: genotype/variation

value: heterozygous (+/-)

value: kidney

source_name: kidney total RNA homozygous (+/+) mice

value: homozygous (+/+) wild type


title: preCC mouse OR857m67

description: preCC mouse OR857m67

value: preCC  OR857

value: lung


title: preB-ALL P8 dose2 CF

value: collected 24 hours after first Cyclophsphamimde infusion


title: preB-ALL P8_before CF

value: collected before the start of Cyclophsphamimde infusion


title: preCC mouse OR1515m165

description: preCC mouse OR1515m165

value: preCC  OR1515


title: SDHD-ESR kidney replicate 4

description: array 121010b_4-4.mev

source_name: kidney total RNA null SDHD-ESR mutant mice

value: null SDHD-ESR mutant


title: SDHD-ESR kidney replicate 2

description: array 121002_4-4.mev


title: het (+/-) kidney replicate 3

description: array 121010b_1-4.mev


title: AML P7 dose2 CF

value: AML


title: AML P7_before CF

value: Male


title: AML P7 dose3 CF

value: Peripheral blood mononuclear cells


title: AML P7 dose1 CF


title: SDHD-ESR kidney replicate 3

description: array 121010b_3-4.mev


title: 600cGy-NOTRT24hr-m7 (2666_7848_33960)

value: male

value: ionizing radiation

value: no treatment

value: peripheral blood


title: 600cGy-LPS24hr-m3 (2666_7848_33959)

value: LPS


title: preCC mouse OR5480m136

description: preCC mouse OR5480m136

value: preCC  OR5480


title: preCC mouse OR4227m141

description: preCC mouse OR4227m141

value: preCC  OR4227


title: ALL P6 dose2 CF

value: ALL


title: 600cGy-GCSF24hr-m3 (2666_7848_33958)

value: GCSF


title: 300cGy-LPS24hr-m3 (2666_7848_33957)


title: SDHD-ESR kidney replicate 1

description: array 121002_3-4.mev

value: 10 weeks

value: kidney

value: homozygous (+/+) wild type


title: preCC mouse OR1246m70

description: preCC mouse OR1246m70

value: preCC  OR1246

value: lung


title: ALL P6 dose1 CF

value: collected 6 hours after first Cyclophsphamimde infusion


title: 200cGy-NOTRT24hr-m3 (2666_7848_33955)

source_name: 200cGy,no treatment,24hr


title: het (+/-) kidney replicate 2

description: array 121002_2-4.mev

value: heterozygous (+/-)


title: SDHD-ESR AM replicate 3

description: array 121123_3-4.mev

source_name: AM total RNA null SDHD-ESR mutant mice

label_protocol: 45 ng of RNA from adrenal medulla were reverse-transcribed into cRNA and labeled with the Two-Color Microarray Low Input Quick Amp Labeling Kit (Agilent Technologies). Samples from 8 homozygous (+/+) individuals were pooled, labeled with cyanine 3-CTP (Cy3), and used as reference samples. Samples from 8 heterozygous (+/-) and 8 SDHD-ESR individuals were labeled with cyanine 5-CTP (Cy5) and used as test samples.

extract_protocol: Tissues were dissected and stored frozen at -80° until processing. Total RNA was prepared from mouse tissues with TRIzol® reagent (Life Technologies), according to the manufacturer's directions for each type of sample. Total RNA from the adrenal medulla, surgically separated from cortex, was prepared using the RNeasy® microkit (Qiagen).

value: null SDHD-ESR mutant

value: adrenal medulla

source_name: AM total RNA homozygous (+/+) mice


title: ALL P6_before CF

value: Male

value: Peripheral blood mononuclear cells

value: collected before the start of Cyclophsphamimde infusion


title: SDHD-ESR AM replicate 4

description: array 121123_4-4.mev


title: het (+/-) kidney replicate 1

description: array 121002_1-4.mev


title: 0cGy-NOTRT24hr-m3 (2666_7848_33953)

value: male

value: control (no ionizing radiation)

value: no treatment

value: peripheral blood


title: preCC mouse OR1496m138

description: preCC mouse OR1496m138

source_name: mouse lung

value: preCC  OR1496


title: 300cGy-GCSF24hr-m3 (2666_7848_33956)

value: ionizing radiation

value: GCSF


title: preCC mouse OR5549m133

description: preCC mouse OR5549m133

value: preCC  OR5549


title: preCC mouse OR4179m174

description: preCC mouse OR4179m174

value: preCC  OR4179


title: preB-ALL P5 dose2 CF

value: preB-ALL

value: collected 24 hours after first Cyclophsphamimde infusion


title: 200cGy-GCSF24hr-m3 (2666_7848_33954)


title: preB-ALL P5_before CF


title: ALL P6 dose3 CF

value: ALL

value: collected 6 hours after second Cyclophsphamimde infusion


title: preCC mouse OR13m69

description: preCC mouse OR13m69

value: preCC  OR136

value: lung


title: preB-ALL P5 dose3 CF

value: Male

value: Peripheral blood mononuclear cells


title: het (+/-) AM replicate 3

description: array 121123_1-4.mev

source_name: AM total RNA heterozygous (+/-) mice

value: 10 weeks

value: heterozygous (+/-)

value: adrenal medulla

value: homozygous (+/+) wild type


title: SDHD-ESR AM replicate 1

description: array 121121_3-4.mev

value: null SDHD-ESR mutant


title: preB-ALL P5 dose1 CF

value: collected 6 hours after first Cyclophsphamimde infusion


title: 0cGy-LPS24hr-m3 (2666_7848_33952)

value: male

value: control (no ionizing radiation)

value: LPS

value: peripheral blood


title: preCC mouse OR5291m125

description: preCC mouse OR5291m125

value: preCC  OR5291


title: SDHD-ESR AM replicate 2

description: array 121121_4-4.mev


title: preCC mouse OR2168m52

description: preCC mouse OR2168m52

value: preCC  OR2168


title: preCC mouse OR3080m40

description: preCC mouse OR3080m40

value: preCC  OR3080


title: 0cGy-GCSF24hr-m3 (2666_7848_33951)

value: GCSF


title: ALL P4 dose3 CF

value: ALL

value: collected 6 hours after second Cyclophsphamimde infusion


title: 600cGy-GCSF6hr-m3 (2666_7848_33948)

value: ionizing radiation


title: 600cGy-NOTRT6hr-m3 (2666_7848_33950)

value: no treatment


title: preCC mouse OR462m61

description: preCC mouse OR462m61

value: preCC  OR462

value: lung


title: het (+/-) AM replicate 4

description: array 121123_2-4.mev

value: 10 weeks

value: heterozygous (+/-)

value: adrenal medulla

value: homozygous (+/+) wild type


title: preCC mouse OR3594m47

description: preCC mouse OR3594m47

value: preCC  OR3594


title: ALL P4 dose2 CF

value: Male

value: Peripheral blood mononuclear cells

value: collected 24 hours after first Cyclophsphamimde infusion


title: AML P3 dose3 CF

value: Female

value: AML


title: het (+/-) AM replicate 1

description: array 121121_1-4.mev


title: 600cGy-LPS6hr-m3 (2666_7848_33949)

value: male

value: LPS

value: peripheral blood


title: het (+/-) AM replicate 2

description: array 121121_2-4.mev


title: ALL P4 dose1 CF

value: ALL

value: collected 6 hours after first Cyclophsphamimde infusion


title: 300cGy-NOTRT6hr-m3 (2666_7848_33947)

value: ionizing radiation

value: no treatment


title: preCC mouse OR3067m51

description: preCC mouse OR3067m51

value: preCC  OR3067

value: lung


title: preCC mouse OR3140m58

description: preCC mouse OR3140m58

value: preCC  OR3140


title: Lin- cells_BCR-ABL+IRF8_Flt3L_day5_exp1

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

hyb_protocol: Slides were hybridized according to the manufacturer's protocol (One-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90040, Version 6.5, May 2010).

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-60502) at 100% in Green channel, with a scan resolution of 3 um.

data_processing: Data are extracted with Agilent Feature Extraction Software and quantile-normalized.

source_name: Lin- cells, MIG-BCR-ABL+MICD8-IRF8 transduced, Flt3L, day 5, experiment 1

label_protocol: Total RNA was labeled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's instructions.

growth_protocol: Murine bone marrow Lin- cells were precultured for 24 hours with 100 ng/mL SCF, 10 ng/mL IL-6, and 10 ng/mL IL-3, and transduced with retroviruses by spinoculation on two consecutive days.

extract_protocol: Total RNA was extracted using RNAiso Plus reagent (Takara) and further purified using RNeasy Mini Kit (Qiagen) according to the manufacturers' instructions.

treatment_protocol: Transduced cells were FACS-sorted and cultured with 100 ng/ml human Flt3L for 5 days.

