title: GW14.5 human neocortex section 63

description:
Sample name: Hs_63
section 63


title: GW14.5 human neocortex section 64

status: Public on Nov 13 2014

type: RNA

city: San Francisco

first: Michael

last: Oldham

state: CA

address: 35 Medical Center Way #0525

country: USA

institute: UCSF

description:
Sample name: Hs_64
section 64

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized in R.  Batch effects associated with Array.ID and Extraction.Date were corrected sequentially with ComBat, as described in Supplementary Methods.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human neocortex

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser 2100.

tag: section

tag: age

value: 14.5 gestational weeks

tag: tissue

value: neocortex

tag: rin

value: H


title: GW14.5 human neocortex section 73

description:
Sample name: Hs_73
section 73

value: D


title: GW14.5 human neocortex section 67

description:
Sample name: Hs_67
section 67


title: GW14.5 human neocortex section 57

description:
Sample name: Hs_57
section 57

value: K


title: GW14.5 human neocortex section 46

description:
Sample name: Hs_46
section 46

value: J


title: GW14.5 human neocortex section 51

description:
Sample name: Hs_51
section 51

value: I


title: GW14.5 human neocortex section 68

description:
Sample name: Hs_68
section 68

value: A


title: GW14.5 human neocortex section 66

description:
Sample name: Hs_66
section 66


title: GW14.5 human neocortex section 78

description:
Sample name: Hs_78
section 78


title: GW14.5 human neocortex section 55

description:
Sample name: Hs_55
section 55


title: GW14.5 human neocortex section 50

description:
Sample name: Hs_50
section 50

value: L


title: GW14.5 human neocortex section 47

description:
Sample name: Hs_47
section 47


title: GW14.5 human neocortex section 62

description:
Sample name: Hs_62
section 62


title: GW14.5 human neocortex section 45

description:
Sample name: Hs_45
section 45


title: GW14.5 human neocortex section 44

description:
Sample name: Hs_44
section 44

value: F


title: GW14.5 human neocortex section 42

description:
Sample name: Hs_42
section 42

value: B


title: GW14.5 human neocortex section 38

description:
Sample name: Hs_38
section 38


title: GW14.5 human neocortex section 41

description:
Sample name: Hs_41
section 41


title: GW14.5 human neocortex section 35

description:
Sample name: Hs_35
section 35


title: GW14.5 human neocortex section 39

description:
Sample name: Hs_39
section 39


title: GW14.5 human neocortex section 36

description:
Sample name: Hs_36
section 36


title: GW14.5 human neocortex section 28

description:
Sample name: Hs_28
section 28

value: E


title: GW14.5 human neocortex section 31

description:
Sample name: Hs_31
section 31


title: GW14.5 human neocortex section 33

description:
Sample name: Hs_33
section 33


title: GW14.5 human neocortex section 26

description:
Sample name: Hs_26
section 26

value: C


title: GW14.5 human neocortex section 34

description:
Sample name: Hs_34
section 34


title: GW14.5 human neocortex section 29

description:
Sample name: Hs_29
section 29


title: GW14.5 human neocortex section 32

description:
Sample name: Hs_32
section 32

value: G


title: GW14.5 human neocortex section 27

description:
Sample name: Hs_27
section 27


title: GW14.5 human neocortex section 25

description:
Sample name: Hs_25
section 25


title: GW14.5 human neocortex section 20

description:
Sample name: Hs_20
section 20


title: GW14.5 human neocortex section 17

description:
Sample name: Hs_17
section 17


title: GW14.5 human neocortex section 22

description:
Sample name: Hs_22
section 22


title: GW14.5 human neocortex section 21

description:
Sample name: Hs_21
section 21


title: GW14.5 human neocortex section 11

description:
Sample name: Hs_11
section 11


title: GW14.5 human neocortex section 14

description:
Sample name: Hs_14
section 14


title: GW14.5 human neocortex section 5

description:
Sample name: Hs_5
section 5


title: GW14.5 human neocortex section 18

description:
Sample name: Hs_18
section 18


title: GW14.5 human neocortex section 12

description:
Sample name: Hs_12
section 12


title: GW14.5 human neocortex section 23

description:
Sample name: Hs_23
section 23


title: GW14.5 human neocortex section 15

description:
Sample name: Hs_15
section 15


title: GW14.5 human neocortex section 10

description:
Sample name: Hs_10
section 10


title: GW14.5 human neocortex section 24

description:
Sample name: Hs_24
section 24


title: Sample16-Th2

city: Sendai

first: Chiaki

last: Ono

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: International Research Institute of Disaster Science

country: Japan

institute: Tohoku University

data_processing: The data were normalised using average normalisation with Illumina genome studio

label: Biotin

source_name: Human PBMC-Th2(CD4+/CCR4+/CXCR3-)

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Round Aminoallyl aRNA amplification kit 1.0 and biotin-X-X-NHS(Epicentre Biotechnologies)

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

tag: cell type

tag: race

value: Japanese

tag: gender

value: M


title: Sample22-Th2


title: DAC treated LNCaP cells replicate 3

city: Toronto

first: Bharati

last: Bapat

address: 60 Murray St

country: Canada

institute: Mount Sinai Hospital

description: Gene expression, LNCaP cells, DAC treated, replicate 3

hyb_protocol: 1650ng cRNA from each sample were loaded onto 4×180 k custom microarray  (GEO platform accession GPL16604) and allowed to hybridize at 65°C for 17hours.

scan_protocol: The arrays were scanned with the Agilent Microarray Scanner G2565CA.

data_processing:
Microarray data were processed with Agilent Feature Extraction Software (v10.7.3.1). A quantile between array normalization was applied and differential expression was determined using a Bayesian adjusted t-statistic from a Linear Models for Microarray Data (LIMMA) linear model.
Gene expression was considered significant if fold change was >1.25 and p <0.05 (adjusted for a false discovery rate of 5%).

source_name: LNCaP cells, DAC treated, replicate 3

label_protocol: 200ng of RNA from each sample was amplified and labeled according to the protocol for One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling Kit, Agilent). The input RNA was reversed transcribed into cDNA, using an oligo-dT-promoter primer, which introduces a T7 promoter region. The subsequent in vitro transcription uses a T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP. cDNA synthesis was performed at 40°C for 2 hours. The labeled cRNA was purified with RNEasy Mini spin columns (Qiagen) and quantified using a Nanodrop-1000.

growth_protocol: The human cell lines DU-145 (ATCC# HTB-81), LNCaP (ATCC# CRL-1740), and 22Rv1 (ATCC# CRL-2505) were cultured in RPMI 1640 media supplemented with 10% fetal bovine serum. Cells were maintained in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini Kit as per the manufacture's instructions. Samples were then analyzed on a Agilent 2100 Bioanayler to ensure high quality and integrity of RNA samples.

treatment_protocol: For treatment with 5-Aza 2’–deoxycitidine (DAC), cells were plated in 6 cm dishes and incubated in culture medium with 2 μg/mL DAC for 4 days with medium change every 2 days.

