title: Serum DNA 87

source_name: genomic DNA from serum sample 87

value: F


title: Serum DNA 98

status: Public on Jun 03 2014

type: genomic

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

country: United Kingdom

institute: University College London

description:
bi-sulphite converted genomic serum DNA from woman
serum DNA from healthy postmenopausal women, a number of which developed breast cancer (cases)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA from serum sample 98

label_protocol: Standard Illumina Protocol for Infinium 27k Chip

extract_protocol: DNA was extracted from serum at Tepnel (www.tepnel.com) using Qiagen QiAamp Blood Mini Kit (51106)

tag: subject

value: healthy postmenopausal women

tag: case/control

tag: ageatdraw (yrs)

tag: season

tag: dna conc. (ug/ml)

value: L


title: SJL/J mouse  liver, treated animal 2

type: RNA

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

country: USA

institute: UNC Eshelman School of Pharmacy

description: Sample name: 178

hyb_protocol: Samples were hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 Array using the Hybridization, Wash and Stain kit (Affymetrix). Following hybridization, arrays were washed and stained using standard Affymetrix procedures.

scan_protocol: GeneChips were scanned with an Affymetrix Gene Chip Scanner.

data_processing: Data were processed using the Affymetrix Power Tools program apt-probeset-summarize. Probes overlapping SNPs in MDP strains were removed and intensity ratios were RMA (Robust Multi-array Analysis) transformed.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: SJL/J liver, isoniazid treated

label_protocol: The GeneChip 3’ IVT Express Kit (Affymetrix) was utilized to generate fragmented, biotin-labeled aRNA.

growth_protocol: 8 female mice in each of 31 strains were 8-10 weeks old at the start of the study.

extract_protocol: 24 hours after the final dose, mice were sacrificed, livers were excised, and left liver lobe tissue was flash frozen in liquid nitrogen. Total liver RNA was isolated with the RNeasy total RNA isolation kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: 4 mice per strain were dosed with vehicle (sterile water) and 4 with isoniazid (100 mg/kg) once daily by oral gavage for 3 days.

tag: gender

value: female

tag: age

tag: tissue

value: left liver lobe

tag: strain

value: SJL/J

tag: treatment

value: Isoniazid

tag: steatosis

value: Yes

tag: scan date


title: Ly3_SPIB.2

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

institute: The University of York

hyb_protocol: Standard Illumina protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: Data were quantile normalised using Lumi for R [64-bit R version 2.15.1 (2012-06-22), lumi version 2.8.0]

source_name: ABC DLBCL_SPIB knock down

label_protocol: Standard Illumina protocol

growth_protocol: cell culture condition: IMDM, each containing 10% heat inactivated fetal calf serum and GlutaMAX™

extract_protocol: RNA was extracted with Trizol and amplified using Illumina® TotalPrepTM-96 RNA Amplification Kit

tag: source gender

value: male

tag: cell line

tag: cell type

value: Diffuse Large B-cell Lymphoma (DLBCL)

tag: transfected with

value: SPIB siRNA (SPIB knock down)


title: AKR/J mouse  liver, control animal 1

description: Sample name: 181

source_name: AKR/J liver, vehicle treated

value: AKR/J

value: Vehicle

value: No


title: Serum DNA 82

source_name: genomic DNA from serum sample 82

value: A


title: SJL/J mouse  liver, treated animal 1

description: Sample name: 177


title: Serum DNA 84

source_name: genomic DNA from serum sample 84

value: G


title: SJL/J mouse  liver, treated animal 4

description: Sample name: 180


title: Serum DNA 88

source_name: genomic DNA from serum sample 88

value: H


title: Serum DNA 83

source_name: genomic DNA from serum sample 83

value: C


title: Serum DNA 93

source_name: genomic DNA from serum sample 93

value: healthy postmenopausal women

value: I


title: Serum DNA 81

source_name: genomic DNA from serum sample 81

value: L


title: Ly3_Scram.2

source_name: ABC DLBCL_Scramble

value: scramble siRNA (control)


title: SJL/J mouse  liver, control animal 3

description: Sample name: 175

source_name: SJL/J liver, vehicle treated

value: female

value: left liver lobe

value: SJL/J


title: SJL/J mouse  liver, control animal 1

description: Sample name: 173

value: Yes


title: Ly3_SPIB.1

value: male

value: Diffuse Large B-cell Lymphoma (DLBCL)


title: SJL/J mouse  liver, control animal 2

description: Sample name: 174


title: DBA/2J mouse  liver, treated animal 3

description: Sample name: 171

source_name: DBA/ J liver, isoniazid treated

value: Isoniazid


title: CD34+ CML 96h Imatinib Hypoxia (0.5% O2) Patient #5

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

description: 5 IM 0.5% 96h

hyb_protocol: 750ng of cRNA from each sample was hybridized to Human HT-12 beadchip microarrays (Illumina) as per manufacturer specifications.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina) at scan factor 2 as per manufacturer specifications.

data_processing: Raw intensity values were subjected to background subtraction performed on the BeadStudio Data Analysis software (Illumina) and normalized using the Cross-correlation method (Chua et al., 2006). Differential gene expression was identified based on a fold change cutoff of >1.5 compared to the DMSO/Normoxia control for each patient and each time point.

source_name: CD34+ Chronic Phase CML 96h Imatinib Hypoxia (0.5% O2) Patient #5

label_protocol: 120ng of total RNA was subjected to cDNA synthesis using the Illumina TotalPrep Amplification kit (Ambion). The cDNA was purified using the MinElute Reaction Cleanup kit (Qiagen). In vitro transcription was performed on the cDNA to generate biotin-labelled cRNA according to manufacturer recommendations followed by purification using the RNeasy Mini kit (Qiagen).

growth_protocol: CML cells were cultured in serum free medium (StemPro−34® SFM complete medium, Gibco) supplemented with 2mM L−Glutamine and cytokines at concentrations similar to those found in stoma conditioned medium (granulocyte−macrophage colony−stimulating factor [GM−CSF], 200pg/mL; granulocyte colony−stimulating factor [G−CSF], 1000pg/mL; stem cell factor [SCF], 200pg/mL; leukemia inhibitory factor [LIF], 50pg/mL; macrophage inflammatory protein-1α [MIP−1α], 200pg/mL; and interleukin 6 [IL−6], 1000pg/mL).

extract_protocol: Total RNA was extracted from the CD34+ CML cells using the RNeasy Micro kit (Qiagen)

treatment_protocol: CD34+ CML cells were isolated from the bone marrow aspirates of 3 chronic phase patients (#3, #4 and #5) using immunomagnetic columns with the CD34 MicroBead kit (Miltenyi Biotec). The cells were then subjected to 24h or 96h of DMSO/Normoxia (21% oxygen, 5% carbon dioxide) control, 2 µM Imatinib, hypoxia (0.5% oxygen, 5% carbon dioxide) or combined Imatinib/hypoxia treatments in a humidified incubator (Innova CO−170, New Brunswick Scientific).

value: CD34+ Chronic Phase CML Cells

tag: marker

value: CD34 Positive

value: 2 µM Imatinib + Hypoxia (0.5% O2)

tag: duration

value: 96 hours


title: CD34+ CML 96h Imatinib Hypoxia (0.5% O2) Patient #3

description: 3 IM 0.5% 96h

source_name: CD34+ Chronic Phase CML 96h Imatinib Hypoxia (0.5% O2) Patient #3


title: CD34+ CML 96h Imatinib Hypoxia (0.5% O2) Patient #4

description: 4 IM 0.5% 96h

source_name: CD34+ Chronic Phase CML 96h Imatinib Hypoxia (0.5% O2) Patient #4


title: Serum DNA 79

source_name: genomic DNA from serum sample 79

tag: subject

tag: case/control

value: H


title: Ly3_Scram.1


title: MH003B-Scr42h2 vs. MH003B-3T3as

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan)

scan_protocol: Features were extracted using Imagene software from Biodiscovery.

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve.

label_protocol: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).

extract_protocol: RNA extraction by Trizol

treatment_protocol: NIH 3T3 cells were cultured in Dulbeccos modified Eagles medium-F10-Pen/Strep-10% fetal calf serum. Transient expression studies were performed by transfecting cells with pGL4.11-Baml1::luciferase (used as circadian reporter) and siRNA oligos against FoxO3 or control. Combined transfection of plasmid DNA and siRNA oligos was performed with Lullaby  (GE Healthcare), according to the manufacturers instructions. After synchronization of intracellular clocks by treatment of confluent cultures with forskolin (dissolved in 100% ethanol, added to the culture medium at a final concentration of 30 µM) cells were harvested for RNA isolation 24h (time1), 30h(time2), 36h(time3) and 42h(time4). As reference a common pool of cRNA (REF=3T3as) was used, which was derived from unsynchronized NIH 3T3 cells.

value: NIH 3T3

tag: transfection

value: pGL4.11-Baml1::luciferase (used as circadian reporter) and siRNA oligos against control

tag: time

tag: sample type

value: unsynchronized NIH 3T3 (REF)


title: Serum DNA 78

source_name: genomic DNA from serum sample 78

value: healthy postmenopausal women

tag: ageatdraw (yrs)

tag: season

tag: dna conc. (ug/ml)

value: F


title: Serum DNA 80

source_name: genomic DNA from serum sample 80

value: J


title: MH003B-Scr36h4 vs. MH003B-3T3as


title: CD34+ CML 96h Hypoxia (0.5% O2) Patient #5

description: 5 DMSO 0.5% 96h

source_name: CD34+ Chronic Phase CML 96h Hypoxia (0.5% O2) Patient #5

tag: treatment

value: Hypoxia (0.5% O2)


title: MH003B-Scr36h2 vs. MH003B-3T3as


title: DBA/2J mouse  liver, treated animal 4

description: Sample name: 172

tag: gender

value: female

tag: age

tag: tissue

value: left liver lobe

tag: strain

tag: steatosis


title: MH003B-Scr42h4 vs. MH003B-3T3as

tag: cell line


title: Serum DNA 75

source_name: genomic DNA from serum sample 75

value: K


title: DBA/2J mouse  liver, treated animal 2

description: Sample name: 170

value: Yes

tag: scan date


title: DBA/2J mouse  liver, control animal 4

description: Sample name: 168

source_name: DBA/ J liver, vehicle treated

value: Vehicle


title: Serum DNA 77

source_name: genomic DNA from serum sample 77

value: D


title: Serum DNA 76

source_name: genomic DNA from serum sample 76

value: B


title: CD34+ CML 96h Hypoxia (0.5% O2) Patient #4

description: 4 DMSO 0.5% 96h

source_name: CD34+ Chronic Phase CML 96h Hypoxia (0.5% O2) Patient #4

tag: cell type

value: CD34+ Chronic Phase CML Cells

tag: marker

value: CD34 Positive

tag: duration


title: CD34+ CML 96h Hypoxia (0.5% O2) Patient #3

description: 3 DMSO 0.5% 96h

source_name: CD34+ Chronic Phase CML 96h Hypoxia (0.5% O2) Patient #3

value: 96 hours


title: DBA/2J mouse  liver, control animal 2

description: Sample name: 166


title: MH003B-Scr30h2 vs. MH003B-3T3as

value: NIH 3T3

tag: transfection


title: DBA/2J mouse  liver, control animal 1

description: Sample name: 165


title: Serum DNA 74

source_name: genomic DNA from serum sample 74

tag: subject

tag: case/control

value: I


title: CD34+ CML 96h Imatinib Normoxia (21% O2) Patient #4

description: 4 IM 21% 96h

source_name: CD34+ Chronic Phase CML 96h Imatinib Normoxia (21% O2) Patient #4

value: 2 µM Imatinib


title: Serum DNA 73

source_name: genomic DNA from serum sample 73

value: healthy postmenopausal women

tag: ageatdraw (yrs)

