title: ZR751_EpEP_16hr_rep5

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM estrogen plus 10nM progesterone for 16hrs. Replicate 5.


title: T47D_PROG_rep3

status: Public on Oct 18 2015

type: RNA

city: Woodville South

first: Eleanor

middle: F

last: Need

state: SA

address: 28 Woodville Rd

department: Discipline of Surgery

country: Australia

institute: The University of Adelaide

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina Scanning protocol

data_processing: Data was normalised using cubic spline normalisation in bead studio. For publication, data was normalised using variance stabilisation normalisation, corrected with ComBat, filtered to likely expressed transcripts and then subjected to linear model fitting as implemented in the bioconductor Limma package in R.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: T47D breast cancer cells, 10nM progesterone treated 16h, rep 3

label_protocol: biotinylated cDNA was prepared using 1ug of total RNA according to standard Illumina protocols

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10% FBS

extract_protocol: Total RNA was isolated using a Qiagen Rneasy RNA extraction kit, incorporating Dnase on-column digestion according to manufacturer's instructions

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM progesterone for 16h. Replicate 3
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).

tag: cell line

tag: cell type

value: breast cancer cell line


title: Myoblasts Subject1 Control

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: Primary proliferating myoblasts isolated from Vastus lateralis muscle treated with vehicle for 24h. Cells isolated from Subject 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG U133 plus2 3'  array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The probe-set level intensities of the arrays were normalized using the Robust Multi-array Analysis method (RMA) implemented within the R statistical software environment using the ‘affy’ package (Bioconductor project).

source_name: Primary proliferating myoblasts, Subject 1, Control

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: Isolated human myoblasts were cultured in DMEM-F12 Glutamax containing 20% FBS and 1% ABAM (high-serum media) at 37° C, 5% CO2. Culture dishes were coated with collagen I (Gibco® Collagen I, Bovine 5 mg/mL Invitrogen) diluted to a final concentration of 50 μg/mL in 0.02 M acetic acid according to the manufacturers manual. Myoblasts were taken through serial passages to increase cell numbers prior to experimentation. All myoblasts were used for experimentation at passage 4-5. For experimentation, myoblasts were harvested and transferred to collagen I coated 6-well plates at a density of 8 x 10^4 cells per well.

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

treatment_protocol: Low-serum media containing 100 nM 1,25(OH)2D3, or vehicle alone for 24 h.

value: Primary proliferating myoblasts

tag: tissue

value: Vastus lateralis

tag: treatment

value: Control

tag: subject

value: Subject 1


title: T47D_MPA_rep3

source_name: T47D breast cancer cells, 10nM medroxyprogesterone acetate treated 16h, rep 3

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM medroxyprogesterone acetate for 16h. Replicate 3
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: Myoblasts Subject2 Control

description: Primary proliferating myoblasts isolated from Vastus lateralis muscle treated with vehicle for 24h. Cells isolated from Subject 2

source_name: Primary proliferating myoblasts, Subject 2, Control

value: Subject 2


title: ZR751_E2s_P_rep2

data_processing: Data was normalised using rank variant normalisation in bead studio. For publication, this data was then normalised using variance stabilisation normalisation, corrected with ComBat, filtered to likely expressed transcripts and then subjected to linear model fitting as implemented in the bioconductor Limma package in R.

growth_protocol: Cells were sourced from ATCC and used at passage 16. Cells were grown in RPMI 1640 (Life Technologies) supplemented with 10% FBS (Sigma-Aldrich)

treatment_protocol: Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 (Life Technologies) supplemented with 10% dextran charcoal stripped FBS (Sigma-Aldrich), and treated with 10nM E2 where indicated (E2L). Cells were subsequently treated for 16h with the nominated hormone(s).

value: breast cancer cells

tag: treatment group

value: 16h 10nM estradiol cotreated with 16h 10nM progesterone


title: ZR751_EpM_16hr_rep1

description: RNA isolation with Qiagen Rneasy kit + Dnase digestion

hyb_protocol: Standard Affymetrix hybridisation protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Raw data was processed in R using bioconductor and Limma. Array data was normalized using RMA

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM medroxyprogesterone acetate for 16hrs. Replicate 1.

label_protocol: Biotinylated cDNA was prepared from 300ng RNA according to standard Affymetrix protocols

growth_protocol: Cells were routinely passaged in RPMI1640 supplemented with 10% FBS. ZR-75-1 cells (passage 16; ATCC) were plated at 500,000 cells/well in 6 well plates in phenol red free RPMI1640 (Life Technologies) supplemented with 10% dextran-charcoal stripped FBS (Hyclone) and treated with hormones as described for each sample. RNA extracted at the timepoints indicated, DNAse treated on column using Qiagen RNeasy kit. An aliquot of each sample was used to synthesise cDNA to validate treatment effects. RNA quality was assessed for each sample via bioanalyser, with an average RIN of  9.6 (range 8.8 to 9.9).

extract_protocol: Extraction was performed using Qiagen Rneasy kit and on-column Dnase digestion according to manufacturer's instructions.

treatment_protocol: Cells were treated using an overlay method involving treatment with 10X concetrated hormone mixture at 1:10 of the cell culture volume, followed by gentle swirling. Treatment times were staggered, and the RNA was isolated as a batch at the culmination of the experiment.

value: breast cancer

tag: biosample number

tag: bioproject id

tag: time


title: Myoblasts Subject1 Vitamin D

description: Primary proliferating myoblasts isolated from Vastus lateralis muscle treated with Vitamin D for 24h. Cells isolated from Subject 1

source_name: Primary proliferating myoblasts, Subject 1, Vitamin D

value: Vitamin D


title: ZR751_EpEP_16hr_rep3

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM estrogen plus 10nM progesterone for 16hrs. Replicate 3.


title: ZR751_E2s_MPA_rep1

value: 16h 10nM estradiol cotreated with 16h 10nM medroxyprogesterone acetate


title: T47D_MPA_rep1

source_name: T47D breast cancer cells, 10nM medroxyprogesterone acetate treated 16h, rep 1

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM medroxyprogesterone acetate for 16h. Replicate 1
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: T47D_PROG_rep1

source_name: T47D breast cancer cells, 10nM progesterone treated 16h, rep 1

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM progesterone for 16h. Replicate 1
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: T47D_PROG_rep2

source_name: T47D breast cancer cells, 10nM progesterone treated 16h, rep 2

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM progesterone for 16h. Replicate 2
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: ZR751_EpEP_16hr_rep1

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM estrogen plus 10nM progesterone for 16hrs. Replicate 1.


title: ZR751_EpEP_16hr_rep4

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM estrogen plus 10nM progesterone for 16hrs. Replicate 4.


title: ZR751_EpEP_16hr_rep2

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM estrogen plus 10nM progesterone for 16hrs. Replicate 2.


title: ZR751_EpEM_16hr_rep2

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM estrogen plus 10nM medroxyprogesterone acetate for 16hrs. Replicate 2.


title: ZR751_E2s_DHT_rep4

value: 16h 10nM estradiol cotreated with 16h 10nM dihydrotestosterone


title: ZR751_EpEM_16hr_rep1

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM estrogen plus 10nM medroxyprogesterone acetate for 16hrs. Replicate 1.


title: T47D_E2_rep2

source_name: T47D breast cancer cells, 10nM estradiol treated 16h, rep2

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM estradiol for 16h. Replicate 2
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: ZR751_EpEM_16hr_rep3

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM estrogen plus 10nM medroxyprogesterone acetate for 16hrs. Replicate 3.


title: T47D_DHT_rep3

source_name: T47D breast cancer cells, 10nM dihydrotestosterone treated 16h, rep3

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM dihydrotestosterone for 16h. Replicate 3
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: T47D_DHT_rep2

source_name: T47D breast cancer cells, 10nM dihydrotestosterone treated 16h, rep2

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM dihydrotestosterone for 16h. Replicate 2
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: T47D_E2_rep3

source_name: T47D breast cancer cells, 10nM estradiol treated 16h, rep3

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM estradiol for 16h. Replicate 3
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: T47D_DHT_rep1

source_name: T47D breast cancer cells, 10nM dihydrotestosterone treated 16h, rep1

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM dihydrotestosterone for 16h. Replicate 1
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: ZR751_EpE_16hr_rep1

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM estrogen for 16hrs. Replicate 1.


title: ZR751_EpE_16hr_rep2

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM estrogen for 16hrs. Replicate 2.


title: T47D_E2_rep1

source_name: T47D breast cancer cells, 10nM estradiol treated 16h, rep1

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM estradiol for 16h. Replicate 1
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: ZR751_EpE_16hr_rep3

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM estrogen for 16hrs. Replicate 3.


title: ZR751_EpVC_0hr_rep3

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 1:1000 EtOH for 0hrs. Replicate 3.


title: T47D_VC_rep3

source_name: T47D breast cancer cells, VC treated 16h, rep3

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 1 part per million vehicle control (VC; ethanol) for 16h. Replicate 3
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: T47D_VC_rep2

source_name: T47D breast cancer cells, VC treated 16h, rep2

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 1 part per million vehicle control (VC; ethanol) for 16h. Replicate 2
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: T47D_VC_rep1

source_name: T47D breast cancer cells, VC treated 16h, rep1

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 1 part per million vehicle control (VC; ethanol) for 16h. Replicate 1
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: ZR751_EpVC_0hr_rep2

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 1:1000 EtOH for 0hrs. Replicate 2.


