title: BXD29 Male H1 10-Aug-05

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: affx-b-actinmur (3'/5')

tag: affx-gapdhmur (3'/5')


title: BXD29 Female H1 13-Jul-05

status: Public on Jul 26 2016

type: RNA

city: Memphis

first: Robert

middle: W.

last: Williams

state: TN

address: 71 Manassas St.

department: Department of Genetics, Genomics and Informatics

country: USA

institute: University of Tennessee

hyb_protocol: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80°C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.

scan_protocol: All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4°C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.

data_processing: The expression values were generated using PDNN. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs. Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1.

growth_protocol: Cells grown in mono layer are lysed directly in a culture dish by adding the RNA STAT-60TM (1 ml/3.5 cm petri dish) and passing the cell lysate several times through a pipette. Cells grown in suspension are sediment then lysed in the RNA STAT-60TM (1 ml per 5-10 x 106 cells) by repetitive pipetting. Washing calls before addition of the RNA STAT-60TM should be avoided as this increases the possibility of mRNA degradation.

extract_protocol: RNA Extraction: In brief, we used the RNA STAT-60 protocol (TEL-TEST B Bulletin No. 1), steps 5.1A (homogenization of tissue), 5.2 (RNA extraction), 5.3 (RNA precipitation), and 5.4 (RNA wash). In Step 5.4 we stopped after adding 75% ethanol (1 ml per 1 ml RNA STAT-60) and stored the mix at -80°C until further use. Before RNA labeling we thawed samples and proceeded with the remainder of Step 5.4; pelleting, drying, and redissolving the pellet in RNase-free water.

treatment_protocol: BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thank Muriel Davisson for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were euthanized and killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria. A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days). All animals were sacrifice between 9 AM and 5 PM during the light phase.

tag: tissue

value: hippocampus

tag: strain

tag: Sex

value: Female

tag: age (days)

tag: batch id

tag: scale factor

tag: background average

tag: present

tag: absent

tag: marginal

tag: source

value: Glenn


title: BXD27 Female H1 13-Jul-05


title: BXD23 Female H1 22-Sep-05


title: BXD24 Female H2 13-Jul-05

value: UMemphis


title: Mouse liver tissue, ZnO sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 1

city: North Ryde

first: Megan

last: Osmond-McLeod

address: 11 Julius Avenue

country: Australia

institute: CSIRO

description:
Long-term sunscreen Group 4-1
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing ZnO nanoparticles with 29kJ/m2 UVR during 30 treatments over 36 weeks.

hyb_protocol: Following fragmentation, ~600-700 ng of single-stranded DNA were hybridised on Affymetrix 1.0 ST mouse gene arrays (17 h, 45˚C, 60 rpm) in an Affymetrix 640 GeneChip® Hybridization Oven. GeneChips were washed and stained in an Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix 7G GeneChip® Scanner.

data_processing: The data was processed and analysed using Matlab Bioinformatics and Statistical toolboxes. RMA was used as the normalisation method. In-house tools were used to remove batch effects and control for false discovery.

label: Biotin

source_name: SKH:QS mouse liver tissue from ZnO sunscreen + 29kJ/m2 UVR-treated mouse, week 36 (30 weekly treatments)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay User Manual, Affymetrix).

growth_protocol: Mice were individually housed in polycarbonate cages in an isolated temperature (~21˚C) and moisture (~55-65% relative humidity) controlled room with a 14-hr light/10-hr dark cycle, with ad libitum access to food and water.

extract_protocol: Total RNA was extracted from liver tissue using the NucleoSpin® RNA II kit (Macherey Nagel, Scientifix) following manufacturer’s instructions.

treatment_protocol: Topical applications of commercially-available sunscreens containing either ZnO nanoparticles, a mixture of TiO2 nanoparticles and organic UVR filters, organic UVR filters only, or no sunscreen were delivered each week to SKH:QS mice. During each treatment, mice were fitted with Elizabethan collars to minimise oral ingestion of sunscreens. Half of the mice in each group were exposed to 29 kJ/m2 UVR 20 min after sunscreen application, and the other half received no UVR treatment. After two hours, the sunscreen was washed from the mice using mild soapy water, and mice were dried before being returned to their cages. Mice received 30 weekly treatments over 36 weeks. Mice were sacrificed at week 36 by intraperitoneal injection of Xylase (50mg/kg)/ketamine (50mg/kg) followed by cervical dislocation.

tag: strain/background

value: liver

tag: sunscreen treatment

value: sunscreen containing ZnO nanoparticles

tag: uvr treatment

value: 29kJ/m2 UVR

tag: time point

value: 36 weeks (30 treatments)


title: BXD22 Male H1 13-Jul-05

value: Male

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: affx-b-actinmur (3'/5')


title: BXD23 Female H2 13-Jun-05

tag: tissue

tag: strain

tag: affx-gapdhmur (3'/5')

value: UTM RW


title: NKTL-JS32

city: Singapore

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level 3

department: Department of Pathology

country: Singapore

institute: National University Health System, Singapore

description:
25008H
Illumina DASL protocol
NKTL Patient

hyb_protocol: Illumina DASL protocol

scan_protocol: not provided

data_processing: Illumina BeadStudio version 3.3.8. No normalization was performed. Raw data were analyzed and used to draw conclusions.

organism: Homo sapiens

label_protocol: Illumina DASL protocol

extract_protocol: For FFPE tissues, total RNA was extracted using High Pure RNA Paraffin Kit (Roche Applied Science, Mannheim, Germany) according to the manufacturer's instruction. For freshly isolated cells, total RNA was extracted using miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) with DNase I treatment protocol by the manufacturer's instruction.

tag: disease

value: NKTL


title: BXD22 Female H1 23-Sep-05

tag: Sex

tag: age (days)

tag: batch id

tag: scale factor

value: UAB


title: NKTL-JS30

description:
25008F
Illumina DASL protocol
NKTL Patient


title: Mouse liver tissue, ZnO sunscreen, no UVR, 30 treatments, biological rep 5

description:
Long-term sunscreen Group 3-5
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing ZnO nanoparticles with no UVR during 30 treatments over 36 weeks.

source_name: SKH:QS mouse liver tissue from ZnO sunscreen no UVR-treated mouse, week 36 (30 treatments)

value: no UVR


title: NKTL-JS26

description:
25008B
Illumina DASL protocol
NKTL Patient


title: NKTL-JS38

description:
25009F
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation

value: EALP


title: BXD21 Female H2 13-Jul-05

tag: background average

tag: present

tag: absent

tag: marginal


title: Mouse liver tissue, ZnO sunscreen, no UVR, 30 treatments, biological rep 3

description:
Long-term sunscreen Group 3-3
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing ZnO nanoparticles with no UVR during 30 treatments over 36 weeks.

tag: strain/background

tag: sunscreen treatment

tag: uvr treatment


title: NKTL-JS29

description:
25008E
Illumina DASL protocol
NKTL Patient


title: Mouse liver tissue, ZnO sunscreen, no UVR, 30 treatments, biological rep 4

description:
Long-term sunscreen Group 3-4
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing ZnO nanoparticles with no UVR during 30 treatments over 36 weeks.

tag: time point


title: BXD20 Male H1 26-Sep-05

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: affx-b-actinmur (3'/5')

tag: source


title: BXD16 Male H1 26-Jul-05

tag: tissue

tag: strain

tag: affx-gapdhmur (3'/5')


title: Mouse liver tissue, ZnO sunscreen, no UVR, 30 treatments, biological rep 2

description:
Long-term sunscreen Group 3-2
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing ZnO nanoparticles with no UVR during 30 treatments over 36 weeks.


title: BXD21 Male H1 6-Dec-05

tag: Sex

tag: age (days)

tag: batch id


title: Mouse liver tissue, no sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 6

description:
Long-term sunscreen Group 2-6
Gene expression data from liver tissue harvested from SKH:QS mouse receiving no sunscreen and weekly treatments with 29kJ/m2 UVR during 30 treatments over 36 weeks.

source_name: SKH:QS mouse liver tissue from no sunscreen + 29kJ/m2 UVR-treated mouse, week 36 (30 weekly treatments)

value: no sunscreen


title: BXD19 Male H1 13-Jun-05

tag: scale factor

tag: background average

tag: present

value: UTM JB


title: NKTL-JS23

description:
71084G
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation

tag: disease


title: BXD19 Female H1 6-Dec-05

tag: absent

tag: marginal


title: NKTL-JS24

description:
71084H
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation


title: BXD20 Female H1 13-Jun-05


title: Mouse liver tissue, ZnO sunscreen, no UVR, 30 treatments, biological rep 1

description:
Long-term sunscreen Group 3-1
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing ZnO nanoparticles with no UVR during 30 treatments over 36 weeks.

tag: strain/background

tag: sunscreen treatment

tag: uvr treatment

tag: time point


title: BXD15 Female H1 22-Sep-05

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: affx-b-actinmur (3'/5')

tag: source


title: NKTL-JS22

description:
71084F
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation


title: NKTL-JS8_repeat

description:
25008A
Illumina DASL protocol
NKTL Patient


title: BXD14 Female H2 6-Dec-05

tag: tissue

tag: strain

tag: Sex

tag: affx-gapdhmur (3'/5')


title: BXD16 Female H1 13-Jun-05

tag: age (days)

tag: batch id

tag: scale factor

tag: background average


title: BXD15 Male H1 13-Jun-05

tag: present

tag: absent

tag: marginal


title: BXD13 Female H1 22-Sep-05


title: BXD13 Male H2 10-Aug-05


title: Mouse liver tissue, no sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 5

description:
Long-term sunscreen Group 2-5
Gene expression data from liver tissue harvested from SKH:QS mouse receiving no sunscreen and weekly treatments with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: strain/background

tag: sunscreen treatment

tag: uvr treatment


title: NKTL-JS21

description:
71084E
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation

tag: disease


title: Mouse liver tissue, no sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 4

description:
Long-term sunscreen Group 2-4
Gene expression data from liver tissue harvested from SKH:QS mouse receiving no sunscreen and weekly treatments with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: time point


title: BXD14 Male H2 6-Dec-05

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: affx-b-actinmur (3'/5')

tag: source


title: Mouse liver tissue, ZnO sunscreen, no UVR, 30 treatments, biological rep 6

description:
Long-term sunscreen Group 3-6
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing ZnO nanoparticles with no UVR during 30 treatments over 36 weeks.