tag: cell type

value: Bone marrow derived Lin- cells

tag: treatment period

value: 5 day

tag: transduction condition

value: MIG-BCR-ABL + MICD8-IRF8


title: Lin- cells_BCR-ABL+IRF8_Flt3L_day5_exp2

source_name: Lin- cells, MIG-BCR-ABL+MICD8-IRF8 transduced, Flt3L, day 5, experiment 2


title: 300cGy-LPS6hr-m3 (2666_7848_33946)

tag: strain

tag: tissue


title: AML P3 dose2 CF

value: Peripheral blood mononuclear cells


title: ALL P4_before CF

value: Male

value: collected before the start of Cyclophsphamimde infusion


title: Lin- cells_BCR-ABL_Flt3L_day5_exp2

source_name: Lin- cells, MIG-BCR-ABL+empty MICD8 transduced, Flt3L, day 5, experiment 2

value: MIG-BCR-ABL + MICD8


title: preCC mouse OR3327m48

description: preCC mouse OR3327m48

value: preCC  OR3327


title: 300cGy-GCSF6hr-m3 (2666_7848_33945)

tag: gender

value: male

tag: stress

value: GCSF


title: AML P3_before CF

value: Female

value: AML


title: AML P3 dose1 CF

value: collected 6 hours after first Cyclophsphamimde infusion


title: 200cGy-LPS6hr-m3 (2666_7848_33943)

value: ionizing radiation

tag: dose

tag: treatment

value: LPS

value: peripheral blood


title: preCC mouse OR5401m137

description: preCC mouse OR5401m137

value: preCC  OR5401

value: lung


title: T-LBL P2 dose3 CF

tag: Sex

value: T-LBL

value: collected 6 hours after second Cyclophsphamimde infusion


title: Lin- cells_MIG+MICD8_Flt3L_day5_exp2

source_name: Lin- cells, empty MIG+empty MICD8 transduced, Flt3L, day 5, experiment 2

value: Bone marrow derived Lin- cells

value: 5 day

value: Empty MIG (MSCV-IRES-GFP) + Empty MICD8 (MSCV-IRES-hCD8t)


title: Lin- cells_MIG+MICD8_Flt3L_day5_exp1

source_name: Lin- cells, empty MIG+empty MICD8 transduced, Flt3L, day 5, experiment 1


title: Lin- cells_BCR-ABL_Flt3L_day5_exp1

source_name: Lin- cells, MIG-BCR-ABL+empty MICD8 transduced, Flt3L, day 5, experiment 1

value: MIG-BCR-ABL + MICD8


title: preCC mouse OR699m69

description: preCC mouse OR699m69

value: preCC  OR699


title: T-LBL P2 dose1 CF

value: Male

tag: sample type

value: Peripheral blood mononuclear cells


title: preCC mouse OR380m69

description: preCC mouse OR380m69

value: preCC  OR380


title: preCC mouse OR5130m140

description: preCC mouse OR5130m140

value: preCC  OR5130


title: preCC mouse OR3061m49

description: preCC mouse OR3061m49

value: preCC  OR3061


title: T-LBL P2 dose2 CF

tag: patient

value: collected 24 hours after first Cyclophsphamimde infusion


title: CLL P1 dose3 CF

tag: tumor type

value: CLL


title: 200cGy-NOTRT6hr-m3 (2666_7848_33944)

source_name: 200cGy,no treatment,6hr

value: male

value: ionizing radiation

value: no treatment

tag: time

value: peripheral blood


title: preCC mouse OR381m65

description: preCC mouse OR381m65

value: preCC  OR381

value: lung


title: PBMCs from rat with large myocardial infarction, biological rep5

city: Warszawa

first: Dorota

middle: Anna

last: Tulacz

address: Pawinskiego 5a

department: Department of Genetics

country: Poland

institute: Institute of Biochemistry and Biophysics of the Polish Academy of Sciences

description: Gene expression data from peripheral blood mononuclear cells (PBMCs) of rat with progressive decompensation of LV and heart failure

hyb_protocol: Following fragmentation, 5.5 ug ssDNA were hybridized for 16 hr at 45˚C on GeneChip® Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GCS 3000 GeneArray Scanner.

data_processing: The data were analyzed with the Partek Genomics Suite software (Partek Inc, St. Louis, MO, USA) using RMA (robust multiarray average) background correction, quantile normalization, median polish method for probesets summarization, and log values of probes signals using base 2.

organism: Rattus norvegicus

source_name: peripheral blood mononuclear cells

label_protocol: Biotin-labeled ssDNA were prepared from 100 ng total RNA by using the Ambion® WT Expression Kit followed by Affymetrix® GeneChip® WT Terminal Labeling Kit according to the manufacturer's instruction.

extract_protocol: Total RNA from left ventricular (LV) tissue and peripheral blood mononuclear cells (PBMCs) samples was isolated using MagNA Pure Compact System (Roche Diagnostics GmbH, Germany) according to the manufacturer's recommendations. LVs were previously homogenized by MagNA Lyser Instrument. The amount of RNA was quantified by UV absorption (Nanodrop, LabTech International, UK) and its quality was determined using an Agilent 2100 Bioanalizer© and RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA). For all RNA samples the RNA integrity number value was above eight.

value: peripheral blood mononuclear cells

tag: samples collection

value: 2 months after the operation of myocardial infarction induction

tag: size of myocardial infarction

value: large infarct size


title: preCC mouse OR219m71

description: preCC mouse OR219m71

value: preCC  OR219


title: T-LBL P2_before CF

source_name: blood

value: Male

value: T-LBL

tag: collection time point

value: collected before the start of Cyclophsphamimde infusion


title: preCC mouse OR937m160

description: preCC mouse OR937m160

value: preCC  OR937


title: preCC mouse OR3181m52

description: preCC mouse OR3181m52

value: preCC  OR3181


title: preCC mouse OR1536m143

description: preCC mouse OR1536m143

value: preCC  OR1536


title: PBMCs from rat with large myocardial infarction, biological rep4


title: M_THP-1(4-UND,48h)

first: Melissa

last: Troester

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

description: Agilent Custom array of THP-1(UND,48h)

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Human Reference B

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

extract_protocol: Qiagen Rneasy Mini

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: THP-1 human monocytic cell line isolated from patient with acute monocytic leukemia

growth_protocol: grown in RMPI media

treatment_protocol: untreated, maintained in RPMI for 48 hr

value: untreated, maintained in RPMI for 48 hr

tag: cell line

tag: cell culture

value: suspension monocytic cell culture


title: preCC mouse OR538m149

description: preCC mouse OR538m149

tag: strain

value: preCC  OR538


title: preCC mouse OR867m181

description: preCC mouse OR867m181

value: preCC  OR867

tag: tissue


title: M_THP-1(4-M2,48h)

description: Agilent Custom array of THP-1(M2,48h)

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

treatment_protocol: treated with PMA for 18 hr, then IL-4 and IL-13 added for additional 30 hr


title: PBMCs from rat with large myocardial infarction, biological rep2


title: PBMCs from sham-operated rat, biological rep5

description: Gene expression data from peripheral blood mononuclear cells (PBMCs) of sham-operated rat

value: 2 months after sham-surgery

value: lack of an infarct area


title: M_THP-1(4-PMA,48h)

description: Agilent Custom array of THP-1(PMA,48h)

treatment_protocol: treated with PMA for 48 hr

value: treated with PMA for 48 hr


title: PBMCs from rat with large myocardial infarction, biological rep3

value: peripheral blood mononuclear cells

value: 2 months after the operation of myocardial infarction induction


title: preCC mouse OR3549m47

description: preCC mouse OR3549m47

value: preCC  OR3549

value: lung


title: PBMCs from rat with large myocardial infarction, biological rep1

description: Gene expression data from peripheral blood mononuclear cells (PBMCs) of rat with compensated LV injury

value: large infarct size


title: preCC mouse OR125m64

description: preCC mouse OR125m64

value: preCC  OR125


title: PBMCs from sham-operated rat, biological rep6


title: preCC mouse OR2390m63

description: preCC mouse OR2390m63

value: preCC  OR2390


title: M_THP-1(3-PMA,48h)

description: Agilent Custom array of THP-1(PMA,48h)


title: preCC mouse OR4410m171

description: preCC mouse OR4410m171

value: preCC  OR4410


title: M_THP-1(3-M2,48h)

description: Agilent Custom array of THP-1(M2,48h)

value: treated with PMA for 18 hr, then IL-4 and IL-13 added for additional 30 hr


title: M_THP-1(4-M1,48h)

description: Agilent Custom array of THP-1(M1,48h)

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

treatment_protocol: treated with PMA for 18 hr, then IFN-g and LPS added for additional 30 hr


title: PBMCs from sham-operated rat, biological rep4


title: M_THP-1(3-UND,48h)

description: Agilent Custom array of THP-1(UND,48h)

value: untreated, maintained in RPMI for 48 hr


title: PBMCs from sham-operated rat, biological rep2


title: PBMCs from sham-operated rat, biological rep3


title: preCC mouse OR3467m61

description: preCC mouse OR3467m61

value: preCC  OR3467


title: preCC mouse OR190m55

description: preCC mouse OR190m55

value: preCC  OR190


title: M_THP-1(3-M1,48h)

description: Agilent Custom array of THP-1(M1,48h)

value: treated with PMA for 18 hr, then IFN-g and LPS added for additional 30 hr

value: suspension monocytic cell culture


title: M_THP-1(2-UND,48h)

description: Agilent Custom array of THP-1(UND,48h)


title: M_THP-1(2-M2,48h)

description: Agilent Custom array of THP-1(M2,48h)


title: hearts from rat with large myocardial infarction, biological rep5

description: Gene expression data from left ventricular (LV) tissue of rat with progressive decompensation of LV and heart failure

source_name: left ventricular tissue

value: left ventricular tissue


title: M_THP-1(2-M1,48h)

description: Agilent Custom array of THP-1(M1,48h)


title: hearts from rat with large myocardial infarction, biological rep1

description: Gene expression data from left ventricular (LV) tissue of rat with compensated LV injury


title: preCC mouse OR5513m128

description: preCC mouse OR5513m128

value: preCC  OR5513


title: preCC mouse OR1057m169

description: preCC mouse OR1057m169

value: preCC  OR1057


title: preCC mouse OR2020m60

description: preCC mouse OR2020m60

value: preCC  OR2020


title: preCC mouse OR5252m131

description: preCC mouse OR5252m131

value: preCC  OR5252


title: M_THP-1(1-UND,48h)

description: Agilent Custom array of THP-1(UND,48h)


title: hearts from rat with large myocardial infarction, biological rep3

value: 2 months after the operation of myocardial infarction induction


title: M_THP-1(1-PMA,48h)

description: Agilent Custom array of THP-1(PMA,48h)

value: treated with PMA for 48 hr


title: hearts from rat with moderate myocardial infarction, biological rep6

value: moderate infarct size


title: preCC mouse OR5528m164

description: preCC mouse OR5528m164

value: preCC  OR5528

value: lung


title: hearts from rat with large myocardial infarction, biological rep4

value: large infarct size


title: preCC mouse OR652m150

description: preCC mouse OR652m150

value: preCC  OR652


title: M_THP-1(2-PMA,48h)

description: Agilent Custom array of THP-1(PMA,48h)