tag: cell line

value: LNCap

tag: treatment

value: DAC treated


title: Control LNCaP cells replicate 3

description: Gene expression, LNCaP cells, control, replicate 3

source_name: LNCaP cells, control, replicate 3

value: Control


title: Control LNCaP cells replicate 2

description: Gene expression, LNCaP cells, control, replicate 2

source_name: LNCaP cells, control, replicate 2


title: DAC treated LNCaP cells replicate 1

description: Gene expression, LNCaP cells, DAC treated, replicate 1

source_name: LNCaP cells, DAC treated, replicate 1


title: GW14.5 human neocortex section 1

description:
Sample name: Hs_1
section 1

value: 14.5 gestational weeks

value: neocortex


title: DAC treated LNCaP cells replicate 2

description: Gene expression, LNCaP cells, DAC treated, replicate 2

source_name: LNCaP cells, DAC treated, replicate 2


title: Control LNCaP cells replicate 1

description: Gene expression, LNCaP cells, control, replicate 1

source_name: LNCaP cells, control, replicate 1


title: Sample11-Th2


title: DAC treated DU-145 cells replicate 3

description: Gene expression, DU-145 cells, DAC treated, replicate 3

source_name: DU-145 cells, DAC treated, replicate 3


title: Control DU-145 cells replicate 3

description: Gene expression, DU-145 cells, control, replicate 3

source_name: DU-145 cells, control, replicate 3


title: Sample12-Th2


title: Sample8-Th2


title: DAC treated DU-145 cells replicate 2

description: Gene expression, DU-145 cells, DAC treated, replicate 2

source_name: DU-145 cells, DAC treated, replicate 2


title: Control DU-145 cells replicate 2

description: Gene expression, DU-145 cells, control, replicate 2

source_name: DU-145 cells, control, replicate 2


title: Sample10-Th2


title: DAC treated DU-145 cells replicate 1

description: Gene expression, DU-145 cells, DAC treated, replicate 1

source_name: DU-145 cells, DAC treated, replicate 1


title: Sample13-Th2


title: DAC treated 22Rv1 cells replicate 3

description: Gene expression, 22Rv1 cells, DAC treated, replicate 3

source_name: 22Rv1 cells, DAC treated, replicate 3


title: Sample6-Th2


title: DAC treated 22Rv1 cells replicate 2

description: Gene expression, 22Rv1 cells, DAC treated, replicate 2

source_name: 22Rv1 cells, DAC treated, replicate 2


title: Sample5-Th2


title: DAC treated 22Rv1 cells replicate 1

description: Gene expression, 22Rv1 cells, DAC treated, replicate 1

source_name: 22Rv1 cells, DAC treated, replicate 1


title: 3#CTL-patient_S12

city: Beijing

first: Jun

last: Chen

address: No.15 Datun Road

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

hyb_protocol: There are many different hybridization protocols, apparatus, and instruments available that may be compatible for use with the OneArray® microarray. Detailed instructions for using the glass cover slide method are described below.

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.

source_name: HBV-associated hepatocellular carcinoma patients

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Promega). And labed with Cy3 and 5 according to the instructions of manufacturer.

growth_protocol: The PBMCs were purified from patients or healthy donors.

extract_protocol: Total RNA were extracted from peripheral NK cells accroding to the  instructions of manufacturer (Promega).

treatment_protocol: The PBMCs were stained with CD56 antibody and sorted out by Flow cytomethy.  Total RNA was extracted.

value: peripheral NK cells

tag: disease status

value: HBV-associated hepatocellular carcinoma


title: Sample1-Th2


title: 3#CTL-healthy_S12

source_name: healthy donors

value: healthy


title: Control 22Rv1 cells replicate 1

description: Gene expression, 22Rv1 cells, control, replicate 1

source_name: 22Rv1 cells, control, replicate 1


title: Sample7-Th2

source_name: Human PBMC-Th2(CD4+/CCR4+/CXCR3-)


title: Control DU-145 cells replicate 1

description: Gene expression, DU-145 cells, control, replicate 1

source_name: DU-145 cells, control, replicate 1


title: Control 22Rv1 cells replicate 2

description: Gene expression, 22Rv1 cells, control, replicate 2

source_name: 22Rv1 cells, control, replicate 2


title: Sample4-Th2


title: Control 22Rv1 cells replicate 3

description: Gene expression, 22Rv1 cells, control, replicate 3

source_name: 22Rv1 cells, control, replicate 3


title: 3#NK-patient_S10


title: 3#NK-healthy_S10


title: 3#CTL-patient_S11


title: 3#NK-healthy_S9


title: 3#NK-patient_S9


title: 4#CD8-patient_S8


title: 2#NK-healthy_S6


title: Sample22-Th1

source_name: Human PBMC-Th1(CD4+/CXCR3+/CCR4-)


title: Sample12-Th1


title: 2#CTL-healthy_s7


title: 2#CTL-healthy_S8


title: 4#CD8-patient_S7


title: 2#NK-healthy_S5


title: Sample16-Th1


title: Sample11-Th1


title: Sample13-Th1


title: 4#CD56-patient_S6


title: 1#CTL-healthy_S4


title: Sample10-Th1


title: 1#CD8-patient_S4


title: 1#CTL-healthy_S3


title: 1#CD8-patient_S3


title: 4#CD56-patient_S5


title: Sample8-Th1


title: 1#CD56-patient_S2


title: Sample7-Th1


title: Sample6-Th1


title: Sample5-Th1


title: Sample4-Th1


title: 1#NK-healthy_S2


title: PARP13 siRNA vs Control siRNA Rep2

city: Cambridge

first: Paul

last: Chang

state: Massachusetts

address: 77 Massachusetts Ave

department: Biology

institute: Massachusetts Institute of Technology

hyb_protocol: Agilent hybridization kit

scan_protocol: SureScan Microarray Scanner (Agilent)

data_processing: Feature Extractor v10.5

source_name: control siRNA_rep2

label_protocol: QuickAmp (Agilent)

growth_protocol: DMEM supplemented with 10% Fetal Bovine serum, 37oC, 5%CO2

extract_protocol: Qiagen Rneasy Mini Kit

treatment_protocol: Two 48-hour transfections with 20nM Control siRNA and PARP13 siRNA. Transfected using Lipofectamine 2000 (Invitrogen) following manufacturer protocol

value: HeLa-Kyoto

source_name: PARP13 siRNA rep2


title: PARP13 siRNA vs Control siRNA Rep1

source_name: control siRNA_rep1

source_name: PARP13 siRNA rep1


title: 1#NK-healthy_S1


title: P3_HF20_W18_A1

status: Public on Nov 12 2014

city: New Delhi

first: Kanury

middle: VS

last: Rao

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: ICGEB

description: Gene expression after Week18

hyb_protocol: Agilent’s In situ Hybridzation kit 5188-5242 was used following the manufacturer's protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal. The normalization (Percentile shift to 75th percentile) has been done using Agilent GeneSpring GX 11.0 software.
Fold_change values for control arrays is calculated by substracting the median values from each probe values (control) of the respective arrays. Fold_change value for treatment arrays is calculated by substracting treated probe values from the median values of each probe (control)  of the respective arrays. The fold_change data is available as a Series supplemetary file.

organism: Mus musculus

label_protocol: Agilent’s Quick-Amp labeling Kit (p/n5190-0444) was used following the manufacturer's protocol. T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis)

extract_protocol: The mice were periodically monitored over an eighteen week period. At the interval of every 3 weeks, five animals from each group were sacrificed and different tissues were extracted and frozen in liquid nitrogen prior to RNA extraction.