tag: tissue


title: BXD12 Female H1 13-Jun-05

tag: strain

tag: Sex

tag: age (days)

tag: affx-gapdhmur (3'/5')


title: BXD12 Male H1 6-Dec-05

tag: batch id

tag: scale factor

tag: background average

tag: present


title: Mouse liver tissue, no sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 3

description:
Long-term sunscreen Group 2-3
Gene expression data from liver tissue harvested from SKH:QS mouse receiving no sunscreen and weekly treatments with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: strain/background

tag: sunscreen treatment


title: Mouse liver tissue, no sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 2

description:
Long-term sunscreen Group 2-2
Gene expression data from liver tissue harvested from SKH:QS mouse receiving no sunscreen and weekly treatments with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: uvr treatment


title: Mouse liver tissue, no sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 1

description:
Long-term sunscreen Group 2-1
Gene expression data from liver tissue harvested from SKH:QS mouse receiving no sunscreen and weekly treatments with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: time point


title: BXD9 Female H2 9-Jun-05

tag: pool size (n of cases used per rna sample)

tag: absent

tag: marginal


title: BXD11 Female H1 22-Sep-05

tag: rma outlier

tag: affx-b-actinmur (3'/5')

tag: source


title: BXD8 Female H1 9-Jun-05

tag: tissue

tag: strain

tag: Sex


title: NKTL-JS14

description:
71082F
Illumina DASL protocol
Normal

tag: disease

value: Normal


title: BXD9 Both H3 6-Dec-05

value: hippocampus

value: Both

tag: age (days)

tag: batch id

tag: scale factor

tag: affx-gapdhmur (3'/5')


title: BXD6 Female H2 9-Jun-05

value: Female

tag: background average

tag: present

value: Glenn


title: Mouse liver tissue, no sunscreen, no UVR, 30 treatments, biological rep 4

description:
Long-term sunscreen Group 1-4
Gene expression data from liver tissue harvested from SKH:QS mouse receiving no sunscreen and no UVR during 30 treatments over 36 weeks.

source_name: SKH:QS mouse liver tissue from no sunscreen no UVR-treated mouse, week 36 (30 treatments)

tag: strain/background

value: liver

tag: sunscreen treatment

tag: uvr treatment

tag: time point


title: BXD6 Male H1 20-Jul-05

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: absent

tag: marginal


title: NKTL-JS20

description:
71084D
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation


title: NKTL-JS19

description:
71084C
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation


title: BXD5 Male H1 15-Jul-05

tag: tissue

tag: strain

tag: affx-b-actinmur (3'/5')

tag: source


title: Mouse liver tissue, no sunscreen, no UVR, 30 treatments, biological rep 3

description:
Long-term sunscreen Group 1-3
Gene expression data from liver tissue harvested from SKH:QS mouse receiving no sunscreen and no UVR during 30 treatments over 36 weeks.


title: shKDM4A

city: Sacramento

first: Ling-Yu

last: Wang

state: CA

department: Biochemistry and Molecular Medicine

institute: University of California, Davis

description: Affymetrix microarray gene expression profiling data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Genechip Human Genome U133 Plus 2 aarays using Affymetrix hybridization kit materials. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol  FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneSpring GX 12.0 software (Agilent Technologies).  Probe intensity values (CEL files) were background-corrected, summarized, and normalized using the Robust Multi-array Average (RMA) algorithm (Irizarry et al., 2003).  Values lower than 50 were filtered out.

source_name: LNCaP cells transduced with shKDM4A contruct

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, Rev3, Affymetrix).

growth_protocol: The cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 100 U/ml penicillin-100 μg/ml streptomycin at 37°C in a humidified environment of 5% CO2 in air, in accordance with the instructions provided by ATCC.

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

treatment_protocol: pLKO.1 control or shKDM4A construct was co-transfected with lentiviral packaging plasmids into HEK293T cell to produce lentiviral particles. 48hrs after transfection, the culture medium was collected and the virus supernatant was concentrated by Lenti-X Concentrator (Clontech, CA). The precipitated viral particle was resuspended in fresh RPMI1640 complete medium for subsequent LNCaP infection. 3 days after viral infection, the cells were harvested for RNA extraction.

tag: cell line

value: LNCaP human prostate carcinoma

tag: genotype/variation

value: KDM4A knockdown


title: Mouse liver tissue, no sunscreen, no UVR, 30 treatments, biological rep 5

description:
Long-term sunscreen Group 1-5
Gene expression data from liver tissue harvested from SKH:QS mouse receiving no sunscreen and no UVR during 30 treatments over 36 weeks.

value: 36 weeks (30 treatments)


title: NKTL-JS12

description:
71082D
Illumina DASL protocol
Normal

tag: disease


title: NKTL-JS13

description:
71082E
Illumina DASL protocol
Normal


title: NKTL-JS15

description:
71082G
Illumina DASL protocol
Normal


title: Mouse liver tissue, no sunscreen, no UVR, 30 treatments, biological rep 6

description:
Long-term sunscreen Group 1-6
Gene expression data from liver tissue harvested from SKH:QS mouse receiving no sunscreen and no UVR during 30 treatments over 36 weeks.


title: NKTL-JS11

description:
71082C
Illumina DASL protocol
Normal


title: BXD5 Female H2 9-Jun-05

tag: Sex

tag: age (days)

tag: batch id

tag: scale factor

tag: background average

tag: affx-gapdhmur (3'/5')


title: Mouse liver tissue, no sunscreen, no UVR, 30 treatments, biological rep 2

description:
Long-term sunscreen Group 1-2
Gene expression data from liver tissue harvested from SKH:QS mouse receiving no sunscreen and no UVR during 30 treatments over 36 weeks.

tag: strain/background

tag: sunscreen treatment

tag: uvr treatment

tag: time point


title: BXD11 Male H1 9-Jun-05

tag: tissue

value: Male

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: present

tag: absent

tag: marginal


title: BXD8 Male H1 23-Sep-05

tag: strain

tag: affx-b-actinmur (3'/5')

tag: source


title: NKTL-JS16

description:
71082H
Illumina DASL protocol
Normal

tag: disease


title: Mouse liver tissue, no sunscreen, no UVR, 30 treatments, biological rep 1

description:
Long-term sunscreen Group 1-1
Gene expression data from liver tissue harvested from SKH:QS mouse receiving no sunscreen and no UVR during 30 treatments over 36 weeks.


title: BXD2 Female H1 9-Jun-05

tag: Sex

tag: age (days)

tag: batch id

tag: scale factor


title: control

source_name: LNCaP cells transduced with control contruct

tag: cell line

tag: genotype/variation

value: control


title: BXD2 Male H1 9-Jun-05

tag: background average

tag: affx-gapdhmur (3'/5')


title: NKTL-JS10

description:
71082B
Illumina DASL protocol
Normal


title: NKTL-JS8

description:
Illumina DASL protocol
71067H
NKTL Patient

source_name: NKTL Patient

value: extranodal NK/T cell lymphoma (NKTL)


title: NKTL-JS4

description:
Illumina DASL protocol
71067D
NKTL Patient


title: NKTL-JS3

description:
Illumina DASL protocol
71067C
NKTL Cell Line

source_name: NKTL Cell Line


title: C57BL/6J Male H2 20-Jul-05

tag: tissue

tag: pool size (n of cases used per rna sample)

value: UTM DG


title: BXD1 Male H1 15-Jul-05

tag: rma outlier

tag: present


title: BXD1 Female H1 6-Dec-05

tag: absent

tag: marginal


title: DBA/2J Female H1 26-Sep-05

tag: strain

tag: affx-b-actinmur (3'/5')

value: UTM RW


title: C57BL/6J Male H2 9-Jun-05

tag: source


title: Nucleus accumbens_RARbeta_KO_2

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

description: Raw microarray data were normalized using a log scale robust multi-array analysis (RMA)

hyb_protocol: Following fragmentation, 3.0 μg of cDNAs were hybridized for 16 hours at 45oC, 60 rpm on GeneChip® Mouse Gene 1.0 ST arrays. The chips were then washed and stained in the GeneChip® Fluidics Station 450.

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G. Raw data were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.1.1

data_processing: CEL files were processed to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms

source_name: nucleus accumbens shell

label_protocol: Biotinylated cDNA targets were prepared from 100 ng of total RNA using  Ambion WT Expression Kit (Cat # 4411974) and  Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations

growth_protocol: RARβ-null mutant male mice as well as their wild type (WT) control littermates were raised on a mixed genetic background (C57BL/6J and 129SvEms/j) from heterozygous crosses, and housed in groups of 4-5 mice per cage. All mice were housed in individually ventilated cages, type “MICE” (Charles River, France) in a 7am-7pm light/dark cycle. Food and water were freely available.

extract_protocol: Behaviorally naive RARβ-null mutant mice (n=6) and their wild type littermates (n=5) were sacrificed by cervical dislocation at the age of 4-5 months. Brains were fresh frozen in Shandon Cryomatrix (Thermo Scientific) and kept in -80°C until use. Nucleus accumbens enriched in its shell part (NAc) was dissected bilaterally, from three subsequent 300µm-thick cryosections with 0.5mm punch and used for RNA extraction. The accurate localization of the NAc was based on visual inspection of each section using a stereomicroscope (Leica, Wild M715) and its comparison with the stereotaxic atlas of mouse brain (Paxinos 2001). RNA was isolated on the affinity column, using RNeasy Micro Kit, according to the manufacturer’s recommendations (Qiagen) and kept in -80°C for further analysis.

tag: Sex

value: male

value: RARβ-null mutant


title: NKTL-JS9

description:
71082A
Illumina DASL protocol
Normal

tag: disease


title: NKTL-JS2

description:
Illumina DASL protocol
71067B
NKTL Cell Line


title: Nucleus accumbens_RARbeta_KO_3


title: Nucleus accumbens_RARbeta_KO_1


title: Nucleus accumbens_RARbeta_WT_6

value: Wild type


title: NKTL-JS1

description:
Illumina DASL protocol
71067A
NKTL Cell Line


title: DBA/2J Female H2 13-Dec-05

tag: age (days)

tag: batch id

value: JAX


title: Nucleus accumbens_RARbeta_KO_5


title: D2B6F1 Female H1 26-Sep-05

value: hippocampus

tag: scale factor


title: Nucleus accumbens_RARbeta_WT_5

tag: genotype/variation


title: C57BL/6J Female H1 23-Sep-05

tag: background average


title: D2B6F1 Female H2 10-Aug-05

tag: affx-gapdhmur (3'/5')


title: Nucleus accumbens_RARbeta_WT_3


title: NKTL-JS7

description:
Illumina DASL protocol
71067G
NKTL Patient


title: Nucleus accumbens_RARbeta_WT_2


title: Nucleus accumbens_RARbeta_WT_4


title: Tumor tissue from patient 5

city: Chengdu

first: Guiquan

last: Zhu

address: No.55 Section 4, Renmin South Road

department: Department of Head Neck Surgery

country: China

institute: Sichuan Cancer Hospital

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) was applied for hybridization as described by the manufacturer. Slides were hybridized at 65°C for 17h in Agilent's SureHyb Hybridization Chambers.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner. Slides were assembled into scanner carousel, and then preceded one-color scanning procedure.