value: G


title: MH003B-Scr30h4 vs. MH003B-3T3as

value: pGL4.11-Baml1::luciferase (used as circadian reporter) and siRNA oligos against control

tag: time

tag: sample type

value: unsynchronized NIH 3T3 (REF)


title: CD34+ CML 96h Imatinib Normoxia (21% O2) Patient #5

description: 5 IM 21% 96h

source_name: CD34+ Chronic Phase CML 96h Imatinib Normoxia (21% O2) Patient #5

tag: treatment


title: DBA/2J mouse  liver, treated animal 1

description: Sample name: 169

source_name: DBA/ J liver, isoniazid treated

tag: gender

value: female

value: Isoniazid


title: MH003B-Scr24h4 vs. MH003B-3T3as


title: Serum DNA 72

source_name: genomic DNA from serum sample 72

tag: season

tag: dna conc. (ug/ml)

value: E


title: DBA/2J mouse  liver, control animal 3

description: Sample name: 167

tag: age

tag: tissue

value: left liver lobe

tag: strain

value: Yes


title: CBA/J mouse  liver, treated animal 4

description: Sample name: 140

source_name: CBA/J liver, isoniazid treated

value: CBA/J

tag: steatosis

tag: scan date


title: CD34+ CML 96h Normoxia (21% O2) Patient #5

description: 5 DMSO 21% 96h

source_name: CD34+ Chronic Phase CML 96h Normoxia (21% O2) Patient #5

tag: cell type

tag: marker

value: Normoxia (21% O2)


title: CBA/J mouse  liver, treated animal 2

description: Sample name: 138


title: MH003B-Scr24h2 vs. MH003B-3T3as

tag: cell line

tag: transfection


title: CD34+ CML 96h Imatinib Normoxia (21% O2) Patient #3

description: 3 IM 21% 96h

source_name: CD34+ Chronic Phase CML 96h Imatinib Normoxia (21% O2) Patient #3

value: CD34+ Chronic Phase CML Cells

tag: duration


title: Serum DNA 71

source_name: genomic DNA from serum sample 71

tag: subject

tag: case/control

tag: ageatdraw (yrs)

value: C


title: CBA/J mouse  liver, treated animal 3

description: Sample name: 139

tag: treatment


title: Serum DNA 66

source_name: genomic DNA from serum sample 66

value: F


title: MH003B-FoxO342h2 vs. MH003B-3T3as

value: NIH 3T3

value: pGL4.11-Baml1::luciferase (used as circadian reporter) and siRNA oligos against FoxO3MH003B-siFoxO3

tag: time

tag: sample type


title: MH003B-FoxO342h4 vs. MH003B-3T3as


title: CBA/J mouse  liver, treated animal 1

description: Sample name: 137

tag: gender


title: CD34+ CML 96h Normoxia (21% O2) Patient #3

description: 3 DMSO 21% 96h

source_name: CD34+ Chronic Phase CML 96h Normoxia (21% O2) Patient #3

value: CD34 Positive

value: 96 hours


title: Serum DNA 69

source_name: genomic DNA from serum sample 69

value: healthy postmenopausal women

tag: season

tag: dna conc. (ug/ml)

value: L


title: Serum DNA 70

source_name: genomic DNA from serum sample 70

value: A


title: Serum DNA 68

source_name: genomic DNA from serum sample 68

value: J


title: Serum DNA 67

source_name: genomic DNA from serum sample 67

value: H


title: Serum DNA 65

source_name: genomic DNA from serum sample 65

value: D


title: CD34+ CML 96h Normoxia (21% O2) Patient #4

description: 4 DMSO 21% 96h

source_name: CD34+ Chronic Phase CML 96h Normoxia (21% O2) Patient #4


title: CBA/J mouse  liver, control animal 4

description: Sample name: 136

source_name: CBA/J liver, vehicle treated

value: female

tag: age

tag: tissue

value: left liver lobe

tag: strain

value: Vehicle


title: MH003B-FoxO330h2 vs. MH003B-3T3as

value: unsynchronized NIH 3T3 (REF)


title: MH003B-FoxO336h4 vs. MH003B-3T3as


title: MH003B-FoxO330h4 vs. MH003B-3T3as


title: CD34+ CML 24h Imatinib Hypoxia (0.5% O2) Patient #3

description: 3 IM 0.5% 24h

source_name: CD34+ Chronic Phase CML 24h Imatinib Hypoxia (0.5% O2) Patient #3

tag: cell type

value: CD34+ Chronic Phase CML Cells

value: 2 µM Imatinib + Hypoxia (0.5% O2)

value: 24 hours


title: MH003B-FoxO324h4 vs. MH003B-3T3as

value: NIH 3T3


title: CD34+ CML 24h Imatinib Hypoxia (0.5% O2) Patient #4

description: 4 IM 0.5% 24h

source_name: CD34+ Chronic Phase CML 24h Imatinib Hypoxia (0.5% O2) Patient #4

tag: marker


title: CD34+ CML 24h Imatinib Hypoxia (0.5% O2) Patient #5

description: 5 IM 0.5% 24h

source_name: CD34+ Chronic Phase CML 24h Imatinib Hypoxia (0.5% O2) Patient #5


title: CBA/J mouse  liver, control animal 3

description: Sample name: 135

value: CBA/J

tag: steatosis

value: Yes

tag: scan date


title: CBA/J mouse  liver, control animal 2

description: Sample name: 134


title: MH003B-FoxO336h2 vs. MH003B-3T3as

tag: cell line

tag: transfection

value: pGL4.11-Baml1::luciferase (used as circadian reporter) and siRNA oligos against FoxO3MH003B-siFoxO3


title: Serum DNA 63

source_name: genomic DNA from serum sample 63

tag: subject

value: healthy postmenopausal women

tag: case/control

value: K


title: CBA/J mouse  liver, control animal 1

description: Sample name: 133

tag: treatment


title: Serum DNA 62

source_name: genomic DNA from serum sample 62

tag: ageatdraw (yrs)

value: I


title: CD34+ CML 24h Hypoxia (0.5% O2) Patient #5

description: 5 DMSO 0.5% 24h

source_name: CD34+ Chronic Phase CML 24h Hypoxia (0.5% O2) Patient #5

value: CD34 Positive

value: Hypoxia (0.5% O2)

tag: duration


title: MH003B-FoxO324h2 vs. MH003B-3T3as

tag: time

tag: sample type


title: CD34+ CML 24h Imatinib Normoxia (21% O2) Patient #5

description: 5 IM 21% 24h

source_name: CD34+ Chronic Phase CML 24h Imatinib Normoxia (21% O2) Patient #5

value: 2 µM Imatinib


title: FVB/NJ mouse  liver, treated animal 4

description: Sample name: 132

source_name: FVB/NJ liver, isoniazid treated

tag: gender

value: female

value: FVB/NJ

value: Isoniazid


title: Serum DNA 64

source_name: genomic DNA from serum sample 64

tag: season

tag: dna conc. (ug/ml)

value: B


title: MH003B-3T3as vs. MH003B-Scr42h3

value: unsynchronized NIH 3T3 (REF)

value: pGL4.11-Baml1::luciferase (used as circadian reporter) and siRNA oligos against control


title: CD34+ CML 24h Hypoxia (0.5% O2) Patient #3

description: 3 DMSO 0.5% 24h

source_name: CD34+ Chronic Phase CML 24h Hypoxia (0.5% O2) Patient #3

value: CD34+ Chronic Phase CML Cells

value: 24 hours


title: CD34+ CML 24h Hypoxia (0.5% O2) Patient #4

description: 4 DMSO 0.5% 24h

source_name: CD34+ Chronic Phase CML 24h Hypoxia (0.5% O2) Patient #4


title: Serum DNA 61

source_name: genomic DNA from serum sample 61

value: G


title: FVB/NJ mouse  liver, treated animal 2

description: Sample name: 130

tag: age

tag: tissue

value: left liver lobe

tag: strain

value: Yes


title: FVB/NJ mouse  liver, treated animal 3

description: Sample name: 131

tag: steatosis


title: MH003B-3T3as vs. MH003B-Scr42h1

value: NIH 3T3


title: CD34+ CML 24h Imatinib Normoxia (21% O2) Patient #4

description: 4 IM 21% 24h

source_name: CD34+ Chronic Phase CML 24h Imatinib Normoxia (21% O2) Patient #4

tag: cell type

tag: marker


title: FVB/NJ mouse  liver, control animal 3

description: Sample name: 127

source_name: FVB/NJ liver, vehicle treated

value: Vehicle

tag: scan date


title: Serum DNA 60

source_name: genomic DNA from serum sample 60

tag: subject

value: healthy postmenopausal women

value: E


title: MH003B-3T3as vs. MH003B-Scr36h1

tag: cell line

tag: transfection


title: Serum DNA 59

source_name: genomic DNA from serum sample 59

tag: case/control

tag: ageatdraw (yrs)

value: C


title: MH003B-3T3as vs. MH003B-Scr30h3

tag: time


title: FVB/NJ mouse  liver, control animal 4

description: Sample name: 128

tag: treatment


title: Serum DNA 58

source_name: genomic DNA from serum sample 58

value: A


title: CD34+ CML 24h Imatinib Normoxia (21% O2) Patient #3

description: 3 IM 21% 24h

source_name: CD34+ Chronic Phase CML 24h Imatinib Normoxia (21% O2) Patient #3

value: CD34 Positive

value: 2 µM Imatinib

tag: duration


title: CD34+ CML 24h Normoxia (21% O2) Patient #5

description: 5 DMSO 21% 24h

source_name: CD34+ Chronic Phase CML 24h Normoxia (21% O2) Patient #5

value: Normoxia (21% O2)


title: MH003B-3T3as vs. MH003B-Scr36h3

tag: sample type


title: Serum DNA 57

source_name: genomic DNA from serum sample 57

tag: season

tag: dna conc. (ug/ml)

value: J


title: CD34+ CML 24h Normoxia (21% O2) Patient #4

description: 4 DMSO 21% 24h

source_name: CD34+ Chronic Phase CML 24h Normoxia (21% O2) Patient #4


title: Serum DNA 55

source_name: genomic DNA from serum sample 55

value: F


title: C57Bl/6J mouse  liver, treated animal 2

description: Sample name: 122

source_name: C57Bl/6J liver, isoniazid treated

tag: gender

value: female

tag: age

tag: tissue

value: Isoniazid

value: No


title: Serum DNA 56

source_name: genomic DNA from serum sample 56

value: H


title: FVB/NJ mouse  liver, control animal 1

description: Sample name: 125

value: left liver lobe

tag: strain

value: FVB/NJ

tag: steatosis


title: MH003B-3T3as vs. MH003B-Scr30h1

value: NIH 3T3

value: unsynchronized NIH 3T3 (REF)

value: pGL4.11-Baml1::luciferase (used as circadian reporter) and siRNA oligos against control