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: hearts from rat with large myocardial infarction, biological rep2


title: hearts from rat with moderate myocardial infarction, biological rep5


title: M_THP-1(1-M2,48h)

description: Agilent Custom array of THP-1(M2,48h)

value: treated with PMA for 18 hr, then IL-4 and IL-13 added for additional 30 hr


title: Proband 5   gluteal

city: Hamburg

first: Sandra

last: Gehrke

address: Unnastraße 48

department: Applied Skin Biology

country: Germany

institute: Beiersdorf AG

hyb_protocol: Standard Miltenyi Protocol

scan_protocol: Standard Miltenyi Protocol

data_processing: The preprocessing proper started with the conversion of the data provided by BDF and Miltenyi in a format suitable for all subsequent analysis steps, which were mainly performed with the R statistical software and its Bioconductor packages. After reading the data files into R, all data were background-corrected. After background correction, data were normalized between arrays (i.e. samples) using quantile-normalization and transformed to log2-scale, which enabled comparison of samples loaded on different arrays. After normalization, a set of quality control steps were performed to filter low-quality probes. Filtering of probes was based on quality flags set by the Agilent Feature Extraction Software.

source_name: subcutaneous adipose tissue gluteal

label_protocol: Standard Miltenyi Protocol

extract_protocol: Total RNA was isolated using the RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer`s instructions

tag: gender

value: female

tag: age

value: 34 years

value: subcutaneous adipose tissue


title: preCC mouse OR1635m174

description: preCC mouse OR1635m174

value: preCC  OR1635


title: preCC mouse OR4445m141

description: preCC mouse OR4445m141

value: preCC  OR4445


title: Proband 5   abdominal

source_name: subcutaneous adipose tissue abdominal


title: hearts from rat with moderate myocardial infarction, biological rep4

value: left ventricular tissue


title: M_THP-1(1-M1,48h)

description: Agilent Catalog 4by44k whole genome array of THP-1(M1,48h)

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

value: treated with PMA for 18 hr, then IFN-g and LPS added for additional 30 hr

value: suspension monocytic cell culture


title: hearts from rat with moderate myocardial infarction, biological rep3

value: 2 months after the operation of myocardial infarction induction


title: hearts from rat with moderate myocardial infarction, biological rep1


title: preCC mouse OR1401m157

description: preCC mouse OR1401m157

value: preCC  OR1401


title: hearts from rat with moderate myocardial infarction, biological rep2

value: moderate infarct size


title: preCC mouse OR559m152

description: preCC mouse OR559m152

value: preCC  OR559


title: Muscle_Subject15_Exercise_Day1_TechRep1of1

city: Loughborough

first: Andrew

last: Murton

state: Leicestershire

address: Sutton Bonington Campus

department: Division of Nutritional Sciences

country: United Kingdom

institute: The University of Nottingham

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the exercise group
Subject15_Day1

hyb_protocol: Protocol per manufacturer's protocol (Affymetrix, Santa Clara, CA)

data_processing: Background corrected by RMA on PM data; quantile normalised; summarisation by median polish regression method. All performed in Bioconductor v2.5

source_name: Vastus lateralis muscle at baseline in subjects assigned to execise group  (day1)

extract_protocol: Total RNA extracted using Trizol according to manufacturer's protocol (Sigma, UK)

value: Vastus lateralis muscle

value: Male

tag: subject

tag: protocol

value: exercise (baseline)

value: day 1

tag: tech rep


title: Muscle_Subject15_Exercise_Day4_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained 24hrs following a repeat bout of resistance exercise
Subject15_Day4

scan_protocol: Protocol per manufacturer's protocol (Affymetrix, Santa Clara, CA)

source_name: Vastus lateralis muscle 24 hrs following a repeat bout of resistance exercise (day4)

value: exercise (2 bouts)

value: day 4


title: Proband 41 gluteal

value: female

value: 28 years


title: hearts from rat with small myocardial infarction, biological rep5

value: small infarct size


title: preCC mouse OR3118m48

description: preCC mouse OR3118m48

source_name: mouse lung

value: preCC  OR3118

value: lung


title: Proband 41 abdominal

value: subcutaneous adipose tissue


title: preCC mouse OR1234m179

description: preCC mouse OR1234m179

value: preCC  OR1234


title: hearts from rat with small myocardial infarction, biological rep6

value: left ventricular tissue

value: 2 months after the operation of myocardial infarction induction


title: preCC mouse OR3156m41

description: preCC mouse OR3156m41

value: preCC  OR3156


title: hearts from rat with small myocardial infarction, biological rep3


title: Proband 45 abdominal

value: 35 years


title: hearts from rat with small myocardial infarction, biological rep4


title: Muscle_Subject15_Exercise_Day2_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained 24hrs following unaccustomed resistance exercise
Subject15_Day2

source_name: Vastus lateralis muscle 24 hrs following a bout of unaccustomed resistance exercise (day2)

label_protocol: Protocol per manufacturer's protocol (Affymetrix, Santa Clara, CA)

value: Vastus lateralis muscle

value: exercise (1 bout)

value: day 2


title: Muscle_Subject14_Control_Day1_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the control (non-exercised) group
Subject14_Day1

source_name: Vastus lateralis muscle at baseline in subjects assigned to control group  (day1)

value: Male

value: control (non-exercised)

value: day 1


title: Muscle_Subject14_Control_Day4_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained on Day 4 from subjects assigned to the control (non-exercised) group
Subject14_Day4

source_name: Vastus lateralis muscle at day 4 in subjects assigned to control group

value: day 4


title: Proband 34 gluteal

value: female

value: 31 years


title: preCC mouse OR1122m139

description: preCC mouse OR1122m139

value: preCC  OR1122


title: Proband 45 gluteal


title: preCC mouse OR220m52

description: preCC mouse OR220m52

value: preCC  OR220

value: lung


title: PBMCs from sham-operated rat, biological rep1

description: Gene expression data from peripheral blood mononuclear cells (PBMCs) for sham-operated rat

value: peripheral blood mononuclear cells

value: 2 months after sham-surgery

value: lack of an infarct area


title: CLL P1 dose2 CF

tag: Sex

tag: sample type

value: Peripheral blood mononuclear cells

value: CLL

value: collected 24 hours after first Cyclophsphamimde infusion


title: Proband 27 gluteal

value: 27 years

value: subcutaneous adipose tissue


title: Muscle_Subject14_Control_Day2_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained on Day 2 from subjects assigned to the control (non-exercised) group
Subject14_Day2

source_name: Vastus lateralis muscle at day 2 in subjects assigned to control group

value: Vastus lateralis muscle

value: Male

value: day 2


title: hearts from rat with small myocardial infarction, biological rep2

value: left ventricular tissue

value: 2 months after the operation of myocardial infarction induction

value: small infarct size


title: preCC mouse OR3415m51

description: preCC mouse OR3415m51

value: preCC  OR3415


title: preCC mouse OR3232m54

description: preCC mouse OR3232m54

value: preCC  OR3232


title: Muscle_Subject13_Control_Day1_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the control (non-exercised) group
Subject13_Day1

value: control (non-exercised)

value: day 1


title: preCC mouse OR3389m51

description: preCC mouse OR3389m51

value: preCC  OR3389

value: lung


title: Proband 27 abdominal

value: female


title: Proband 26 gluteal

value: 29 years


title: Muscle_Subject12_Control_Day2_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained on Day 2 from subjects assigned to the control (non-exercised) group
Subject12_Day2


title: Muscle_Subject12_Control_Day1_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the control (non-exercised) group
Subject12_Day1


title: preCC mouse OR739m165

description: preCC mouse OR739m165

value: preCC  OR739


title: Proband 23 gluteal

value: 35 years


title: Muscle_Subject11_Exercise_Day2_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained 24hrs following unaccustomed resistance exercise
Subject11_Day2

value: exercise (1 bout)


title: Proband 34 abdominal

value: 31 years

value: subcutaneous adipose tissue


title: Proband 23 abdominal


title: Muscle_Subject10_Control_Day4_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained on Day 4 from subjects assigned to the control (non-exercised) group
Subject10_Day4

value: Vastus lateralis muscle

value: Male

value: day 4


title: Muscle_Subject11_Exercise_Day1_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the exercise group
Subject11_Day1

value: exercise (baseline)


title: preCC mouse OR820m63

description: preCC mouse OR820m63

value: preCC  OR820


title: preCC mouse OR896m61

description: preCC mouse OR896m61

value: preCC  OR896


title: preCC mouse OR5612m133

description: preCC mouse OR5612m133

value: preCC  OR5612


title: Proband 22 abdominal

value: 34 years


title: Muscle_Subject13_Control_Day4_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained on Day 4 from subjects assigned to the control (non-exercised) group
Subject13_Day4

value: control (non-exercised)


title: preCC mouse OR5410m133

description: preCC mouse OR5410m133

value: preCC  OR5410

value: lung


title: Muscle_Subject10_Control_Day1_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the control (non-exercised) group
Subject10_Day1