data_processing:
Data was extracted using Agilent Feature Extraction software. Results were provided in the Raw Data Files. Normalization was performed using the Agilent GeneSpring GX v12.0 software.
After quantile normalization of the raw data, lncRNAs that had at least 6 out of 12 samples with flags in Present or Marginal ("All Targets Value") were chosen for further data analysis. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: OSCC tissue

label_protocol: Arraystar Flash RNA Labeling Kit was used for sample labeling.

extract_protocol: Total RNA from tissues were extracted using TRIzol reagent following the manufacturer's instructions.

treatment_protocol: Fresh OSCC tissues and normal oral mucosa were stored in liquid nitrogen.

tag: disease status

value: oral squamous cell carcinoma (OSCC)

tag: Stage

tag: tissue

value: OSCC tissue

tag: site

value: tungue

tag: age

tag: patient identifier


title: Nucleus accumbens_RARbeta_KO_4


title: B6D2F1 Male H4 26-Sep-05

description: technical duplicate of R1291H3

tag: strain

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: present

tag: absent

tag: marginal


title: Normal oral mucosa from patient 6

source_name: normal oral mucosa

value: normal oral mucosa

value: sofe palate

tag: Sex


title: B6D2F1 Female H2 26-Sep-05

value: Female

tag: age (days)

tag: batch id

tag: scale factor

tag: affx-b-actinmur (3'/5')

tag: source


title: Normal oral mucosa from patient 3

tag: disease status

tag: Stage

value: buccal


title: B6D2F1 Male H3 9-Jun-05

tag: tissue

value: Male

tag: background average

tag: affx-gapdhmur (3'/5')


title: Tumor tissue from patient 6

tag: site

tag: age

tag: patient identifier


title: Normal oral mucosa from patient 4

value: gingiva


title: Nucleus accumbens_RARbeta_WT_1

tag: genotype/variation


title: Tumor tissue from patients 3


title: Tumor tissue from patient 4


title: Cal-27 cells cultured under hypoxia, replicate 3

data_processing:
Data was extracted using Agilent Feature Extraction software. Results were provided in the Raw Data Files. Normalization was performed using the Agilent GeneSpring GX v12.0 software.
After quantile normalization of the raw data, lncRNAs that had at least 3 out of 6 samples with flags in Present or Marginal ("All Targets Value") were chosen for further data analysis. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: OSCC cell line, hypoxia

growth_protocol: Cal-27 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum, 2mM L-glutamine, 25mM HEPES, and 100 units/ml penicillin and 100 ug/ml streptomycin in a humidified 5% CO2 atmosphere.

extract_protocol: Total RNA from cells grown in monolayer were extracted using TRIzol reagent following the manufacturer's instructions.

treatment_protocol: The Cal-27 cells were cultured under 20% O2 (normoxic) or 1% O2 (hypoxic) conditions, balanced with N2 in a 3-gas incubator.

tag: cell line

tag: cell type

value: oral squamous cell carcinoma (OSCC) cell line

tag: origin

value: human tongue squamous cell carcinoma

tag: growth condition

value: hypoxia (1% oxygen)


title: Cal-27 cells cultured under hypoxia, replicate 2


title: Normal oral mucosa from patient 1

tag: Sex

value: male


title: Normal oral mucosa from patient 5


title: Tumor tissue from patients 1


title: Cal-27 cells cultured under hypoxia, replicate 1


title: Normal oral mucosa from patient 2


title: Tumor tissue from patients 2


title: Paired adjacent normal tissue obtained from patient 10

city: Shanghai

first: Jianjun

last: Zhang

state: Shanghai

address: No.639, Zhizaoju road

institute: Shanghai Jiaotong University

description: lncRNA expression

hyb_protocol: 1.5 ug of Cy3-labelled cDNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Human Gene Expression Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B).

data_processing: Feature Extraction software (version 10.7.1.1, Agilent Technologies) was used to analyze array images to obtain raw data. GeneSpring software (version 12.5, Agilent Technologies) was employed to finish the basic analysis of the raw data. Initially, the raw data were normalized using the quantile algorithm. The probes with at least 100 percent of samples in any 1 condition out of 2 conditions having flags that indicate “Detected” were chosen for further data analysis. Differentially expressed lncRNAs were then identified through fold change, and p values were calculated using t-tests. The thresholds set for up- and down-regulated genes were a fold change ≥ 2.0 and a p value ≤ 0.05.

label_protocol: The RNA samples were first reverse transcribed into cDNA, and these cDNA samples were then labeled using a Low Input Quick-Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: All cancer samples and paired normal samples obtained from GC patients with primary GC from Zhongshan hospital, Fudan University.

extract_protocol: Total RNA was extracted from cancer cells using TRIzol Reagent (Invitrogen, Shanghai, China), and cDNA was synthesized using a PrimeScript RT reagent kit (Takara, Kusatsu, Shiga, Japan).

treatment_protocol: All clinical samples were quickly stored in liquid nitrogen after surgical resection.

tag: cancer status

value: normal sample

value: stomach

tag: gender


title: Paired adjacent normal tissue obtained from patient 7

description: lncRNA expression


title: Paired adjacent normal tissue obtained from patient 8

description: lncRNA expression

value: female


title: Paired adjacent normal tissue obtained from patient 9

description: lncRNA expression


title: Cal-27 cells cultured under normoxia, replicate 3

source_name: OSCC cell line, normoxia

value: normoxia (20% oxygen)


title: D2B6F1 Female H2 9-Jun-05

value: hippocampus

tag: strain

tag: age (days)

tag: batch id

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: scale factor

tag: present

tag: absent

tag: marginal

tag: affx-b-actinmur (3'/5')

tag: source

value: UTM RW


title: siControl BV2 cells coculture with C6 cells for 6h (average 3 indep. exps)

city: London

first: Miguel

middle: Angel

last: Burguillos

address: 4 Newark Street

country: United Kingdom

institute: Queen Mary University of London

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of two housekeeping genes: GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; deltaCt=(Ct_Target − Ct_HKG)
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
The fold_change.txt reports test/control (siCaspase 3 monoculture/siControl monoculture, siControl coculture/siControl monoculture and siCaspase3 coculture/siControl monoculture) ratios.

label: SYBR Green

source_name: BV2 microglia cell line transformed with a v-raf/v-myc recombinant retro-virus

label_protocol: PCR assays were performed using the Wound Healing  Pathway PCR assay panel (SA Biosciences) following the Manufacturer’s instructions. Reverse transcription was performed from 1000 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (AB7500 Real Time PCR, Applied Biosystems) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

growth_protocol: DMEM 10%FCS Pen/Strep during the knockdwon (48h); Then DMEM reduced to 5% FCS for the final 6h for both conditions (monoculture  and coculture set ups)

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: cell line

tag: cell type

value: Microglia cell line

tag: transformed with

value: a v-raf/v-myc recombinant retro-virus

tag: transfected with

value: siRNA negative control

tag: co-cultured with

value: C6 glioma cells for 6hrs


title: Paired adjacent normal tissue obtained from patient 6

description: lncRNA expression

tag: cancer status

tag: tissue

tag: gender


title: Paired adjacent normal tissue obtained from patient 5

description: lncRNA expression


title: siControl BV2 cells monoculture (average 3 indep. exps)

description: Control

value: none (monoculture)


title: Paired adjacent normal tissue obtained from patient 4

description: lncRNA expression


title: Cal-27 cells cultured under normoxia, replicate 1

tag: origin

tag: growth condition


title: Cal-27 cells cultured under normoxia, replicate 2


title: chondrocytes_soft ECM_24h_rep2

city: beijing

first: YAN

last: ZU

address: tsinghua university

institute: TSINGHUA

hyb_protocol: The pre-hybridization of MOA v2 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The Matrix value is normalized intensities. The pairwise comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

source_name: mouse chondrocytes，soft ECM，24h，Rep2

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: The articular cartilage was isolated and chondrocytes were extracted by collagenase digestion. After configuring the chondrocytes were plated in monolayer culture in DMEM high glucose supplemented with 10% FBS, 1% glutamine, 1% penicillin-streptomycin at 37 °C in 5% CO2.

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: Polyacrylamide gels with 500 Pa and 100 KPa Young’s moduli were prepared. Chondrocytes were palted in stiff, soft and normal ECM for 24h.

value: Articular cartilage

value: chondrocytes


title: chondrocytes_stiff ECM_24h_rep2

source_name: mouse chondrocytes，stiff ECM，24h，Rep2


title: Paired adjacent normal tissue obtained from patient 1

description: lncRNA expression


title: Paired adjacent normal tissue obtained from patient 3

description: lncRNA expression


title: chondrocytes_soft ECM_24h_rep1

source_name: mouse chondrocytes，soft ECM，24h，Rep1


title: Paired adjacent normal tissue obtained from patient 2

description: lncRNA expression


title: chondrocytes_soft ECM_24h_rep3

source_name: mouse chondrocytes，soft ECM，24h，Rep3


title: siCaspase3 BV2 cells coculture with C6 cells for 6h (average 3 indep. exps)

description: Test

value: siRNA against caspase-3


title: chondrocytes_stiff ECM_24h_rep3

source_name: mouse chondrocytes，stiff ECM，24h，Rep3


title: chondrocytes_normal_24h_rep3

source_name: mouse chondrocytes，normal，24h，Rep3


title: chondrocytes_normal_24h_rep1

source_name: mouse chondrocytes，normal，24h，Rep1


title: chondrocytes_stiff ECM_24h_rep1

source_name: mouse chondrocytes，stiff ECM，24h，Rep1


title: chondrocytes_normal_24h_rep2

source_name: mouse chondrocytes，normal，24h，Rep2


title: KO_HFD 1

status: Public on Jul 25 2016

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Mouse430_2 whole genome expression array chips were washed and stained in the Affymetrix Fluidics Station 400s

scan_protocol: Chips were scanned with an Affymetrix Scanner with standard settings

data_processing: Data was analyzed with RMA using the program Partek 6.6

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA

growth_protocol: RNA were isolated from wild type and mutants.