title: CD34+ CML 24h Normoxia (21% O2) Patient #3

description: 3 DMSO 21% 24h

source_name: CD34+ Chronic Phase CML 24h Normoxia (21% O2) Patient #3

tag: cell type

value: CD34+ Chronic Phase CML Cells

tag: marker

value: 24 hours


title: C57Bl/6J mouse  liver, treated animal 1

description: Sample name: 121

tag: scan date


title: FVB/NJ mouse  liver, treated animal 1

description: Sample name: 129

source_name: FVB/NJ liver, isoniazid treated

value: Yes


title: MH003B-3T3as vs. MH003B-FoxO342h3

tag: cell line

tag: transfection

value: pGL4.11-Baml1::luciferase (used as circadian reporter) and siRNA oligos against FoxO3MH003B-siFoxO3


title: MH003B-3T3as vs. MH003B-Scr24h1


title: FVB/NJ mouse  liver, control animal 2

description: Sample name: 126

value: Vehicle


title: Serum DNA 52

source_name: genomic DNA from serum sample 52

tag: subject

value: healthy postmenopausal women

tag: case/control

tag: ageatdraw (yrs)

value: I


title: Serum DNA 53

source_name: genomic DNA from serum sample 53

value: B


title: C57Bl/6J mouse  liver, treated animal 4

description: Sample name: 124

value: female

tag: treatment


title: MH003B-3T3as vs. MH003B-Scr24h3

tag: sample type

tag: time


title: MH003B-3T3as vs. MH003B-FoxO336h1


title: Serum DNA 50

source_name: genomic DNA from serum sample 50

tag: season

tag: dna conc. (ug/ml)

value: E


title: Serum DNA 54

source_name: genomic DNA from serum sample 54

value: D


title: MH003B-3T3as vs. MH003B-FoxO336h3


title: Serum DNA 51

source_name: genomic DNA from serum sample 51

value: G


title: C57Bl/6J mouse  liver, control animal 3

description: Sample name: 119

source_name: C57Bl/6J liver, vehicle treated

tag: gender

tag: age

value: left liver lobe

value: No


title: MH003B-3T3as vs. MH003B-FoxO324h3

value: NIH 3T3


title: MH003B-3T3as vs. MH003B-FoxO330h1

value: unsynchronized NIH 3T3 (REF)


title: Serum DNA 49

source_name: genomic DNA from serum sample 49

value: A


title: MH003B-3T3as vs. MH003B-FoxO330h3


title: C57Bl/6J mouse  liver, control animal 2

description: Sample name: 118

tag: tissue

tag: strain


title: C57Bl/6J mouse  liver, treated animal 3

description: Sample name: 123

value: Isoniazid

tag: steatosis


title: Serum DNA 47

source_name: genomic DNA from serum sample 47

value: J


title: Serum DNA 46

source_name: genomic DNA from serum sample 46

value: H


title: Serum DNA 45

source_name: genomic DNA from serum sample 45

value: F


title: Serum DNA 48

source_name: genomic DNA from serum sample 48

value: L


title: C3H/HeJ mouse  liver, treated animal 4

description: Sample name: 116

source_name: C3H/HeJ liver, isoniazid treated


title: Serum DNA 43

source_name: genomic DNA from serum sample 43

value: healthy postmenopausal women


title: C3H/HeJ mouse  liver, treated animal 2

description: Sample name: 114


title: MH003B-3T3as vs. MH003B-FoxO324h1

value: pGL4.11-Baml1::luciferase (used as circadian reporter) and siRNA oligos against FoxO3MH003B-siFoxO3


title: MH003A-FoxO6-time3-b vs. MH003A-3T3as

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

treatment_protocol: NIH 3T3 cells were cultured in Dulbeccos modified Eagles medium-F10-Pen/Strep-10% fetal calf serum. Transient expression studies were performed by transfecting cells with plasmids pFoxO6-egfp or empty vector (Clontech) using Fugene reagent (Roche) according to the manufacturers instructions. After synchronization of intracellular clocks by treatment of confluent cultures with forskolin (dissolved in 100% ethanol, added to the culture medium at a final concentration of 30 µM) cells were harvested for RNA isolation 24h (time1), 30h(time2), 36h(time3) and 42h(time4). As reference a common pool of cRNA (REF=3T3as) was used, which was derived from unsynchronized NIH 3T3 cells.


title: MH003A-FoxO6-time4-b vs. MH003A-3T3as


title: Serum DNA 42

source_name: genomic DNA from serum sample 42

value: K


title: C3H/HeJ mouse  liver, treated animal 3

description: Sample name: 115

value: female


title: C3H/HeJ mouse  liver, control animal 4

description: Sample name: 112

source_name: C3H/HeJ liver, vehicle treated

value: Vehicle


title: C3H/HeJ mouse  liver, control animal 3

description: Sample name: 111


title: Serum DNA 44

source_name: genomic DNA from serum sample 44

value: D


title: C3H/HeJ mouse  liver, control animal 2

description: Sample name: 110


title: Serum DNA 40

source_name: genomic DNA from serum sample 40

value: G


title: C3H/HeJ mouse  liver, control animal 1

description: Sample name: 109

value: left liver lobe


title: MH003A-FoxO6-time2-b vs. MH003A-3T3as


title: C3H/HeJ mouse  liver, treated animal 1

description: Sample name: 113

value: No


title: MH003A-FoxO6-time4-d vs. MH003A-3T3as

value: NIH 3T3


title: MH003A-FoxO6-time1-b vs. MH003A-3T3as

value: unsynchronized NIH 3T3 (REF)


title: MH003A-FoxO6-time3-d vs. MH003A-3T3as


title: MH003B-3T3as vs. MH003B-FoxO342h1


title: MH003A-FoxO6-time2-d vs. MH003A-3T3as


title: BALB/cJ mouse  liver, treated animal 4

description: Sample name: 108

source_name: BALB/cJ liver, isoniazid treated

value: BALB/cJ

value: Yes


title: Serum DNA 39

source_name: genomic DNA from serum sample 39

value: E


title: MH003A-FoxO6-time1-d vs. MH003A-3T3as


title: Serum DNA 38

source_name: genomic DNA from serum sample 38

value: C


title: BALB/cJ mouse  liver, treated animal 3

description: Sample name: 107

value: Isoniazid


title: Serum DNA 36

source_name: genomic DNA from serum sample 36

value: L


title: BALB/cJ mouse  liver, control animal 4

description: Sample name: 104

source_name: BALB/cJ liver, vehicle treated


title: Serum DNA 37

source_name: genomic DNA from serum sample 37

value: healthy postmenopausal women

value: A


title: MH003A-EV-time4-d vs. MH003A-3T3as

value: empty vector


title: BALB/cJ mouse  liver, treated animal 1

description: Sample name: 105

value: female


title: Serum DNA 33

source_name: genomic DNA from serum sample 33

value: F


title: BALB/cJ mouse  liver, treated animal 2

description: Sample name: 106


title: MH003A-EV-time4-b vs. MH003A-3T3as


title: Serum DNA 32

source_name: genomic DNA from serum sample 32

value: B


title: Serum DNA 41

source_name: genomic DNA from serum sample 41

value: I


title: Serum DNA 35

source_name: genomic DNA from serum sample 35

value: J


title: BALB/cJ mouse  liver, control animal 2

description: Sample name: 102

value: left liver lobe

value: Vehicle


title: BALB/cJ mouse  liver, control animal 1

description: Sample name: 101


title: Serum DNA 30

source_name: genomic DNA from serum sample 30


title: Serum DNA 31

source_name: genomic DNA from serum sample 31

value: K


title: MH003A-EV-time3-b vs. MH003A-3T3as

value: NIH 3T3

value: unsynchronized NIH 3T3 (REF)


title: MH003A-EV-time2-b vs. MH003A-3T3as


title: Serum DNA 28

source_name: genomic DNA from serum sample 28

value: E


title: MH003A-EV-time1-b vs. MH003A-3T3as


title: MH003A-3T3as vs. MH003A-FoxO6-time4-c


title: Serum DNA 34

source_name: genomic DNA from serum sample 34

value: H


title: BMDM, Tpl2 KO, LPS treated, biological replicate 2

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

description: Gene expression data from BMDM

hyb_protocol: Approximately 10 ug of biotinylated cRNA was hybridized to GeneChip Mouse Genome 430 2.0 arrays (Affymetrix) at 45 degree for 16 hours in accordance with the manufacturer’s protocols

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

data_processing: Expression values were determined with GeneChip Operating Software (GCOS) v1.1.1 software. All data analysis was performed using GeneSpring software GX 11.0. Expression values for each probe were normalized using the Robust Multichip Average (RMA) method.

source_name: Bone marrow derive macrophage

label_protocol: Approximately 10 ug of total RNA was labeled using MessageAmp™ II-Biotin Enhanced Kit (Ambion)

growth_protocol: BM was harvested from tibiae and femurs of mice by flushing with supplemented DMEM using a 10 mL syringe and 25-gauge needle.  Cells were disaggregated by gentle pipetting and centrifuged at 1200 rpm for 10 min at RT.  The cells were then re-suspended in ACK lysing buffer (Invitrogen) for 30 sec to lyse red blood cells.  Cells were washed in PBS (20-30 mL) and centrifuged again at 1200 rpm for 10 min. Cell pellet was resuspended in supplemented DMEM for cell counting.  Differentiated macrophages were obtained by culturing BM cells on sterile petri dishes at 2 x 106/mL in supplemented DMEM with the addition of macrophage colony-stimulating factor (M-CSF; 10 ng/mL) for 7-10 days at 37°C, 5% CO2.  Cells were adherence purified on day 7-10 by removing media, washing adherent cells with PBS and then harvesting by incubating in 10 mL cell dissociation buffer (Invitrogen) for 15 min at 37°C.  Plates were washed with PBS to collect dislodged cells, and cells were centrifuged at 1200 rpm for 10 min. Cell pellets were resuspended in supplemented DMEM for cell counting.

extract_protocol: Total cellular RNA was extracted using an RNeasy Mini kit (Qiagen).

treatment_protocol: For individual experiments, murine BMDMs or adherence purified PECs were plated at either 0.5 x 106/mL or 1 x 106/mL in supplemented DMEM medium.  Cells were left unstimulated (as a control) or stimulated with lipopolysaccharide (LPS) from Escherichia coli (0111:B4, 1 μg/mL) for various time-points at 37°C, 5% CO2.  For inhibition studies, BMDMs were pre-treated with the following inhibitors in supplemented DMEM medium for 30 min at 37°C, 5% CO2 prior to stimulation with LPS:  LY-294,002 hydrochloride, 20 μM (Sigma); Rapamycin, 30 nM (Sigma); U0126 ethanolate, 20 μM (Sigma).