treatment_protocol: The mice were kept at 12:12 hr light: dark photoperiod with ad libitum access to food and water. Weaned mice at the age of 3-4 weeks were divided randomly into five groups- (each group contains 30 animals): first group was fed on normal diet (ND) with 10% of calories coming from fat, the second group was HFHSD fed group with increased sucrose and 60% of calories coming from fat (Research diets Inc.USA), and the third, fourth and fifth group of mice were fed on HFHSD with different doses of an ethano-botanical formulation, KAL-1 and we named them as HF5 (5µg of KAL-1+ HFHSD), HF20 (20µg of KAL-1+ HFHSD) and HF75 (75µg of KAL-1+ HFHSD). The daily weight of this aqueous formulation was 700 mg/ml. This dataset consists of gene expression changes in spleen.

tag: strain

tag: fed with

value: High fat+20µg of KAL diet

value: Spleen

tag: time point


title: 1#CD56-patient_S1


title: P3_HF20_W18_A3

description: Gene expression after Week18


title: P3_HF75_W18_SPL_A4

description: Gene expression after Week18

value: High fat+75µg of KAL diet


title: P3_HF5_W18_SPL_A3

description: Gene expression after Week18

value: High fat+5µg of KAL diet


title: P3_HFC_W18_A3

description: Gene expression after Week18

value: High fat diet


title: Sample1-Th1


title: P3_HFC_W18_A2

description: Gene expression after Week18


title: P3_HF75_W18_A3

description: Gene expression after Week18


title: P3_HFC_W18R1_SplA

description: Gene expression after Week18


title: P3_HF75_W18_A1

description: Gene expression after Week18


title: P3_HF5_W18_A1

description: Gene expression after Week18


title: P3_HF20_W18_A2

description: Gene expression after Week18


title: P3_HF75_W15R2_A3

description: Gene expression after Week15


title: P3_LFC_W18_A4

description: Gene expression after Week18

value: Low fat diet


title: P3_LFC_W18_A5

description: Gene expression after Week18


title: P3_HF5_W18_A2

description: Gene expression after Week18


title: P3_LFC_W18_A2

description: Gene expression after Week18


title: P3_HF5_W15R2_A3

description: Gene expression after Week15


title: P3_HF20_W15R2_A3

description: Gene expression after Week15


title: P3_HF75_W15R2_A1

description: Gene expression after Week15


title: P3_HF5_W15R2_D2

description: Gene expression after Week15


title: P3_HFC_W15R2_A2

description: Gene expression after Week15


title: P3_HF5_W15R2_D1

description: Gene expression after Week15


title: P3_HF20_W15R2_A1

description: Gene expression after Week15


title: P3_HF20_W15R2_D2

description: Gene expression after Week15


title: 3#CTL-healthy_S11


title: P3_HFC_W15R2_D3(a1)

description: Gene expression after Week15


title: P3_LFC_W15R2_D1

description: Gene expression after Week15


title: P3_LFC_W15R2_A3

description: Gene expression after Week15


title: P3_HFC_W12_A2_Cy3

description: Gene expression after Week12


title: P3_HF75_Spl_A6_Cy3

description: Gene expression after Week12


title: P3_HFC_W12_A4_Cy3

description: Gene expression after Week12


title: P3_HF5_W12_A2_Cy3

description: Gene expression after Week12


title: P3_HFC_W15R2_A3

description: Gene expression after Week15


title: P3_LFC_W15R2_D2

description: Gene expression after Week15


title: P3_HFC_W12_A3_Cy3

description: Gene expression after Week12


title: P3_HF20_A5_Cy3

description: Gene expression after Week12


title: P3_HF20_A3_Cy3

description: Gene expression after Week12


title: P3_HF5_W12_A3_Cy3

description: Gene expression after Week12


title: P3_HF75_Spl_A1_Cy3

description: Gene expression after Week12


title: P3_HF20_W12_A1_Cy3

description: Gene expression after Week12


title: P3_LFC_W12_A1_Cy3

description: Gene expression after Week12


title: P3_HF75_W9R3_2

description: Gene expression after Week9


title: P3_HF75_W9R3_3

description: Gene expression after Week9


title: P3_LFC_W12_A3_Cy3

description: Gene expression after Week12


title: P3_HF75_SpL_A3_Cy3

description: Gene expression after Week12


title: P3_LFC_W12_A2_Cy3

description: Gene expression after Week12


title: P3_HFC_W9R3_A5

description: Gene expression after Week9


title: P3_HF5_W12_A1_Cy3

description: Gene expression after Week12


title: P3_HFC_W9R3_A1

description: Gene expression after Week9


title: P3_HFC_W9R3_A3

description: Gene expression after Week9


title: P3_HF75_W9R3_1

description: Gene expression after Week9


title: P3_HF20_W9R3_3

description: Gene expression after Week9


title: P3_HF20_W9R3_A1

description: Gene expression after Week9


title: P3_HF20_W9R3_A2

description: Gene expression after Week9


title: P3_HF5_W9R3_A2

description: Gene expression after Week9


title: P3_HF5_W9R3_A1

description: Gene expression after Week9


title: P3_LFC_W9R3_A2

description: Gene expression after Week9


title: P3HF5_W6_A1

description: Gene expression after Week6


title: P3_HF5_W9R3_A3

description: Gene expression after Week9


title: P3HF20_W6_A1

description: Gene expression after Week6


title: P3_LFC_W9R3_A1

description: Gene expression after Week9


title: P3_LFC_W9R3_A3

description: Gene expression after Week9


title: P3HF20_W6_A2

description: Gene expression after Week6


title: P3LFC_W6_A2

description: Gene expression after Week6


title: P3_HF75_W3_A2

description: Gene expression after Week3


title: P3HFC_W6_A1

description: Gene expression after Week6


title: P3_HF75_W3_A1

description: Gene expression after Week3


title: P3_HFC_W3R_A5

description: Gene expression after Week3


title: P3HFC_W6_A2

description: Gene expression after Week6


title: P3LFC_W6_A1

description: Gene expression after Week6


title: P3_HFC_W3R_A2

description: Gene expression after Week3


title: P3HF75_W6_A2

description: Gene expression after Week6


title: P3_HF5_W3R2_A2

description: Gene expression after Week3


title: P3_HF75_W15R2_A2

description: Gene expression after Week15


title: P3HF75_W6_A1

description: Gene expression after Week6


title: P3HF5_W6_A2

description: Gene expression after Week6


title: P3_HF20_W3R2_A1

description: Gene expression after Week3


title: P3_HF5_W3R2_A1

description: Gene expression after Week3


title: P3_HF5_W3R_A1

description: Gene expression after Week3


title: P3_HF20_W3_A1

description: Gene expression after Week3


title: P3_LFC_W3R2_Ts_A1

description: Gene expression after Week3


title: P3_HF20_W3_A2

description: Gene expression after Week3


title: P3_LFC_W3R_A5

description: Gene expression after Week3


title: P3_LFC_W3R_A1

description: Gene expression after Week3


title: P3_HFC_W3R_A3

description: Gene expression after Week3


title: P3_HF75_W3R2_A2

description: Gene expression after Week3


title: P3_Day_14_HFC_3

description: Gene expression after 14 Day

value: 14 Day


title: P3_LFC_W0_R2_Spl_A2

description: Gene expression after Week0


title: P3_LFC_W0_R2_Spl_A5

description: Gene expression after Week0


title: P3_HFC_W0_R2_Spl_A2

description: Gene expression after Week0


title: P3_HFC_W0_R2_Spl_A3

description: Gene expression after Week0


title: P3_LFC_W0_R2_Spl_A1

description: Gene expression after Week0


title: P3_HFC_W0_R2_Spl_A1

description: Gene expression after Week0


title: P3_Day_14_HFC_cells

description: Gene expression after 14 Day


title: P3_Day_14_LFC_cells 2

description: Gene expression after 14 Day


title: P3_Day_14_HFC_cells 1

description: Gene expression after 14 Day


title: P3_Day_14_LFC_cells 3

description: Gene expression after 14 Day


title: P3_HFC_Day 10_Cells_1

description: Gene expression after 10 Day

value: 10 Day


title: P3_LFC_Day 10_Cells_3

description: Gene expression after 10 Day


title: P3_HFC_Day 10_Cells_2

description: Gene expression after 10 Day


title: P3_HFC_Day 10_Cells_3

description: Gene expression after 10 Day


title: P2_HFC_D6_3 [spleen]