value: day 1


title: preCC mouse OR3011m48

description: preCC mouse OR3011m48

value: preCC  OR3011


title: Proband 22 gluteal

value: female


title: hearts from rat with small myocardial infarction, biological rep1

description: Gene expression data from left ventricular (LV) tissue of rat with compensated LV injury

value: left ventricular tissue

value: 2 months after the operation of myocardial infarction induction

value: small infarct size


title: Muscle_Subject09_Exercise_Day2_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained 24hrs following unaccustomed resistance exercise
Subject09_Day2

value: Vastus lateralis muscle

value: exercise (1 bout)

value: day 2


title: Proband 17 abdominal

value: 24 years

value: subcutaneous adipose tissue


title: hearts from sham-operated rat, biological rep6

description: Gene expression data from left ventricular (LV) tissue of sham-operated rat

value: 2 months after sham-surgery

value: lack of an infarct area


title: hearts from sham-operated rat, biological rep3


title: Muscle_Subject09_Exercise_Day1_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the exercise group
Subject09_Day1

value: Male

value: exercise (baseline)


title: Proband 10 gluteal

value: 26 years


title: hearts from sham-operated rat, biological rep2


title: Proband 26 abdominal

value: 29 years


title: hearts from sham-operated rat, biological rep4


title: Proband 17 gluteal


title: preCC mouse OR3009m54

description: preCC mouse OR3009m54

value: preCC  OR3009

value: lung


title: Proband 10 abdominal

value: female


title: hearts from sham-operated rat, biological rep5

value: left ventricular tissue


title: preCC mouse OR2580m61

description: preCC mouse OR2580m61

value: preCC  OR2580


title: Muscle_Subject08_Control_Day2_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained on Day 2 from subjects assigned to the control (non-exercised) group
Subject08_Day2

value: control (non-exercised)


title: Muscle_Subject08_Control_Day4_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained on Day 4 from subjects assigned to the control (non-exercised) group
Subject08_Day4

value: Vastus lateralis muscle

value: day 4


title: preCC mouse OR3078m52

description: preCC mouse OR3078m52

value: preCC  OR3078


title: preCC mouse OR3401m39

description: preCC mouse OR3401m39

value: preCC  OR3401


title: Muscle_Subject08_Control_Day1_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the control (non-exercised) group
Subject08_Day1

value: day 1


title: Muscle_Subject07_Exercise_Day4_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained 24hrs following a repeat bout of resistance exercise
Subject07_Day4

value: exercise (2 bouts)


title: hearts from sham-operated rat, biological rep1

value: 2 months after sham-surgery

value: lack of an infarct area


title: preCC mouse OR3180m54

description: preCC mouse OR3180m54

value: preCC  OR3180


title: Muscle_Subject07_Exercise_Day1_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the exercise group
Subject07_Day1

value: Male

value: exercise (baseline)


title: Muscle_Subject07_Exercise_Day2_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained 24hrs following unaccustomed resistance exercise
Subject07_Day2

value: exercise (1 bout)

value: day 2


title: preCC mouse OR792m76

description: preCC mouse OR792m76

value: preCC  OR792

value: lung


title: preCC mouse OR5516m139

description: preCC mouse OR5516m139

value: preCC  OR5516


title: DL nucleus motor neurons bio rep 1

city: New York

first: Krista

middle: Joan

last: Spiller

state: New York

address: 630 W 168th street

institute: Columbia University

description: gene expression data from dorsolateral nucleus motor neurons of young wild type mouse

hyb_protocol: µg of biotinylated cRNA from three independent samples for each motor neuron group isolated by LCM was hybridized to on Affymetrix Mouse Genome 430 2.0 Arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition

data_processing: GeneSpring and BioconductorLIMMA package was used for statistical analysis

source_name: motor neurons laser captured from sections of dorsolateral nucleus at L6 level of the spinal cord of P7 male mouse

label_protocol: At least 1.5 ng of purified RNA was the starting material used in the WT-Ovation Pico RNA Amplification System (Nugen, San Carlos,CA) with the FL-Ovation cDNA Biotin Module V2 (Nugen) to generate labeled probe.

growth_protocol: Mice were obtained from Jackson Labs and were housed under standerd condicition as per IACUC protocol.

extract_protocol: Postnatal day 7 male animals were perfused with 30% sucrose, lumbosacral spinal cord and midbrain regions were rapidly recovered, embedded in OCT compound, and frozen in liquid nitrogen. 12 µm-thick cryosections were mounted on RNAse-free, PEN-foil covered glass slides (Zeiss), fixed for 2 min in 100% EtOH, rinsed in 50% EtOH, stained with 1% cresyl violet for 2 min, rinsed with 50% EtOH, dehydrated in graded solutions of ethanol and air dried prior to LCM using PALM Microbeam system. From each animal, ~200 DL, L5, and oculomotor motor neurons were collected directly in lysis buffer.  RNA was purified using Absolutely RNA, NanoPrep kit. RNA integrity was assessed on the Bioanalyzer 2100.

value: male

value: postnatal day 7

tag: cell type

value: DL nucleus motor neurons


title: preCC mouse OR1009m158

description: preCC mouse OR1009m158

value: preCC  OR1009


title: oculomotor nucleus  motor neurons bio rep 3

description: gene expression data from oculomotor motor neurons of youg wildtype mouse

source_name: motor neurons laser captured from sections of the oculomotor nucleus in the midbrain  of P7 male mouse

value: oculomotor nucleus  motor neurons


title: preCC mouse OR1390m66

description: preCC mouse OR1390m66

value: preCC  OR1390


title: DL nucleus motor neurons bio rep 2


title: DL nucleus motor neurons bio rep 3


title: Muscle_Subject06_Control_Day1_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the control (non-exercised) group
Subject06_Day1

value: Vastus lateralis muscle

value: control (non-exercised)

tag: time

value: day 1


title: preCC mouse OR549m62

description: preCC mouse OR549m62

value: preCC  OR549


title: preCC mouse OR2558m55

description: preCC mouse OR2558m55

value: preCC  OR2558


title: lumbar motor neurons bio rep 2

description: gene expression data from lumbar motor neurons of young wildtype mouse

source_name: motor neurons laser captured from sections of L5 levesl of the spinal cord of P7 male mouse

value: lumbar motor neurons


title: oculomotor nucleus  motor neurons bio rep 1


title: Muscle_Subject05_Exercise_Day4_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained 24hrs following a repeat bout of resistance exercise
Subject05_Day4

value: Male

value: exercise (2 bouts)

value: day 4


title: lumbar motor neurons bio rep 3


title: preCC mouse OR1566m188

description: preCC mouse OR1566m188

value: preCC  OR1566

value: lung


title: oculomotor nucleus  motor neurons bio rep 2

value: male


title: Muscle_Subject06_Control_Day2_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained on Day 2 from subjects assigned to the control (non-exercised) group
Subject06_Day2

value: day 2


title: Muscle_Subject05_Exercise_Day1_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the exercise group
Subject05_Day1

value: exercise (baseline)


title: lumbar motor neurons bio rep 1

value: postnatal day 7


title: Muscle_Subject06_Control_Day4_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained on Day 4 from subjects assigned to the control (non-exercised) group
Subject06_Day4


title: preCC mouse OR3513m61

description: preCC mouse OR3513m61

value: preCC  OR3513


title: Muscle_Subject05_Exercise_Day2_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained 24hrs following unaccustomed resistance exercise
Subject05_Day2

value: exercise (1 bout)


title: Muscle_Subject04_Control_Day4_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained on Day 4 from subjects assigned to the control (non-exercised) group
Subject04_Day4

value: Vastus lateralis muscle


title: preCC mouse OR822m147

description: preCC mouse OR822m147

value: preCC  OR822


title: preCC mouse OR3431m38

description: preCC mouse OR3431m38

value: preCC  OR3431


title: Ectoderm replicate 3

city: Barcelona

first: William

middle: M

last: Keyes

address: Carrer del Dr. Aiguader, 88

department: Gene Regulation, Stem Cells and Cancer

institute: Centre for Genomic Regulation (CRG)

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent). The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples. Data processing was performed using limma package under R/Bioconductor environment.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 75ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

tag: strain background

value: embryonic day 11.5

value: Ectoderm


title: Ectoderm replicate 2


title: AER replicate 2

value: Apical Ectodermal Ridge (AER)


title: AER replicate 1


title: preCC mouse OR5066m143

description: preCC mouse OR5066m143

value: preCC  OR5066


title: Ectoderm replicate 1


title: Muscle_Subject04_Control_Day1_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the control (non-exercised) group
Subject04_Day1

value: Male

value: control (non-exercised)

value: day 1


title: Muscle_Subject03_Exercise_Day4_TechRep1of2

description:
Gene expression data from vastus lateralis samples obtained 24hrs following a repeat bout of resistance exercise
Subject03_Day4_A

value: exercise (2 bouts)

value: day 4


title: Ectoderm replicate 4


title: preCC mouse OR1427m53

description: preCC mouse OR1427m53

value: preCC  OR1427

value: lung


title: Muscle_Subject04_Control_Day2_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained on Day 2 from subjects assigned to the control (non-exercised) group
Subject04_Day2

value: day 2


title: AER replicate 3


title: preCC mouse OR3612m60

description: preCC mouse OR3612m60

value: preCC  OR3612


title: Muscle_Subject03_Exercise_Day4_TechRep2of2

description:
Gene expression data from vastus lateralis samples obtained 24hrs following a repeat bout of resistance exercise
Subject03_Day4_B