title: ZR751_EpVC_0hr_rep1

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 1:1000 EtOH for 0hrs. Replicate 1.


title: 57_12w_2

status: Public on Oct 17 2015

city: Tsurumi-ku,

first: Michie

last: Kobayashi

state: Yokohama

address: 1-1-43, Suehirocho,

country: Japan

institute: DNA Chip Research Inc.

description: Gene expression profile in the peripheral blood after Placebo intake.

hyb_protocol: Agilent one-color gene expression hyb/wash protocol.

scan_protocol: Microarrays were scanned using a G2505C DNA Microarray Scanner.

data_processing: The images were converted to numerical values by Feature Extraction Software ver. 10.7.3.1. Data analysis used GeneSpring GX v11.5 (Agilent Technologies) with which inter-array normalization was done using the 75th percentile.

source_name: Peripheral Blood, 12 week

label_protocol: Cyanine 3-labeled cRNA was prepared from 100 ng total RNA using the Low Input Quick Amp Labeling Kit according to the manufacturer’s protocol.

extract_protocol: The stored tube was used for total RNA extraction with the PAXgene Blood miRNA Kit (QIAGEN, City, CA, USA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: A peripheral blood sample was collected in a PAXgene blood RNA tube (BD, City, NJ, USA), left at room temperature for 2 hours after sufficient mixing, and then stored at −20℃.

value: whole blood

tag: gender

value: male

tag: time point

value: after intake

value: Placebo


title: 8_0w_1

description: Gene expression profile in the peripheral blood before Placebo intake.

source_name: Peripheral Blood, 0 week

value: before intake


title: 60_12w_1


title: 8_12w_1


title: 9_12w_1

description: Gene expression profile in the peripheral blood after Chlorella intake.

value: Chlorella


title: 58_0w_1

description: Gene expression profile in the peripheral blood before Chlorella intake.


title: 59_0w_1


title: 6_12w_1


title: 7_0w_1


title: 59_12w_1


title: 58_12w_1


title: 9_0w_1


title: 7_12w_1


title: 6_0w_1


title: 57_0w_1


title: 56_12w_1


title: 60_0w_1


title: 56_0w_1


title: 55_12w_1


title: 54_12w_1


title: 55_0w_1


title: 53_0w_1


title: 53_12w_1


title: 54_0w_1


title: 52_12w_1


title: ZR751_VC_rep1

value: 16h eqivalent vehicle (ethanol; 2 parts per million)


title: 52_0w_1


title: 51_0w_1


title: 48_0w_1


title: 49_12w_1


title: 46_12w_1


title: 50_12w_2


title: 46_0w_1


title: 5_12w_1


title: 47_12w_1


title: 50_0w_1


title: 49_0w_1


title: 47_0w_1


title: 5_0w_1


title: 45_12w_2


title: 51_12w_2


title: 48_12w_1


title: 45_0w_1


title: 44_0w_2


title: 44_12w_1


title: 43_12w_1


title: 42_12w_1


title: 43_0w_1


title: 42_0w_2


title: Rh_Ileum_12D-7.4 Gy_2

city: Houston

first: David

middle: S

last: Loose

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharm

country: USA

institute: University of Texas

description: US23502373_252680610574_S01_GE1_1100_Jul11_1_4_sample 72

hyb_protocol: Hybridization was done at 65C overnight per Agilent's protocol

scan_protocol: Scaning was done with on a Agilent Technologies Scanner G2505C

data_processing: Raw data was imported into Genespring GX13

organism: Macaca mulatta

source_name: Total RNA Ileum

label_protocol: RNA was labeled with Cy3 following Agilent's low-input quick amp labeling one color protocol

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted with the use of RNeasy microarray tissue mini kits (Qiagen, Germantown, MD) and cleaned by TURBO DNase (Life Technologies/Thermo Fisher Scientific, Grand Island, NY).

treatment_protocol: Animals received 6.7 or 7.4 Gy of total body irradiation and were killed after 4, 7, or 21 days. Approximately 3 cm of ileum was removed and RNA extracted.

tag: day

tag: dose


title: 41_0w_1


title: Rh_Ileum_12D-6.7 Gy_2

description: US23502373_252680610572_S01_GE1_1100_Jul11_1_4_sample 70


title: Rh_Ileum_12D-6.7 Gy_1

description: US23502373_252680610571_S01_GE1_1100_Jul11_1_4_sample 69


title: Rh_Ileum_12D-7.4 Gy_1

description: US23502373_252680610573_S01_GE1_1100_Jul11_1_4_sample 71


title: 4_12w_2


title: 41_12w_1


title: Rh_Ileum_7D-7.4 Gy_3

description: US23502373_252680610556_S01_GE1_1100_Jul11_1_4_sample 67


title: 40_0w_2


title: Rh_Ileum_7D-7.4 Gy_4

description: US23502373_252680610557_S01_GE1_1100_Jul11_1_4_sample 68


title: Rh_Ileum_7D-7.4 Gy_2

description: US23502373_252680610574_S01_GE1_1100_Jul11_1_3_sample 66


title: Rh_Ileum_7D-6.7 Gy_4

description: US23502373_252680610572_S01_GE1_1100_Jul11_1_3_sample 64


title: 40_12w_1


title: 38_12w_1


title: Rh_Ileum_7D-6.7 Gy_3

description: US23502373_252680610571_S01_GE1_1100_Jul11_1_3_sample 63


title: Rh_Ileum_7D-6.7 Gy_2

description: US23502373_252680610557_S01_GE1_1100_Jul11_1_3_sample 62


title: 4_0w_1


title: 39_0w_1


title: Rh_Ileum_4D-7.4 Gy_4

description: US23502373_252680610574_S01_GE1_1100_Jul11_1_2_sample 60


title: Rh_Ileum_7D-7.4 Gy_1

description: US23502373_252680610573_S01_GE1_1100_Jul11_1_3_sample 65


title: 37_0w_1


title: 38_0w_1


title: 37_12w_2


title: 39_12w_1


title: Rh_Ileum_4D-7.4 Gy_3

description: US23502373_252680610573_S01_GE1_1100_Jul11_1_2_sample 59


title: 35_12w_1


title: Rh_Ileum_4D-7.4 Gy_1

description: US23502373_252680610571_S01_GE1_1100_Jul11_1_2_sample 57


title: Rh_Ileum_4D-7.4 Gy_2

description: US23502373_252680610572_S01_GE1_1100_Jul11_1_2_sample 58


title: Rh_Ileum_7D-6.7 Gy_1

description: US23502373_252680610556_S01_GE1_1100_Jul11_1_3_sample 61


title: Rh_Ileum_4D-6.7 Gy_4

description: US23502373_252680610557_S01_GE1_1100_Jul11_1_2_sample 56


title: 36_12w_1

description: Gene expression profile in the peripheral blood after Placebo intake.


title: 36_0w_2

description: Gene expression profile in the peripheral blood before Placebo intake.


title: 34_12w_1

description: Gene expression profile in the peripheral blood after Chlorella intake.


title: Rh_Ileum_4D-CONTROL_4

description: US23502373_252680610572_S01_GE1_1100_Jul11_1_1_sample 52


title: Rh_Ileum_4D-6.7 Gy_3

description: US23502373_252680610556_S01_GE1_1100_Jul11_1_2_sample 55


title: 35_0w_1

description: Gene expression profile in the peripheral blood before Chlorella intake.


title: Rh_Ileum_4D-6.7 Gy_2

description: US23502373_252680610574_S01_GE1_1100_Jul11_1_1_sample 54


title: Rh_Ileum_4D-CONTROL_1

description: US23502373_252680610556_S01_GE1_1100_Jul11_1_1_sample 49


title: 34_0w_1


title: Rh_Ileum_4D-6.7 Gy_1

description: US23502373_252680610573_S01_GE1_1100_Jul11_1_1_sample 53


title: Rh_Ileum_4D-CONTROL_2

description: US23502373_252680610557_S01_GE1_1100_Jul11_1_1_sample 50


title: 19_WholeBlood_KO LRRK2

city: New York

first: Maria

middle: D

last: Chikina

state: NY

address: One Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
19

hyb_protocol: Reporter and Capture probes against markers of interest were prepared as previously described by Geiss et al. (2008; PMID: 18278033). Data were collected and analyzed using the nCounter Digital Analyzer.

scan_protocol: not provided

data_processing: Using NanoString spike control data, a generalized linear model was fitted with 8 negative and 6 positive spike controls, where the counts for each control followed a Poisson distribution with the mean modeled as a linear function of concentration. Each sample was then normalized to the median slope and intercept of all samples. The median background value, median intercept from the fit of the generalized linear model above, was added to the data before they were log2 transformed. Using the transformed data of all genes, a Bland-Altman plot (or an MA plot without the log2 transformation) was done for each sample to compare the sample and the average of all samples. A loess curve was fitted for each Bland-Altman plot to globally normalize the transformed data. A marker whose 95 percentile value over all the samples was below the 95 percentile value of the negative spike controls was deemed undetectable and removed. Outliers were detected by reducing to 3 dimensions via principal component analysis (PCA) and calculating the probability (using a chisq distribution) of the observed sample mahalanobis distances to the center. No outliers were detected in the mouse dataset.