description: Gene expression after 6 Day

value: 6 Day


title: P2_HFC_D6_2 [spleen]

description: Gene expression after 6 Day


title: P3_LFC_Day 10_Cells_1

description: Gene expression after 10 Day


title: P2_LFC_D6_3 [spleen]

description: Gene expression after 6 Day


title: P2_HFC_D6_1 [spleen]

description: Gene expression after 6 Day


title: P2_LFC_D6_2 [spleen]

description: Gene expression after 6 Day


title: P2_LFC_D6_1 [spleen]

description: Gene expression after 6 Day


title: P3_Day 1_LF_A2

description: Gene expression after 1 Day

value: 1 Day


title: P3_HFC_D1_1

description: Gene expression after 1 Day


title: P3_HFC_D1_2

description: Gene expression after 1 Day


title: P3_Day 1_LF 1

description: Gene expression after 1 Day


title: P3_Day 1_LF_A1

description: Gene expression after 1 Day


title: P6_HF20_W18_SMT_A3

description: Gene expression after Week18

source_name: HF20_Skeletal Muscles

treatment_protocol: The mice were kept at 12:12 hr light: dark photoperiod with ad libitum access to food and water. Weaned mice at the age of 3-4 weeks were divided randomly into five groups- (each group contains 30 animals): first group was fed on normal diet (ND) with 10% of calories coming from fat, the second group was HFHSD fed group with increased sucrose and 60% of calories coming from fat (Research diets Inc.USA), and the third, fourth and fifth group of mice were fed on HFHSD with different doses of an ethano-botanical formulation, KAL-1 and we named them as HF5 (5µg of KAL-1+ HFHSD), HF20 (20µg of KAL-1+ HFHSD) and HF75 (75µg of KAL-1+ HFHSD). The daily weight of this aqueous formulation was 700 mg/ml. This dataset consists of gene expression changes in Subcutaneous SVCs.