extract_protocol: Trizol extraction of total RNA was performed according to standard affymetrix labeling protocols

treatment_protocol: Genotype mouse(WT vs KO )were treated  with Normal and High Fat  foods.

tag: genotype

tag: diet

value: high fat

tag: strain


title: KO-Norm 3

value: normal


title: WT_HFD 3

value: Wild type


title: KO_HFD 2


title: siCaspase3 BV2 cells monoculture (average 3 indep. exps)

description: Control


title: WT_HFD 1


title: KO_HFD 3


title: KO-Norm 2


title: KO-Norm 1


title: WT-Norm 3


title: WT-Norm 2


title: WT_HFD 2


title: MEF_Lats2KO_#121_rep2_dyeswap

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

hyb_protocol: Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction, LOWESS normalization, and dye-normalization .

source_name: Embryonic fibroblast cells derived from LAT2+/+ C57BL/6J mice

label_protocol: 500 ng of total RNA was labeled using Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 500ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 5-CTP (Cy5-CTP) or 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A650nm for Cy5-CTP and at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Mouse embyonic fibroblasts (MEFs) were cultured in DMEM + 10% inactivated fetal bovine serum (FBS), penicillin (100U/mL), and streptomycin (100μg/mL) at 37°C, 5% CO2.

extract_protocol: Cultured cells were lysed by QIAzol Lysis Reagent (Qiagen), then total RNA was extracted from aqueous phase of QIAzol homogenate with RNeasy Mini Kit (Qiagen) and processed according to the manufacturer’s protocol. The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA).

treatment_protocol: no treatment

value: embryonic fibroblasts

tag: clone name

source_name: Embryonic fibroblast cells derived from LAT2-/- C57BL/6J mice


title: MEF_Lats2KO_#121_rep2


title: MEF_Lats2KO_#121_rep1


title: MEF_Lats2KO_#112


title: MEF_Lats2KO_#116


title: MEF_Lats2KO_#116_dyeswap


title: MEF_KO_Contact_inhibition

extract_protocol: Total RNA was extracted from cultured cells with miRNeasy Mini Kit (Qiagen) and processed according to the manufacturer’s protocol. The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were cultured for 48h until subconfluet and for 3 - 5 days prior to RNA sampling for low density sample and high density sample respectively.

tag: condition

value: high density

value: low density


title: MEF_Lats2KO_#121_rep1_dyeswap


title: MEF_KO_Contact_inhibition_dyeswap


title: MEF_WT_Contact_inhibition_dyeswap


title: PARTICIPANT-117

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

description:
10011068017_C.AVG_Signal
Illumina Human HT-12 BeadArray

hyb_protocol: Standard Illumina hybridization protocol for cRNA target (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All probe and gene values are provided, with no additional filtering.

source_name: Whole blood (PAXgene RNA)

label_protocol: Ambion TotalPrep target synthesis for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from primary peripheral blood samples (PAXgene) using Qiagen RNEasy reagents.

tag: age

tag: bmi

tag: alcohol

tag: smoking

tag: income

tag: hedonic

tag: eudaimonic

tag: jobevaluation

tag: selfindependent

tag: selfinterdependent

tag: otherindependent

tag: otherinterdependent


title: PARTICIPANT-114

description:
10010265114_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-110

description:
10010265114_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-115

description:
10011068017_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-119

description:
10011068017_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-108

description:
10010265114_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-116

description:
10011068017_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: MEF_WT_Contact_inhibition

tag: genotype

tag: cell type


title: PARTICIPANT-109

description:
10010265114_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-118

description:
10011068017_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-105

description:
10010265114_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-111

description:
10010265114_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-103

description:
10010265114_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-104

description:
10010265114_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-107

description:
10010265114_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-102

description:
10010265114_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-106

description:
10010265114_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: MEF_Lats2KO_#112_dyeswap

tag: strain


title: PARTICIPANT-100

description:
9992555015_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-101

description:
9992555015_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-96

description:
9992555015_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-97

description:
9992555015_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-83

description:
9992555003_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-85

description:
9992555003_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-90

description:
9992555015_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-98

description:
9992555015_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-99

description:
9992555015_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-93

description:
9992555015_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-91

description:
9992555015_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-94

description:
9992555015_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-92

description:
9992555015_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-86

description:
9992555003_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-84

description:
9992555003_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-88

description:
9992555003_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-87

description:
9992555003_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-80

description:
9992555003_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-82

description:
9992555003_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-81

description:
9992555003_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-77

description:
9967453055_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: IL8-3 30DAF rep2

city: Sendai

first: Yoshinori

last: Kanayama

state: Miyagi

address: 1-1, Tsutsumidori-amamiyamachi, Aobaku

department: Graduate School of Agricultural Science

institute: Tohoku University

description: Gene expression of IL8-3 fruit

hyb_protocol: Hybridization was performed according to the manual of the Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies). Following hybridization, we washed the probe array.

scan_protocol: We scanned tomato custom-designed microarray images with Agilent DNA Microarray Scanner G2565CA (Agilent Technologies).

data_processing: Scanned microarray images were converted to signal data with Feature Extraction software (Agilent Technologies).

organism: Solanum lycopersicum

source_name: Tomato introgression line 'IL8-3' fruit, 30 day after flowering, replicate 2

label_protocol: Target labeling was performed according to the manual of the Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies).

growth_protocol: M82 and IL8-3 plants were grown in a planting bed with culture soil containing slow-release fertilizer (CDU TamagokaseiS555, Co-op Chemical) and granular dolomite (Magutan, Gausukogyo) in a greenhouse, as described previously (Ikeda et al. 2013). Fruits were sampled at 10, 20, 30 DAF, and ripening stage (breaker stage) from 8 plants. Pericarp tissues were frozen in liquid nitrogen and stored at −80°C¬.

extract_protocol: Total RNA was extracted from fruit by the SDS–phenol method (Mohammed et al. 2012) and further purified with an RNeasy Plant Mini Kit (Qiagen). The optical density of the RNA was measured to check the quality, and high-quality RNA was subjected to transcriptome analysis using three independent biological replicates.

tag: cultivar

tag: tissue

value: Fruit pericarp

tag: developmental stage

value: 30 day after flowering


title: IL8-3 30DAF rep3

description: Gene expression of IL8-3 fruit

source_name: Tomato introgression line 'IL8-3' fruit, 30 day after flowering, replicate 3


title: IL8-3 Ripe rep2

description: Gene expression of IL8-3 fruit

source_name: Tomato introgression line 'IL8-3' fruit, Ripening stage, replicate 2

value: Ripening stage


title: PARTICIPANT-78

description:
9992555003_A.AVG_Signal
Illumina Human HT-12 BeadArray

tag: age

tag: bmi


title: IL8-3 Ripe rep1

description: Gene expression of IL8-3 fruit

source_name: Tomato introgression line 'IL8-3' fruit, Ripening stage, replicate 1


title: IL8-3 Ripe rep3

description: Gene expression of IL8-3 fruit

source_name: Tomato introgression line 'IL8-3' fruit, Ripening stage, replicate 3


title: PARTICIPANT-79

description:
9992555003_B.AVG_Signal
Illumina Human HT-12 BeadArray

tag: alcohol

tag: smoking


title: PARTICIPANT-76

description:
9967453055_K.AVG_Signal
Illumina Human HT-12 BeadArray

tag: income

tag: hedonic


title: IL8-3 30DAF rep1

description: Gene expression of IL8-3 fruit

source_name: Tomato introgression line 'IL8-3' fruit, 30 day after flowering, replicate 1


title: IL8-3 20DAF rep3

description: Gene expression of IL8-3 fruit

source_name: Tomato introgression line 'IL8-3' fruit, 20 day after flowering, replicate 3

value: 20 day after flowering


title: PARTICIPANT-89

description:
9992555003_L.AVG_Signal
Illumina Human HT-12 BeadArray

tag: eudaimonic

tag: jobevaluation


title: WT-Norm 1

tag: diet


title: IL8-3 20DAF rep2

description: Gene expression of IL8-3 fruit

source_name: Tomato introgression line 'IL8-3' fruit, 20 day after flowering, replicate 2


title: IL8-3 10DAF rep1

description: Gene expression of IL8-3 fruit

source_name: Tomato introgression line 'IL8-3' fruit, 10 day after flowering, replicate 1

value: 10 day after flowering


title: M82 Ripe rep2

description: Gene expression of M82 fruit

source_name: Tomato cultivated variety 'M82' fruit, Ripening stage, replicate 2


title: M82 30DAF rep3

description: Gene expression of M82 fruit

source_name: Tomato cultivated variety 'M82' fruit, 30 day after flowering, replicate 3


title: IL8-3 10DAF rep3

description: Gene expression of IL8-3 fruit

source_name: Tomato introgression line 'IL8-3' fruit, 10 day after flowering, replicate 3


title: M82 Ripe rep1

description: Gene expression of M82 fruit

source_name: Tomato cultivated variety 'M82' fruit, Ripening stage, replicate 1


title: IL8-3 20DAF rep1

description: Gene expression of IL8-3 fruit

source_name: Tomato introgression line 'IL8-3' fruit, 20 day after flowering, replicate 1


title: PARTICIPANT-70

description:
9967453055_E.AVG_Signal
Illumina Human HT-12 BeadArray

tag: selfindependent

tag: selfinterdependent

tag: otherindependent


title: PARTICIPANT-74

description:
9967453055_I.AVG_Signal
Illumina Human HT-12 BeadArray

tag: otherinterdependent


title: M82 30DAF rep1

description: Gene expression of M82 fruit

source_name: Tomato cultivated variety 'M82' fruit, 30 day after flowering, replicate 1


title: IL8-3 10DAF rep2

description: Gene expression of IL8-3 fruit

source_name: Tomato introgression line 'IL8-3' fruit, 10 day after flowering, replicate 2


title: M82 30DAF rep2

description: Gene expression of M82 fruit

source_name: Tomato cultivated variety 'M82' fruit, 30 day after flowering, replicate 2


title: M82 20DAF rep3

description: Gene expression of M82 fruit

source_name: Tomato cultivated variety 'M82' fruit, 20 day after flowering, replicate 3


title: PARTICIPANT-72

description:
9967453055_G.AVG_Signal
Illumina Human HT-12 BeadArray

source_name: Whole blood (PAXgene RNA)


title: M82 20DAF rep2

description: Gene expression of M82 fruit

source_name: Tomato cultivated variety 'M82' fruit, 20 day after flowering, replicate 2


title: PARTICIPANT-75

description:
9967453055_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-69

description:
9967453055_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: M82 10DAF rep1

description: Gene expression of M82 fruit

source_name: Tomato cultivated variety 'M82' fruit, 10 day after flowering, replicate 1


title: PARTICIPANT-67

description:
9967453055_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: M82 10DAF rep3

description: Gene expression of M82 fruit

source_name: Tomato cultivated variety 'M82' fruit, 10 day after flowering, replicate 3


title: PARTICIPANT-71

description:
9967453055_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: M82 Ripe rep3

description: Gene expression of M82 fruit

source_name: Tomato cultivated variety 'M82' fruit, Ripening stage, replicate 3


title: PARTICIPANT-66

description:
9967453055_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: M82 10DAF rep2

description: Gene expression of M82 fruit

source_name: Tomato cultivated variety 'M82' fruit, 10 day after flowering, replicate 2


title: M82 20DAF rep1

description: Gene expression of M82 fruit

source_name: Tomato cultivated variety 'M82' fruit, 20 day after flowering, replicate 1


title: PARTICIPANT-65

description:
9967453052_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-61

description:
9967453052_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-64

description:
9967453052_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-62

description:
9967453052_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-57

description:
9967453052_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: HeLa-S3_siLATS1/LATS2

description: HeLa-S3 cell, siLATS1/LATS2

hyb_protocol: Before hybridization, 1650 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations to Agilent-014850 arrays were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual.