tag: genotype/variation

value: Tpl2 deficient

value: stimulated with LPS


title: BMDM, Tpl2 KO, LPS treated, biological replicate 1

description: Gene expression data from BMDM


title: C57Bl/6J mouse  liver, control animal 4

description: Sample name: 120

source_name: C57Bl/6J liver, vehicle treated

value: No

tag: scan date


title: MH003A-EV-time2-d vs. MH003A-3T3as

tag: cell line


title: MH003A-3T3as vs. MH003A-FoxO6-time4-a

tag: transfection


title: Serum DNA 27

source_name: genomic DNA from serum sample 27

tag: subject

value: healthy postmenopausal women

value: C


title: Serum DNA 29

source_name: genomic DNA from serum sample 29

tag: case/control

value: G


title: MH003A-3T3as vs. MH003A-FoxO6-time3-c


title: BALB/cJ mouse  liver, control animal 3

description: Sample name: 103

value: female

value: BALB/cJ

value: Yes


title: MH003A-EV-time3-d vs. MH003A-3T3as

value: empty vector


title: MH003A-3T3as vs. MH003A-FoxO6-time3-a


title: MH003A-EV-time1-d vs. MH003A-3T3as


title: BMDM, Tpl2 WT, LPS treated, biological replicate 1

description: Gene expression data from BMDM

value: Tpl2 wild type


title: BMDM, Tpl2 WT, LPS treated, biological replicate 2

description: Gene expression data from BMDM


title: Serum DNA 26

source_name: genomic DNA from serum sample 26

tag: ageatdraw (yrs)

value: A


title: Serum DNA 22

source_name: genomic DNA from serum sample 22

value: F


title: C57Bl/6J mouse  liver, control animal 1

description: Sample name: 117

value: left liver lobe

tag: treatment

value: Vehicle


title: BMDM, Tpl2 KO, unstimulated, biological replicate 1

description: Gene expression data from BMDM

value: unstimulated


title: BMDM, Tpl2 KO, unstimulated, biological replicate 2

description: Gene expression data from BMDM


title: KF_NN_animal4

city: Brisbane

first: Ross

middle: L

last: Tellam

state: QLD

address: 306 Carmody Road St.Lucia

department: Level 6 Queensland Biosciences Precinct

country: Australia

institute: CSIRO Animal, Food and Health Sciences

description: Gene expression data from Dorset/Suffolk/Rambouillet cross-bred sheep lambs at 12 weeks development from kidney fat (KF)

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genomer Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, GCOSvs1.4

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

organism: Ovis aries

source_name: Kidney fat, lamb, 12 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Animals were reared and euthanased in accordance with the animal ethics guidelines of Utah State University (Utah, USA)

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

treatment_protocol: Kidney fat was dissected from each animal at a pre-determined site within 15 minutes of euthanasia, snap frozen under liquid nitrogen and stored at -80oC.

tag: genotype

value: wildtype

tag: developmental stage

value: 12 week

value: perirenal adipose

value: Dorset/Suffolk/Rambouillet cross-bred


title: BMDM, Tpl2 WT, unstimulated, biological replicate 1

description: Gene expression data from BMDM


title: MH003A-3T3as vs. MH003A-FoxO6-time2-a

value: NIH 3T3

tag: sample type

value: unsynchronized NIH 3T3 (REF)

tag: time


title: MH003A-3T3as vs. MH003A-EV-time4-c


title: Serum DNA 24

source_name: genomic DNA from serum sample 24

value: healthy postmenopausal women

tag: season

tag: dna conc. (ug/ml)

value: J


title: MH003A-3T3as vs. MH003A-FoxO6-time1-a


title: MH003A-3T3as vs. MH003A-FoxO6-time2-c


title: KF_NN_animal1

tag: tissue


title: KF_NN_animal2

tag: strain


title: KF_NCpat_animal4

value: Callipyge


title: MH003A-3T3as vs. MH003A-EV-time4-a


title: MH003A-3T3as vs. MH003A-EV-time3-c


title: Serum DNA 25

source_name: genomic DNA from serum sample 25

value: L


title: BMDM, Tpl2 WT, unstimulated, biological replicate 2

description: Gene expression data from BMDM


title: Serum DNA 21

source_name: genomic DNA from serum sample 21

value: D


title: MH003A-3T3as vs. MH003A-FoxO6-time1-c


title: MH003A-3T3as vs. MH003A-EV-time2-c

value: empty vector


title: KF_NCpat_animal3


title: Serum DNA 20

source_name: genomic DNA from serum sample 20

value: B


title: KF_NN_animal3


title: MH003A-3T3as vs. MH003A-EV-time3-a


title: Serum DNA 17

source_name: genomic DNA from serum sample 17

value: G


title: KF_NCpat_animal2


title: MH003A-3T3as vs. MH003A-EV-time2-a


title: Serum DNA 15

source_name: genomic DNA from serum sample 15

value: A


title: KF_NCpat_animal1


title: MH003A-3T3as vs. MH003A-EV-time1-c


title: Serum DNA 18

source_name: genomic DNA from serum sample 18

value: I


title: Serum DNA 10

source_name: genomic DNA from serum sample 10

value: C


title: Serum DNA 12

source_name: genomic DNA from serum sample 12

value: K


title: Serum DNA 9

source_name: genomic DNA from serum sample 9


title: Serum DNA 13

source_name: genomic DNA from serum sample 13


title: Serum DNA 16

source_name: genomic DNA from serum sample 16


title: kidney-old-fasted-41

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

hyb_protocol: Gene chip hybridization, washing and scanning were carried out according to Affymetrix protocols.

scan_protocol: Scanning was carried out according to Affymetrix protocols

data_processing: Quality control was performed using the pipeline at the www.arrayanalysis.org website (Maastricht University, the Netherlands). Normalization was done via the Robust Multichip Average (RMA) algorithm.

source_name: 3 days fasting

label_protocol: RNA was further processed for hybridization to Affymetrix HT MG-430 PM Array Plates at the Microarray Department of the University of Amsterdam, the Netherlands. RNA amplication and labeling were carried out according to Affymetrix protocols

growth_protocol: All aged mice were bred, raised and kept under identical SPF conditions. Young (male C57BL/6J, weight range 22–25 grams age range 10–14 weeks ) and aged (male FVB-C57BL/6J F1-hybrid, average age 73 weeks, weight ~ 47 grams) mice were used for this experiment. Before start of the experiment, the animals were transferred to separate rooms within the animal facility and were given an acclimatization period of 1-2 weeks. Animals were kept under standard laboratory conditions (temperature ± 20°C, 12 hour light/12 hour dark) and were allowed free access to water and food unless noted otherwise. All experiments were performed with the approval of the local Animal Experiments Committee of the National Institute of Public Health and the Environment (RIVM) and of the Erasmus Medical Center, the Netherlands.

extract_protocol: Half of both the left and the right kidney were snap frozen in liquid nitrogen until further analysis. For gene expression analysis, total RNA was extracted from frozen kidney tissue using the QIAzol lysis Reagent and miRNAeasy Mini Kit (QIAGEN, Hilden, Germany), as described in the Qiagen protocol. Addition of wash buffers RPE and RWT (QIAGEN) was done mechanically by using the QIAcube (QIAGEN, Hilden, Germany) via the miRNeasy program; animal tissues; aqueous phase. RNA was eluted in RNase free water and stored at -80°C. The concentration of RNA was measured by Nanodrop (Thermo Scientific). Subsequently, quality assessment of the RNA was done using the 2100 Bio-Analyzer (Agilent Technologies, Amstelveen, the Netherlands) and RNA kits and reagents belonging to the same manufacturer.

treatment_protocol: The first group had unlimited access to food and water preoperatively. The second group was fasted for three days preoperatively with no access to food and unlimited access to water.

tag: gender

value: male

tag: protocol

value: 3 days fasting

tag: age

value: old

value: kidney


title: Serum DNA 11

source_name: genomic DNA from serum sample 11

value: E


title: kidney-old-fasted-42


title: kidney-old-control-40

source_name: control

value: control


title: Serum DNA 8

source_name: genomic DNA from serum sample 8

value: healthy postmenopausal women


title: kidney-old-fasted-39


title: kidney-old-control-43


title: Serum DNA 7

source_name: genomic DNA from serum sample 7

value: J


title: kidney-old-fasted-33


title: kidney-old-fasted-38


title: Serum DNA 6

source_name: genomic DNA from serum sample 6

value: H


title: Serum DNA 5

source_name: genomic DNA from serum sample 5

value: D


title: kidney-old-control-36


title: Serum DNA 1

source_name: genomic DNA from serum sample 1


title: Serum DNA 23

source_name: genomic DNA from serum sample 23


title: kidney-young-fasted-339

value: young


title: Serum DNA 2

source_name: genomic DNA from serum sample 2


title: kidney-young-fasted-344


title: technical rep vs. quasi-technical rep

city: Lubbock

first: Christopher

middle: Dale

last: Rock

state: TX

address: Flint and Main Sts.

department: Biological Sciences

institute: Texas Tech University

description:
slide # ATv3.6.1.299
technical rep: 50% wild type_rep1 + 50% wild type_rep3 vs. quasi-technical rep: 50% hlq mutant_rep4 + 25% hlq mutant_rep1 + 25% hlq mutant rep_3

hyb_protocol: A pair of Cy5- and Cy3-labeled samples were mixed in equimolar proportions (~1000 ng per sample) and hybridized.  Conditions of hybridization and washing were according to the protocol published by Galbraith DW, Janda J, Lambert GM: Multiparametric analysis, sorting, and transcriptional profiling of plant protoplasts and nuclei according to cell type. In: Methods in Molecular Biology: Flow Cytometry Protocols. vol. 699; 2011: 407-429.

scan_protocol: GenePix Autoloader 4200AL Scanner (Molecular Devices, Sunnyvale, CA) with laser excitation at 532 and 635 nm at the resolution of ten pixels per micron, and saved as 16-bit grayscale multi-image TIFF files.

data_processing: Intensity values were extracted using GenePix Pro 6.0 (Molecular Devices, Sunnyvale, CA) and saved as gpr and txt files for each block individually.  The data for each array were lowess normalized followed by ANOVA analysis of differential gene expression using empirical Bayes methods to moderate the standard deviations between genes.  This was done by the software package Linear Models for Microarray Data (limma) (Smyth, G.K., Michaud, J., and Scott, H.S. (2005). Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21, 2067-2075) written in R language under the BioConductor platform (Gentleman, R., Carey, V., Bates, D., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Hornik, K., Hothorn, T., Huber, W., Iacus, S., Irizarry, R., Leisch, F., Li, C., Maechler, M., Rossini, A., Sawitzki, G., Smith, C., Smyth, G., Tierney, L., Yang, J., and Zhang, J. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5, R80) version R2.5.1 (http://www.r-project.org/).  Normalization “within” and “between arrays” scaled the log2-ratios of each two color experiment to have the same median-absolute-deviation across arrays.  We calculated a dye effect coefficient in addition to the genotype coefficient and signal amplitude across all probes and samples.

organism: Arabidopsis thaliana

source_name: whole seedling

label_protocol: ~2.5 µg of total RNA was used per sample per labeling reaction for reverse transcription into cDNA.  Strand-specific cRNA was labeled with Amino Allyl MessageAmp aRNA Amplification Kit (Ambion; cat#: AM1753) according to the manufacturer's protocol (Grand Island, NY, USA).  Each sample was run on a Bioanalyzer (Agilent Technologies, Santa Clara, CA) before and after labeling.

growth_protocol: ~1,000 Arabidopsis thaliana seeds from a self-fertilization of heterozygote for the mutant hlq gene in the genetic background abi2-1/abi2-1 homozygous (Landsberg erecta ecotype) were soaked in water and kept in the dark at 4°C for 3 days before being placed in rows and germinated on Petri plates containing 0.5x Murashige & Skoog salts (Research Products International, Mt. Prospect, IL), 1% sucrose, 0.5% phytagel (SIGMA-ALDRICH, St. Louis, MO). Plates were kept vertically under continuous light (~ 100 µE/m-2s-1) at 21°C for two weeks. Then seedlings were collected in microfuge tubes, frozen in liquid nitrogen and stored at -80°C before RNA extraction.  The accessions used in this study are listed as follows: Col-0 (stock # CS60000), abi2-1 (CS23), Landsberg erecta (Ler) (CS20), available from the Arabidopsis Biological Resource Center (Ohio State University; http://abrc.osu.edu/).

extract_protocol: For each individual pool, 100mg sample (~40 seedlings) was ground in a mortar with liquid nitrogen. Total RNA was extracted by using Trizol (Invitrogen, Carlsbad, CA) according to manufacturer's guidelines. Nucleotide pellet was washed with 70% EtOH twice and dried in air. After dissolving pellet in DEPC-treated water, the RNA concentration was measured by Nano Drop and the final concentration was adjusted to 1 µg/µL with DEPC water.

treatment_protocol: samples were not treated.

value: abi2-1, erecta homozygous, hlq/+ heterozygous and +/+ wild type

value: abi2-1, erecta homozygous, hlq/hlq homozygous


title: kidney-old-control-34


title: Positive_control_1_pool_dye_swap

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: Animal treated with phenobarbital and beta-naphthoflavone VS pooled samples from 10 animals treated with saline

hyb_protocol: Channel 1 sample was mixed with channel 2 sample, hybridization buffer was added (final concentration was 3xSSC, 0.2% SDS) and samples were denatured. Using LifterSlip cover glasses (Erie Scientific Company, Portsmouth, NH, USA) samples were hybridized for 16h at 65ºC in a water bath using humidified hybridization chambers (HybChambers, GeneMachines, San Carlos, CA, USA). Prior hybridizations Sterolgene v1 Mouse slides were pre-hybridized for 1 hour at 42ºC in 5xSSC, 0.1%SDS and 1%BSA, then washed at room temperature for 5 min in 2xSSC and 0.1%SDS, 3 min in 0.2xSSC and 2 min in MilliQ water and dried by centrifugation. After hybridization slides were washed at room temperature for 5 min in 2xSSC and 0.5%SDS, 5 min in 0.5xSSC, 5 min in 0.05xSSC, and then dried using vacuum centrifuge.