value: skeletal muscle


title: P3_HFC_D1_3

description: Gene expression after 1 Day


title: P6_HF20_W18_SMT_A2

description: Gene expression after Week18


title: P6_HF75_W18_SMT_A2

description: Gene expression after Week18

source_name: HF75_Skeletal Muscles


title: P6_HF75_W18_SMT_A1

description: Gene expression after Week18


title: P6 LFC W18 SMT_A3

description: Gene expression after Week18

source_name: LFC_Skeletal Muscles


title: P6_HF5_W18_SMT_A3

description: Gene expression after Week18

source_name: HF5_Skeletal Muscles


title: P3_LFC_Day10_cells_2

description: Gene expression after 10 Day


title: P6 LFC W18 SM_A1

description: Gene expression after Week18


title: P6 LFC W18 SMT_A2

description: Gene expression after Week18


title: P6_HF20_W15_SMT_A3

description: Gene expression after Week15


title: P6_HF75_W15_SMT_A2

description: Gene expression after Week15


title: P6_HF20_W15_SMT_A1

description: Gene expression after Week15


title: P6_HF75_W15_SMT_A3

description: Gene expression after Week15


title: P6_HF5_W18_SMT_A2

description: Gene expression after Week18


title: P6_HF5_W15_SMT_A3

description: Gene expression after Week15


title: P6_HF20_W15_SMT_A2

description: Gene expression after Week15


title: P6_HF20_W18_SMT_A1

description: Gene expression after Week18


title: P3_Day_14_LFC_cells 1

description: Gene expression after 14 Day


title: P6_HF5_W15_SMT_A2

description: Gene expression after Week15


title: P6_HF75_W15_SMT_A1

description: Gene expression after Week15


title: P6_HFC_W15_SMT_A2

description: Gene expression after Week15

source_name: HFC_Skeletal Muscles


title: P6_HF5_W15_SMT_A1

description: Gene expression after Week15


title: P6_HFC_W15_SMT_A3

description: Gene expression after Week15


title: P6_LFC_W15_SMT_A3

description: Gene expression after Week15


title: P6_HF5_TS_A2_Cy3

description: Gene expression after Week12


title: P6_HFC_W15_SMT_A1

description: Gene expression after Week15


title: P6_HF5_Ts_A3_Cy3

description: Gene expression after Week12


title: P6_LFC_W15_SMT_A1

description: Gene expression after Week15


title: P6_HF75_SMT_A2_Cy3

description: Gene expression after Week12


title: P6_HFC_A1_Cy3

description: Gene expression after Week12


title: P6_LFC_TS-A4_Cy3

description: Gene expression after Week12


title: P6_HF5_Ts_A1_Cy3

description: Gene expression after Week12


title: P6_LFC_W15R2_A1

description: Gene expression after Week15


title: P6_HF75_SMT_A3_Cy3

description: Gene expression after Week12


title: P6_HF20_Ts_A2_Cy3

description: Gene expression after Week12


title: P6_HF20_Ts_A3_Cy3

description: Gene expression after Week12


title: P6_HF75_W18_SMT_A3

description: Gene expression after Week18


title: P6_LFC_Ts_A1_Cy3

description: Gene expression after Week12


title: P6_LFC_W9R3_SMT_D1

description: Gene expression after Week9


title: P6_HFC_A3_Cy3

description: Gene expression after Week12


title: P6_HFC_A2_Cy3

description: Gene expression after Week12


title: P6_HF20_Ts_A1_Cy3

description: Gene expression after Week12


title: P6_LFC-Ts_A5_Cy3

description: Gene expression after Week12


title: P6_HF5_W9R3_SMT_D2

description: Gene expression after Week9


title: P6_HFC_W9R3_SMT_D1

description: Gene expression after Week9


title: P6_HF75_W9R3_SMT_D1

description: Gene expression after Week9


title: P6-HFC-W6R-SMT-A2

description: Gene expression after Week6


title: P6_HF20_W9R3_SMT_D2

description: Gene expression after Week9


title: P6-H75-W6R-SMT-A3

description: Gene expression after Week6


title: P6-HF5-W6R-SMT-A3

description: Gene expression after Week6


title: P6-HF5-W6R-SMT-A2

description: Gene expression after Week6


title: P6_HF75_SMT_A1_Cy3

description: Gene expression after Week12


title: P6-HF75-W6R-SMT-A1

description: Gene expression after Week6


title: P6-HFC-W6R-SMT-A3

description: Gene expression after Week6


title: P6-HFC-W6R-SMT-A1

description: Gene expression after Week6


title: P6-HF20-W6R-SMT-A3

description: Gene expression after Week6


title: P6-LFC-W6R-SMT-A3

description: Gene expression after Week6


title: P6-HF5-W6R-SMT-A1

description: Gene expression after Week6


title: P6_HFC_W3R2_SMT_A2

description: Gene expression after Week3


title: P6-LFC-W6R-SMT-A2

description: Gene expression after Week6


title: P6_HFC_W3R2_SMT_A3

description: Gene expression after Week3


title: P6_HF75_W3R2_SMT_A3

description: Gene expression after Week3


title: P6-HF75-W6R-SMT-A2

description: Gene expression after Week6


title: P6-HF20-W6R-SMT-A2

description: Gene expression after Week6


title: P6_HF75_W3R2_SMT_A1

description: Gene expression after Week3


title: P6-LFC-W6R-SMT-A1

description: Gene expression after Week6


title: P6_HF5_W3R2_SMT_A3

description: Gene expression after Week3


title: P6_HF75_W3R2_SMT_A2

description: Gene expression after Week3


title: P6_HF5_W3R2_SMT_A2

description: Gene expression after Week3


title: P6_HF5_W3R2_SMT_A1

description: Gene expression after Week3


title: P6_LFC_W3R2_SMT_A3

description: Gene expression after Week3


title: P6_HF20_W3R2_SMT_A3

description: Gene expression after Week3


title: P6_HFC_W3R2_SMT_A1

description: Gene expression after Week3


title: P6_HF20_W3R2_SMT_A1

description: Gene expression after Week3


title: P6_HF20_W3R2_SMT_A2

description: Gene expression after Week3


title: P6_LFC_W3R2_SMT_A1

description: Gene expression after Week3


title: P6_LFC_W3R2_SMT_A2

description: Gene expression after Week3


title: P6_HFC_W0_R2_SMT_A3

description: Gene expression after Week0


title: P6_LFC_W0_R2_SMT_A4

description: Gene expression after Week0


title: P6_LFC_W0_R2_SMT_A5

description: Gene expression after Week0


title: P6_LFC_W0_R2_SMT_A3

description: Gene expression after Week0


title: P6_HFC_W0_R2_SMT_A1

description: Gene expression after Week0


title: P6_HFC_W0_R2_SMT_A2

description: Gene expression after Week0


title: P6_Day_14_HFC_3

description: Gene expression after 14 Day


title: P6_Day_14_HFC_2

description: Gene expression after 14 Day


title: P6_HFC_Day 10_2

description: Gene expression after 10 Day


title: P6_Day_14_LFC_3

description: Gene expression after 14 Day


title: P6_HFC_Day 10_1

description: Gene expression after 10 Day


title: P6_HFC_D6_3

description: Gene expression after 6 Day


title: P6_Day_14_HFC_1

description: Gene expression after 14 Day


title: P6_LFC_Day 10_3

description: Gene expression after 10 Day


title: P6_LFC_Day 10_2

description: Gene expression after 10 Day


title: P6_HFC_Day 10_3

description: Gene expression after 10 Day


title: P6_HFC_D6_1

description: Gene expression after 6 Day


title: P6_Day_14_LFC_2

description: Gene expression after 14 Day


title: P6_LFC_Day 10_1

description: Gene expression after 10 Day


title: P6-HF20-W6R-SMT-A1

description: Gene expression after Week6


title: P6_LFC_D6_2

description: Gene expression after 6 Day


title: P6_Day_14_LFC_1

description: Gene expression after 14 Day


title: P6_HFC_D6_2

description: Gene expression after 6 Day


title: P6_LFC_D6_3

description: Gene expression after 6 Day


title: P6_LFC_D6_1

description: Gene expression after 6 Day


title: P6_HFC_D1_2

description: Gene expression after 1 Day


title: P6_HFC_D1_3

description: Gene expression after 1 Day


title: P2_HFC_W18_A1

description: Gene expression after Week18

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal. These intensities are used to calculate '75-percentile normalized data' and then fold changes using Agilent GeneSpring GX 11.0 software.

treatment_protocol: The mice were kept at 12:12 hr light: dark photoperiod with ad libitum access to food and water. Weaned mice at the age of 3-4 weeks were divided randomly into five groups- (each group contains 30 animals): first group was fed on normal diet (ND) with 10% of calories coming from fat, the second group was HFHSD fed group with increased sucrose and 60% of calories coming from fat (Research diets Inc.USA), and the third, fourth and fifth group of mice were fed on HFHSD with different doses of an ethano-botanical formulation, KAL-1 and we named them as HF5 (5µg of KAL-1+ HFHSD), HF20 (20µg of KAL-1+ HFHSD) and HF75 (75µg of KAL-1+ HFHSD). The daily weight of this aqueous formulation was 700 mg/ml. This dataset consists of gene expression changes in liver.