label: Biotin & color-coded tag

organism: Mus musculus

source_name: Whole blood

label_protocol: Using 100 ng total RNA, mRNA levels were assayed by direct digital detection following the manufacturer’s guidelines (NanoString Technologies, Seattle, WA). The marker panel was selected for suspected biological relevance to neurodegenerative diseases and mostly low coefficient of variation (CV below 70%) in blood-based expression profiles of healthy control-reference datasets available in the public domain.

growth_protocol: N=5 male mice were used in each of four groups: wild-type controls (WTC), transgenic over-expressing either wild-type LRRK2 (LRRK2-WT) or G2019S LRRK2 (LRRK2-GS), and LRRK2 null mutant (knockout; KO). Transgenic LRRK2 models were previously developed using bacterial artificial chromosome (BAC)-mediated transgenesis and characterized (Li et al., 2010; PMID: 20130188). LRRK2 knockout mice were kindly provided by Dr. Huaibin Cai (Lin et al., 2009; PMID: 20064389).

extract_protocol: Mouse blood samples were collected via heart puncture method. Total RNA was immediately isolated using the QIAamp RNA Blood Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations.

tag: lrrk2 genotype

value: KO


title: 18_WholeBlood_KO LRRK2

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
18


title: 16_WholeBlood_KO LRRK2

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
16


title: 17_WholeBlood_KO LRRK2

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
17


title: 20_WholeBlood_KO LRRK2

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
20


title: 15_WholeBlood_Tg_LRRK2-GS

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
15

value: Transgenic GA (G2019S)


title: 33_12w_1


title: Rh_Ileum_4D-CONTROL_3

description: US23502373_252680610571_S01_GE1_1100_Jul11_1_1_sample 51


title: 30_12w_2


title: 14_WholeBlood_Tg_LRRK2-GS

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
14


title: 32_0w_1


title: Rh_Colon_12D-6.7 Gy_1

description: US23502373_252680610550_S01_GE1_1100_Jul11_1_4_sample 45

data_processing: Raw data was imported into Genespring v

source_name: Total RNA Colon

treatment_protocol: Animals received 6.7 or 7.4 Gy of total body irradiation and were killed after 4, 7, or 21 days. Approximately 3 cm of colon was removed and RNA extracted.


title: 31_12w_1

description: Gene expression profile in the peripheral blood after Placebo intake.


title: 13_WholeBlood_Tg_LRRK2-GS

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
13


title: 33_0w_1

description: Gene expression profile in the peripheral blood before Placebo intake.


title: 12_WholeBlood_Tg_LRRK2-GS

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
12


title: Rh_Colon_12D-7.4 Gy_2

description: US23502373_252680610555_S01_GE1_1100_Jul11_1_4_sample 48


title: 32_12w_1

description: Gene expression profile in the peripheral blood after Chlorella intake.


title: 31_0w_1


title: Rh_Colon_12D-6.7 Gy_2

description: US23502373_252680610551_S01_GE1_1100_Jul11_1_4_sample 46


title: 11_WholeBlood_Tg_LRRK2-GS

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
11


title: 10_WholeBlood_Tg_LRRK2-WT

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
10

value: Transgenic GG (WT)


title: 9_WholeBlood_Tg_LRRK2-WT

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
9


title: Rh_Colon_7D-7.4 Gy_4

description: US23502373_252680610546_S01_GE1_1100_Jul11_1_4_sample 44


title: Rh_Colon_12D-7.4 Gy_1

description: US23502373_252680610554_S01_GE1_1100_Jul11_1_4_sample 47


title: 30_0w_1

description: Gene expression profile in the peripheral blood before Chlorella intake.


title: Rh_Colon_7D-7.4 Gy_3

description: US23502373_252680610545_S01_GE1_1100_Jul11_1_4_sample 43


title: 3_12w_1


title: 7_WholeBlood_Tg_LRRK2-WT

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
7


title: 8_WholeBlood_Tg_LRRK2-WT

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
8


title: Rh_Colon_7D-7.4 Gy_2

description: US23502373_252680610555_S01_GE1_1100_Jul11_1_3_sample 42


title: 6_WholeBlood_Tg_LRRK2-WT

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
6


title: 5_WholeBlood_WT_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
5

value: GG (WT)


title: 4_WholeBlood_WT_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
4


title: Rh_Colon_7D-7.4 Gy_1

description: US23502373_252680610554_S01_GE1_1100_Jul11_1_3_sample 41


title: 29_0w_1


title: 3_0w_1

description: Gene expression profile in the peripheral blood before Placebo intake.


title: 3_WholeBlood_WT_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
3


title: 1_WholeBlood_WT_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
1


title: 94_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
94

data_processing: Using NanoString spike control data, a generalized linear model was fitted with 8 negative and 6 positive spike controls, where the counts for each control followed a Poisson distribution with the mean modeled as a linear function of concentration. Each sample was then normalized to the median slope and intercept of all samples. The median background value, median intercept from the fit of the generalized linear model above, was added to the data before they were log2 transformed. Using the transformed data of all genes, a Bland-Altman plot (or an MA plot without the log2 transformation) was done for each sample to compare the sample and the average of all samples. A loess curve was fitted for each Bland-Altman plot to globally normalize the transformed data. A marker whose 95 percentile value over all the samples was below the 95 percentile value of the negative spike controls was deemed undetectable and removed. Six markers were removed by this criteria in the human dataset. Outliers were detected by reducing to 3 dimensions via principal component analysis (PCA) and calculating the probability (using a chisq distribution) of the observed sample mahalanobis distances to the center. One sample in the human dataset was a clear outlier, with the remaining p-values following a uniform distribution, and was removed from further analysis.

extract_protocol: Human venous blood was collected in PAXgene® blood RNA tubes (Beckton Dickinson, Franklin Lakes, NJ), and stored at -80°C until RNA isolation. Total RNA was extracted using the PAXgene® blood miRNA kit, following the manufacturer’s instructions (Qiagen).

tag: disease status

value: PD

tag: proband status

value: F

tag: personal status

value: Patient

tag: age at blood draw

tag: age at onset

tag: l-dopa dose (mg)

tag: updrs motor score


title: 29_12w_1

description: Gene expression profile in the peripheral blood after Chlorella intake.

tag: tissue

tag: treatment


title: 2_WholeBlood_WT_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
2


title: 28_12w_1


title: Rh_Colon_7D-6.7 Gy_4

description: US23502373_252680610551_S01_GE1_1100_Jul11_1_3_sample 40


title: Rh_Colon_7D-6.7 Gy_3

description: US23502373_252680610550_S01_GE1_1100_Jul11_1_3_sample 39


title: Rh_Colon_7D-6.7 Gy_1

description: US23502373_252680610545_S01_GE1_1100_Jul11_1_3_sample 37


title: 92_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
92


title: 27_0w_1


title: 91_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
91

value: M


title: 28_0w_1

description: Gene expression profile in the peripheral blood before Chlorella intake.


title: 27_12w_2

description: Gene expression profile in the peripheral blood after Placebo intake.


title: Rh_Colon_7D-6.7 Gy_2

description: US23502373_252680610546_S01_GE1_1100_Jul11_1_3_sample 38


title: 89_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
89


title: Rh_Colon_4D-7.4 Gy_4

description: US23502373_252680610555_S01_GE1_1100_Jul11_1_2_sample 36


title: 87_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
87

value: healthy

value: Spouse


title: 88_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
88

value: whole blood


title: 85_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
85

value: unknown


title: 26_12w_1

value: male

value: after intake


title: 84_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
84


title: 90_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
90


title: 83_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
83


title: 81_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
81


title: 80_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
80


title: 93_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
93


title: Rh_Colon_4D-7.4 Gy_2

description: US23502373_252680610551_S01_GE1_1100_Jul11_1_2_sample 34


title: 71_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
71

value: First degree


title: 77_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
77


title: 25_12w_1

description: Gene expression profile in the peripheral blood after Chlorella intake.

value: Chlorella


title: 69_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
69


title: Rh_Colon_4D-7.4 Gy_3

description: US23502373_252680610554_S01_GE1_1100_Jul11_1_2_sample 35


title: 68_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
68


title: Rh_Colon_4D-7.4 Gy_1

description: US23502373_252680610550_S01_GE1_1100_Jul11_1_2_sample 33


title: 26_0w_1

description: Gene expression profile in the peripheral blood before Placebo intake.

value: before intake

value: Placebo


title: 66_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
66


title: 24_12w_1

description: Gene expression profile in the peripheral blood after Placebo intake.


title: Rh_Colon_4D-6.7 Gy_4

description: US23502373_252680610546_S01_GE1_1100_Jul11_1_2_sample 32


title: Rh_Colon_4D-6.7 Gy_3

description: US23502373_252680610545_S01_GE1_1100_Jul11_1_2_sample 31


title: 61_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
61


title: 60_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
60


title: 24_0w_1


title: 67_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
67


title: 59_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
59


title: Rh_Colon_4D-CONTROL_4

description: US23502373_252680610551_S01_GE1_1100_Jul11_1_1_sample 28


title: Rh_Colon_4D-6.7 Gy_2

description: US23502373_252680610555_S01_GE1_1100_Jul11_1_1_sample 30


title: 56_WholeBlood_Ctrl

description:
No clinical data
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
56

value: Not available


title: 54_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
54


title: 57_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
57


title: 25_0w_1

description: Gene expression profile in the peripheral blood before Chlorella intake.


title: 23_0w_1


title: 22_12w_1

description: Gene expression profile in the peripheral blood after Chlorella intake.