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

data_processing: Features were filtered out according to the following criteria: coefficient of variation (CV, ratio between standard deviation of the background and the median feature intensity) above 0.5 and foreground to background ratio above 1.5. Saturated features were removed. Log2 ratios were normalized using LOESS fit to spike in control RNAs and housekeeping controls. Filtration and normalization was done in Orange software. Normalized log ratios can be compared across samples. Data normalization and analysis was performed using Orange software (Demsar, 2006; Curk, 2005; http://www.ailab.si/orange).

label_protocol: cDNA synthesis and incorporation of aa-dUTP by reverse transcription was performed using SuperScript™ III Reverse Transcriptase (Invitrogen, USA), 100mM dNTPs (Promega, USA), amino-allyl dUTP (Sigma Aldrich, USA), oligo dT primers (Invitrogen, USA) and 20µg of total RNA, protected with RNase OUT  RNase inhibitor (Invitrogen, USA). Negative control group RNA was pooled from all mice and used as a reference in all hybridizations. Final dNTP concentration was of 25mM for dATP, dCTP and dGTP; dTTP and amino-allyl-dUTP were in ratio 3:2 (final concentration 15mM and 10mM, respectively). 250 pg of Firefly Luciferase mRNA (Promega, Madison, WI, USA), and 0.5 μL of test spike mix from Lucidea Universal ScoreCard kit were added as internal controls and calibrators. After the reverse transcription, RNA was alkaline-hydrolysed and amino-allyl cDNA was purified on MinElute PCR Purification Kit columns (Qiagen, Germany). Cy3 and Cy5 NHS esters were coupled to aa-cDNA (Cy3, resp. Cy5 Mono-Reactive Dye Pack (Amersham Biosciences, USA)). Uncoupled dye was removed on MinElute columns.

growth_protocol: Female mice of the inbred strain C57BL/6, 8-10 weeks old were kept in transparent plastic cages and maintained in an Independent Environmental Air Flow Animal Cabinet with lighting from 6AM  to 6PM, temperature 22 °C.

extract_protocol: Total RNA was isolated from liver tissue samples stored in RNAlater (Qiagen, Germany) using TRI REAGENT (MRC, USA). RNA concentration and purity was measured by spectrophotometry at 260, 280 and 230 nm using an Infinite M200 micro plate reader (Tecan, Switzerland). RNA integrity was determined on an Agilent 2100 Bioanalyzer using an RNA 6000 Nano LabChip kit (both Agilent Technologies, USA).

treatment_protocol: Animals were randomly separated into 4 groups of 5 and treated for three days by intraperitoneal injections as following: AD and TD groups were given 25 mg/kg of AD or TD intraperitoneally for three days. PC (positive control) group of four animals was treated with 60 mg/kg phenobarbital plus one dose of 80 mg/kg of β-naphthoflavone on day two. 5 animals of NC (negative control) group were injected 200µl of 0.9% saline solution. On day four, animals were killed by cervical dislocation.

value: liver

value: phenobarbital and beta-naphthoflavone

tag: animal

value: pool PC_1,PC_2,PC_3,PC_4

source_name: Pooled samples from 10 animals treated with saline

value: saline


title: Positive_control_4_pool

source_name: Animal treated with phenobarbital and beta-naphthoflavone


title: Positive_control_3_pool_dye_swap


title: Positive_control_2_pool


title: kidney-young-control-350

value: male


title: kidney-young-fasted-343

value: 3 days fasting


title: kidney-young-control-349


title: kidney-young-control-348


title: kidney-old-control-37

value: old


title: hlq mutant_rep2_vs wild type_rep2

description:
slide # ATv3.6.1.297
hlq mutant_rep2_vs wild type_rep2


title: kidney-young-fasted-340

value: kidney


title: kidney-young-control-347


title: Serum DNA 19

source_name: genomic DNA from serum sample 19

value: K


title: MB28

status: Public on Jun 02 2014

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

description: Gene expression data from a medulloblastoma tumor sample

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

source_name: Primary medulloblastoma tumor tissue

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from biopsy samples was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using the TRIzol reagent (Invitrogen, Carlsbad, USA), and subsequently passed over a RNeasy Mini Spin Column (Qiagen, Hilden, Germany) for the removal of small fragments. Integrity control and sample quantitation of total extracted RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

value: M

tag: histology

value: desmoplastic


title: wild type_rep3 vs. hlq_rep3

description:
slide # ATv3.6.1.298
wild type_rep3 vs. hlq_rep3


title: Serum DNA 4

source_name: genomic DNA from serum sample 4

tag: subject

value: healthy postmenopausal women

value: B


title: MB34

value: F

value: LCA


title: Ptprd-/-p16-/- tumor, biolofical rep 2

city: New York

first: Timothy

last: Chan

state: NY

address: 1275 York Avenue

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan-Kettering Cancer Center

description: Ptprd-/-p16-/- GFP+ DAPI- tumor cells from RCAS PDGFB GFP gliomas

hyb_protocol: 6.5ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray scanner 7G.

data_processing: Data was RMA normalized and analyzed using Partek software (v.6.6).

label_protocol: 75 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

growth_protocol: Cerebral injections of RCAS PDGF GFP were performed on post-neonatal day 1-3.

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

treatment_protocol: GFP+ tumors were dissected manually under a fluorescence microscope and digested enzymatically with papain. GFP+DAPI- cells were sorted into Trizol and stored at -80 degrees.

tag: strain background

value: mixed background of C57/BL6 and FVB/N

tag: genotype/variation

value: brain

tag: cell type

value: RCAS PDGF GFP glioma cells


title: LFS_MB1


title: MB35


title: Ptprd+/-p16-/- tumor, biological rep 2

description: Ptprd+/-p16-/- GFP+ DAPI- tumor cells from RCAS PDGFB GFP gliomas

value: HET; Ptprd+/-p16-/-


title: MB79

value: medulloblastoma, NOS


title: Vehicle treated sample

city: Memphis

first: Ramesh

last: Narayanan

state: Tennessee

address: 19 S. Manassas, Room 120

department: Medicine

institute: University of Tennessee Health Science Center

description:
Gene Expression Data
Vehicle

hyb_protocol: According to Affymetrix protocol

scan_protocol: Scan was done on GCS3000 7G

data_processing: Normalization was done using Affymetrix Expression Console

source_name: MDA-MB-231-AR vehicle

label_protocol: Affymetrix WT labeling kit Cat #900671

growth_protocol: Tumors were grown in nude mice (MDA-MB-231 cells stably transfected with AR)

extract_protocol: RNA was extracted using Qiagen Rneasy kit. Amplification was done with Ambion WT Amplification kit Cat #4411974 using 100 ng total RNA.

treatment_protocol: Mice were treated with vehicle or GTx-027

tag: disease state

value: MDA-MB-231-AR tumor grown in nude mice

tag: treatment

value: treated orally with vehicle


title: MB37


title: GTx-027-treated sample

description:
Gene Expression Data
GTx-027 (30 mpk)

source_name: MDA-MB-231-AR GTx-027

value: treated orally with selective androgen receptor modulator (SARM) GTx-027


title: Serum DNA 14

source_name: genomic DNA from serum sample 14

tag: case/control

tag: ageatdraw (yrs)

value: L


title: Ptprd-/-p16-/- tumor, biological rep 3

source_name: Ptprd-/-p16-/- GFP+ DAPI- tumor cells from RCAS PDGFB GFP gliomas


title: MB21


title: wild type_rep1 vs. hlq mutant_rep1

description:
slide # ATv3.6.1.296
wild type_rep1 vs. hlq mutant_rep1

tag: genotype

value: abi2-1, erecta homozygous, hlq/+ heterozygous and +/+ wild type

value: abi2-1, erecta homozygous, hlq/hlq homozygous


title: Par_MB 310

value: M


title: MBRep_T78

value: desmoplastic


title: kidney-young-control-346

source_name: control

value: male

value: control

value: young

value: kidney


title: Ptprd-/-p16-/- tumor, biological rep 1

value: mixed background of C57/BL6 and FVB/N


title: MB1

value: F

value: classic


title: MB104


title: MB82


title: MBRep_T59


title: MH003A-3T3as vs. MH003A-EV-time1-a

tag: cell line

value: NIH 3T3

tag: sample type

value: unsynchronized NIH 3T3 (REF)

tag: transfection

value: empty vector

tag: time


title: MB81

tag: gender

value: medulloblastoma, NOS


title: Ptprd+/+p16-/- tumor, biological rep 2

description: Ptprd+/+p16-/- GFP+ DAPI- tumor cells from RCAS PDGFB GFP gliomas

value: wild type; Ptprd+/+p16-/-

tag: tissue

value: brain

value: RCAS PDGF GFP glioma cells


title: Ptprd+/-p16-/- tumor, biological rep 1

source_name: Ptprd+/-p16-/- GFP+ DAPI- tumor cells from RCAS PDGFB GFP gliomas

value: HET; Ptprd+/-p16-/-


title: SARS_Mu_Mock_young_24h_34_2

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505C) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

label_protocol: cRNA probes were generated from each sample by the use of an Agilent one-color Quick-Amp labeling kit. The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: Young (8 weeks old) and aged (1 year old) female BALB/c mice were  intranasally infected with 10^5 PFU of either MA15, MA15 gamma, MA15 epsilon, or phosphate buffer solution (PBS; mock-infection). Lungs from aged mice were harvested at 12, 24, and 48 hours post-infection. Lungs from young mice were harvested at 12, 24, 48, and 96 hours post-infection.

extract_protocol: All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Lung samples for microarray analysis were stored as TRIzol homogenates at -80 degrees C prior to RNA extraction.