value: liver


title: P2_HFC_W18_A2

description: Gene expression after Week18


title: P6_HFC_D1_1

description: Gene expression after 1 Day


title: P6_D1_LF 3

description: Gene expression after 1 Day

source_name: LF_Skeletal Muscles


title: P2_HFC_W18_A5

description: Gene expression after Week18


title: P2_HF75_W18_A1

description: Gene expression after Week18


title: P2_HF75_W18_A3

description: Gene expression after Week18


title: P2_HF5_W18_A2

description: Gene expression after Week18


title: P2_LFC_W18_A6

description: Gene expression after Week18


title: P2_HF5_W18_A3

description: Gene expression after Week18


title: P6_D1_LF 2

description: Gene expression after 1 Day


title: P2_HF5_W18_A1

description: Gene expression after Week18


title: P2_HF75_W18_A6

description: Gene expression after Week18


title: P2_HF20_W18_A5

description: Gene expression after Week18


title: P6_D1_LF 1

description: Gene expression after 1 Day


title: P2_HF5_W15_A6

description: Gene expression after Week15


title: P2_HFC_W15_A4

description: Gene expression after Week15


title: P2_HF20_W18_A2

description: Gene expression after Week18


title: P2_LFC_W18_A5

description: Gene expression after Week18


title: P2_HF75_W15_A1

description: Gene expression after Week15


title: P2_HFC_W15_A6

description: Gene expression after Week15


title: P2_LFC_W18_A10

description: Gene expression after Week18


title: P2_HF20_W18_A6

description: Gene expression after Week18


title: P2_HF5_W15_A2

description: Gene expression after Week15


title: P2_HF20_W15_A4

description: Gene expression after Week15


title: P2_HF75_W15_A4

description: Gene expression after Week15


title: P2_HFC_W15_A3

description: Gene expression after Week15


title: P2_HF20_W15_A1

description: Gene expression after Week15


title: P2_HF5_W15_A3

description: Gene expression after Week15


title: P2_HF75_W15_A2

description: Gene expression after Week15


title: P2_HF20_W15_A5

description: Gene expression after Week15


title: P2_LFC_W15_A3

description: Gene expression after Week15


title: P2_LFC_W15_A1

description: Gene expression after Week15


title: P2_HFC_W12_A4

description: Gene expression after Week12


title: P2_LFC_W15_A2

description: Gene expression after Week15


title: P2_HF75_W12_A1

description: Gene expression after Week12


title: P2_HFC_W12_A6

description: Gene expression after Week12


title: P2_HF5_W12_A1

description: Gene expression after Week12


title: P2_LFC_W12_A4

description: Gene expression after Week12


title: P2_HF5_W12_A2

description: Gene expression after Week12


title: P2_HF75_W12_A3

description: Gene expression after Week12


title: P2_HFC_W12_A5

description: Gene expression after Week12


title: P2_HF20_W12_A2

description: Gene expression after Week12


title: P2_HF75_W12_A2

description: Gene expression after Week12


title: P2_HF5_W12_A3

description: Gene expression after Week12


title: P2_HF20_W12_A1

description: Gene expression after Week12


title: P2_LFC_W12_A6

description: Gene expression after Week12


title: P2_LFC_W12_A5

description: Gene expression after Week12


title: P2_HFC_W9_A1

description: Gene expression after Week9


title: P2_HF75_W9_A3

description: Gene expression after Week9


title: P2_HF5_W9_A2

description: Gene expression after Week9


title: P2_HF75_W9_A2

description: Gene expression after Week9


title: P2_HF75_W9_A1

description: Gene expression after Week9


title: P2_HFC_W9_A2

description: Gene expression after Week9


title: P2_HF5_W9_A1

description: Gene expression after Week9


title: P2_HF20_W9_A2

description: Gene expression after Week9


title: P2_LFC_W9_A3

description: Gene expression after Week9


title: P2_HF20_W9_A1

description: Gene expression after Week9


title: P2_LFC_W9_A1

description: Gene expression after Week9


title: P2_LFC_W9_A2

description: Gene expression after Week9


title: P2_HF5_W9_A3

description: Gene expression after Week9


title: P2HF75_W6_A1

description: Gene expression after Week6


title: P2HF5_W6_A2

description: Gene expression after Week6


title: P2HF75_W6_A3

description: Gene expression after Week6


title: P2HFC_W6_A3

description: Gene expression after Week6


title: P2HFC_W6_A1

description: Gene expression after Week6


title: P2HF5_W6_A1

description: Gene expression after Week6


title: P2LFC_W6_A3

description: Gene expression after Week6


title: P2HF5_W6_A3

description: Gene expression after Week6


title: P2HFC_W6_A2

description: Gene expression after Week6


title: P2_HF20_W9_A3

description: Gene expression after Week9


title: P2HF20_W6_A2

description: Gene expression after Week6


title: P2LFC_W6_A2

description: Gene expression after Week6


title: P2HF20_W6_A3

description: Gene expression after Week6


title: P2HF20_W6_A1

description: Gene expression after Week6


title: P2LFC_W6_A1

description: Gene expression after Week6


title: P2_HF75_W3_A2

description: Gene expression after Week3


title: P2_HF75_W3_A1

description: Gene expression after Week3


title: P2_HFC_W3_A3

description: Gene expression after Week3


title: P2_HFC_W3_A1

description: Gene expression after Week3


title: P2_HFC_W3_A2

description: Gene expression after Week3


title: P2_HF5_W3_A3

description: Gene expression after Week3


title: P2HF75_W6_A2

description: Gene expression after Week6


title: P2_HF20_W3_A3

description: Gene expression after Week3


title: P2_HF5_W3_A2

description: Gene expression after Week3


title: P2_HF5_W3_A1

description: Gene expression after Week3


title: P2_LFC_W3_A3

description: Gene expression after Week3


title: P2_HF20_W3_A1

description: Gene expression after Week3


title: P2_HFC_W0_A3

description: Gene expression after Week0


title: P2_LFC_W3_A1

description: Gene expression after Week3


title: P2_HF75_W3_A3

description: Gene expression after Week3


title: P2_Day_14_HFC_1

description: Gene expression after 14 Day


title: P2_HFC_W0_A2

description: Gene expression after Week0


title: P2_HF20_W3_A2

description: Gene expression after Week3


title: P2_Day_14_HFC_3

description: Gene expression after 14 Day


title: P2_LFC_W0_A1

description: Gene expression after Week0


title: P2_LFC_W3_A2

description: Gene expression after Week3


title: P2_Day_14_LFC_3

description: Gene expression after 14 Day


title: P2_LFC_W0_A2

description: Gene expression after Week0


title: P2_HFC_W0_A1

description: Gene expression after Week0


title: P2_Day_14_LFC_2

description: Gene expression after 14 Day


title: P2_Day_14_LFC_1

description: Gene expression after 14 Day


title: P2_LFC_Day 10_1

description: Gene expression after 10 Day


title: P2_HFC_Day 10_3

description: Gene expression after 10 Day


title: P2_LFC_Day 10_3

description: Gene expression after 10 Day


title: P2_LFC_Day 10_2

description: Gene expression after 10 Day


title: P2_HFC_Day 10_1

description: Gene expression after 10 Day


title: P2_HFC_W9_A3

description: Gene expression after Week9


title: P2_HFC_Day 10_2

description: Gene expression after 10 Day


title: P2_HFC_D6_3

description: Gene expression after 6 Day


title: P2_Day_14_HFC_2

description: Gene expression after 14 Day


title: P2_HF20_W12_A3

description: Gene expression after Week12


title: P2_LFC_D6_2

description: Gene expression after 6 Day


title: P2_HFC_D6_1

description: Gene expression after 6 Day


title: P2_HFC_D1_2

description: Gene expression after 1 Day


title: P2_HFC_D6_2

description: Gene expression after 6 Day


title: P2_LFC_D6_1

description: Gene expression after 6 Day


title: P2_Day 1_LF 1

description: Gene expression after 1 Day


title: P2_HFC_D1_3

description: Gene expression after 1 Day


title: P2_LFC_D6_3

description: Gene expression after 6 Day


title: P2_Day 1_LF 3

description: Gene expression after 1 Day


title: P2_HFC_D1_1

description: Gene expression after 1 Day


title: P2_Day 1_LF 2

description: Gene expression after 1 Day


title: P1_HFC_W18_A2

description: Gene expression after Week18

treatment_protocol: The mice were kept at 12:12 hr light: dark photoperiod with ad libitum access to food and water. Weaned mice at the age of 3-4 weeks were divided randomly into five groups- (each group contains 30 animals): first group was fed on normal diet (ND) with 10% of calories coming from fat, the second group was HFHSD fed group with increased sucrose and 60% of calories coming from fat (Research diets Inc.USA), and the third, fourth and fifth group of mice were fed on HFHSD with different doses of an ethano-botanical formulation, KAL-1 and we named them as HF5 (5µg of KAL-1+ HFHSD), HF20 (20µg of KAL-1+ HFHSD) and HF75 (75µg of KAL-1+ HFHSD). The daily weight of this aqueous formulation was 700 mg/ml. This dataset consists of gene expression changes in  Hippocampus.