title: preCC mouse OR113m87

description: preCC mouse OR113m87

value: preCC  OR113


title: Muscle_Subject03_Exercise_Day1_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the exercise group
Subject03_Day1

value: Vastus lateralis muscle

value: exercise (baseline)


title: Muscle_Subject03_Exercise_Day2_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained 24hrs following unaccustomed resistance exercise
Subject03_Day2

value: exercise (1 bout)


title: preCC mouse OR5046m132

description: preCC mouse OR5046m132

value: preCC  OR5046


title: preCC mouse OR5308m141

description: preCC mouse OR5308m141

value: preCC  OR5308


title: Muscle_Subject02_Control_Day4_TechRep2of2

description:
Gene expression data from vastus lateralis samples obtained on Day 4 from subjects assigned to the control (non-exercised) group
Subject02_Day4_B


title: Muscle_Subject02_Control_Day4_TechRep1of2

description:
Gene expression data from vastus lateralis samples obtained on Day 4 from subjects assigned to the control (non-exercised) group
Subject02_Day4_A


title: preCC mouse OR237m72

description: preCC mouse OR237m72

value: preCC  OR237


title: Muscle_Subject02_Control_Day2_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained on Day 2 from subjects assigned to the control (non-exercised) group
Subject02_Day2


title: Muscle_Subject01_Exercise_Day4_TechRep2of2

description:
Gene expression data from vastus lateralis samples obtained 24hrs following a repeat bout of resistance exercise
Subject01_Day4_B


title: Muscle_Subject01_Exercise_Day4_TechRep1of2

description:
Gene expression data from vastus lateralis samples obtained 24hrs following a repeat bout of resistance exercise
Subject01_Day4_A


title: E3Stro

city: Cincinnati

first: Daesuk

last: Chung

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Childrens Hospital Medical Center

hyb_protocol: hybridized to GeneChip® mouse gene 1.0 ST array

scan_protocol: Affymetrix GeneChip Scanner 3000 7G used to scan

data_processing:
RMA
Differentially expressed genes were selected based on the GeneSpring GX10 program, with a threshold of unpaired t-test (P-value #0.05), false discovery rate (FDR) #5%, and a fold change cut off = 2.0.

source_name: Stromal cells of co-culture

label_protocol: Biotin-labeled cRNAs were generated using the Affymetrix Whole Transcript Sense Target Labeling Assay (Affymetrix)

growth_protocol: Uterine epithelial and stromal cells were isolated by enzymatic digestion of uterine tissues on day 4 of pseudopregnancy. Epithelial sheets were grown on matrigel coated cell culture inserts and the stromal cells were grown on cover slips in six-well plates. After initiation of the co-culture, the cells were depleted in phenol-red free DMEM/F12 media supplemented with charcoal-stripped 1% FBS for overnight prior to the initiation of treatments with E2 (10 nM) or vehicle (0.01% ethanol). Both cell layers were analyzed separately after 2 days.

extract_protocol: Cells were harvested from co-culture and RNAs were extracted from epithelial and stromal cell populations using RNeasy Mini Kit (Bio-rad, Valencia, CA)

treatment_protocol: Vehicle control vs. E2

tag: treatment

value: Stromal cells of co-culture


title: E1Stro


title: E2Stro


title: V2Stro

value: Vehicle control


title: V3Stro


title: Muscle_Subject01_Exercise_Day2_TechRep2of2

description:
Gene expression data from vastus lateralis samples obtained 24hrs following unaccustomed resistance exercise
Subject01_Day2_B

value: Male


title: Muscle_Subject02_Control_Day1_TechRep1of1

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the control (non-exercised) group
Subject02_Day1

value: control (non-exercised)

value: day 1


title: tup1_deletion_rapamycin_rep1

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description: replicate 1 of rapamycin-treated tup1 deletion strain

organism: Saccharomyces cerevisiae

source_name: tup1 deletion strain

growth_protocol: Yeast cells were grown to mid-log phase (O.D 600 nm of 0.6 to 0.8) at 30°C in YPD media with shaking at 250 rpm, and frozen in liquid nitrogen right after treatment.

extract_protocol: The collected yeast cells were re-suspended with AE buffer (50 mM Sodium Acetate pH 5.2, 10 mM EDTA) containing 2% of SDS, and total RNA was extracted with a hot phenol method (Iyer et al. PNAS 93(11):5208-12).

treatment_protocol: For rapamycin treatment, either DMSO or rapamycin was added to mid-log phase yeast cells and incubated for 30 min at 30°C. Since DMSO is a solvent for rapamycin, control and rapamycin-added cells were treated with DMSO and rapamycin to be a final concentration of 0.1% and 100 nM, respectively

tag: genotype

value: tup1 deletion strain

tag: background genotype

value: rapamycin


title: wild_type_rapamycin_rep4

description: replicate 4 of rapamycin-treated wild type

source_name: wild type

value: wild type


title: tup1_deletion_rapamycin_rep2

description: replicate 2 of rapamycin-treated tup1 deletion strain


title: tup1_deletion_DMSO_rep2

description: replicate 2 of DMSO-treated tup1 deletion strain

value: DMSO


title: tup1_deletion_DMSO_rep1

description: replicate 1 of DMSO-treated tup1 deletion strain


title: 16 AP_genomic DNA from subcutaneous adipose tissue

type: genomic

description:
16 AP
normal adipose tissue sample

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Illumina GenomeStudio Software. Non_normalized data matrix contains unmethylated (Signal A) and methylated (Signal B) signal intensities.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using the MasterPureTMDNA Purification Kit (Epicentre Biotechnologies) according to the manufacturer`s instructions

value: female

value: 26 years

tag: disease state

value: normal state


title: 26 GLM_genomic DNA from subcutaneous adipose tissue

description:
26 GLM
normal adipose tissue sample

value: 29 years


title: Muscle_Subject01_Exercise_Day2_TechRep1of2

description:
Gene expression data from vastus lateralis samples obtained 24hrs following unaccustomed resistance exercise
Subject01_Day2_A

value: Vastus lateralis muscle

value: exercise (1 bout)

value: day 2


title: V1Stro


title: E3Epi

source_name: Epithelial cells of co-culture

value: Epithelial cells of co-culture


title: Muscle_Subject01_Exercise_Day1_TechRep1of2

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the exercise group
Subject01_Day1_A

value: exercise (baseline)


title: Muscle_Subject01_Exercise_Day1_TechRep2of2

description:
Gene expression data from vastus lateralis samples obtained at baseline in subjects assigned to the exercise group
Subject01_Day1_B


title: wild_type_rapamycin_rep3

description: replicate 3 of rapamycin-treated wild type


title: E2Epi


title: ARID3A Neg 13

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

description: A Qiagen human oligonucleotide library was spotted on glass slides. Control spots containing positive controls, negative controls, and printing buffer lacking oligonucleotides were not used in the normalization or analysis protion of the project, and were therefore eliminated from the matrix data on the GP14867 array.

hyb_protocol: Labeled cDNA was added to ChipHyb ™ buffer (Ventana, Tuscon) containing Cot-1 DNA (0.5 mg/ml), yeast tRNA (0.2 mg/ml), and poly(dA)40-60 (0.4 mg/ml). Hybridization was performed on a Ventana Dioscovery system for 6 hr at 42C. Microarrays were washed to a final stringency of 0.1X SSC.

scan_protocol: Microarrays were scanned using an Agilent model G2505B scanner. Signal intensity was dertermined using Imagene software (BioDiscovery, Marina del Rey).

data_processing: Data were normalized as described previoulsy in Arthritis Res Ther, 2004, 6:R15-32. In brief, the procedure is based on the fact that spot intensities from genes not expressed by the samples of interest constitute noise and are therefore normally distributed. The method models the signals from nonexpressed genes to a normal distribution with a mean of 0 and standard deviation (SD) of 1, using an iterative nonlinear curve-fitting procedure. A second normalization step is then performed using the genes significantly expressed above background (> 3 SD above background). Gene expression values are log-transformed, with negative values replaced by the lowest positive logarithmic value obtained.

source_name: ARID3A Neg 13

label_protocol: 2 microgram total RNA was labeles with Clontech Powerscript reverse transcriptase and labeled with Cy3-dUTP

growth_protocol: Cells were grown in RPMI 1640 supplemented with 7% heat inactivated fetal calf serum, 5x 10-5 M β mercaptoethanol, 100U/ ml penicillin, 100µg/ ml streptomycin, 2mM glutamine and 1mM sodium pyruvate at 370C in a CO2 incubator.

extract_protocol: RNA was isolated using Trireagent following manufacturer's recommenations

treatment_protocol: Electroporation was performed at 0.22 mV and 960 microF capacitance. Cells were sorted by MoFlo cell sorter for GFP positive cells 48 hr after electroporation.