tag: strain

value: BALB/c

value: female

tag: age

value: 8 wks old (young)

value: lung

tag: sample collection time post infection

tag: infected with

value: phosphate buffer solution (PBS), mock infection

tag: biological replicate


title: 2m20

value: M

tag: histology

value: desmoplastic


title: SARS_Mu_Mock_young_24h_35


title: Ptprd+/+p16-/- tumor, biological rep 1

source_name: Ptprd+/+p16-/- GFP+ DAPI- tumor cells from RCAS PDGFB GFP gliomas

tag: strain background

value: mixed background of C57/BL6 and FVB/N

tag: genotype/variation

tag: cell type


title: Serum DNA 3

source_name: genomic DNA from serum sample 3

tag: subject

value: healthy postmenopausal women

tag: case/control

tag: ageatdraw (yrs)

tag: season

tag: dna conc. (ug/ml)

value: I


title: SARS_Mu_Mock_young_12h_49


title: SARS_Mu_Mock_young_48h_1


title: SARS_Mu_Mock_young_96h_19


title: SARS_Mu_Mock_young_12h_47


title: TAL1_3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

hyb_protocol: Hybridization was performed in the hybridization oven (Agilent Technologies, 17h, 10 rpm, 65˚C)

scan_protocol: Cy3 intensities were detected by a one-color microarray scanner (G2505C, Agilent Technologies) at 5 µm resolution

data_processing: Data were quantile normalized and log2 transformed using R and Bioconductor package limma.

source_name: HEL cells transduced with shRNA against Tal1 expressing virus

label_protocol: For each array 200 ng RNA was processed and Cy3 labeled by the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Human erythroleukemia (HEL) cell were obtained from ATCC (HEL 92.1.7 (ATCC® TIB-180™). Cells were grown in RPMI-Medium supplemented with 10% fetal bovine serum, 1% peniciline/streptamycine. Cell density was at a range between 10E5 to 10E6 cell/ml.

extract_protocol: mRNA was isolated from HEL cells, which were transduced with lentiviruses harboring shconstructs against the transcription factor Tal1 and PADI4 respectively, in biological triplicates. Two control samples with a control lentivirus with an shRNA against LacZ were included. RNA was prepared 6 days after transduction.. Tissue samples were transferred into trizol buffer, homogenized and mRNA was isolated in a single-step acid guanidinium thiocyanate-phenol-chloroform extraction following manufacturer´s instructions (http://tools.invitrogen.com/content/sfs/manuals/trizol_reagent.pdf)

treatment_protocol: HEL cells were lentivirally transduced with a virus harboring an shRNA cassette. Transduction effciency was more than 90% as measured by GFP fluorescence. Cells were harvested 6 days after transduction.

tag: cell line

value: HEL

tag: proband sex

value: Male

tag: treatment


title: SARS_Mu_Mock_young_48h_2

tag: strain

tag: gender

tag: tissue


title: BalbC_SARS_Mock_Aged_12h_B

tag: age

value: 1 yr (aged)

tag: sample collection time post infection

tag: infected with

value: B


title: SARS_Mu_Mock_young_12h_46

tag: biological replicate


title: SARS_Mu_Mock_young_24h_33


title: TAL1_1

value: transduced with shRNA against Tal1 expressing virus


title: BalbC_SARS_Mock_Aged_12h_C

value: C


title: SARS_Mu_Mock_young_12h_48_2


title: TAL1_2


title: SARS_Mu_Mock_young_96h_20


title: BalbC_SARS_Mock_Aged_48h_B


title: PAD4_3

source_name: HEL cells transduced with shRNA against PADI4 expressing virus


title: SARS_Mu_Mock_young_96h_18


title: PAD4_1

value: transduced with shRNA against PADI4 expressing virus


title: SARS_Mu_Mock_young_48h_3_2

value: BALB/c


title: BalbC_SARS_Mock_Aged_48h_A

value: female

value: A


title: SARS_Mu_Mock_young_48h_4

value: 8 wks old (young)

value: lung


title: BalbC_SARS_Mock_Aged_24h_A

value: phosphate buffer solution (PBS), mock infection


title: BalbC_SARS_Mock_Aged_12h_A


title: C_2

source_name: HEL cells transduced with an control shRNA expressing virus (LacZ)


title: SARS_Mu_MA15g_young_24h_40

value: SARS mouse adapted variants

tag: variant type

value: MA15 gamma


title: SARS_Mu_MA15g_young_12h_54


title: BalbC_SARS_Mock_Aged_24h_B


title: ATL-acu#2-N

city: Tokyo

first: Kazumi

last: Nakano

address: 4-6-1, Sirokanedai, Minatoku

department: Department of Medical Genome Sciences, Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

description: mRNA expression in ATL

hyb_protocol: Hybridization was performed at 65oC for 17h in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) for 1min and with GE Wash buffer 2 (Agilent)  for 1min at 37oC.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner C using the one color scan setting for 4x44K microarray slides (Scan Area: 61x21.6 mm, Scan resolution: 5um, Dye channel: Green, Tiff: 20bit, XDR ratio: NoXDR)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol : GE1-107  and Grid: 014850_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PBMC

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from FACS-sorted samples using TriZol (Invitrogen) following the manufacturer's recommendations.  The protocol includes DNaseI treatment to eliminate any genomic DNA contamination. The extracted total RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from ATL patients, HTLV-1 carriers and healthy volunteers was subjected to PBMCs isolation. Then PBMCs were subjected to multicolor FACS-sorting based on CADM1 and CD7 expression levels in  CD4+ T cells.

value: whole blood

tag: atl subtype

value: ATL-acute

value: male


title: PAD4_2

value: HEL

value: Male


title: SARS_Mu_MA15g_young_24h_39_2


title: ATL-acu#3-N

description: mRNA expression in ATL


title: SARS_Mu_MA15g_young_12h_56


title: ATL-sm#2-D

description: mRNA expression in ATL

value: ATL-smoldering


title: C_1

value: transduced with an control shRNA expressing virus


title: ATL-acu#1-N

description: mRNA expression in ATL


title: SARS_Mu_MA15g_young_96h_28


title: ATL-ch#1-N

description: mRNA expression in ATL

value: ATL-chronic


title: ATL-ch#1-D

description: mRNA expression in ATL


title: ATL-sm#2-N

description: mRNA expression in ATL


title: SARS_Mu_MA15g_young_48h_11


title: 6-9mm_P_vs_G_Array2

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: Biological replicate 2 of 4

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.

organism: Bos taurus

label_protocol: The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

extract_protocol:
Slaughterhouse ovaries from dairy cattle were kept on ice during transport and throughout the collection procedure in order to maintain RNA integrity. Individual follicle (6-9mm) collection of the mural granulosa cell layer was performed by scraping. Briefly, the follicle diameter was measured with a ruler at the ovary surface and part of the follicular fluid was aspirated using an 18 gauge syringe. A small, rounded weighing spatula was then inserted through the hole and used to gently scrape the follicular walls, limiting the chances of collecting theca cells. Each follicle’s granulosa cells were transferred to individual 1.5 ml centrifuge tube containing 500 μl PBS.   The samples were passed through a light vortex (half speed for 5 seconds) and centrifuged at 600 X g for 30 seconds at 4°C. The supernatant was discarded to remove cellular debris or blood in the sample leaving only about 10 μl not to disturb pellet, especially for small follicles where it was barely visible. Immediately after supernatant removal, the pellet was re-suspended by light vortexing in 50 μl of the same cold PBS solution.  For each sample, the 50 μl cell suspension, 25 μl was transferred to a new 750 μl tube on ice for propidium iodide (PI) staining and flow cytometry analysis. The volume remaining in the original 1.5 ml tubes was frozen for RNA extraction.
Briefly, the fixed samples were centrifuged at 600 X g for 2 min at room temperature to remove the alcohol and DNA fragments. The granulosa pellet was then re-suspended in 500 μl of PI solution (50 μg/ml)  in PBSE containing 0.1% Triton X-100, and RNase A at 50 μg/ml (50 U/mg) [14]. The samples were then incubated 30 min at room temperature.The flow cytometry to analyze the DNA content in PI-stained cells was performed with a Beckman-Coulter EPICS XL equipped with a 488 nm laser. Peak versus integrated fluorescence were used to gate out doublets; two cells stuck together. 10,000 events were acquired once the gates had been applied.
Total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

tag: breed (cattle)

value: holstein

tag: follicular size

tag: follicular status

value: plateau phase

value: ovary

tag: cell type

value: granulosa cells

value: growing phase


title: SARS_Mu_MA15g_young_48h_10

value: BALB/c

value: female

value: 8 wks old (young)

value: lung


title: SARS_Mu_MA15g_young_96h_25

value: SARS mouse adapted variants

value: MA15 gamma


title: ATL-ch#1-P

description: mRNA expression in ATL

value: whole blood


title: 6-9mm_P_vs_G_Array4

description: Biological replicate 4 of 4


title: SARS_Mu_MA15g_young_96h_27


title: ATL-sm#1-N

description: mRNA expression in ATL

value: male


title: 6-9mm_P_vs_G_Array1

description: Biological replicate 1 of 4


title: SARS_Mu_MA15g_young_24h_41


title: 6-9mm_P_vs_G_Array3

description: Biological replicate 3 of 4


title: SARS_Mu_MA15g_young_12h_57


title: ATL-sm#2-P

description: mRNA expression in ATL


title: ATL-sm#1-D

description: mRNA expression in ATL


title: SARS_Mu_MA15g_young_96h_26


title: AC#2-N

description: mRNA expression in ATL

value: HTLV-1 asymptomatic carrier


title: AC#1-D

description: mRNA expression in ATL


title: SARS_Mu_MA15g_young_48h_12


title: BalbC_SARS_MA15g_Aged_48h_C_2

value: 1 yr (aged)

value: C


title: BalbC_SARS_MA15g_Aged_12h_B

value: B


title: BalbC_SARS_MA15g_Aged_24h_A_2


title: 6-9mm_G_vs_P_Array1

description: Biological replicate 1 of 4

value: holstein


title: BalbC_SARS_MA15g_Aged_48h_B


title: SARS_Mu_Mock_young_96h_17

value: phosphate buffer solution (PBS), mock infection


title: 6-9mm_G_vs_P_Array3

description: Biological replicate 3 of 4

value: ovary

value: plateau phase


title: BalbC_SARS_MA15g_Aged_12h_A

value: A


title: SARS_Mu_MA15g_young_12h_55

value: BALB/c


title: AC#1-N

description: mRNA expression in ATL


title: 6-9mm_P_vs_ A_Array3

description: Biological replicate 3 of 4

value: granulosa cells

value: attretic


title: ATL-sm#1-P

description: mRNA expression in ATL

value: ATL-smoldering


title: AC#2-P

description: mRNA expression in ATL


title: AC#2-D

description: mRNA expression in ATL


title: 6-9mm_P_vs_ A_Array1

description: Biological replicate 1 of 4


title: Normal#3-P

description: mRNA expression in ATL

value: Normal

value: female


title: BalbC_SARS_MA15g_Aged_24h_C

value: lung

value: SARS mouse adapted variants

value: MA15 gamma


title: AC#1-P

description: mRNA expression in ATL

value: whole blood

value: HTLV-1 asymptomatic carrier

value: male


title: SARS_Mu_MA15g_young_48h_9

value: 8 wks old (young)


title: 6-9mm_P_vs_ A_Array4

description: Biological replicate 4 of 4

value: holstein


title: 6-9mm_G_vs_P_Array2

description: Biological replicate 2 of 4

value: growing phase

value: ovary


title: BalbC_SARS_MA15g_Aged_12h_C

value: 1 yr (aged)

value: C


title: 6-9mm_A_vs_ P_Array3

description: Biological replicate 3 of 4

value: granulosa cells

value: plateau phase


title: 6-9mm_P_vs_ A_Array2

description: Biological replicate 2 of 4

value: attretic


title: Normal#2-P

description: mRNA expression in ATL

value: Normal


title: 6-9mm_G_vs_P_Array4

description: Biological replicate 4 of 4


title: BalbC_SARS_MA15g_Aged_48h_A_2

value: BALB/c

value: female

value: A


title: 6-9mm_A_vs_ P_Array1

description: Biological replicate 1 of 4


title: SARS_Mu_MA15e_young_48h_14

value: lung

value: SARS mouse adapted variants

value: MA15 epsilon


title: Normal#1-P

description: mRNA expression in ATL

value: whole blood

value: male


title: SARS_Mu_MA15e_young_96h_31

value: 8 wks old (young)


title: BalbC_SARS_MA15g_Aged_24h_B

value: MA15 gamma

value: B


title: 6-9mm_A_vs_ P_Array2

description: Biological replicate 2 of 4

value: holstein

value: ovary


title: SARS_Mu_MA15e_young_24h_42


title: SARS_Mu_MA15e_young_48h_16


title: SARS_Mu_MA15e_young_12h_59


title: DU145 AR

city: Chicago

first: Hong-Jian

last: Jin

state: IL - Illinois

address: 303 E Superior St

institute: Northwestern University

description: SAMPLE 2

hyb_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

data_processing: The bead-level data were preprocessed using GenomeStudio (Illumina) and the expression data was analyzed using the beadarray package in Bioconductor,quantile normalized using the beadarray package.