scan_protocol: Scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies). The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction, LOWESS normalization, and dye-normalization.

source_name: HeLa-S3 cell, siLATS1/LATS2

label_protocol: 100 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

growth_protocol: HeLa-S3 cells were cultured in DMEM + 10% fetal bovine serum (FBS), penicillin (100U/mL), and streptomycin (100μg/mL) at 37°C, 5% CO2.

treatment_protocol: siRNAs for LATS1 and/or LATS2 were transfected in HeLa-S3 cells using Lipofectamine 2000 (Life technologies), then cells were cultured for 48h prior to RNA sampling.

tag: cell line

value: cervix


title: HeLa-S3_siLATS2

description: HeLa-S3 cell, siLATS2

source_name: HeLa-S3 cell, siLATS2


title: PARTICIPANT-63

description:
9967453052_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: WD_Tumor_6L

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina System Manual

scan_protocol: Refer to the Illumina System Manual

data_processing: Raw scan data were normalized with the use of cubic spline algorithm implemented in Illumina Normalizer module of GenePattern software (www.broadinstitute.org/genepattern).

label_protocol: Refer to the Illumina System Manual

extract_protocol: Using RNA later-soaked tissue specimens, total RNA was extracted using RNeasy Mini kit (Qiagen).

treatment_protocol: 129S1/SvImJ;C57Bl/6J (129/B6) mice were fed with high-fat diet (Western Diet) and high fructose-glucose solution (Sugar Water) (WD SW) or chow diet (CD) for 52 weeks, and total RNA samples were isolated from liver and tumor tissues for genome-wide expression profiling.

value: WD SW

tag: tissue type

value: Tumor

tag: strain


title: PARTICIPANT-58

description:
9967453052_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: HeLa-S3_siLATS1

description: HeLa-S3 cell, siLATS1

source_name: HeLa-S3 cell, siLATS1

tag: tissue


title: PARTICIPANT-56

description:
9967453052_C.AVG_Signal
Illumina Human HT-12 BeadArray

tag: age


title: PARTICIPANT-60

description:
9967453052_G.AVG_Signal
Illumina Human HT-12 BeadArray

tag: bmi


title: WD_Liver_5R

value: Liver


title: WD_Liver_6L


title: HeLa-S3_mock

description: HeLa-S3 cell, mock

source_name: HeLa-S3 cell, mock


title: WD_Liver_4R


title: PARTICIPANT-55

description:
9967453052_B.AVG_Signal
Illumina Human HT-12 BeadArray

tag: alcohol


title: WD_Tumor_4N


title: PARTICIPANT-59

description:
9967453052_F.AVG_Signal
Illumina Human HT-12 BeadArray

tag: smoking


title: WD_Tumor_5N


title: WD_Tumor_4R


title: WD_liver_4N


title: WD_Tumor_5R


title: CD_Liver_3N

value: CD


title: WD_Liver_5N


title: PARTICIPANT-54

description:
9967453052_A.AVG_Signal
Illumina Human HT-12 BeadArray

tag: income


title: CD_Liver_2L


title: CD_Liver_2N


title: Chow_14N

treatment_protocol: 129S1/SvImJ;C57Bl/6J (129/B6) mice were fed with high-fat diet (Western Diet) and high fructose-glucose solution (Sugar Water) (WD SW) or chow diet (CD) for 8 weeks, and total RNA samples were isolated from liver tissues for genome-wide expression profiling.

value: liver


title: CD_Liver_1L


title: Chow_13R


title: PARTICIPANT-52

description:
9967453048_K.AVG_Signal
Illumina Human HT-12 BeadArray

tag: hedonic


title: PARTICIPANT-49

description:
9967453048_H.AVG_Signal
Illumina Human HT-12 BeadArray

tag: eudaimonic


title: WDSW_7L


title: WDSW_7N


title: WDSW_7R


title: WDSW_5R


title: CD_Liver_1R


title: Chow_12N


title: PARTICIPANT-46

description:
9967453048_E.AVG_Signal
Illumina Human HT-12 BeadArray

tag: jobevaluation


title: PARTICIPANT-53

description:
9967453048_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: Chow_12R

tag: diet


title: PARTICIPANT-48

description:
9967453048_G.AVG_Signal
Illumina Human HT-12 BeadArray

tag: selfindependent


title: PARTICIPANT-50

description:
9967453048_I.AVG_Signal
Illumina Human HT-12 BeadArray

tag: selfinterdependent


title: RV_LRAT_VAD_2

city: Scarborough

first: Douglas

last: Sawyer

state: ME

address: 81 Research Dr

department: Cardiovascular Institute

institute: Maine Medical Center

description: Gene expression data from right ventricle

hyb_protocol: TdT-labeled cRNA was hybridized to mouse gene 1.0 ST arrays.

scan_protocol: Affymetrix gene-chip scanner using AGCCv.1.1.

data_processing:
Data were normalized using RMA procedure.  ANOVA was used to model variation in probe expression as a function of the 3 different treatment groups.  FDR was calculated for the p-values of the overall ANOVA F statistic using the p.adjust function of R (version 3.1.2 using method BH.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r2.dt1.mm8.mps

source_name: right ventricle of LRAT -/- on VAD

label_protocol: sample RNA was normalized to 43.44 ng/ul and amplified using AMBION RNA and labeled with Affymetrix GeneChip WT terminal labeling.

growth_protocol: mice were group housed in plastic cages with Alpha-Dri bedding and were maintained on their own air system in a temperature controlled room with a 12h light/12h dark cycle.

extract_protocol: the heart was dissected from the chest cavity and immersed in RNAlater.  The right ventricle was separated from the left ventricle by cutting along the septum.  Tissue was cut into small pieces and RNA was extracted using a modified guanidine isothiocyanate-cesium chloride centrifugation method.  Samples were treated with DNAse.

treatment_protocol: acidified water was supplied in water bottles.  Custom vitamin A deficieint (CSMD130C) and sufficient (960220) color-coded, pelleted, diets were prepared by MP BioMedical, Solon, OH.  The VAS diet was same as VAD, but supplemented with 250,000 U/kg retinol palmitate as a source of vitamin A.  Animals were sacrificed after 50 days on the diet.

tag: gender

value: male

tag: genotype/variation

value: LRAT -/-

value: right ventricle

value: vitamin A deficient


title: RV_LRAT_VAD_3


title: RV_LRAT_VAD_1


title: RV_LRAT_VAS_3

source_name: right ventricle of LRAT -/- on VAS

value: vitamin A sufficient


title: WDSW_5N


title: PARTICIPANT-47

description:
9967453048_F.AVG_Signal
Illumina Human HT-12 BeadArray

tag: otherindependent

tag: otherinterdependent


title: RV_LRAT_VAS_1


title: PARTICIPANT-51

description:
9967453048_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-45

description:
9967453048_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: RV_LRAT_VAS_2


title: Chow_13N

tag: strain


title: PARTICIPANT-44

description:
9967453048_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: RV_WT_VAS_1

source_name: right ventricle of wild-type

value: wild-type

tag: tissue


title: RV_WT_VAS_3


title: RV_WT_VAS_2


title: PARTICIPANT-43

description:
9967453048_B.AVG_Signal
Illumina Human HT-12 BeadArray

tag: age


title: Sample_51_Feces_EU_Patient_MCS-3

type: genomic

city: San Francisco

first: Jordan

middle: Samuel

last: Mar

state: Ca

address: 513 Parnassus Ave., S-357

department: Medicine, Division of Gastroenterology

institute: University Of California, San Francisco

description:
Feces_EU_Patient_MCS-3
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

hyb_protocol: Next, the labeled DNA was denatured at 99ºC for 5 min and hybridized to custom-made Affymetrix GeneChips (16S rRNA genes PhyloChips) at 48ºC and 60 rpm for 16 h. PhyloChip washing and staining were performed according to the standard Affymetrix protocols described previously (Masuda and Church 2002).

scan_protocol: Each PhyloChip was scanned and recorded as a pixel image, and initial data acquisition and intensity determination were performed using standard Affymetrix software (GeneChip microarray analysis suite, version 5.1).

data_processing:
Fluorescence intensities were normalized to spike-in control oligonucleotides provided by SecondGenome, Inc. (San Bruno, CA, USA) using the proprietary PhyCA processing technique developed by SecondGenome, Inc, which utilizes aggregate measures (“r scores”) that incorporate mismatch probe fluorescence intensity as well as distribution of total chip fluorescence. Quartile r score cutoffs were chosen based on r scores retrieved for control probes spiked-in at known concentrations, as recorded from all Phylochip microarrays of the current study, and were as follows: rQ1 > .38, rQ2 > .57, rQ3 > .82. For more information on normalization procedure, see Ivanov, II, et al. Cell 2009; 139:485-98.
Values in the matrix template represent total, normalized flourescence intensities for each OUT found present in at least on sample. These values are untransformed and represent a the relative abundance of the OTU in question.