tag: transfection

value: vector only

tag: cell line

value: RAJI


title: ARID3A Neg 14

source_name: ARID3A Neg 14


title: E1Epi

tag: strain


title: wild_type_rapamycin_rep2

description: replicate 2 of rapamycin-treated wild type


title: V3Epi

value: Vehicle control


title: 23 AP_genomic DNA from subcutaneous adipose tissue

description:
23 AP
normal adipose tissue sample

source_name: subcutaneous adipose tissue abdominal

tag: gender

value: 35 years


title: 22 AP_genomic DNA from subcutaneous adipose tissue

description:
22 AP
normal adipose tissue sample

tag: age

value: 34 years


title: ARID3A Neg 12

source_name: ARID3A Neg 12


title: wild_type_rapamycin_rep1

description: replicate 1 of rapamycin-treated wild type

value: rapamycin


title: 23 GLL_genomic DNA from subcutaneous adipose tissue

description:
23 GLL
normal adipose tissue sample

source_name: subcutaneous adipose tissue gluteal


title: ARID3A Pos 14

source_name: ARID3A Pos 14

value: ARID3A and vector


title: wild_type_DMSO_rep4

description: replicate 4 of DMSO-treated wild type

value: wild type

value: DMSO


title: wild_type_DMSO_rep3

description: replicate 3 of DMSO-treated wild type


title: V1Epi


title: wild_type_DMSO_rep2

description: replicate 2 of DMSO-treated wild type


title: 16 GRM_genomic DNA from subcutaneous adipose tissue

description:
16 GRM
normal adipose tissue sample

value: female

value: 26 years


title: ARID3A Neg 11

source_name: ARID3A Neg 11


title: 22 GLL_genomic DNA from subcutaneous adipose tissue

description:
22 GLL
normal adipose tissue sample

value: normal state


title: V2Epi


title: wild_type_DMSO_rep1

description: replicate 1 of DMSO-treated wild type


title: ARID3A Pos 12

source_name: ARID3A Pos 12


title: 17 AP_genomic DNA from subcutaneous adipose tissue

description:
17 AP
normal adipose tissue sample

value: 24 years


title: ARID3A Pos 13

source_name: ARID3A Pos 13


title: 17 GLM_genomic DNA from subcutaneous adipose tissue

description:
17 GLM
normal adipose tissue sample


title: ARID3A Pos 11

source_name: ARID3A Pos 11


title: 02_C2C12-Bex10-1

city: San Francisco

first: Baoming

last: Nie

state: CA

address: 1650 Owens St.

department: GICD

institute: Gladstone Institutes

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: The labeled cDNA was hybridized to mouse Gene 1.0 ST microarrays (Affymetrix, Santa Clara, CA).

scan_protocol: The signal intensity fluorescent images produced during Affymetrix GeneChip hybridizations were read using the Affymetrix Model 3000 Scanner.

data_processing: Data were normalized and analyzed using Affymetrix Expression Console and Transcriptome Analysis Console (TAC) software. A gene was regarded as significantly changed if the P-value was <0.05 and fold was >1.5 or < -1.5.

label_protocol: Purified RNA was analyzed for quality using chip-based capillary electrophoresis (Bioanalyzer, Agilent, Inc) and quantity and purity was determined with a NanoDrop spectrometer. The NuGEN Pico V2, based on Ribo-SPIA technology, was used for amplification, fragmentation and biotin-labeling.

growth_protocol: C2C12 cells were cultured in 20% to confluent, then switched to basal adipogenesis medium(AM,Ctrl) or AM+Bex10(10uM) for 48h.

extract_protocol: RNA was isolated with the RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: 2 batches of C2C12 cells were treated as growth protocol


title: 03_C2C12-Ctrl-2


title: 26 AP_genomic DNA from subcutaneous adipose tissue

description:
26 AP
normal adipose tissue sample

value: 29 years


title: 10 GLM_genomic DNA from subcutaneous adipose tissue

description:
10 GLM
normal adipose tissue sample


title: 10 AP_genomic DNA from subcutaneous adipose tissue

description:
10 AP
normal adipose tissue sample


title: 01_C2C12-Ctrl-1


title: SAMPLE 118 T5_Norring

status: Public on Nov 14 2013

city: Aarhus

first: Michael

last: Hansen

address: Ny Munkegade 114

country: Denmark

institute: Aarhus University

hyb_protocol: As outlined in the Genisphere Array 50 Protocol Revised version 5 available at http://web.uvic.ca/cbr/grasp/microarray/array.html

scan_protocol: Scanned using a ScanArray scanner (PerkinElmer) at a resolution of 10μm and 90% laser power, manually equilibrating intensity between dyes for each slide using the photomultiplier tube settings.

data_processing: Spots were localized and quantified with the QuantArray 3.0 software (Perkin- Elmer Life Sciences), using the histogram quantification method and keeping the mean value of intensity for each spot. Local background was removed and the data from bad spots were manually excluded from the data set. For each of the two dyes on each array, spots with signal intensities lower than the mean intensity of the empty spots plus twice their standard deviation were flagged as non-expressed. Spots that had no non-expressed flag in at least one of the six studied groups (3 rivers and 2 temperatures) were kept.

organism: Salmo trutta

source_name: Temperature and river effect

label_protocol: Cy5 and Cy3 dyes of the Array50 kit (Genisphere) following the procedures at http://web.uvic.ca/cbr/grasp/microarray/array.html (Genisphere Array 50 Protocol Revised version 5), using 15microgram of RNA per reverse transcription reaction and sunbsequently OPTION 1 Ð concentration of cDNA using Millipore Microcon YM-30 concentrators.

growth_protocol: Common garden experiment in wet lab. Each full-sib family of eggs was divided into two batches, which were incubated at 5 and 8 degrees C in hatching troughs with circulated water, biological filter and temperature control. Each family was placed in separate compartments of hatching boxes, but all families and individuals experienced similar conditions.

extract_protocol: RNA was extracted from whole individuals on ice using the RNA Pure Link Minikit (Invitrogen, Paisley, UK). Each fry was homogenized individually in 0.8ml lysis buffer containing 1% 2-mercaptoethanol using a Tissuelyzer (QIAGEN, Hilden, Germany). Samples were then centrifuged at 2600 g for 5 min and 0.6 ml of the supernatant was transferred to a new 2 ml tube, 0.6 ml Trizol and 0.6 ml chloroform was added, mixed and centrifuged at 13,000 g at 4¡C for 15 min. Then, 800 µl of the upper phase was transferred to a new tube and RNA was extracted according to the manufacturer's recommendations. After RNA extraction, 1 µl of RNase inhibitor (20 units/µl, Ambion, Invitrogen, Paisley, UK) was added to prevent RNA degradation and samples were DNase treated with DNase I, amplification grade (1 unit/µl) (Invitrogen, Paisley, UK) following the manufacturer's recommendation. RNA quantity and integrity was checked on a Nanodrop instrument (ND-1000; Thermo Fisher Scientific Inc., Wilmington, Delaware, USA) and on an Experion automated electrophoresis station using RNA HighSens chips (BIORAD, Copenhagen, Denmark).

tag: tissue

value: Whole larva

tag: river

value: Norring

tag: temperature


title: SAMPLE 120 T5_Norring


title: SAMPLE 114 T5_Norring


title: SAMPLE 111 T8_Norring


title: SAMPLE 117 T8_Norring


title: SAMPLE 116 T5_Norring


title: SAMPLE 115 T8_Norring


title: SAMPLE 108 T5_Norring


title: SAMPLE 119 T8_Norring


title: SAMPLE 112 T5_Norring


title: SAMPLE 109 T8_Norring


title: SAMPLE 110 T5_Norring


title: SAMPLE 107 T8_Norring


title: SAMPLE 106 T5_Norring


title: SAMPLE 105 T8_Norring


title: SAMPLE 102 T5_Norring


title: SAMPLE 96 T5_Norring


title: SAMPLE 99 T8_Norring


title: SAMPLE 104 T5_Norring


title: SAMPLE 97 T8_Norring


title: SAMPLE 101 T8_Norring


title: SAMPLE 103 T8_Norring


title: SAMPLE 98 T5_Norring


title: 04_C2C12-Bex10-2


title: SAMPLE 92 T5_Norring


title: SAMPLE 100 T5_Norring


title: SAMPLE 93 T8_Norring


title: SAMPLE 94 T5_Norring


title: SAMPLE 88 T5_Norring


title: SAMPLE 90 T5_Norring


title: SAMPLE 95 T8_Norring


title: A. baumannii MMC rep2

city: A CORUÑA

first: JESUS

last: ARANDA

address: AS XUBIAS

institute: CHUAC

description: Biological replicates 2 of 3

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).
Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Acinetobacter baumannii ATCC 17978

label_protocol: Two-Color Microarray-Based Prokaryote Analysis Fair Play III Labeling v. 1.3 (Agilent)

growth_protocol: A. baumannii ATCC 17978 wild-type strain was grown in Luria Bertani (LB) medium and incubated at 37ºC with shaking at 180 rpm.

extract_protocol: Total RNA was extracted with a High Pure RNA Isolation kit (Roche), according to the manufacturer’s instructions. Samples were treated with DNaseI (Invitrogen) and purified using the RNeasy MinElute Clean up kit (Qiagen).

treatment_protocol: At the mid-exponential growth phase (OD600=0.6), MMC was added to the culture at a final concentration of 0.5 µg ml-1 and incubated for an additional 2 h. The control was performed in the same way without MMC addition.

tag: condition

value: MMC-

value: MMC+


title: SAMPLE 85 T8_Norring


title: SAMPLE 86 T5_Norring


title: A. baumannii MMC rep3

description: Biological replicates 3 of 3


title: SAMPLE 87 T8_Norring


title: A. baumannii MMC rep1

description: Biological replicates 1 of 3


title: C 32

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

hyb_protocol: according to Honda et al. Hepatology. 2006 Nov;44(5):1122-38, Honda M, et al. Gastroenterology. 2001 Mar;120(4):955-66.

scan_protocol: Quantitative assessment of the signals on the slides was carried out by scanning on a ScanArray 5000 (General Scanning, Watertown, MA, USA) followed by image analysis using GenePix Pro 4.1 (Axon Instruments, Union City, CA, USA).

data_processing: Because the levels of expression of some housekeeping genes were also changed, especially in advanced stages of liver disease, for the  normalization of data we averaged intensities of all spots obtained with  Cy3 and Cy5 in each of the 16 rectangles and adjusted intensity of each  corrected DNA spot as the average intensity ratio Cy5/Cy3 = 1.0. This  global normalization of intensity provided smaller variance of CyS/Cy3  ratio and almost equivalent results to normalization using the housekeeping genes [Honda et al. Hepatology. 2006 Nov;44(5):1122-38, Honda M, et al. Gastroenterology. 2001 Mar;120(4):955-66]. From the 9643 expression data, duplicated genes were averaged and final 8516 non redundant expression results were obtained.