title: 22_0w_1


title: Rh_Colon_4D-CONTROL_3

description: US23502373_252680610550_S01_GE1_1100_Jul11_1_1_sample 27


title: 23_12w_1


title: 53_WholeBlood_PD

description:
No clinical data
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
53


title: 21_12w_1


title: Rh_Jejunum_12D-7.4 Gy_2

description: US23502373_252680610544_S01_GE1_1100_Jul11_1_4_sample 24

data_processing: Raw data was imported into Genespring 13GX

source_name: Total RNA jejunum

treatment_protocol: Animals received 6.7 or 7.4 Gy of total body irradiation and were killed after 4, 7, or 21 days. Approximately 3 cm of jejunum was removed and RNA extracted.


title: Rh_Colon_4D-CONTROL_2

description: US23502373_252680610546_S01_GE1_1100_Jul11_1_1_sample 26


title: 52_WholeBlood_Ctrl

description:
No clinical data
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
52


title: Rh_Colon_4D-6.7 Gy_1

description: US23502373_252680610554_S01_GE1_1100_Jul11_1_1_sample 29


title: 44_WholeBlood_Ctrl

description:
No clinical data
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
44

value: First degree of affected non-proband


title: 21_0w_1


title: 43_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
43


title: 20_12w_1


title: Rh_Jejunum_12D-7.4 Gy_1

description: US23502373_252680610543_S01_GE1_1100_Jul11_1_4_sample 23


title: Rh_Jejunum_12D-6.7 Gy_2

description: US23502373_252680610542_S01_GE1_1100_Jul11_1_4_sample 22


title: 20_0w_2


title: Rh_Colon_4D-CONTROL_1

description: US23502373_252680610545_S01_GE1_1100_Jul11_1_1_sample 25


title: 39_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
39


title: 38_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
38


title: Rh_Jejunum_12D-6.7 Gy_1

description: US23502373_252680610541_S01_GE1_1100_Jul11_1_4_sample 21


title: 35_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
35

value: GG (WT)


title: 34_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
34


title: 41_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
41


title: 33_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
33


title: 31_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
31


title: 30_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
30


title: 40_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
40

value: PD


title: 29_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
29

value: F


title: Rh_Jejunum_7D-7.4 Gy_3

description: US23502373_252680610539_S01_GE1_1100_Jul11_1_4_sample 19


title: Rh_Jejunum_7D-7.4 Gy_2

description: US23502373_252680610544_S01_GE1_1100_Jul11_1_3_sample 18


title: 2_12w_1

description: Gene expression profile in the peripheral blood after Chlorella intake.


title: 37_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
37

value: Patient


title: 19_0w_1

description: Gene expression profile in the peripheral blood before Chlorella intake.


title: 27_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
27

value: M


title: 36_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
36


title: 28_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
28

value: First degree, affected with tremor


title: 58_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
58


title: 26_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
26


title: 25_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
25


title: 2_0w_1


title: Rh_Jejunum_7D-6.7 Gy_4

description: US23502373_252680610542_S01_GE1_1100_Jul11_1_3_sample 16


title: 19_12w_1


title: 18_12w_1

description: Gene expression profile in the peripheral blood after Placebo intake.


title: 23_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
23


title: Rh_Jejunum_7D-6.7 Gy_3

description: US23502373_252680610541_S01_GE1_1100_Jul11_1_3_sample 15


title: 15_0w_1

description: Gene expression profile in the peripheral blood before Placebo intake.


title: Rh_Jejunum_7D-7.4 Gy_4

description: US23502373_252680610540_S01_GE1_1100_Jul11_1_4_sample 20


title: 21_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
21


title: Rh_Jejunum_7D-6.7 Gy_2

description: US23502373_252680610540_S01_GE1_1100_Jul11_1_3_sample 14


title: Rh_Jejunum_7D-7.4 Gy_1

description: US23502373_252680610543_S01_GE1_1100_Jul11_1_3_sample 17


title: 19_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
19


title: 20_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
20

value: healthy


title: 18_0w_1

value: whole blood


title: 17_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
17


title: 15_12w_1


title: 14_12w_1


title: 15_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
15


title: 16_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
16


title: 24_WholeBlood_Ctrl

description:
No clinical data
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
24

value: Affected non carrier, non-first degree relative


title: 13_12w_1

description: Gene expression profile in the peripheral blood after Chlorella intake.

value: male


title: 14_0w_1


title: 14_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
14


title: 13_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
13

value: unknown


title: Rh_Jejunum_4D-7.4 Gy_4

description: US23502373_252680610544_S01_GE1_1100_Jul11_1_2_sample 12


title: 13_0w_1

description: Gene expression profile in the peripheral blood before Chlorella intake.


title: 12_12w_1

description: Gene expression profile in the peripheral blood after Placebo intake.

value: after intake


title: Rh_Jejunum_4D-7.4 Gy_3

description: US23502373_252680610543_S01_GE1_1100_Jul11_1_2_sample 11


title: Rh_Jejunum_7D-6.7 Gy_1

description: US23502373_252680610539_S01_GE1_1100_Jul11_1_3_sample 13


title: Rh_Jejunum_4D-7.4 Gy_2

description: US23502373_252680610542_S01_GE1_1100_Jul11_1_2_sample 10


title: Rh_Jejunum_4D-7.4 Gy_1

description: US23502373_252680610541_S01_GE1_1100_Jul11_1_2_sample 9


title: 12_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
12

value: Unaffected non-first degree relative


title: 11_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
11

value: First degree


title: 10_WholeBlood_PD

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
10


title: 9_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
9


title: 12_0w_1

description: Gene expression profile in the peripheral blood before Placebo intake.

value: before intake

value: Placebo


title: 7_WholeBlood_Ctrl

description:
No clinical data
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
7

value: Spouse

value: Not available


title: 6_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
6


title: 5_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
5

value: GG (WT)


title: Rh_Jejunum_4D-6.7 Gy_4

description: US23502373_252680610540_S01_GE1_1100_Jul11_1_2_sample 8


title: 11_12w_1

description: Gene expression profile in the peripheral blood after Chlorella intake.

value: Chlorella


title: Rh_Jejunum_4D-6.7 Gy_2

description: US23502373_252680610544_S01_GE1_1100_Jul11_1_1_sample 6


title: 1_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
1

value: F

value: N/A (Not Applicable)


title: Rh_Jejunum_4D-CONTROL_4

description: US23502373_252680610542_S01_GE1_1100_Jul11_1_1_sample 4


title: 10_0w_1

description: Gene expression profile in the peripheral blood before Chlorella intake.


title: Rh_Jejunum_4D-6.7 Gy_1

description: US23502373_252680610543_S01_GE1_1100_Jul11_1_1_sample 5


title: 3_WholeBlood_Ctrl

description:
No clinical data
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
3

value: M


title: 10_12w_1


title: Rh_Jejunum_4D-CONTROL_2

description: US23502373_252680610540_S01_GE1_1100_Jul11_1_1_sample 2


title: SciaticNerve_14day_rep3

city: Tianjin China

first: Bin

last: Pan

address: 154 Anshan Road, Heping District, Tianjin, People's Republic of China

country: China

institute: Orthopedics Department of General Hospital, Tianjin Medical University

description:
14_3SciaticNerve
lncrna expression in the distal end of the crushed sciatic nerve after 14 day

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing:
Data were extracted with Feature Extraction software10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
The default normalization scheme for Agilent one-color exon data in the GeneSpring GX 11.5 (or later) program is 75th percentile scaling.

source_name: sciatic nerve_14 day after injury

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Mice was anaesthetized by intraperitoneal injection of chloral hydrate, a proper incision was made into its right lateral thigh to expose and lift the sciatic nerve.  The right sciatic nerve crush were performed at the upper thigh level using acute naculum.The nerve was compressed for 30s to ensure that it was transparent so that axon was disconnected while epineurium was integral. Then a ligation on crush site was served as a marker. And the incision sites were then closed.The distal segments of crushed sciatic nerves (0.5cm) were isolated and harvested from mice of each group at 0, 3, 7, 14d post-surgery respectively.

tag: strain

tag: age

value: ~2 months

tag: tissure

value: sciatic nerve

tag: time after peripheral nerve injury

value: 14 day


title: SciaticNerve_14day_rep2

description:
14_2SciaticNerve
lncrna expression in the distal end of the crushed sciatic nerve after 14 day


title: SciaticNerve_14day_rep1

description:
14_1SciaticNerve
lncrna expression in the distal end of the crushed sciatic nerve after 14 day


title: Maize_TC208cytoline_cytTC316_rep2

city: Cluj-Napoca

first: Simona

last: Visan

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute “Prof Dr. Ion Chiricuta”,

hyb_protocol: The probes were hybridized on Agilent maize custom arrays 4X180k. Hybridization was carried out for 17 hours at 65°C, followed by washing. In addition, to avoid the ozone effects on Cy-3 signal, a supplementary organic solvent containing an ozone scavenging compound dissolved in acetonitrile was used after washing step.

scan_protocol: The slides were scanned on Agilent Microarray Scanner (G2565CA) at 2 µm

data_processing: The scanned images were analyzed with Feature Extraction Software v.11 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 062494_D_F_20131129) to obtain median signal intensities. Data processing were done in R.Control features as well as saturated and non-uniformed features were removed. Data were normalized using quantile method.