molecule: genomic DNA

organism: human gut metagenome

source_name: Feces

label_protocol: DNA was extracted from individual fecal samples using a combination of bead beating and the commercially available QIAamp® DNA Stool Kit (Cat. No. 51504; QIAGEN, CA). Initially, 1.6mL of Buffer ASL was added to approximately 100mg of feces and bead beat for 30 s at 6.0 m/s in a FastPrep-24 instrument (Cat. No. 116004500; MP Biomedicals). Following bead beating, samples were incubated at 95ºC for 5 minutes to improve lysis efficiency of difficult to lyse microbes. The remainder of the DNA isolation was conducted using a QIAcube (Cat. No. 9001292; QIAGEN, CA) according to the QIAamp® DNA Stool Kit Protocol: Isolation of DNA from Stool for Pathogen Detection. Isolated DNA was stored at -80ºC. Blank extractions were included as negative controls to monitor for bacterial contamination

extract_protocol: Study participants were provided detailed instructions and necessary materials for fecal sample collection. Standardized fecal samples (first stool of the morning) were collect at home by defecating onto a sterile stool collection device (Cat. No. Protocult #120; Ability Building Center, MN ) placed over a toilet seat and using a sterile collection cup with an attached sterile scoop (Cat. No. 80.734.311; Sarstedt, Germany). Following collection, fecal samples were placed in a pre-paid overnight mailer with a frozen ice pack (Cat. No. S-9902; ULINE, CA) and shipped overnight via USPS in accordance with federal regulations. Upon arrival, fecal sample were immediately stored at -80ºC.

value: Feces

value: Patient

tag: origin

value: EU

value: X

tag: Sex

tag: bmi

tag: mcs

tag: scca


title: LV_LRAT_VAS_3

description: Gene expression data from left ventricle

source_name: left ventricle of LRAT -/- on VAS

extract_protocol: the heart was dissected from the chest cavity and immersed in RNAlater.  The right ventricle was separated from the left ventricle by cutting along the septum.  Tissue was cut into small pieces and RNA was extracted using a Trizol according to manufacturers instructions.  Samples were treated with DNAse.

treatment_protocol: acidified water was supplied in water bottles.  Custom vitamin A deficient VAD (CSMD130C) and sufficient VAS (960220) color-coded, pelleted, diets were prepared by MP BioMedical, Solon, OH.  The VAS diet was same as VAD, but supplemented with 250,000 U/kg retinol palmitate as a source of vitamin A.  Animals were sacrificed after 50 days on the diet.

value: left ventricle


title: PARTICIPANT-38

description:
9967453044_I.AVG_Signal
Illumina Human HT-12 BeadArray

tag: alcohol

tag: smoking

tag: income

tag: hedonic

tag: eudaimonic


title: PARTICIPANT-42

description:
9967453048_A.AVG_Signal
Illumina Human HT-12 BeadArray

tag: jobevaluation

tag: selfindependent

tag: selfinterdependent


title: PARTICIPANT-34

description:
9967453044_F.AVG_Signal
Illumina Human HT-12 BeadArray

tag: otherindependent

tag: otherinterdependent


title: PARTICIPANT-36

description:
9967453044_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: LV_LRAT_VAD_2

source_name: left ventricle of LRAT -/- on VAD

tag: gender

tag: genotype/variation

tag: tissue

tag: diet


title: LV_LRAT_VAD_3


title: LV_WT_VAS_1

source_name: left ventricle of wild-type


title: LV_LRAT_VAD_1


title: LV_WT_VAS_3


title: PARTICIPANT-41

description:
9967453044_L.AVG_Signal
Illumina Human HT-12 BeadArray

source_name: Whole blood (PAXgene RNA)

tag: age

tag: bmi


title: Sample_41_Feces_EU_Patient_MCS-2

description:
Feces_EU_Patient_MCS-2
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

tag: origin

tag: Sex

tag: mcs

tag: scca


title: Sample_50_Feces_EU_Patient_MCS-1

description:
Feces_EU_Patient_MCS-1
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.


title: Sample_44_Feces_EU_Patient_MCS-2


title: LV_LRAT_VAS_2


title: PARTICIPANT-40

description:
9967453044_K.AVG_Signal
Illumina Human HT-12 BeadArray

tag: alcohol

tag: smoking

tag: income

tag: hedonic


title: LV_WT_VAS_2


title: Sample_49_Feces_EU_Patient_MCS-2


title: LV_LRAT_VAS_1


title: PARTICIPANT-37

description:
9967453044_H.AVG_Signal
Illumina Human HT-12 BeadArray

tag: eudaimonic

tag: jobevaluation

tag: selfindependent

tag: selfinterdependent


title: Sample_43_Feces_EU_Patient_MCS-2


title: Sample_46_Feces_EU_Patient_MCS-2


title: PARTICIPANT-68

description:
9967453055_C.AVG_Signal
Illumina Human HT-12 BeadArray

tag: otherindependent

tag: otherinterdependent


title: PARTICIPANT-32

description:
9967453044_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: HT-29 cells; 5 ng/ml TNF, 0 ng/ml EGF, 5 ng/ml insulin for 16 hr, replicate #2

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

hyb_protocol: Following fragmentation, complementary RNA was hybridized to GeneChip Human Genome U133A Arrays (Affymetrix) according to the manufacturer's recommendation.

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

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

source_name: HT-29 colon adenocarcinoma cells sensitized with 200 U/ml interferon-gamma for 24 hr

label_protocol: Biotin-labeled complementary RNA was synthesized with the T7-based BioArray HighYield RNA Transcript Labeling Kit (Enzo) according to the manufacturer's recommendation.

growth_protocol: HT-29 cells were grown according to ATCC recommendations, plated at 50,000 cells/cm2 for 24 hr, and sensitized with 200 U/ml interferon-gamma before treatment.

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer's recommendation, and RNA integrity was confirmed on an Agilent Bioanalyzer.

treatment_protocol: Cells were stimulated with 0, 5, or 100 ng/ml TNF; 0, 1, or 100 ng/ml EGF; and 0, 5, or 500 ng/ml insulin for 4, 8, or 16 hr.

tag: cell line

value: HT-29 colorectal adenocarcinoma cell line

tag: seeding density

value: 50,000 cells/cm2 at 24 hr before interferon-gamma sensitization

tag: treatment

value: 16 hr


title: Sample_40_Feces_EU_Patient_MCS-1

tag: tissue

tag: origin

tag: age

tag: bmi


title: PARTICIPANT-33

description:
9967453044_E.AVG_Signal
Illumina Human HT-12 BeadArray

tag: alcohol


title: HT-29 cells; 5 ng/ml TNF, 1 ng/ml EGF, 0 ng/ml insulin for 16 hr, replicate #2


title: PARTICIPANT-30

description:
9967453044_B.AVG_Signal
Illumina Human HT-12 BeadArray

tag: smoking


title: PARTICIPANT-29

description:
9967453044_A.AVG_Signal
Illumina Human HT-12 BeadArray

tag: income


title: Sample_38_Feces_EU_Control_Control

description:
Feces_EU_Control_Control
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

value: Control

value: Y

tag: Sex

tag: mcs

tag: scca


title: Sample_34_Feces_EU_Control_Control


title: HT-29 cells; 5 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 16 hr, replicate #2


title: Sample_32_Feces_EU_Patient_Porphyromonadaceae

description:
Feces_EU_Patient_Porphyromonadaceae
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

value: Porphyromonadaceae


title: HT-29 cells; 100 ng/ml TNF, 0 ng/ml EGF, 500 ng/ml insulin for 16 hr, replicate #2


title: Sample_33_Feces_EU_Patient_MCS-1


title: HT-29 cells; 0 ng/ml TNF, 0 ng/ml EGF, 500 ng/ml insulin for 16 hr, replicate #2


title: Sample_37_Feces_EU_Patient_MCS-2


title: HT-29 cells; 0 ng/ml TNF, 100 ng/ml EGF, 0 ng/ml insulin for 16 hr, replicate #2


title: Sample_29_Feces_EU_Patient_MCS-1


title: PARTICIPANT-27

description:
9967453043_K.AVG_Signal
Illumina Human HT-12 BeadArray

tag: hedonic

tag: eudaimonic

tag: jobevaluation

tag: selfindependent


title: Sample_31_Feces_EU_Patient_MCS-1


title: PARTICIPANT-26

description:
9967453043_J.AVG_Signal
Illumina Human HT-12 BeadArray

tag: selfinterdependent

tag: otherindependent

tag: otherinterdependent


title: Sample_28_Feces_EU_Control_Control

tag: tissue


title: HT-29 cells; 100 ng/ml TNF, 100 ng/ml EGF, 0 ng/ml insulin for 16 hr, replicate #2

tag: cell line

tag: seeding density

tag: treatment


title: PARTICIPANT-23

description:
9967453043_G.AVG_Signal
Illumina Human HT-12 BeadArray

tag: age

tag: bmi

tag: alcohol


title: PARTICIPANT-28

description:
9967453043_L.AVG_Signal
Illumina Human HT-12 BeadArray

tag: smoking

tag: income


title: PARTICIPANT-24

description:
9967453043_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-25

description:
9967453043_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: HT-29 cells; 0 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 16 hr, replicate #2


title: HT-29 cells; 100 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 16 hr, replicate #2


title: HT-29 cells; 5 ng/ml TNF, 0 ng/ml EGF, 5 ng/ml insulin for 8 hr, replicate #2

value: 8 hr


title: HT-29 cells; 5 ng/ml TNF, 1 ng/ml EGF, 0 ng/ml insulin for 8 hr, replicate #2


title: Sample_26_Feces_EU_Patient_MCS-1

tag: origin

tag: Sex

tag: mcs

tag: scca


title: Sample_27_Feces_EU_Control_Control


title: PARTICIPANT-20

description:
9967453043_F.AVG_Signal
Illumina Human HT-12 BeadArray

tag: hedonic

tag: eudaimonic

tag: jobevaluation

tag: selfindependent


title: Sample_25_Feces_EU_Control_Control

tag: tissue


title: Sample_22_Feces_SA_Control_Control

description:
Feces_SA_Control_Control
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

value: SA

value: C


title: PARTICIPANT-18

description:
9967453043_D.AVG_Signal
Illumina Human HT-12 BeadArray

tag: selfinterdependent

tag: otherindependent

tag: otherinterdependent


title: Sample_24_Feces_EU_Patient_MCS-1

description:
Feces_EU_Patient_MCS-1
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

tag: age


title: HT-29 cells; 100 ng/ml TNF, 100 ng/ml EGF, 0 ng/ml insulin for 8 hr, replicate #2