growth_protocol: DU145 cells were maintained in RPMI supplemented with 10% FBS

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer.

treatment_protocol: Cells were collected at 48 hours after adenoviral overexpression of LacZ, AR, FOXA1 or AR+FOXA1 proteins.

tag: genotype/variation

value: AR overexpression


title: SARS_Mu_MA15e_young_96h_30


title: DU145 Ctrl

description: SAMPLE 1

scan_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

tag: cell line

value: control


title: DU145 AR+FOXA1

description: SAMPLE 4

label_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

value: AR+FOXA1 overexpression


title: BCpc primary breast cancer cell line-replicate1

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

description: Biological replicate 1 of 4. Prmary culture derived  from a patient with breast IDC with molecular mesenchymal characteristics.

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to an established protocol by Agilent Technologies (Santa Clara, CA, USA). Two-channel arrays were hybridized using Cy3 and Cy5 and quantified using Feature Extraction v9.5 software. The Agilent Whole Human Genome Array (4x44K) was used for competitive hybridization and the slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Images were scanned using Agilent scanner, G2505B (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Statistical data analysis, background correction, normalization and summary of expression measure were conducted with GeneSpring GX 10.0.2 software (Agilent Technologies). Data were filtered using two-step procedure: first the entities were filtered based on their flag values P (present) and M (marginal) and then filtered based on their signal intensity values, this enables to remove very low signal values or those that have reached saturation. Statistically significant differences were computed by Student’s t-test and the significance level was set at p<0.05. False discovery rate (FDR) was applied as multiple test correction method.

source_name: BCpc primary breast cancer cell culture

label_protocol: 500 ng of total RNA was amplified according to the manufacturer’s instructions by double strand cDNA synthesis, followed by T7-based in vitro transcription. MCF10A breast cancer cell line was used as a control for all samples. Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA from MCF10A was labeled with cyanine 3 (Cy3)-conjugated dUTP.

growth_protocol: BCpc primary breast cancer cell line were collected at the 4th growth passage

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: BCpc primary breast cancer cell

tag: growth passage

tag: original tissue

value: breast

value: non-tumorigenic breast epithelial MCF10A cell line


title: SARS_Mu_MA15e_young_24h_44

tag: strain

value: BALB/c

value: female


title: BCpc primary breast cancer cell line-replicate3

description: Biological replicate 3 of 4. Prmary culture derived  from a patient with breast IDC with molecular mesenchymal characteristics.


title: DU145 FOXA1

description: SAMPLE 3

value: FOXA1 overexpression


title: BCpc primary breast cancer cell line-replicate4

description: Biological replicate 4 of 4. Prmary culture derived  from a patient with breast IDC with molecular mesenchymal characteristics.


title: Stressed MEFs, biological repl 3, frac 9-14

city: Indianapolis

first: Ronald

middle: C

last: Wek

state: Indiana

address: 6238 Brokenhurst Road

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

description:
RW03M024.CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation

hyb_protocol: Labeled cRNA was hybridized for 17 hours to the Affymetrix Mouse Genome 430 2.0 Array.

scan_protocol: Arrays were scanned using GCOS.

data_processing:
MAS5 data was generated using Affymetrix GeneChip Operating Software (GCOS) and scaling = 1 so that no scaling was done. Arrays were scaled using the 3' and M poly-A bacterial spike-in probe set values as stated in Sampth, et al.: PMID 18462695.
Please note that the treatment plus fractionation based on association with different numbers of ribosomes did yield different populations of mRNAs, which resulted in considerable variation in normalized data across the samples.

source_name: RNA from polysome fractions

label_protocol: RNA preparations were labeled using the standard Affymetrix protocol for 3'-IVT arrays (Affymetrix, Santa Clara, CA) using 2ug of RNA for all samples. The poly A spike-in was omitted because they were spiked into the riobosomal fractions before RNA extraction to be used for normalization later.

growth_protocol: Mouse embryonic fibroblast (MEF) cells were grown in DMEM media supplemented with mM non-essential amino acids, 10% fetal bovine serum, 100 units/mL penicillin, and 100 ug/mL streptomycin at 37C.

extract_protocol: Cell lysates were subjected to sucrose gradient centrifugation and polysome fractionation.  A total of 14 fractions were collected from the top of the gradients into cold  microfuge tubes and immediately placed on ice. Each fraction was adjusted to 0.5% SDS, and fractions were combined to form three pools as follows: fractions 1-4, 5-8, 9-14  were combined as pools 1, 2, and 3, respectively. In parallel, total RNA was isolated from unfractionated lysates for analysis of total gene transcript levels. Synthetic Poly(A)  luciferase RNA (10ng/mL) (Promega), along with a bacterial spike-in control RNA (Affymetrix), were added to each gradient fraction pool. RNA was precipitated at -70C with 2.5  volumes 100% ethanol and purified using QIAGEN RNeasy midi-columns.

treatment_protocol: MEF cells were treated with 1 uM thapsigargin for 6 hours, or without treatment, and rinsed twice with chilled PBS before Trizol extraction. For polysome analysis, both treatment groups were also subjected to a 10 minute (50 ug/mL) cyclohexidime treatment prior to sucrose gradient ultracentrifugation and RNA extraction.

value: Mouse Embryonic Fibroblast (MEF) cells

tag: treated with

value: 1 uM thapsigargin for 6 hrs

tag: rna fraction

value: polysomal (≥ 4 ribosomes per mRNA, sucrose gradient fractions 9-14)

tag: molecule subtype

value: RNA from polysome fractions

tag: replicate


title: 6mM SB (GSBPC)

city: Valhalla

first: Bistra

last: Nankova

address: 95 Grassland Rd

institute: New York Medical College

description: Gene expression data from PC12 cells exposed for 48 hrs to 6mM SB

hyb_protocol: Following fragmentation in the presence of heat and Mg2+ the biotinylated cRNA was hybridized to Affymetrix Rat Genome 230_2.0 array for 16 hrs at 450C. The array was washed and stained with streptavidin phycoerythrin (SAPE) using fluidics station

scan_protocol: The array was scanned using GeneChip Scanner 3000

data_processing: The data were analyzed using Affymetrix GeneChipOperating Software and default setting. The comparison analyses follow the format Experimental_vbaselinechanges.txt and Experimental_vBaselinechanges2X.txt for probe sets shown to give a fold change of 2 or more in gene expression between the two samples.

organism: Rattus norvegicus

source_name: 6mM SB (GSBPC)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression analysis technical manual, 2001, Affymetrix

growth_protocol: PC12 cells were maintained in Dulbecco's modified eagle's medium (DMEM) supplemented with 10% horse serum, 5% fetal bovine serum, 50 ug/ml streptomycin and 50IU/ml penicillin in humidified atmosphere at 370C and 10% CO2

extract_protocol: Total RNA from individual petri dishes was isolated using RNasol (Tel-Test, Inc. Friendswood, TX). For microarray analyses the samples from each experimental group were pooled (n=6) purified over Qiagen columns as recommended by Affymetrix and sent to Keck Microarray Facility at Yale, New Haven, CT for RT and microarray analyses.

treatment_protocol: Two days before confluence, PC12 cells were treated with butyrate (SB, at doses of 1mM and 6mM final concentration in media) or with propionate (PA, 1mM and 10mM). Control cells received vehicle.


title: 10mM PA (10PAPC)

description: Gene expression data from PC12 cells exposed for 48 hrs to 10mM PA

source_name: 10mM PA (10PAPC)


title: 1mM PA (1PAPC)

description: Gene Expression data from PC12 cells exposed for 48 hrs to 1mM PA

source_name: 1mM PA (1PAPC)


title: BCpc primary breast cancer cell line-replicate2

description: Biological replicate 2 of 4. Prmary culture derived  from a patient with breast IDC with molecular mesenchymal characteristics.


title: Transformed C3H10T1/2+DEM(0.25mM), C1

city: Lucknow

first: Dr Sushil

last: Kumar

state: Uttar Pradesh

address: M G Marg

department: Environmental Carcinogenesis

country: India

institute: Indian Institute of Toxicology Research

hyb_protocol: The labeled cRNA samples were hybridized onto an Agilent Custom Mouse Whole Genome 8x60k gene expression designed by Genotypic Technology Private Limited (AMADID No: 026986). 600ng of Cy3-labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software.

data_processing: The normalization was done using GeneSpring GX 11.5 Software. 75th percentile shift normalization.

source_name: Transformed C3H10T1/2, DEM (0.25mM)

label_protocol: The samples for gene expression were labeled using the Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and converted to double-stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double-stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3-CTP (Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Mouse embryo fibroblast cell line C3H10T1/2 was procured from National Centre For Cell Science (Pune, India). DMEM (GIBCO, Grand Island, NY, USA) media were supplemented with 10% v/v fetal bovine serum (GIBCO, Grand Island, NY, USA), 1.5 g/l NaHCo3, 4.5 g/l Glucose (SRL,India),1X Antibiotic-Antimycotic (GIBCO, Grand Island, NY, USA). The cell lines were maintained in a humidiﬁed, 5% CO2 incubator at 37 0C and sub-cultured twice weekly using 0.25% v/v trypsin/EDTA (GIBCO, Grand Island, NY, USA). All experiments were performed using cells in exponential growth phase .