organism: Zea mays subsp. mays

source_name: maize, TC208 nucleus in TC316 cytoplasm, replicate 2

label_protocol: Cy-3 labeled microarray probes (cRNA-Cy3) were synthesized from 200 ng of total RNA using one-color Low Input Quick Amp Labeling Kit, according to Agilent manufacturer’s protocol. The quality of synthesized cRNAs was checked with Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies) considering a minimal yield of 1.65 μg and a specific activity of more than 6 pmol/μl Cy3/μg cRNA.

growth_protocol: The plants were grown in the green house for nine days and were used for RNA extraction afterwards

extract_protocol: Total RNA was isolated with TriReagent (Sigma-Aldrich) and purified with RNeasy Mini Kit (Qiagen) according to the manufacture's protocol. The quality of the total RNA was evaluated with Bioanalyzer 2100 (Agilent Technologies) based on RNA integrity number (RIN). All samples had the RIN greater than 8.

value: 9-days-old seedling

tag: donor type

value: cytoplasm donor


title: Rh_Jejunum_4D-6.7 Gy_3

description: US23502373_252680610539_S01_GE1_1100_Jul11_1_2_sample 7

tag: day


title: Maize_TC208cytoline_cytTC316_rep3

source_name: maize, TC208 nucleus in TC316 cytoplasm, replicate 3


title: Maize_TC208cytoline_cytW633_rep2

source_name: maize, TC208 nucleus in W633 cytoplasm, replicate 2


title: Rh_Jejunum_4D-CONTROL_1

description: US23502373_252680610539_S01_GE1_1100_Jul11_1_1_sample 1

tag: dose


title: SciaticNerve_7day_rep1

description:
7_1SciaticNerve
lncrna expression in the distal end of the crushed sciatic nerve after 7 day

source_name: sciatic nerve_7 day after injury

value: 7 day


title: Maize_TC208cytoline_cytW633_rep3

source_name: maize, TC208 nucleus in W633 cytoplasm, replicate 3


title: Maize_TC208_nucleus_donor_rep3

source_name: maize, nucleus donor, replicate 3

value: nucleus donor


title: SciaticNerve_3day_rep3

description:
3_3SciaticNerve
lncrna expression in the distal end of the crushed sciatic nerve after 3 day

source_name: sciatic nerve_3 day after injury

value: 3 day


title: SciaticNerve_7day_rep2

description:
7_2SciaticNerve
lncrna expression in the distal end of the crushed sciatic nerve after 7 day


title: Maize_TC208cytoline_cytTC316_rep1

source_name: maize, TC208 nucleus in TC316 cytoplasm, replicate 1


title: Rh_Jejunum_4D-CONTROL_3

description: US23502373_252680610541_S01_GE1_1100_Jul11_1_1_sample 3


title: Maize_TC208cytoline_cytW633_rep1

source_name: maize, TC208 nucleus in W633 cytoplasm, replicate 1


title: Maize_TC208_nucleus_donor_rep2

source_name: maize, nucleus donor, replicate 2


title: SciaticNerve_3day_rep2

description:
3_2SciaticNerve
lncrna expression in the distal end of the crushed sciatic nerve after 3 day


title: SciaticNerve_0day_rep3

description:
0_3SciaticNerve
lncrna expression in the distal end of the crushed sciatic nerve after 0 day

source_name: sciatic nerve_0 day after injury

value: 0 day


title: SciaticNerve_7day_rep3

description:
7_3SciaticNerve
lncrna expression in the distal end of the crushed sciatic nerve after 7 day


title: 11_0w_1

source_name: Peripheral Blood, 0 week

value: whole blood

tag: gender

value: male

tag: time point

value: before intake


title: FlowerBud_PedroXimenes_rep1

status: Public on Oct 16 2015

city: Logrono

first: Pablo

last: Carbonell-Bejerano

state: La Rioja

address: Madre de Dios, 51

department: Instituto de las Ciencias de la Vid y del Vino

country: Spain

institute: CSIC

description:
This sample is of Vitis vinifera cv. Pedro Ximenes flower buds collected just before anthesis on 2011/05/24 morning time. It is the first of three Pedro Ximenes replicates, each from a different plant.
PX-1

hyb_protocol: If the quality control was correct, then 4 µg of labelled cDNA were hybridized. Hybridization solution (NimbleGen Hybridization kit) was added to each labelled cDNA and hybridization was performed for 16 h at 42ºC in a HS 4 Hybridization station (NimbleGen-Roche).

scan_protocol: Hybridized microarrays were washed with Wash buffer kit (NimbleGen-Roche) and scanned at 532 nm and 2 µm resolution in a DNA Microarray Scanner with Surescan High-Resolution Technology (Agilent technologies).

data_processing: After evaluation of hybridization quality by Experimental metrics report implemented in NimbleScan Software version 2.6 (NimbleGen-Roche), probeset signal values from all the microarray hybridizations were background corrected and normalized together using Robust Microarray Average (RMA) (Irizarry et al., 2003) in NimbleScan Software, which produces a calls file for each sample with normalized expression data for each gene.

organism: Vitis vinifera

source_name: Vitis vinifera cv Pedro Ximenes flower buds collected just before anthesis

label_protocol: cDNA was synthesized from 10 µg of total RNA using cDNA Synthesis System Kit (NimbleGen-Roche). The cDNA preparation (1 µg) was amplified and labelled with Cy3-random nonamers using One color labeling kit (NimbleGen-Roche).

growth_protocol: Every CB and PX plants used (20-30 years old)were grafted in Richter-110 rootstocks, trellised in double cordon Royat system in the Grapevine Germplasm Collection of the Instituto de Ciencias de la Vid y del Vino (ICVV) (ESP-217) located at 'Finca Valdegón' (VALD, in Agoncillo, La Rioja, Spain).

extract_protocol: Total RNA was extracted from frozen CB and PX flower buds using the Spectrum Plant Total RNA kit (Sigma-Aldrich) with the manufacturer?s protocol. An in column DNase digestion step with the RNase-Free DNase Set (QIAGEN) was added

treatment_protocol: Three biological replicates of CB and PX 1 dba flowers were hybridized to NimbleGen microarrays. Inflorescences collected from different VALD plants on 24/05/2011 were used for each replicate.

tag: somatic variant

value: Pedro Ximenes

tag: fruit type

value: seeded

value: flower bud

tag: developmental stage

value: just before anthesis


title: FlowerBud_PedroXimenes_rep2

description:
This sample is of Vitis vinifera cv. Pedro Ximenes flower buds collected just before anthesis on 2011/05/24 morning time. It is the second of three Pedro Ximenes replicates, each from a different plant.
PX-2


title: FlowerBud_PedroXimenes_rep3

description:
This sample is of Vitis vinifera cv. Pedro Ximenes flower buds collected just before anthesis on 2011/05/24 morning time. It is the third of three Pedro Ximenes replicates, each from a different plant.
PX-3


title: SciaticNerve_0day_rep2

description:
0_2SciaticNerve
lncrna expression in the distal end of the crushed sciatic nerve after 0 day


title: FlowerBud_CorintoBianco_rep2

description:
This sample is of Vitis vinifera cv. Corinto Bianco flower buds collected just before anthesis on 2011/05/24 morning time. It is the second of three Corinto Bianco replicates, each from a different plant.
CB-2

source_name: Vitis vinifera cv Corinto Bianco flower buds collected just before anthesis

value: Corinto Bianco

value: parthenocarpic


title: Maize_TC208_nucleus_donor_rep1

source_name: maize, nucleus donor, replicate 1


title: FlowerBud_CorintoBianco_rep3

description:
This sample is of Vitis vinifera cv. Corinto Bianco flower buds collected just before anthesis on 2011/05/24 morning time. It is the third of three Corinto Bianco replicates, each from a different plant.
CB-3


title: SciaticNerve_3day_rep1

description:
3_1SciaticNerve
lncrna expression in the distal end of the crushed sciatic nerve after 3 day

value: ~2 months

value: sciatic nerve


title: FlowerBud_CorintoBianco_rep1

description:
This sample is of Vitis vinifera cv. Corinto Bianco flower buds collected just before anthesis on 2011/05/24 morning time. It is the first of three Corinto Bianco replicates, each from a different plant.
CB-1


title: SciaticNerve_0day_rep1

description:
0_1SciaticNerve
lncrna expression in the distal end of the crushed sciatic nerve after 0 day


title: LPS_0.025_2

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: THP-1 gene expression after 20 hrs treatment with 0.025 µg/mL LPS (in cRPMI supplemented with 0.5% DMSO).

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing. Hybridization was completed by Labcorp, Seattle, WA (previously called Covance).

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505C). Scanning was completed by Labcorp, Seattle, WA (previously called Covance).