tag: cell line

tag: seeding density

tag: treatment


title: HT-29 cells; 5 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 8 hr, replicate #2


title: Sample_17_Feces_SA_Control_Control

tag: bmi


title: PARTICIPANT-17

description:
9967453043_C.AVG_Signal
Illumina Human HT-12 BeadArray

tag: alcohol

tag: smoking

tag: income


title: PARTICIPANT-14

description:
9967453042_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: PARTICIPANT-19

description:
9967453043_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: HT-29 cells; 0 ng/ml TNF, 100 ng/ml EGF, 0 ng/ml insulin for 8 hr, replicate #2


title: HT-29 cells; 100 ng/ml TNF, 0 ng/ml EGF, 500 ng/ml insulin for 8 hr, replicate #2


title: Sample_15_Feces_SA_Patient_MCS-3

description:
Feces_SA_Patient_MCS-3
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

tag: origin

value: A

tag: Sex

tag: mcs

tag: scca


title: HT-29 cells; 5 ng/ml TNF, 0 ng/ml EGF, 5 ng/ml insulin for 4 hr, replicate #2

value: 4 hr


title: PARTICIPANT-15

description:
9967453043_A.AVG_Signal
Illumina Human HT-12 BeadArray

tag: hedonic

tag: eudaimonic

tag: jobevaluation

tag: selfindependent


title: PARTICIPANT-11

description:
9967453042_K.AVG_Signal
Illumina Human HT-12 BeadArray

tag: selfinterdependent

tag: otherindependent

tag: otherinterdependent


title: HT-29 cells; 0 ng/ml TNF, 0 ng/ml EGF, 500 ng/ml insulin for 8 hr, replicate #2

tag: cell line

tag: seeding density


title: Sample_14_Feces_SA_Patient_MCS-1

description:
Feces_SA_Patient_MCS-1
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

tag: tissue

tag: age

tag: bmi


title: HT-29 cells; 0 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 8 hr, replicate #2

tag: treatment


title: Sample_13_Feces_SA_Patient_MCS-3

tag: origin


title: PARTICIPANT-9

description:
9967453042_I.AVG_Signal
Illumina Human HT-12 BeadArray

tag: alcohol

tag: smoking

tag: income


title: PARTICIPANT-8

description:
9967453042_H.AVG_Signal
Illumina Human HT-12 BeadArray

tag: hedonic


title: Sample_16_Feces_SA_Control_Control

tag: Sex

tag: mcs

tag: scca


title: HT-29 cells; 5 ng/ml TNF, 1 ng/ml EGF, 0 ng/ml insulin for 4 hr, replicate #2


title: HT-29 cells; 100 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 8 hr, replicate #2


title: PARTICIPANT-10

description:
9967453042_J.AVG_Signal
Illumina Human HT-12 BeadArray

tag: eudaimonic

tag: jobevaluation

tag: selfindependent

tag: selfinterdependent


title: Sample_11_Feces_SA_Patient_MCS-4

description:
Feces_SA_Patient_MCS-4
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.


title: PARTICIPANT-7

description:
9967453042_G.AVG_Signal
Illumina Human HT-12 BeadArray

tag: otherindependent

tag: otherinterdependent


title: HT-29 cells; 5 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 4 hr, replicate #2

tag: cell line

tag: seeding density


title: PARTICIPANT-4

description:
9967453042_D.AVG_Signal
Illumina Human HT-12 BeadArray

tag: age

tag: bmi


title: Sample_3_Feces_SA_Patient_MCS-1

tag: tissue

tag: origin


title: Sample_5_Feces_SA_Patient_MCS-3


title: Sample_4_Feces_SA_Patient_MCS-4


title: PARTICIPANT-5

description:
9967453042_E.AVG_Signal
Illumina Human HT-12 BeadArray

tag: alcohol

tag: smoking

tag: income


title: HT-29 cells; 100 ng/ml TNF, 0 ng/ml EGF, 500 ng/ml insulin for 4 hr, replicate #2

tag: treatment


title: HT-29 cells; 0 ng/ml TNF, 0 ng/ml EGF, 500 ng/ml insulin for 4 hr, replicate #2


title: HT-29 cells; 100 ng/ml TNF, 100 ng/ml EGF, 0 ng/ml insulin for 4 hr, replicate #2


title: Sample_2_Feces_SA_Patient_MCS-2

description:
Feces_SA_Patient_MCS-2
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

tag: Sex

tag: mcs

tag: scca


title: Sample_1_Feces_SA_Patient_MCS-1


title: HT-29 cells; 0 ng/ml TNF, 100 ng/ml EGF, 0 ng/ml insulin for 4 hr, replicate #2


title: PARTICIPANT-6

description:
9967453042_F.AVG_Signal
Illumina Human HT-12 BeadArray

tag: hedonic

tag: eudaimonic

tag: jobevaluation

tag: selfindependent


title: PARTICIPANT-2

description:
9967453042_B.AVG_Signal
Illumina Human HT-12 BeadArray

tag: selfinterdependent

tag: otherindependent

tag: otherinterdependent


title: Sample_9_Feces_SA_Patient_MCS-2

tag: age

tag: bmi


title: Sample_10_Feces_SA_Patient_MCS-1

tag: tissue

tag: origin


title: HT-29 cells; 100 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 4 hr, replicate #2

tag: cell line

tag: seeding density


title: BMDCs_Lyn-KO_CpG-B_Rep3

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

institute: Yokohama City University

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

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

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

source_name: Lyn-KO BMDCs, stimulated with CpG-B ODN, replicate 3

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

growth_protocol: Bone marrow cells were cultured with 100 ng/ml human fms-like tyrosine kinase-3 (Flt3)-ligand (PeproTech) to induce dendritic cell differentiation. After 9 days, cells were harvested and used as BMDCs.

extract_protocol: The total RNA was prepared using NucleoSpin RNA (Macherey-Nagel) according to the manufacturers' instructions.

treatment_protocol: BMDCs were unstimulated or stimulated with 150 nM CpG-B ODN (1668) for 6 h.

tag: genotype

value: Lyn KO

tag: stimulation

value: CpG-B ODN

tag: replicate

value: Replicate 3

tag: cell type

value: BMDC

tag: genetic background


title: PARTICIPANT-3

description:
9967453042_C.AVG_Signal
Illumina Human HT-12 BeadArray

tag: alcohol

tag: smoking

tag: income

tag: hedonic

tag: eudaimonic


title: BMDCs_Irf5-KO_CpG-B_Rep3

source_name: Irf5-KO BMDCs, stimulated with CpG-B ODN, replicate 3

value: Irf5 KO


title: HT-29 cells; 5 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 16 hr, replicate #1

tag: treatment


title: HT-29 cells; 5 ng/ml TNF, 0 ng/ml EGF, 5 ng/ml insulin for 16 hr, replicate #1


title: HT-29 cells; 0 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 4 hr, replicate #2


title: HT-29 cells; 0 ng/ml TNF, 0 ng/ml EGF, 500 ng/ml insulin for 16 hr, replicate #1


title: HT-29 cells; 5 ng/ml TNF, 1 ng/ml EGF, 0 ng/ml insulin for 16 hr, replicate #1


title: HT-29 cells; 100 ng/ml TNF, 0 ng/ml EGF, 500 ng/ml insulin for 16 hr, replicate #1


title: BMDCs_Lyn-KO_US_Rep3

source_name: Lyn-KO BMDCs, unstimulated, replicate 3

value: Unstimulated


title: BMDCs_DKO_US_Rep3

source_name: Lyn/Irf5-DKO BMDCs, unstimulated, replicate 3

value: Lyn/Irf5 DKO


title: BMDCs_Irf5-KO_US_Rep3

source_name: Irf5-KO BMDCs, unstimulated, replicate 3


title: BMDCs_DKO_CpG-B_Rep3

source_name: Lyn/Irf5-DKO BMDCs, stimulated with CpG-B ODN, replicate 3


title: HT-29 cells; 100 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 16 hr, replicate #1

value: HT-29 colorectal adenocarcinoma cell line

value: 50,000 cells/cm2 at 24 hr before interferon-gamma sensitization


title: HT-29 cells; 5 ng/ml TNF, 0 ng/ml EGF, 5 ng/ml insulin for 8 hr, replicate #1


title: HT-29 cells; 100 ng/ml TNF, 100 ng/ml EGF, 0 ng/ml insulin for 16 hr, replicate #1

value: 16 hr


title: BMDCs_Lyn-KO_CpG-B_Rep2

source_name: Lyn-KO BMDCs, stimulated with CpG-B ODN, replicate 2

value: Replicate 2


title: HT-29 cells; 0 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 16 hr, replicate #1


title: HT-29 cells; 100 ng/ml TNF, 0 ng/ml EGF, 500 ng/ml insulin for 8 hr, replicate #1


title: BMDCs_DKO_CpG-B_Rep2

source_name: Lyn/Irf5-DKO BMDCs, stimulated with CpG-B ODN, replicate 2


title: BMDCs_Irf5-KO_CpG-B_Rep2

source_name: Irf5-KO BMDCs, stimulated with CpG-B ODN, replicate 2


title: HT-29 cells; 5 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 8 hr, replicate #1


title: BMDCs_DKO_US_Rep2

source_name: Lyn/Irf5-DKO BMDCs, unstimulated, replicate 2


title: BMDCs_Lyn-KO_US_Rep2

source_name: Lyn-KO BMDCs, unstimulated, replicate 2


title: BMDCs_Irf5-KO_US_Rep2

source_name: Irf5-KO BMDCs, unstimulated, replicate 2


title: HT-29 cells; 0 ng/ml TNF, 100 ng/ml EGF, 0 ng/ml insulin for 16 hr, replicate #1


title: BMDCs_WT_CpG-B_Rep3

source_name: WT BMDCs, stimulated with CpG-B ODN, replicate 3

value: WT


title: BMDCs_WT_US_Rep2

source_name: WT BMDCs, unstimulated, replicate 2


title: HT-29 cells; 100 ng/ml TNF, 100 ng/ml EGF, 0 ng/ml insulin for 8 hr, replicate #1

value: 8 hr


title: HT-29 cells; 100 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 8 hr, replicate #1


title: BMDCs_WT_CpG-B_Rep2

source_name: WT BMDCs, stimulated with CpG-B ODN, replicate 2


title: HT-29 cells; 5 ng/ml TNF, 1 ng/ml EGF, 0 ng/ml insulin for 8 hr, replicate #1


title: HT-29 cells; 0 ng/ml TNF, 100 ng/ml EGF, 0 ng/ml insulin for 8 hr, replicate #1