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Exponentially growing cells were seeded at a density of 1X10^4 cells/25-cm2. 3MC (2.5µg/ml) was given to each flask after 24 h of seeding for 2 days. Cells were washed with phosphate-buffered saline (PBS) and replaced with fresh normal medium for next 4 days.TPA (100ng/ml) exposure was given twice a week and was given to each 3MC treated flask for next two weeks . After the removal of TPA treatment, cells were cultured in normal DMEM media for next 4 weeks. After 6 weeks, flasks were divided into two groups: one was used for the gimesa staining and counting and the other one was used for the microarray experiment. The methanol fixed, stained with 10% Giemsa solution, rinsed three times with water and observed by light microscopy for foci scoring and classification. Transformed foci were counted and classified. Foci showing deep basophilic, dense multilayering of cells, random cell orientation at any part of the focus edge, invasion into the surrounding contact-inhibited mono-layer, and domination of spindle-shaped cells were scored as positive transformation foci. Now these transformed cells were exposed to DEM (0.25mM) and gene expression study was done.

value: chemically transformed C3H10T1/2

value: mouse embryo fibroblasts

tag: treatment


title: Stressed MEFs, biological repl 3, frac 1-4

description:
RW03M022.CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation

tag: tissue

value: free mRNA (sucrose gradient fractions 1-4)


title: 1mM SB (ISBPC)

description: Gene expression data from PC12 cells exposed for 48 hrs to 1mM SB

source_name: 1mM SB (ISBPC)


title: Stressed MEFs, biological repl 3, frac 5-8

description:
RW03M023.CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation

value: 1_to_3 ribosomes per mRNA (sucrose gradient fractions 5-8)


title: SARS_Mu_MA15e_young_96h_32

tag: gender

tag: age

value: 8 wks old (young)

value: lung

tag: sample collection time post infection

tag: infected with

value: SARS mouse adapted variants

tag: variant type

value: MA15 epsilon

tag: biological replicate


title: SARS_Mu_MA15e_young_24h_43


title: SARS_Mu_MA15e_young_48h_15_2


title: Transformed C3H10T1/2, B1

source_name: Transformed C3H10T1/2, untreated

tag: cell type


title: Control PC12 cells (CPC)

description: Gene expression data from control, vehicle treated PC12 cells

source_name: Control PC12 cells (CPC)


title: OB_125_rep2

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

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.).

source_name: MC3T3-E1 cells differentiated for 15 days

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

growth_protocol: MC3T3-E1 cells were cultured in alpha MEM with 10% heat-inactivated fetal bovine serum from Hyclone (Logan, UT) and 1% penicillin-streptomycin.  Differentiated cells were cultured in complete media plus 10mM glycerol-2-phosphate and 50ug/mL ascorbic acid for 15 days, changing media every 2-3 days.

extract_protocol: RNA was isolated using the TRI-Reagent protocol (MRC, Cincinnati, OH) and amplification methods according Roche NimbleGen protocols.

treatment_protocol: Cells were treated with 100nM 1,25(OH)2D3 or ethanol vehicle for 24 hours.

tag: passage

tag: cell line


title: OB_125_rep3

value: MC3T3-E1 cells differentiated for 15 days


title: Transformed C3H10T1/2, B2


title: Stressed MEFs, biological repl 2, frac 5-8

description:
RW03M019.CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation


title: Transformed C3H10T1/2+DEM(0.25mM), C2


title: OB_125_rep1


title: hUtSMC_E2_72h_X2

city: Galway

last: Cairns

address: University Road

department: NCBES

country: Ireland

institute: NUI Galway

hyb_protocol: All hybridizations were carried out using the OpArray (Operon) hybridization and wash solutions as recommended by the manufacturer.

scan_protocol: Slides were scanned at 543 nm (Cy3) with a ScanArray Express HT scanner (Perkin Elmer). PMT settings were optimal at 70 %. Resolution was 10 micrometeres.

data_processing: Images were processes using GenePix Pro 6.1.0.4. gpr files were imported into GeneSpring GX 12.0 (Agilent Technologies). Data was log transformed and normalised by the Percentile Shift Method using the 75th percentile. Subsequently all normalised data was baseline transformed to the median of all samples. Three control samples (C1_0h, C2_0h, C3_0h) have been included as raw data (as they were included in the normalised experiment) but these were not part of the analysis (control vs treated).

source_name: normal, non-pregnant female, 72h 17beta estradiol treatment

label_protocol: All samples were prepared for microarray hybridization using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion) according to the manufacturer’s recommendations. Probes were hybridized against the Operon Human Genome Array-Ready Oligo Set Microarrays™ ((AROS) Version 4.0).

growth_protocol: hUtSMCs (Lonza) were cultured in complete Dulbecco’s modified essential medium (DMEM), supplemented with 10 % (v/v) fetal bovine serum (FBS), 100 units/ml penicillin and 0.1 mg/ml streptomycin (Sigma-Aldrich) until cells reached 90 % confluence.

extract_protocol: Total RNA was isolated from the cells using a combination of Trizol (Ambion) and Qiagen RNeasy Mini Kit (Qiagen). Cells were lysed in Trizol reagent (1 ml Trizol per 1x107 cells) and 0.2ml chloroform (Sigma-Aldrich) per millilitre of Trizol reagent was added, vortexed for 2 min and incubated at room temperature for 10 min. The mixture was centrifuged (13,000 rpm for 15 min at 4 °C), the upper phase mixed with an equal volume of 70% ethanol and loaded onto the RNeasy column (Qiagen). Total RNA was subsequently isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. RNA was quantified using a NanoDrop ND-1000 spectrophotomer (Thermo Scientific) and quality checked using the Agilent 2100 Bioanalyzer. All RNA yielded RNA integrity numbers (RIN) of greater than 9.0 (average 9.8)

treatment_protocol: At 90% confluence cells were preconditioned overnight with Phenol Red Free DMEM (PRF-DMEM), supplemented with 10% double charcoal-stripped fetal bovine serum (CS-FBS) (Biosera) and containing antibiotics. Cells were starved of endogenous steroids in ‘starvation media’ - PRF-DMEM supplemented with 2% CS-FBS and antibiotics until the cells attained 100% confluence. Subsequently, cells in ‘starvation media’ were supplemented with 10 nM 17β-estradiol (E2) (Sigma Aldrich). Control cells were grown in ‘starvation media’ in the absence of E2 until harvest. Cells were harvested after 6 h, 24 h and 72 h of E2 treatment along with corresponding controls and total RNA was isolated. The complete experiment was replicated three times

value: passage 5-8

value: normal, non-pregnant female

value: myometrial smooth muscle cell

tag: smooth muscle markers

value: calponin, smoothelin positive (RT-PCR)

tag: other markers

value: oxytocin receptor and ER-alpha positive (RT-PCR)

tag: estrogen response

value: monitored by CD38 and CX43 gene and protein levels


title: SARS_Mu_MA15e_young_96h_29

tag: strain

value: BALB/c

value: female


title: Stressed MEFs, biological rep 3

description:
RW03M021.CEL
Gene expression data from whole MEF cell lysate for transcriptional regulation

source_name: Total RNA from MEF cells

value: Mouse Embryonic Fibroblast (MEF) cells

tag: treated with

value: 1 uM thapsigargin for 6 hrs

tag: rna fraction

value: total RNA (no fractionation)

tag: molecule subtype

value: Total RNA


title: hUtSMC_E2_72h_X3

tag: tissue


title: SARS_Mu_MA15e_young_24h_45

tag: gender

value: 8 wks old (young)


title: 6-9mm_A_vs_ P_Array4

description: Biological replicate 4 of 4

tag: breed (cattle)

value: holstein

tag: follicular size

tag: follicular status

value: attretic

value: ovary

value: granulosa cells

value: plateau phase


title: hUtSMC_CON_72h_X3

source_name: normal, non-pregnant female, 72h Control

value: passage 5-8

value: normal, non-pregnant female


title: Stressed MEFs, biological repl 2, frac 1-4

description:
RW03M018.CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation

value: free mRNA (sucrose gradient fractions 1-4)

value: RNA from polysome fractions

tag: replicate


title: Stressed MEFs, biological rep 2

description:
RW03M017.CEL
Gene expression data from whole MEF cell lysate for transcriptional regulation


title: POB_125_rep2

source_name: MC3T3-E1 cells

value: MC3T3-E1 cells

tag: treatment


title: SARS_Mu_MA15e_young_12h_60

value: BALB/c

tag: age

value: lung

tag: sample collection time post infection

tag: infected with

value: SARS mouse adapted variants

tag: variant type

value: MA15 epsilon

tag: biological replicate


title: Stressed MEFs, biological repl 2, frac 9-14

description:
RW03M020.CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation

value: Mouse Embryonic Fibroblast (MEF) cells

value: 1 uM thapsigargin for 6 hrs

value: polysomal (≥ 4 ribosomes per mRNA, sucrose gradient fractions 9-14)


title: Control MEFs, biological rep 3, frac 5-8

description:
RW03M011.CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation

value: none (control)

value: 1_to_3 ribosomes per mRNA (sucrose gradient fractions 5-8)


title: SARS_Mu_MA15e_young_12h_61

value: female

value: 8 wks old (young)


title: hUtSMC_E2_72h_X1

tag: passage

tag: cell type

value: myometrial smooth muscle cell

tag: smooth muscle markers

value: calponin, smoothelin positive (RT-PCR)

tag: other markers

value: oxytocin receptor and ER-alpha positive (RT-PCR)

tag: estrogen response

value: monitored by CD38 and CX43 gene and protein levels


title: SARS_Mu_MA15e_young_12h_58

tag: strain

tag: tissue


title: Stressed MEFs, biological rep 1

description:
RW03M013.CEL
Gene expression data from whole MEF cell lysate for transcriptional regulation

tag: treated with

tag: rna fraction

value: total RNA (no fractionation)

tag: molecule subtype

value: Total RNA


title: Voluntary Termination of Pregnancy (patient 8)

city: Valencia

first: Juan

middle: M

last: Moreno-Moya

address: Catedrático Agustín Escardino

country: Spain

institute: FIVI

description: each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer

hyb_protocol: After H2O resuspended, samples were mixed with another Spike, mixed with blocking agent and Hi-RPM hybridization buffer and heated at 100ºC for 5' and cooled at 4ºC. Then samples were loaded onto gaskets slides and microarrays slides were put on them. Finally Samples were hybridized for 20h at 55ºC.

scan_protocol: Microarrays slides were washed and scanned in Genepix Personal 4100A Scanner and scanned in Genepix Pro Software with a spot resolution of 5um in the green channel

data_processing: Median intensity value of each spot data was normalized and log2 transformed using R software and libraries from bioconductor database. Next, replicated probes were merged by mean using GEPAS.

source_name: Trophoblast tissue

label_protocol: 100ng of total RNA were mixed with spike and treated with phosphatase for 30' at 37º then cooled at 4ºC. Next DMSO was added and heated at 100ºC for 7.5' then cooled at 4ºC. Next mixed with Cy3-pCp and T4 RNA Ligase for 2 hours at 16ºC and cooled at 4ºC. Samples were dried in a vacuum for 3h at 45ºC. Then H2O added.

growth_protocol: Endometrial fluid aspiration samples were immediately fast frozen at -80ºC until day of RNA extraction.

extract_protocol: To ensure that miRNA fraction will be recovered we performed RNA extraction using the miRNeasy Kit (Qiagen, Valencia, CA, USA). RNA extracted was quantified using a NanoDrop (Thermo Fisher Scientific Inc, MA, USA) spectrophotometer and the proportion of miRNAs was evaluated using the Small RNA LabChip BioAnalyzer 2100,  (Agilent Technologies Inc, DE, USA)

tag: type

value: tissue

tag: week of gestation

tag: status

value: voluntary termination of pregnancy


title: hUtSMC_E2_24h_X5

source_name: normal, non-pregnant female, 24h 17beta estradiol treatment

value: passage 5-8

value: normal, non-pregnant female


title: Control MEFs, biological rep 3, frac 9-14

description:
RW03M012.CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation

value: Mouse Embryonic Fibroblast (MEF) cells

value: RNA from polysome fractions

tag: replicate


title: hUtSMC_E2_24h_X4


title: Voluntary Termination of Pregnancy (patient 7)

tag: age