source_name: non HCC lesion with chronic hepatitis C

label_protocol: As a reference for each microarray analysis, aRNA samples prepared from the normal liver tissue from one of the patients were used. Test RNA samples fluorescently labeled with cyanine (Cy) 5 and reference RNA labeled with Cy3 were used for microarray hybridization.

extract_protocol: Total RNA was isolated from liver biopsy or operated samples using an RNA extraction kit (Micro RNA Extraction Kit, Stratagene, La Jolla, CA, USA). Aliquots of total RNA (5 ug) were subjected to amplification with antisense RNA (aRNA) using a Message AmpTM aRNA kit (Ambion, Austin, TX, USA) as recommended by the manufacturer

treatment_protocol: HCC and non-cancerous liver specimens were obtained from 17 patients with HCV-related HCC and 17 with HBV-related HCC who underwent surgical resection of the liver. For the control normal liver, a surgically obtained tissue sample from a patient who showed no clinical signs of hepatitis was used as described previously

tag: specimen group

value: non HCC lesion with chronic hepatitis C [CH-C]

value: liver

source_name: normal liver sample from a patient

tag: sample type

value: reference


title: C 34


title: C 33


title: C 31


title: C 35


title: C 30


title: SAMPLE 82 T5_Norring


title: C 29


title: SAMPLE 83 T8_Norring


title: C 28


title: SAMPLE 89 T8_Norring


title: SAMPLE 76 T5_Karup

value: Karup


title: SAMPLE 81 T8_Norring


title: SAMPLE 84 T5_Norring


title: SAMPLE 79 T8_Karup


title: SAMPLE 78 T5_Karup


title: SAMPLE 80 T5_Karup


title: C 27


title: SAMPLE 77 T8_Karup


title: SAMPLE 75 T8_Karup


title: C 25


title: C 26


title: C 23


title: C 24


title: SAMPLE 72 T5_Karup


title: C 21


title: SAMPLE 73 T8_Karup


title: C 20


title: SAMPLE 74 T5_Karup


title: SAMPLE 71 T8_Karup


title: C 16


title: C 17


title: C 19


title: C 18


title: SAMPLE 63 T8_Karup


title: SAMPLE 70 T5_Karup


title: C 15


title: SAMPLE 69 T8_Karup


title: C 14


title: SAMPLE 66 T5_Karup


title: SAMPLE 68 T5_Karup


title: SAMPLE 65 T8_Karup


title: C 22


title: C 13


title: SAMPLE 62 T5_Karup


title: SAMPLE 67 T8_Karup


title: SAMPLE 61 T8_Karup


title: SAMPLE 64 T5_Karup


title: C 12


title: SAMPLE 60 T5_Karup


title: SAMPLE 113 T8_Norring


title: SAMPLE 59 T8_Karup


title: C 11


title: C 6


title: C 10


title: C 5


title: C 7


title: C 9


title: C 8


title: C 3


title: C 2


title: SAMPLE 57 T8_Karup


title: C 4


title: SAMPLE 58 T5_Karup


title: C 1


title: B 35

source_name: non HCC lesion with chronic hepatitis B

value: non HCC lesion with chronic hepatitis B [CH-B]


title: B 36


title: SAMPLE 55 T8_Karup


title: B 34


title: SAMPLE 56 T5_Karup


title: SAMPLE 53 T8_Karup


title: 0304103 cells treated by FLC + BBR vs FLC 0304103 cells

city: Beijing

first: Dedong

last: Li

state: Beijing

address: Fuxing Road 28

department: department of clinical pharmacology

country: China

institute: PLA General Hospital

description: Biological replicate 1 of 3.

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio) Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. There was no reversal fluorescent strategy used. All test samples was labeled with Cy5 and all control samples was labeled with Cy3.

organism: Candida albicans

source_name: Candida albicans 0304103 treated by  FLC + BBR

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

growth_protocol: Candida albicans 0304103 cells were propagated in yeast-peptone-dextrose (YPD) medium (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose).

extract_protocol: Total RNA was isolated by the hot phenol method.

treatment_protocol: 0304103 cells were cultured to 0.4 - 1.0×106 cells/ml in YPD, then divided into two parts: one was exposed to fluconazole  (64 μg/ml) and berberine (16 μg/ml) whereas the other was exposed to fluconazole  (64 μg/ml) and grown an additional 6 h, at which point they were pelleted by centrifugation for 5 min at room temperature and frozen in liquid nitrogen.

source_name: Candida albicans 0304103 treated with fluconazole for 6 h


title: SAMPLE 54 T5_Karup


title: 01010 cells treated by FLC + BBR vs FLC 01010 cells

description: Biological replicate 2 of 3.

source_name: Candida albicans 01010 treated by  FLC + BBR

growth_protocol: Candida albicans 01010 cells were propagated in yeast-peptone-dextrose (YPD) medium (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose).

treatment_protocol: 01010 cells were cultured to 0.4 - 1.0×106 cells/ml in YPD, then divided into two parts: one was exposed to fluconazole  (64 μg/ml) and berberine (16 μg/ml) whereas the other was exposed to fluconazole  (64 μg/ml) and grown an additional 6 h, at which point they were pelleted by centrifugation for 5 min at room temperature and frozen in liquid nitrogen.

source_name: Candida albicans 01010 treated with fluconazole for 6 h


title: 632 cells treated by BBR vs control 632 cells

description: Biological replicate 3 of 3.

source_name: Candida albicans 632 treated by  BBR

growth_protocol: Candida albicans 632 cells were propagated in yeast-peptone-dextrose (YPD) medium (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose).

treatment_protocol: 632 cells were cultured to 0.4 - 1.0×106 cells/ml in YPD, then divided into two parts: one was exposed to berberine (16 μg/ml)  whereas the other was the control and grown an additional 6 h, at which point they were pelleted by centrifugation for 5 min at room temperature and frozen in liquid nitrogen.

source_name: Candida albicans 632 untreated


title: SAMPLE 52 T5_Karup


title: 632 cells treated by FLC + BBR vs FLC 632 cells

description: Biological replicate 3 of 3.

source_name: Candida albicans 632 treated by  FLC + BBR

treatment_protocol: 632 cells were cultured to 0.4 - 1.0×106 cells/ml in YPD, then divided into two parts: one was exposed to fluconazole  (64 μg/ml) and berberine (16 μg/ml) whereas the other was exposed to fluconazole  (64 μg/ml) and grown an additional 6 h, at which point they were pelleted by centrifugation for 5 min at room temperature and frozen in liquid nitrogen.

source_name: Candida albicans 632 treated with fluconazole for 6 h


title: B 33


title: SAMPLE 51 T8_Karup


title: SAMPLE 50 T5_Karup


title: 01010 cells treated by BBR vs control 01010 cells

description: Biological replicate 2 of 3.

source_name: Candida albicans 01010 treated by  BBR

treatment_protocol: 01010 cells were cultured to 0.4 - 1.0×106 cells/ml in YPD, then divided into two parts: one was exposed to berberine (16 μg/ml)  whereas the other was the control and grown an additional 6 h, at which point they were pelleted by centrifugation for 5 min at room temperature and frozen in liquid nitrogen.

source_name: Candida albicans 01010 untreated


title: 0304103 cells treated by BBR vs control 0304103 cells

description: Biological replicate 1 of 3.

source_name: Candida albicans 0304103 treated by  BBR

treatment_protocol: 0304103 cells were cultured to 0.4 - 1.0×106 cells/ml in YPD, then divided into two parts: one was exposed to berberine (16 μg/ml)  whereas the other was the control and grown an additional 6 h, at which point they were pelleted by centrifugation for 5 min at room temperature and frozen in liquid nitrogen.

source_name: Candida albicans 0304103 untreated


title: Sp_RNA_5FU_t240

city: Salamanca

first: Luis

last: Quintales

address: Calle Zacarías González, 2

department: Universidad de Salamanca / CSIC

institute: Instituto de Biología Funcional y Genómica (IBFG)

description: RNA 5FU 240 min

hyb_protocol: 220 ml 1x hybridization mixture containing 5.5 mg of fragmented and labeled DNA target, 7% DMSO, 1.5, 5, 25 and 100 pM of Eukaryotic Hibridization Controls (bioB, bioC, bioD, cre) respectively, and 50 pM control oligonucleotide B2 were prepared using the Affymetrix GeneChip Hybridization Kit as described in the Affymetrix GeneChip Whole Transcript (WT) Sense Target Assay Labeling Manual. The final DNA target mixture was hybridized to Affymetrix S. pombe Tiling 1.0FR arrays and incubated in a hybridization oven at 45 °C and 60 rpm for 17 h ±1h.

scan_protocol: Affymetrix standard protocol using Affymetrix Fluidics 450 and Scanner 3000

data_processing:
The eigth *.CEL files were quantile normalized (PMID:12538238). Mean signal intensities (log2) of biological replicates were reported in WIG files.
All the results files are in Wiggle Track Format (WIG) containing RNA log2 raw signal for RNA samples (transcription mapping). The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.

organism: Schizosaccharomyces pombe

source_name: RNA 5FU 240 min

label_protocol: 5.5 mg of the fragmented single-stranded DNA samples resuspended in 45 ml were incubated with a labeling master mix containing DNA Labeling Reagent (5 mM), terminal deoxynucleotidyl transferase (30 U/ul) and 1× Terminal Deoxynucleotidyl Transferase Buffer in a thermal cycler as described in the Affymetrix GeneChip Whole Transcript (WT) Sense Target Assay Labeling Manual.