value: Hippocampus


title: P1_HFC_W18_A12

description: Gene expression after Week18


title: P1_HF5_W18_A7

description: Gene expression after Week18


title: P1_HF75_W18_A5

description: Gene expression after Week18


title: P1_HF75_W18_A8

description: Gene expression after Week18


title: P1_HFC_W18_A4

description: Gene expression after Week18


title: P1_HF5_W18_A8

description: Gene expression after Week18


title: P1_LFC_W18_A5

description: Gene expression after Week18


title: P1_LFC_W18_A2

description: Gene expression after Week18


title: P1_HF20_W18_A1

description: Gene expression after Week18


title: P1_HF20_W18_A4

description: Gene expression after Week18


title: P1_HFC_W15_A2

description: Gene expression after Week15


title: P1_HFC_W15_A4

description: Gene expression after Week15


title: P1_HF20_W18_A7

description: Gene expression after Week18


title: P1_LFC_W18_A3

description: Gene expression after Week18


title: P1_HF75_W15_A7

description: Gene expression after Week15


title: P1_HF5_W15_A3

description: Gene expression after Week15


title: P1_HF75_W15_A3

description: Gene expression after Week15


title: P1_HF75_W18_A6

description: Gene expression after Week18


title: P1_HFC_W15_A3

description: Gene expression after Week15


title: P1_HF5_W15_A6

description: Gene expression after Week15


title: P1_HF20_W15_A5

description: Gene expression after Week15


title: P1_HF5_W15_A4

description: Gene expression after Week15


title: P1_LFC_W15_A6

description: Gene expression after Week15


title: P1_HF20_W15_A3

description: Gene expression after Week15


title: P1_HF75_W15_A8

description: Gene expression after Week15


title: P1_HF20_W15_A7

description: Gene expression after Week15


title: P1_LFC_W15_A3

description: Gene expression after Week15


title: P1_LFC_W15_A8

description: Gene expression after Week15


title: P1_HFC_W12_A7

description: Gene expression after Week12


title: P1_HF5_W12_A1

description: Gene expression after Week12


title: P1_HF5_W12_A3

description: Gene expression after Week12


title: P1_HF75_W12_A2

description: Gene expression after Week12


title: P1_LFC_W12_A2

description: Gene expression after Week12


title: P1_HF20_W12_A1

description: Gene expression after Week12


title: P1_HFC_W12_A6

description: Gene expression after Week12


title: P1_HF75_W9_A3

description: Gene expression after Week9


title: P1_HF75_W12_A3

description: Gene expression after Week12


title: P1_HF75_W12_A1

description: Gene expression after Week12


title: P1_HFC_W9_A3

description: Gene expression after Week9


title: P1_HFC_W9_A1

description: Gene expression after Week9


title: P1_HF75_W9_A1

description: Gene expression after Week9


title: P1_LFC_W12_A6

description: Gene expression after Week12


title: P1_HFC_W12_A8

description: Gene expression after Week12


title: P1_HF75_W9_A2

description: Gene expression after Week9


title: P1_HF20_W12_A2

description: Gene expression after Week12


title: P1_HF20_W9_A3

description: Gene expression after Week9


title: P1_HF5_W9_A1

description: Gene expression after Week9


title: P1_HF5_W9_A2

description: Gene expression after Week9


title: P1_HF20_W9_A1

description: Gene expression after Week9


title: P1_HF5_W12_A2

description: Gene expression after Week12


title: P1_HF5_W9_A3

description: Gene expression after Week9


title: P1_LFC_W12_A1

description: Gene expression after Week12


title: P1_LFC_W9_A3

description: Gene expression after Week9


title: P1_HF20_W12_A3

description: Gene expression after Week12


title: P1_HF20_W9_A2

description: Gene expression after Week9


title: P1HFC_W6_A3

description: Gene expression after Week6


title: P1_HFC_W9_A2

description: Gene expression after Week9


title: P1_LFC_W9_A1

description: Gene expression after Week9


title: P1_LFC_W9_A2

description: Gene expression after Week9


title: P1HFC_W6_A1

description: Gene expression after Week6


title: P1HFC_W6_A2

description: Gene expression after Week6


title: P1HF75_W6_A2

description: Gene expression after Week6


title: P1HF75_W6_A3

description: Gene expression after Week6


title: P1HF5_W6_A2

description: Gene expression after Week6


title: P1HF20_W6_A3

description: Gene expression after Week6


title: P1HF5_W6_A1

description: Gene expression after Week6


title: P1HF20_W6_A2

description: Gene expression after Week6


title: P1HF5_W6_A3

description: Gene expression after Week6


title: P1HF20_W6_A1

description: Gene expression after Week6


title: P1HF75_W6_A1

description: Gene expression after Week6


title: P1LFC_W6_A1

description: Gene expression after Week6


title: P1HFC_W3_A3

description: Gene expression after Week3


title: P1_HF5_W18_A3

description: Gene expression after Week18


title: P1LFC_W6_A3

description: Gene expression after Week6


title: P1HFC_W3_A2

description: Gene expression after Week3


title: P1HF75_W3_A3

description: Gene expression after Week3


title: P1HF75_W3_A2

description: Gene expression after Week3


title: P1LFC_W6_A2

description: Gene expression after Week6


title: P1HFC_W3_A1

description: Gene expression after Week3


title: P1HF20_W3_A2

description: Gene expression after Week3


title: P1LFC_W3_A3

description: Gene expression after Week3


title: P1LFC_W3_A2

description: Gene expression after Week3


title: P1HF20_W3_A3

description: Gene expression after Week3


title: P1_HFC_W0_A2

description: Gene expression after Week0


title: P1HF20_W3_A1

description: Gene expression after Week3


title: P1_LFC_W0_A2

description: Gene expression after Week0


title: P1_LFC_W0_A1

description: Gene expression after Week0


title: P1_Day_14_HFC_2

description: Gene expression after 14 Day


title: P1_HFC_W0_A3

description: Gene expression after Week0


title: P1LFC_W3_A1

description: Gene expression after Week3


title: P1_HFC_W0_A1

description: Gene expression after Week0


title: P1_LFC_W0_A3

description: Gene expression after Week0


title: P1_LFC_Day 10_3

description: Gene expression after 10 Day


title: P1_Day_14_HFC_1

description: Gene expression after 14 Day


title: P1HF75_W3_A1

description: Gene expression after Week3


title: P1_LFC_D6_2

description: Gene expression after 6 Day


title: P1_Day_14_LFC_3

description: Gene expression after 14 Day


title: P1_LFC_D6_1

description: Gene expression after 6 Day


title: P1_Day_14_LFC_2

description: Gene expression after 14 Day


title: P1_HFC_D1_3

description: Gene expression after 1 Day


title: P1_HFC_D1_1

description: Gene expression after 1 Day


title: P4_HF75_W18_S-A

description: Gene expression after Week18

source_name: HF20_Subcutaneous SVCs

value: Subcutaneous SVCs


title: P1_HFC_Day 10_3

description: Gene expression after 10 Day


title: P1_HFC_Day 10_2

description: Gene expression after 10 Day


title: P1_Day_14_LFC_1

description: Gene expression after 14 Day


title: P1_LFC_Day 10_2

description: Gene expression after 10 Day


title: P1_Day_14_HFC_3

description: Gene expression after 14 Day


title: P4_HF5_W18_S-A

description: Gene expression after Week18

source_name: HF5_Subcutaneous SVCs


title: P1_HFC_Day 10_1

description: Gene expression after 10 Day


title: P1_LFC_Day 10_1

description: Gene expression after 10 Day


title: P4 HFC W15-S-A

description: Gene expression after Week15