title: HT-29 cells; 0 ng/ml TNF, 0 ng/ml EGF, 500 ng/ml insulin for 8 hr, replicate #1


title: BMDCs_DKO_CpG-B_Rep1

source_name: Lyn/Irf5-DKO BMDCs, stimulated with CpG-B ODN, replicate 1

value: Replicate 1


title: HT-29 cells; 0 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 8 hr, replicate #1

source_name: HT-29 colon adenocarcinoma cells sensitized with 200 U/ml interferon-gamma for 24 hr


title: BMDCs_DKO_US_Rep1

source_name: Lyn/Irf5-DKO BMDCs, unstimulated, replicate 1


title: HT-29 cells; 5 ng/ml TNF, 1 ng/ml EGF, 0 ng/ml insulin for 4 hr, replicate #1


title: HT-29 cells; 5 ng/ml TNF, 0 ng/ml EGF, 5 ng/ml insulin for 4 hr, replicate #1


title: BMDCs_WT_CpG-B_Rep1

source_name: WT BMDCs, stimulated with CpG-B ODN, replicate 1


title: BMDCs_Irf5-KO_CpG-B_Rep1

source_name: Irf5-KO BMDCs, stimulated with CpG-B ODN, replicate 1


title: BMDCs_Lyn-KO_US_Rep1

source_name: Lyn-KO BMDCs, unstimulated, replicate 1


title: MEF_Lats2WT_PDL90

description: Embryonic fibroblast cells derived from LAT2+/+ C57BL/6J mice

hyb_protocol: Refer to Agilent miRNA hybridisation protocol. Probes were hybridized at 55°C for 20 hours with rotation. Then the slides were washed by Gene expression wash buffer 1 at room temperature for 5 minutes and by Gene expression wash buffer 2 at 37°C for 5 minutes.

scan_protocol: After hybridization and washing, the slides were scanned using an Agilent scanner (G2505C).

data_processing: Images were extracted using Agilent Feature Extraction software (v 10.5.1.1).

label_protocol: 100 ng of aliquots of total RNA was used for making miRNA probes according to the Agilent protocol (ver. 1.6). Briefly, total RNA was dephosphorylated with calf intestine alkaline phosphatase (Takara Bio, Shiga, Japan), denatured with dimethyl sulfoxide, and labeled with pCp-Cy3 using T4 RNA ligase (Takara Bio, Shiga, Japan) using the miRNA Labeling Reagent and Hybridization Kit (5190-0408, Agilent).

tag: strain

value: embryonic fibroblasts

tag: clone name

tag: pdl


title: HT-29 cells; 100 ng/ml TNF, 0 ng/ml EGF, 500 ng/ml insulin for 4 hr, replicate #1


title: BMDCs_WT_US_Rep3

source_name: WT BMDCs, unstimulated, replicate 3


title: HT-29 cells; 0 ng/ml TNF, 0 ng/ml EGF, 500 ng/ml insulin for 4 hr, replicate #1


title: MEF_Lats2KO_PDL96

description: Embryonic fibroblast cells derived from LAT2-/- C57BL/6J mice

tag: tissue


title: BMDCs_Irf5-KO_US_Rep1

source_name: Irf5-KO BMDCs, unstimulated, replicate 1


title: HT-29 cells; 5 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 4 hr, replicate #1

tag: cell line


title: MEF_Lats2KO_PDL70

source_name: Embryonic fibroblast cells derived from LAT2-/- C57BL/6J mice


title: HT-29 cells; 100 ng/ml TNF, 100 ng/ml EGF, 0 ng/ml insulin for 4 hr, replicate #1

tag: seeding density


title: MEF_Lats2WT_PDL68

source_name: Embryonic fibroblast cells derived from LAT2+/+ C57BL/6J mice

tag: genotype


title: HT-29 cells; 100 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 4 hr, replicate #1


title: BMDCs_WT_US_Rep1

source_name: WT BMDCs, unstimulated, replicate 1

tag: stimulation


title: HT-29 cells; 0 ng/ml TNF, 0 ng/ml EGF, 0 ng/ml insulin for 4 hr, replicate #1


title: HT-29 cells; 0 ng/ml TNF, 100 ng/ml EGF, 0 ng/ml insulin for 4 hr, replicate #1


title: HeLa-S3_LATS2_KO

description: HeLa-S3 cell, LATS2 KO, clone#25

source_name: HeLa-S3 cell, LATS2 KO, clone#25

growth_protocol: LATS2 KO HeLa-S3 cells and parental wild type cells were cultured in DMEM + 10% fetal bovine serum (FBS), penicillin (100U/mL), and streptomycin (100μg/mL) at 37°C, 5% CO2.

value: cervix


title: BMDCs_Lyn-KO_CpG-B_Rep1

source_name: Lyn-KO BMDCs, stimulated with CpG-B ODN, replicate 1

tag: replicate


title: HeLa-S3_parental_WT_rep1

description: HeLa-S3 cell, wild type, technical replicate1


title: CD8-T_Adult_AD40_rep1

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

institute: TAGC INSERM U1090

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

source_name: CD8-T, Adult, rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Adult T cells were obtained from leukocyte concentrates of healthy adult donors donated by Hospital de Zona of Instituto Mexicano del Seguro Social in Cuernavaca.  Neonatal blood was collected from the cord vein of full term vaginal deliveries of healthy babies at Hospital General Parres in Cuernavaca.  Blood was collected just after the delivery and before placenta expulsion. The procedure was approved by the Hospital Parres Ethical Committee and was performed on informed mothers that consented to donate their babies’ cord blood. Total blood was separated through a ficoll-hypaque gradient and plastic adhesion. PBMCs or CBMCs were further depleted of unwanted cell populations with a cocktail of antibodies followed by G protein-magnetic-beads (invitrogen) binding and depletion with a magnet. Antibodies used were CD57 (NK1, Zymed), CD19 (HD37, Santa Cruz Biotechnology), CD16 (3G8, BioLegend) and CD4 (MT310, Santa Cruz Biotechnology) antibodies.  To eliminate memory and effector cells in PBMCs, antibodies against CD45RO (UCH-L1 Santa Cruz Biotechnology), and CD44 (BJ18, BioLegend) were also used. Then CD8+T cells were obtained with an anti-CD8 (SK1, BioLegend) antibody. The pure cells were centrifuged and placed in Trizol (Invitrogen, cat. 15596-018), were shipped on dry ice to the transcriptome platform in Marseille. RNA was extracted according to manufacturer's instructions. The integrity of the RNA was determined by RNA chip in the bioanalyzer (Agilent), and only samples with RNA integrity (RIN) over 8.0 were used for transcriptome evaluation.

tag: status

value: Adult

tag: cell type


title: CD8-T_Neonate_N49_rep1

source_name: CD8-T, Neonate, rep1

value: Neonate


title: CD8-T_Adult_AD41_rep1


title: CD8-T_Neonate_N42_rep1


title: CD8-T_Neonate_N44_rep1


title: CD8-T_Neonate_N46_rep1


title: HeLa-S3_parental_WT_rep2

description: HeLa-S3 cell, wild type, technical replicate2


title: CD8-T_Adult_AD39_rep1


title: CD8-T_Adult_AD36_rep1


title: hMSC G line in NSS

city: Daejeon

first: Bic-Na

last: Song

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

department: Korean Bioinformation Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

description:
Sample name: 13_G
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array data processin were performed on Illumina GenomeStudio software.  We normalized gene expression data using Quantile normalization and log2 transformation.

source_name: human bone marrow_non-stimulatory serum

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX).

growth_protocol: MSC cultures were established from BM mononuclear cells and passaged in the Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (stimulatory (SS) serum and non-stimulatory (NSS) serums). MSCs that had been maintained in each culture media were sub-cultured for at least two passages before analysis.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer's protocol.

tag: gender

value: Male

tag: age

value: Bone marrow

value: G


title: hMSC SS15 line in NSS

description:
Sample name: 13_15
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.


title: hMSC SS15 line in SS

description:
Sample name: 97_15
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.

source_name: human bone marrow_stimulatory serum


title: hMSC SS10 line in NSS

description:
Sample name: 13_10
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.


title: hMSC SS10 line in SS

description:
Sample name: 97_10
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.


title: OVCAR3_PBX1KD_48hr

city: baltimore

first: Jin

last: Jung

address: 1550 orleans street, CRB2, Rm 376

department: OB/GYN

institute: Johns Hopkins Medical Institutes

data_processing: The data were background subtracted, quantile normalized, and log2 transformed.

source_name: OVCAR3 cell culture PBX1KD

label_protocol: Biotin labeled cRNA samples for hybridization were prepared by using Illumina Total Prep RNA Amplification Kit.

growth_protocol: RPMI-1640 supplemented with 10% fetal calf serum and 1% penicillin-Streptomycin

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit.

treatment_protocol: OVCAR3 cells were infected with viral supernatant expressing small RNAs complementary to either PBX1 RNA or a Control RNA (scrambled seq).  After two repeated infections (24 h each), cells were then harvested 24h and 48h later.

tag: cell lines


title: OVCAR3_Control_48hr

source_name: OVCAR3 cell culture control

value: Control


title: LacZ knockdown MCF-7 (clone#18)

city: Kyotanabe

first: Tsuyoshi

last: Waku

address: 1-3 Tatara Miyakodani

institute: Doshisha University

description: Sample data of shLacZ clone

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

scan_protocol: GeneChips were scanned using the AFFYMETRIX GeneChip Scanner GCS3000.

data_processing: The data were analyzed using GeneSpring software with the default settings.

source_name: LacZ knockdown MCF-7, isolated

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

growth_protocol: MCF-7 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was extracted using Fast pure RNA kit (TAKARA) according to the manufacturer's instructions.

treatment_protocol: MCF-7 cells were incubated with the shCHIP- or shLacZ-containing retroviral supernatant in the presence of 8 μg/ml polybrene.  Twenty-four hours after infection, the viral supernatant was replaced with fresh DMEM containing 10% FBS.  The infected cells were selected with 1 mg/ml G418.  Clones were isolated from shLacZ or shCHIP cells.

value: LacZ knockdown


title: LacZ knockdown MCF-7 (clone#147)

description: Sample data of shLacZ clone


title: LacZ knockdown MCF-7 (clone#153)

description: Sample data of shLacZ clone


title: LacZ knockdown MCF-7 (clone#16)

description: Sample data of shLacZ clone


title: LacZ knockdown MCF-7 (clone#115)

description: Sample data of shLacZ clone