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 10.7.3.1) and the GE1_107_Sep09 extraction protocol, all by Labcorp, Seattle, WA (previously called Covance). Data was then read into R (version 3.2.1)/Bioconductor (Biobase version 2.28.0), where it was background corrected and quantile normalized using the limma package (version 3.24.15).

source_name: THP-1, LPS, 0.025 µg/mL, replicate 2

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing. Labeling was completed by Labcorp, Seattle, WA (previously called Covance).

growth_protocol: THP-1 cells were cultured in complete RPMI (Invitrogen) supplemented with 10% heat-inactivated FBS (Hyclone).

extract_protocol: Total RNA was extracted according to manufacturer’s protocol using the RNeasy® Mini kit (QIAGEN).

treatment_protocol: Cells were differentiated in complete RPMI supplemented with 40nM PMA for 30 hrs. Cells were then treated for 20 hrs with complete RPMI  either supplemented with 0.5% (v/v) DMSO or or transfected with 2 µg/mL appropriate RNA.

tag: transfected

value: not transfected


title: IFNb_100_3

description: THP-1 gene expression after 20 hrs treatment with 100 IU/mL IFNβ (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, IFNb, 100 IU/mL, replicate 3


title: LPS_0.025_1

source_name: THP-1, LPS, 0.025 µg/mL, replicate 1


title: IFNb_100_2

source_name: THP-1, IFNb, 100 IU/mL, replicate 2


title: SeV_100_3

description: THP-1 gene expression after 20 hrs infection with 100 HAU/mL SeV (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, SeV, 100 HAU/mL, replicate 3


title: DMSO_2

description: THP-1 gene expression after 20 hrs mock treatment with cRPMI supplemented with 0.5% DMSO.

source_name: THP-1, 0.5% DMSO alone, replicate 2


title: IFNb_25_3

description: THP-1 gene expression after 20 hrs treatment with 25 IU/mL IFNβ (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, IFNb, 25 IU/mL, replicate 3


title: XRNA_1

description: THP-1 gene expression after 20 hours transfection with 2 µg/mL HCV XRNA using the TransIT®-mRNA Transfection kit (Mirus Bio LLC).

source_name: THP-1, HCV XRNA, 2 µg/mL, replicate 1

value: transfected with HCV XRNA


title: IFNb_25_1

source_name: THP-1, IFNb, 25 IU/mL, replicate 1


title: SeV_100_2

source_name: THP-1, SeV, 100 HAU/mL, replicate 2


title: SeV_25_3

description: THP-1 gene expression after 20 hrs infection with 25 HAU/mL SeV (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, SeV, 25 HAU/mL, replicate 3


title: LPS_0.25_2

description: THP-1 gene expression after 20 hrs treatment with 0.25 µg/mL LPS (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, LPS, 0.25 µg/mL, replicate 2


title: IFNb_100_1

source_name: THP-1, IFNb, 100 IU/mL, replicate 1


title: PUUC_2

description: THP-1 gene expression after 20 hours transfection with 2 µg/mL HCV pU/UC RNA using the TransIT®-mRNA Transfection kit (Mirus Bio LLC).

source_name: THP-1, HCV pU/UC, 2 µg/mL, replicate 2

value: transfected with HCV pU/UC RNA


title: SeV_100_1

source_name: THP-1, SeV, 100 HAU/mL, replicate 1


title: LPS_0.25_3

source_name: THP-1, LPS, 0.25 µg/mL, replicate 3


title: SeV_25_2

source_name: THP-1, SeV, 25 HAU/mL, replicate 2


title: XRNA_2

source_name: THP-1, HCV XRNA, 2 µg/mL, replicate 2


title: PUUC_1

source_name: THP-1, HCV pU/UC, 2 µg/mL, replicate 1


title: KIN1409_0.625_2

description: THP-1 gene expression after 20 hrs treatment with 0.625 µM KIN1409 (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, KIN1409, 0.625 µM, replicate 2


title: IFNb_25_2

source_name: THP-1, IFNb, 25 IU/mL, replicate 2


title: PUUC_3

source_name: THP-1, HCV pU/UC, 2 µg/mL, replicate 3


title: DMSO_1

source_name: THP-1, 0.5% DMSO alone, replicate 1


title: LPS_0.25_1

source_name: THP-1, LPS, 0.25 µg/mL, replicate 1


title: DMSO_3

source_name: THP-1, 0.5% DMSO alone, replicate 3


title: SeV_25_1

source_name: THP-1, SeV, 25 HAU/mL, replicate 1


title: KIN1409_0.625_3

source_name: THP-1, KIN1409, 0.625 µM, replicate 3


title: KIN1409_0.625_1

source_name: THP-1, KIN1409, 0.625 µM, replicate 1


title: KIN1409_2.5_2

description: THP-1 gene expression after 20 hrs treatment with 2.5 µM KIN1409 (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, KIN1409, 2.5 µM, replicate 2


title: 8_WholeBlood_Ctrl

description:
mRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
8

source_name: Whole blood

tag: disease status

value: healthy

tag: lrrk2 genotype

value: GG (WT)

tag: proband status

value: M

tag: personal status

value: First degree

tag: age at blood draw

tag: age at onset

tag: l-dopa dose (mg)


title: KIN1409_2.5_3

source_name: THP-1, KIN1409, 2.5 µM, replicate 3


title: KIN1409_2.5_1

source_name: THP-1, KIN1409, 2.5 µM, replicate 1


title: KIN1408_0.625_1

description: THP-1 gene expression after 20 hrs treatment with 0.625 µM KIN1408 (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, KIN1408, 0.625 µM, replicate 1


title: KIN1400_0.625_1

description: THP-1 gene expression after 20 hrs treatment with 0.625 µM KIN1400 (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, KIN1400, 0.625 µM, replicate 1


title: KIN1400_0.625_3

source_name: THP-1, KIN1400, 0.625 µM, replicate 3


title: KIN1408_2.5_2

description: THP-1 gene expression after 20 hrs treatment with 2.5 µM KIN1408 (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, KIN1408, 2.5 µM, replicate 2


title: KIN1400_0.625_2

source_name: THP-1, KIN1400, 0.625 µM, replicate 2


title: KIN1400_2.5_1

description: THP-1 gene expression after 20 hrs treatment with 2.5 µM KIN1400 (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, KIN1400, 2.5 µM, replicate 1


title: KIN1408_2.5_1

source_name: THP-1, KIN1408, 2.5 µM, replicate 1


title: KIN1408_2.5_3

source_name: THP-1, KIN1408, 2.5 µM, replicate 3


title: KIN1400_10_1

description: THP-1 gene expression after 20 hrs treatment with 10 µM KIN1400 (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, KIN1400, 10 µM, replicate 1


title: KIN1400_10_2

source_name: THP-1, KIN1400, 10 µM, replicate 2


title: XRNA_3

source_name: THP-1, HCV XRNA, 2 µg/mL, replicate 3


title: KIN1409_10_1

description: THP-1 gene expression after 20 hrs treatment with 10 µM KIN1409 (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, KIN1409, 10 µM, replicate 1


title: KIN1408_10_1

description: THP-1 gene expression after 20 hrs treatment with 10 µM KIN1408 (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, KIN1408, 10 µM, replicate 1


title: KIN1408_0.625_2

source_name: THP-1, KIN1408, 0.625 µM, replicate 2


title: KIN1400_2.5_2

source_name: THP-1, KIN1400, 2.5 µM, replicate 2


title: KIN1408_10_2

source_name: THP-1, KIN1408, 10 µM, replicate 2


title: TB12.3199_6_B

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Bead level data were pre-processed to remove spatial artifacts, log2 transformed and quantile normalized using the beadarray package in Bioconductor prior to analysis (Dunning et al, 2007). The ComBAT method (Johnson et al., 2007), as implemented in the sva Bioconductor package, was used address batch effects in the expression data.  Downstream analyses were restricted to 'perfect' probes only (Barbosa-Morais et al., 2010), and whenever a gene-centric analysis was required we chose the probe with the highest Inter-quartile range (IQR) to represent each gene. Probes (genes) were ranked by IQR values, and the 100 most variable probes across expression data were selected for clustering, based on k-means method (see Chalise et al. (2014) for a review on clustering methods), where each observation belongs to the cluster with the nearest mean that best describes that cluster. A linear modelling approach was used to estimate the expression of each probe in the five subtypes, and the set of matched benign samples. Differential expression statistics for the comparison of each subtype to benign were then generated following Bayes' shrinkage of variance (Smyth 2004).

source_name: tissue from robotic radical prostatectomy (RRP) surgery

label_protocol: cRNA was generated and biotin-labelled using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: N/A - surgical tissue samples

extract_protocol: Qiagen AllPrep, according to manufacturer's instructions.

treatment_protocol: Matched tumour and benign tissues were identified and prepared from RP surgical tissue as described in Warren et al. (2013).  The Prostate.  73:  194-202.

tag: individual

tag: primary biopsy gleason grade

tag: secondary biopsy gleason grade

tag: clinical stage

tag: psa nmol/ml

tag: pre op serum testosterone (nmol/l)

tag: serum testosterone on day of surgery nmol/l

tag: secondary surgical specimen pathological gleason grade

tag: tissue

value: benign tissue


title: TB12.2829_17_B

tag: surgical specimen pathological gleason grade


title: TB12.2888_11_B


title: TB12.2888_16_T

value: tumor


title: TB12.2945_20_T


title: TB12.2829_1_T


title: TB12.3085_13_B


title: TB12.2890_9_B


title: TB12.3199_7_T


title: TB12.2564_3_B


title: TB12.3085_10_T


title: TB12.2560_9_B


title: TB12.2560_17_T


title: TB12.2564_1_T


title: TB12.2269_7_T


title: TB12.0807_3_T


title: TB12.2269_12_B


title: TB12.0672_1_T


title: TB12.0672_12_B


title: TB12.0445_1_B


title: TB11.1315_2_T


title: TB11.1450_3_T


title: TB11.2080_11_B


title: TB11.1634_16_B


title: HCT116 TP53 knockout treated with miRNA 3189, rep1

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R.

source_name: HCT116 TP53 knockout, miR-3189 mimic

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: HCT116 p53KO cells were cultured in DMEM with 10% FBS, at 37oC, 5% CO2.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: HCT116 p53KO cells were transfected with miR-3189 mimics or control siRNA for 48hr.