growth_protocol: YE medium at 30 °C to OD595 = 0.2 (~4 × 106 cells/ml)

extract_protocol: Total RNA was immediately extracted using the MasterPure Yeast RNA Purification Kit (Epicentre, Madison, WI) according to the manufacturer’s recommendations. The purified RNA was immediately frozen in liquid nitrogen and stored at -70 °C. The quality and quantity of total RNA were determined by Nanodrop ND-1000 UV spectroscopy (Thermo Scientific), and RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies). We obtained high-quality RNA from all the samples since the RNA Integrity Number  (RIN) was greater than 9 in each case.

treatment_protocol: 5FU was added to the culture to a final concentration of 500 μM and incubation was allowed to proceed for 240 minutes.

tag: culture type

value: Asynchronous mitosis

tag: time

value: 240 min


title: Sp_RNA_5FU_t060

description: RNA 5FU 60 min

source_name: RNA 5FU 60 min

treatment_protocol: 5FU was added to the culture to a final concentration of 500 μM and incubation was allowed to proceed for 60 minutes.

value: 60 min


title: Sp_RNA_5FU_t015

description: RNA 5FU 15 min

source_name: RNA 5FU 15 min

treatment_protocol: 5FU was added to the culture to a final concentration of 500 μM and incubation was allowed to proceed for 15 minutes.

value: 15 min


title: B 31

source_name: normal liver sample from a patient


title: B 32

source_name: non HCC lesion with chronic hepatitis B


title: B 29


title: B 30


title: Sp_RNA_5FU_t000

description: RNA 5FU 0 min

source_name: RNA 5FU 0 min

value: 0 min


title: B 27


title: SAMPLE 49 T8_Karup

source_name: Temperature and river effect


title: B 26


title: SAMPLE 48 T5_Karup


title: B 25


title: SAMPLE 47 T8_Karup


title: B 23


title: B 24


title: SAMPLE 91 T8_Norring


title: SAMPLE 46 T5_Karup


title: B 17


title: B 19


title: B 20


title: B 21


title: SAMPLE 45 T8_Karup


title: B 28


title: SAMPLE 44 T5_Karup


title: B 22


title: B 15


title: B 14


title: B 13


title: SAMPLE 43 T8_Karup


title: ALDH+ flow sorted cells, biological rep 7

city: Houston

first: yang

last: CONG

address: 6565 Fannin St.,

department: Department of Systems Medicine and Bioengineering

institute: Houston Methodist Research Institution

hyb_protocol: Gene expression analyses used Affymetrix U133 Plus 2.0 human oligonucleotide microarrays. Preparation of cRNA, hybridizations, washes and detection were done as recommended by the supplier.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (GeneChip® Scanner 3000).

data_processing: Expression data were analyzed by the Robust Multi-array Average method (RMA) in R using Bioconductor and associated packages.

source_name: human breast tumor_ALDH+

label_protocol: 50 ng total RNA and the Affymetrix two-cycle labelling Affymetrix kit (P/N 900494) were used. Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA was extracted from frozen ALDEFLUOR-positive and -negative cells using DNA/RNA All Prep Maxi Kit, according to the manufacturer's instructions.

tag: aldh status

value: ALDH+


title: SAMPLE 42 T5_Karup


title: B 12


title: B 11


title: ALDH+ flow sorted cells, biological rep 8


title: B 18


title: ALDH- flow sorted cells, biological rep 8

source_name: human breast tumor_ALDH-

value: ALDH-


title: ALDH+ flow sorted cells, biological rep 6


title: SAMPLE 40 T5_Lilleaa

value: Lilleaa


title: ALDH- flow sorted cells, biological rep 7


title: ALDH+ flow sorted cells, biological rep 5


title: B 16


title: ALDH- flow sorted cells, biological rep 6


title: SAMPLE 39 T8_Lilleaa

value: Whole larva


title: B 8


title: B 9


title: B 7


title: B 6


title: B 5


title: B 2


title: B 4


title: B 10


title: SAMPLE 37 T8_Lilleaa


title: HCC 34

description: HCVmoderate

source_name: hepatocellular carcinoma (HCC)

value: hepatitis C virus [HCV]-related


title: SAMPLE 36 T5_Lilleaa


title: B 1


title: ALDH+ flow sorted cells, biological rep 4


title: ALDH- flow sorted cells, biological rep 5


title: ALDH+ flow sorted cells, biological rep 3


title: SAMPLE 38 T5_Lilleaa


title: SAMPLE 41 T8_Karup


title: HCC 31

description: HCVmoderate


title: SAMPLE 34 T5_Lilleaa


title: B 3


title: SAMPLE 33 T8_Lilleaa


title: ALDH+ flow sorted cells, biological rep 2


title: SAMPLE 35 T8_Lilleaa


title: HCC 32

description: HCVmoderate


title: HCC 33

description: HCVmoderate


title: ALDH- flow sorted cells, biological rep 4


title: ALDH- flow sorted cells, biological rep 3


title: HCC 28

description: HCVmoderate


title: HCC 26

description: HCVmoderate


title: HCC 30

description: HCVmoderate


title: ALDH- flow sorted cells, biological rep 2


title: SAMPLE 32 T5_Lilleaa


title: SAMPLE 30 T5_Lilleaa


title: SAMPLE 31 T8_Lilleaa


title: ALDH- flow sorted cells, biological rep 1


title: HCC 25

description: HCVmoderate


title: HCC 23

description: HCVwell


title: HCC 22

description: HCVwell


title: SAMPLE 29 T8_Lilleaa


title: HCC 29

description: HCVmoderate


title: ALDH+ flow sorted cells, biological rep 1


title: HCC 21

description: HCVwell


title: HCC 27

description: HCVmoderate


title: HCC 20

description: HCVwell


title: HCC 18

description: HCVwell


title: HCC 19

description: HCVwell


title: HCC 24

description: HCVwell


title: HCC 16

description: HBV moderate

value: hepatitis B virus [HBV]-related


title: HCC 17

description: HBV moderate


title: HCC 15

description: HBV moderate


title: Glioblastoma stem-like cell line 12.1

city: Madison

last: Zorniak

state: WI

address: 600 Highland Ave

department: Neurological Surgery

institute: University of Wisconsin-Madison

description:
Whole genome expression profile
12.1 GSC

hyb_protocol: Hybridized cRNA was labeled with streptavidin-phycoerythrin for visualization.

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Devices, Sunnyvale, CA, USA) and digitized using Array-Pro image analysis software (Media Cybernetics, Bethesda, MD, USA).

data_processing: All of the expression profiles were batch normalized by a robust multichip average (RMA) algorithm using Geospiza GeneSifter (PerkinElmer) online microarray database and analysis software. No statistics were applied. The data was then exported into Microsoft Office Excel 2010 and organized for GSC transcripts with raw intensity values 10 fold or higher over normal brain, hNSCs, GBM primary and recurrent tumor samples. The reverse sorting algorithm was done to obtain downregulated GSC trascripts. This analysis provided a list of upregulated plasma membrane transcripts in GSCs.

source_name: Glioblastoma stem-like cells

label_protocol: Total RNA was  sent to LC Sciences (Houston, TX) for final gene expression processing and analysis. In brief, total RNA was reverse transcribed with T7-Oligo(dT) primers. After cleanup of cDNA, cRNA was synthesized using in vitro transcription (3’ IVT). cRNA was biotinylated and fragmented before hybridization to an U133 plus 2.0 array (Affymetrix, Santa Clara, CA), containing probes for over 47,000 transcripts.

growth_protocol: All studies were performed with approval from the University of Wisconsin-Madison Institutional Review Board (2012-0024) with informed consent obtained from patients, and with approval from the Animal Care and Use Committee (M02223). Glioblastoma stem-like cells (GSC) were isolated without the use of surface markers. Briefly, tumor tissue was collected directly from the University of Wisconsin Pathology Archives, weighed, coarsely minced with a scalpel blade, and subsequently chopped 2× at 200 µm using a tissue chopper (Sorvall TC-2 Smith-Farquahar). Chopped tissue was directly plated in suspension and cultured in passaging medium: 70% Dulbecco modified Eagle medium-high glucose, 30% Ham’s F12, 1× B27 supplement, 5 µg/mL heparin, penicillin-streptomycin-amphotericin (PSA), supplemented with 20 ng/ml each of human recombinant epidermal growth factor (EGF) and bovine fibroblast growth factor (bFGF). Sphere cultures were passaged approximately every 7 days by tissue chopping 2× at 100 µm. GSC lines 12.1 and 22 were cultured in suspension with each number corresponding to a different delinked patient. Each GSC line was validated for self-renewal by neurosphere formation, expression of stem cell markers (i.e. AC/CD133), multipotency, tumor initiation, and serial implantation in non-obese diabetic severe combined immunodeficient (NOD-SCID) mice (Harlan Sprague-Dawley) at high efficiency before experiments were performed.

extract_protocol: Total RNA was extracted from GSCs with an RNeasy kit (Qiagen).

value: glioblastoma stem-like cell (GSC) line 12.1

tag: gsc line validated for self-renewal by neurosphere formation

value: yes


title: Glioblastoma stem-like cell line 22

description:
Whole genome expression profile
22 GSC

value: glioblastoma stem-like cell (GSC) line 22


title: HCC 14

description: HBV moderate

value: liver

value: reference


title: SAMPLE 24 T5_Lilleaa


title: SAMPLE 27 T8_Lilleaa


title: SAMPLE 25 T8_Lilleaa


title: SAMPLE 26 T5_Lilleaa