tag: cell line

value: HCT116 TP53 knockout

tag: treatment

value: miR-3189 mimic


title: TB11.1315_8_B


title: TB11.1634_9_T


title: TB11.1450_13_B


title: LPS_0.025_3

description: THP-1 gene expression after 20 hrs treatment with 0.025 µg/mL LPS (in cRPMI supplemented with 0.5% DMSO).

source_name: THP-1, LPS, 0.025 µg/mL, replicate 3

tag: transfected


title: TB11.1182_4_B


title: HCT116 TP53 knockout treated with miRNA 3189, rep2


title: HCT116 TP53 knockout control, rep1

source_name: HCT116 TP53 knockout, control siRNA

value: control siRNA


title: TB11.2080_1_T


title: HCT116 treated with miRNA 3189, rep2

source_name: HCT116, miR-3189 mimic

growth_protocol: HCT116 cells were cultured in DMEM with 10% FBS, at 37oC, 5% CO2.

treatment_protocol: HCT116 cells were transfected with miR-3189 mimics or control siRNA for 48hr.


title: HCT116 treated with miRNA 3189, rep3


title: TB11.1182_17_T


title: HCT116 TP53 knockout control, rep2


title: HCT116 TP53 knockout treated with miRNA 3189, rep3


title: HCT116 control, rep3

source_name: HCT116, control siRNA


title: HCT116 TP53 knockout control, rep3


title: HCT116 treated with miRNA 3189, rep1


title: HCT116 control, rep2


title: HCT116 control, rep1


title: CNCMI-2493_test 4

city: jouy en josas

first: elsa

last: jacouton

address: Allée de Vilvert

department: MICA

country: France

institute: INRA

description: replicate 4

scan_protocol: Standard Illumina scanning protocol

data_processing: All microarray analysis, including pre-processing, normalization and statistical analysis was carried out using Bioconductor packages in R programming language (version 2.14). The robust spline normalization (RSN) of lumi package was applied. This function combines the features of quantile and loess normalization and is designed to normalize the variance-stabilized data.

label_protocol: Biotinylated cDNA were prepared with the Ovation PicoSL WTA System v2 and Encore BiotinIL Module kits, Nugen

growth_protocol: cells were incubated in DMEM medium (antibiotic free - 10% FCS) during 48h before putting in contact with bacteria and wash with PBS before extraction

extract_protocol: RNA were extract using Rneasymini kit, Qiagen

treatment_protocol: cells were incubated 6h with controls or bacterial strains before extraction

tag: cell type

value: human intestinal epithelial cell

tag: infectious agent

value: L. rhamnosus CNCMI-2493

tag: passage

value: passage 12


title: rosi.control_test 8

description: replicate 8

source_name: HT-29, rosiglitazone

value: passage 15


title: neg.control_test 6

description: replicate 6

source_name: HT-29, DMEM

value: passage 13


title: CNCMI-2493_test 3

description: replicate 3


title: rosi.control_test 6

description: replicate 6


title: CNCMI-4317_test 8

description: replicate 8

value: L. rhamnosus CNCMI-4317


title: neg.control_test 5

description: replicate 5

value: passage 2


title: neg.control_test 7

description: replicate 7

value: passage 14


title: neg.control_test 8

description: replicate 8


title: CNCMI-4317_test 7

description: replicate 7


title: rosi.control_test 3

description: replicate 3

value: passage 10


title: CNCMI-4317_test 5

description: replicate 5


title: rosi.control_test 4

description: replicate 4

value: passage 1


title: rosi.control_test 7

description: replicate 7


title: CNCMI-2493_test 2

description: replicate 2

value: passage 7


title: rosi.control_test 5

description: replicate 5


title: rosi.control_test 2

description: replicate 2

value: passage 6


title: CNCMI-4317_test 6

description: replicate 6


title: CNCMI-4317_test 4

description: replicate 4


title: neg.control_test 3

description: replicate 3


title: CNCMI-4317_test 1

description: replicate 1


title: CNCMI-4317_test 3

description: replicate 3


title: neg.control_test 4

description: replicate 4


title: neg.control_test 2

description: replicate 2


title: CNCMI-4317_test 2

description: replicate 2


title: NSC11 cells treated with 2Gy, collected at 6h, total RNA, biological replicate 3

first: Philip

middle: J

last: Tofilon

state: Maryland

address: 10 Center Drive-MSC 1002

department: Radiation Oncology

description:
NSC11 Total 2Gy6h 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

hyb_protocol: cDNA was hybridized to GeneChip Human Genome U133A 2.0 Array chips (Affymetrix) per manufacturer's protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 300 7G.

data_processing: The data were analyzed with Expression Console using MAS5 normalization.

label: Biotin

source_name: NSC11 GSCs, 2Gy, 6h, total RNA

label_protocol: The isolated RNA was amplified with GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: GSCs were grown at 37°C, 5%CO2/5%O2.

extract_protocol: For polysome-bound RNA, cells incubated in 100 μg of cycloheximide/mL for 15 minutes before collection. Cytoplasmic RNA was obtained by lysing cells in 1 mL of polysome buffer [15 mmol/L Tris-HCl (pH 7.5), 300 mmol/L NaCl, 15 mmol/L MgCl2, 1% Triton X100, 100 μg/mL cycloheximide, 1 mg/mL heparin, and 500 units/mL RNasin (Promega)]. After 15 minutes on ice, lysates were centrifuged (12,000 x g for 15 minutes), and the resulting cytosolic supernatant was layered onto a 10% to 50% sucrose gradient. Gradients were then centrifuged at 35,000 x g for 3 hours at 4°C and polysome-bound fractions were collected using an ISCO Density Gradient Fractionation System (ISCO, Lincoln, NE) with continuous monitoring based on A254. The RNA in each fraction was extracted using TRIzol LS (Invitrogen). Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were grown to ~80% confluence in 150-mm2 tissue culture dishes and irradiated with 2Gy and collected either 1h or 6h after irradiation. Radiation was delivered using a 320 kV X-ray machine (Precision XRay Inc.) at a dose rate of 2.3 Gy/min.

value: glioblastoma stem-like cells (GSCs)

value: 2Gy radiation

tag: time point

tag: rna type

value: total


title: NSC11 cells treated with 2Gy, collected at 6h, total RNA, biological replicate 2

description:
NSC11 Total 2Gy6h 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: NSC11 cells treated with 2Gy, collected at 1h, total RNA, biological replicate 2

description:
NSC11 Total 2Gy1h 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: NSC11 GSCs, 2Gy, 1h, total RNA


title: NSC11 cells treated with 2Gy, collected at 6h, total RNA, biological replicate 1

description:
NSC11 Total 2Gy6h 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: NSC11 cells treated with 2Gy, collected at 1h, total RNA, biological replicate 3

description:
NSC11 Total 2Gy1h 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: rosi.control_test 1

description: replicate 1


title: CNCMI-2493_test 1

description: replicate 1


title: neg.control_test 1

description: replicate 1


title: NSC11 cells treated with 2Gy, collected at 1h, total RNA, biological replicate 1

description:
NSC11 Total 2Gy1h 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: NSC11 cells treated with 2Gy, collected at 1h, polysome-bound RNA, biological replicate 3

description:
NSC11 Polysome 2Gy1h 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: NSC11 GSCs, 2Gy, 1h, polysome-bound RNA

value: polysome-bound


title: NSC11 cells treated with 2Gy, collected at 6h, polysome-bound RNA, biological replicate 1

description:
NSC11 Polysome 2Gy6h 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: NSC11 GSCs, 2Gy, 6h, polysome-bound RNA


title: NSC11 cells treated with 2Gy, collected at 1h, polysome-bound RNA, biological replicate 2

description:
NSC11 Polysome 2Gy1h 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: GBMJ1 cells treated with 2Gy, collected at 6h, total RNA, biological replicate 2

description:
GBMJ1 Total 2Gy6h 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: GBMJ1 GSCs, 2Gy, 6h, total RNA


title: NSC11 cells treated with 0Gy, control, total RNA, biological replicate 2

description:
NSC11 Total Control 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: NSC11 GSCs, control, total RNA

value: 0Gy radiation


title: GBMJ1 cells treated with 2Gy, collected at 6h, total RNA, biological replicate 3

description:
GBMJ1 Total 2Gy6h 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: NSC11 cells treated with 0Gy, control, polysome-bound RNA, biological replicate 1

description:
NSC11 Polysome Control 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: NSC11 GSCs, control, polysome-bound RNA


title: NSC11 cells treated with 0Gy, control, polysome-bound RNA, biological replicate 2

description:
NSC11 Polysome Control 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: NSC11 cells treated with 2Gy, collected at 1h, polysome-bound RNA, biological replicate 1

description:
NSC11 Polysome 2Gy1h 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: NSC11 cells treated with 0Gy, control, total RNA, biological replicate 1

description:
NSC11 Total Control 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: GBMJ1 cells treated with 2Gy, collected at 6h, total RNA, biological replicate 1

description:
GBMJ1 Total 2Gy6h 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: GBMJ1 cells treated with 0Gy, control, total RNA, biological replicate 1

description:
GBMJ1 Total Control 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: GBMJ1 GSCs, control, total RNA


title: GBMJ1 cells treated with 0Gy, control, total RNA, biological replicate 2

description:
GBMJ1 Total Control 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: GBMJ1 cells treated with 2Gy, collected at 1h, total RNA, biological replicate 1

description:
GBMJ1 Total 2Gy1h 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: GBMJ1 GSCs, 2Gy, 1h, total RNA


title: NSC11 cells treated with 0Gy, control, polysome-bound RNA, biological replicate 3

description:
NSC11 Polysome Control 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: GBMJ1 cells treated with 2Gy, collected at 1h, total RNA, biological replicate 3

description:
GBMJ1 Total 2Gy1h 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: GBMJ1 cells treated with 0Gy, control, total RNA, biological replicate 3

description:
GBMJ1 Total Control 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: NSC11 cells treated with 2Gy, collected at 6h, polysome-bound RNA, biological replicate 3

description:
NSC11 Polysome 2Gy6h 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: GBMJ1 cells treated with 0Gy, control, polysome-bound RNA, biological replicate 3

description:
GBMJ1 Polysome Control 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: GBMJ1 GSCs, control, polysome-bound RNA


title: GBMJ1 cells treated with 2Gy, collected at 6h, polysome-bound RNA, biological replicate 2

description:
GBMJ1 Polysome 2Gy6h 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: GBMJ1 GSCs, 2Gy, 6h, polysome-bound RNA


title: GBMJ1 cells treated with 2Gy, collected at 6h, polysome-bound RNA, biological replicate 1

description:
GBMJ1 Polysome 2Gy6h 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: GBMJ1 cells treated with 0Gy, control, polysome-bound RNA, biological replicate 1

description:
GBMJ1 Polysome Control 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: GBMJ1 cells treated with 0Gy, control, polysome-bound RNA, biological replicate 2

description:
GBMJ1 Polysome Control 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: GBMJ1 cells treated with 2Gy, collected at 1h, polysome-bound RNA, biological replicate 2

description:
GBMJ1 Polysome 2Gy1h 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: GBMJ1 GSCs, 2Gy, 1h, polysome-bound RNA


title: GBMJ1 cells treated with 2Gy, collected at 1h, polysome-bound RNA, biological replicate 3

description:
GBMJ1 Polysome 2Gy1h 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: NSC11 cells treated with 2Gy, collected at 6h, polysome-bound RNA, biological replicate 2

description:
NSC11 Polysome 2Gy6h 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: GBMJ1 cells treated with 2Gy, collected at 1h, total RNA, biological replicate 2

description:
GBMJ1 Total 2Gy1h 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: NSC11 cells treated with 0Gy, control, total RNA, biological replicate 3

description:
NSC11 Total Control 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: GBMJ1 cells treated with 2Gy, collected at 6h, polysome-bound RNA, biological replicate 3

description:
GBMJ1 Polysome 2Gy6h 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: 0923 cells treated with 0Gy, control, total RNA, biological replicate 2

description:
0923 Total Control 2
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: 923 GSCs, control, total RNA


title: 0923 cells treated with 0Gy, control, total RNA, biological replicate 1

description:
0923 Total Control 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: 0923 cells treated with 2Gy, collected at 6h, total RNA, biological replicate 2

description:
0923 Total 2Gy6h 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: 923 GSCs, 2Gy, 6h, total RNA


title: 0923 cells treated with 2Gy, collected at 1h, total RNA, biological replicate 1

description:
0923 Total 2Gy1h 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: 923 GSCs, 2Gy, 1h, total RNA


title: 0923 cells treated with 2Gy, collected at 1h, total RNA, biological replicate 2

description:
0923 Total 2Gy1h 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: 0923 cells treated with 2Gy, collected at 6h, total RNA, biological replicate 1

description:
0923 Total 2Gy6h 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: 0923 cells treated with 2Gy, collected at 6h, total RNA, biological replicate 3

description:
0923 Total 2Gy6h 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: 0923 cells treated with 0Gy, control, total RNA, biological replicate 3

description:
0923 Total Control 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: 0923 cells treated with 0Gy, control, polysome-bound RNA, biological replicate 1

description:
0923 Polysome Control 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: 923 GSCs, control, polysome-bound RNA


title: 0923 cells treated with 0Gy, control, polysome-bound RNA, biological replicate 3

description:
0923 Polysome Control 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: Asthmatic 5

city: Newcastle

first: QIAN

last: LI

address: University drive

institute: University of Newcastle

description: baseline

hyb_protocol: 750 ng cRNA was hybridised to Illumina Sentrix HumanRef-8 V3 Expression BeadChips (Illumina, San Diego, CA, USA) using standard protocols

scan_protocol: Each BeadChip measured the expression of 24,354 genes and was scanned using the Illumina Bead Station and captured using BeadScan 3.5.11 (Illumina)

data_processing: Sample and gene profiling results were included in the analysis if the sample was of suitable purity (OD 260/280 ratio between 1.7-2.1) and was successfully amplified (sufficient cRNA generated) and hybridized (95th percentile of fluorescence score>500) and the data passed quality control criteria in GeneSpring GX (correlation coefficients and priciple component analysis plots)

source_name: induced sputum

label_protocol: A total of 500 ng of sputum RNA was amplified and labelled with biotin-uridine triphosphate using the Total Prep RNA amplification kit as per manufacturer’s instructions (Life Technologies)

extract_protocol: RNA was extracted from induced sputum using the RNeasy Mini Kit (Qiagen, Hilden, Germany);RNA quatitation was performed using the Quanti-iT RiboGreen RNA

tag: disease state

value: asthmatic

tag: gender

value: male

tag: age

tag: bmi

tag: smoking pack-years

tag: ID


title: 0923 cells treated with 2Gy, collected at 6h, polysome-bound RNA, biological replicate 3

description:
0923 Polysome 2Gy6h 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: 923 GSCs, 2Gy, 6h, polysome-bound RNA


title: Asthmatic 9

description: postmeal


title: 0923 cells treated with 2Gy, collected at 1h, polysome-bound RNA, biological replicate 2

description:
0923 Polysome 2Gy1h 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

source_name: 923 GSCs, 2Gy, 1h, polysome-bound RNA


title: 0923 cells treated with 0Gy, control, polysome-bound RNA, biological replicate 2

description:
0923 Polysome Control 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: 0923 cells treated with 2Gy, collected at 6h, polysome-bound RNA, biological replicate 1

description:
0923 Polysome 2Gy6h 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: Asthmatic 3

description: baseline


title: 0923 cells treated with 2Gy, collected at 1h, polysome-bound RNA, biological replicate 3

description:
0923 Polysome 2Gy1h 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: 0923 cells treated with 2Gy, collected at 1h, total RNA, biological replicate 3

description:
0923 Total 2Gy1h 3.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: Asthmatic 7

description: postmeal

value: female


title: 0923 cells treated with 2Gy, collected at 1h, polysome-bound RNA, biological replicate 1

description:
0923 Polysome 2Gy1h 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: Asthmatic 10

description: postmeal


title: 0923 cells treated with 2Gy, collected at 6h, polysome-bound RNA, biological replicate 2

description:
0923 Polysome 2Gy6h 2.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.


title: Asthmatic 4

description: baseline


title: Asthmatic 8

description: postmeal


title: Asthmatic 2

description: baseline


title: Asthmatic 6

description: postmeal


title: Asthmatic 1

description: baseline


title: 77C

city: Beijing

first: Xiaoyu

last: Shi

address: Chao Yang District Pan Jia Yuan Nan Li No.17

department: Cancer Institute (Hospital)

institute: Peking Union Medical College and Chinese Academy of Medical Sciences

description: Gene expression in colorectal tissue

hyb_protocol: 1.65 ug of Cy3-labeled cRNA (specific activity >9.0 pmol Cy3 per ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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 p/n 5188-5325) and 1 minute with 37°C GE Wash buffer 2 (Agilent p/n 5188-5326).

scan_protocol: After washing, slides were scanned immediately on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100% and 10%, dynamic range is extended).

data_processing: The scanned images were analyzed with the Agilent's Feature Extraction Software (v10.5)  using default parameters (protocol GE1_105_Dec08 and Grid 014850_D_20070207) to obtain background subtracted and spatially detrended processed signal intensities. The raw data was normalized by the GenespringGX Software (Agilent, version 11.5).

source_name: Colorectal adenocarcinoma

label_protocol: 500ng purified total RNA was reverse transcribed into cDNA, transcribed into cRNA and labeled with Cyanine-3 (Cy3) using the Agilent’s Quick Amp Labeling Kit (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from frozen tissue using TRIzol RNA isolation reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s specifications, and purified by the RNeasy mini Kit (Cat No.74106, Qiagen, Germany). RNA integrity was detected using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA concentration was determined using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: Colorectal epithelial neoplasms were obtained from patients undergoing polypectomy, and colorectal normal mucosae were obtained from patients with hemorrhoid undergoing surgical excision. Fresh tissue samples were frozen in liquid nitrogen after surgery and stored at -80℃ for subsequent molecular analysis.

value: Male

tag: age(years)

tag: pathologic grade

value: Adenocarcinoma

tag: ptnm


title: Healthy control 2

description: baseline

value: healthy


title: Healthy control 6

description: postmeal


title: 89C

description: Gene expression in colorectal tissue


title: 86C

description: Gene expression in colorectal tissue


title: 60C

description: Gene expression in colorectal tissue


title: Healthy control 5

description: postmeal


title: 76C

description: Gene expression in colorectal tissue


title: 44C

description: Gene expression in colorectal tissue

value: Female


title: Healthy control 3

description: baseline


title: Healthy control 4

description: postmeal