source_name: HFC_Subcutaneous SVCs


title: P4_HFC_W9R3_WS_1

description: Gene expression after Week9


title: P4-HF75-W12S-A

description: Gene expression after Week12

source_name: HF75_Subcutaneous SVCs


title: P1_HFC_D6_2

description: Gene expression after 6 Day


title: P4_HF5_W15_S-A

description: Gene expression after Week15


title: P1_LFC_D6_3

description: Gene expression after 6 Day


title: P1_HFC_D6_3

description: Gene expression after 6 Day


title: P4_LFC_sub_A3

description: Gene expression after Week12

source_name: LFC_Subcutaneous SVCs


title: P1_Day 1_LF 1

description: Gene expression after 1 Day


title: P1_HFC_D6_1

description: Gene expression after 6 Day


title: P4_HF75_W9_S-A

description: Gene expression after Week9


title: P4-HFC-W6RS-A

description: Gene expression after Week6


title: P4-HF75-W6RS-A

description: Gene expression after Week6


title: P4 LFC W15-S-A

description: Gene expression after Week15


title: P1_HFC_D1_2

description: Gene expression after 1 Day


title: P4_LFC_W9R3_WS_A1

description: Gene expression after Week9


title: P4-HF5-W6RS-A

description: Gene expression after Week6


title: P4_HF5_W9R3_WS_1

description: Gene expression after Week9


title: P4_HFC_W18_S-A2

description: Gene expression after Week18


title: P4_HF20_W18_S-A

description: Gene expression after Week18


title: P4_HF75_W3R_S_A

description: Gene expression after Week3


title: P4_HF75_W15_S-A

description: Gene expression after Week15


title: P4-HF20-W6RS-A

description: Gene expression after Week6


title: P4_HF20_SA2

description: Gene expression after Week12


title: P4-HF5-W12S-A

description: Gene expression after Week12


title: P4_HF20_W15R2_SA

description: Gene expression after Week15


title: P4_LFC_W18_S-A

description: Gene expression after Week18


title: P4_HFC_W0_R2_S-A

description: Gene expression after Week0


title: P4_LFC_Day 10_S

description: Gene expression after 10 Day


title: P4_LFC_W3R2_S_A

description: Gene expression after Week3


title: P4_Day_14_LFC_S

description: Gene expression after 14 Day


title: P4_LFC_W0_R2_S-A

description: Gene expression after Week0


title: P4-HFC-W12S-A

description: Gene expression after Week12


title: P5_HF20_W18_S-A

description: Gene expression after Week18

source_name: HF20_subcutaneous adipose

label_protocol: Agilent’s Quick-Amp labeling Kit (p/n5190-0444) was used following the manufacturer's protocol. T7 promoter based-linear amplification to generate labeled complementary  RNA (One-Color Microarray-Based Gene Expression Analysis)

treatment_protocol: The mice were kept at 12:12 hr light: dark photoperiod with ad libitum access to food and water. Weaned mice at the age of 3-4 weeks were divided randomly into five groups- (each group contains 30 animals): first group was fed on normal diet (ND) with 10% of calories coming from fat, the second group was HFHSD fed group with increased sucrose and 60% of calories coming from fat (Research diets Inc.USA), and the third, fourth and fifth group of mice were fed on HFHSD with different doses of an ethano-botanical formulation, KAL-1 and we named them as KAL-5 (5µg of KAL-1+ HFHSD), KAL-20 (20µg of KAL-1+ HFHSD) and KAL-75 (75µg of KAL-1+ HFHSD). The daily weight of this aqueous formulation was 700 mg/ml. This dataset consists of gene expression changes in Subcutaneous Adipose.

value: subcutaneous adipose


title: P5_LFC_D6_S_Rep

description: Gene expression after 6 Day


title: P4_H20_W9R3_WS_1

description: Gene expression after Week9

source_name: H20_Subcutaneous SVCs


title: P5_HF75_W18_STA

description: Gene expression after Week18

source_name: HF75_subcutaneous adipose


title: P5_HFC_W18_S-A

description: Gene expression after Week18

source_name: HFC_subcutaneous adipose


title: P4_HFC_Day 1_S

description: Gene expression after 1 Day


title: P4-LFC-W6RS-A

description: Gene expression after Week6


title: P4_HFC_W3R2_S_A

description: Gene expression after Week3


title: P4_HF20_W3R2_S_A

description: Gene expression after Week3


title: P5_HFC_W15_S-A

description: Gene expression after Week15


title: P5_HF20_W15_S-A

description: Gene expression after Week15


title: P4_HF5_W3_S-A

description: Gene expression after Week3


title: P5_HF75_W15_S-A

description: Gene expression after Week15


title: P5_HF5_W15_S-A

description: Gene expression after Week15

source_name: HF5_subcutaneous adipose


title: P4_Day_14_HFC_S

description: Gene expression after 14 Day


title: P5_HFC_D6_S Ts

description: Gene expression after 6 Day


title: P5_HF5_W18_S-A

description: Gene expression after Week18


title: P4_Day1_LFS

description: Gene expression after 1 Day

source_name: LF_Subcutaneous SVCs


title: P4_HFC_Day 10_S

description: Gene expression after 10 Day


title: P5_HFC-W12S-A

description: Gene expression after Week12


title: P5_LFC_W15_S-A

description: Gene expression after Week15

source_name: LFC_subcutaneous adipose


title: P5_HFC_W0_R2_S-A

description: Gene expression after Week0


title: P5_LFC_W18_S-A

description: Gene expression after Week18


title: P5_HF75-W12S Ts-A

description: Gene expression after Week12


title: P5_LFC_W0_R2_S-A

description: Gene expression after Week0


title: P5-HF5-W6RS-A

description: Gene expression after Week6


title: P5_HF75_W3R_S-A

description: Gene expression after Week3


title: P5_HF20-W12S Ts-A

description: Gene expression after Week12


title: P5_Day_14_HFC_S

description: Gene expression after 14 Day


title: P5_Day_14_LFC_S

description: Gene expression after 14 Day


title: P5_HF75_W9_S-A

description: Gene expression after Week9


title: P5_HFC_W9_S(T)

description: Gene expression after Week9


title: P5_HF20_W9_S-A

description: Gene expression after Week9


title: P5_HFC_W3R3_WS_1

description: Gene expression after Week3


title: P5_LFC_A3

description: Gene expression after Week12


title: P5_LFC_W9_S-A

description: Gene expression after Week9


title: P5-HFC-W6RS-A

description: Gene expression after Week6


title: P5_HF5_W9_S-A

description: Gene expression after Week9


title: P5_HFC_Day 1_S

description: Gene expression after 1 Day


title: P5_LFC_D6_S

description: Gene expression after 6 Day


title: P5_HFC_D6_S

description: Gene expression after 6 Day


title: P5-HF20-W6RS-A

description: Gene expression after Week6


title: P5_HF5-W12B Ts-A

description: Gene expression after Week12


title: P5-LFC-W6RS-A

description: Gene expression after Week6


title: P4_HF20_W15_E-A

description: Gene expression after Week15

source_name: HF20_Epididymal SVCs

treatment_protocol: The mice were kept at 12:12 hr light: dark photoperiod with ad libitum access to food and water. Weaned mice at the age of 3-4 weeks were divided randomly into five groups- (each group contains 30 animals): first group was fed on normal diet (ND) with 10% of calories coming from fat, the second group was HFHSD fed group with increased sucrose and 60% of calories coming from fat (Research diets Inc.USA), and the third, fourth and fifth group of mice were fed on HFHSD with different doses of an ethano-botanical formulation, KAL-1 and we named them as HF5 (5µg of KAL-1+ HFHSD), HF20 (20µg of KAL-1+ HFHSD) and HF75 (75µg of KAL-1+ HFHSD). The daily weight of this aqueous formulation was 700 mg/ml. This dataset consists of gene expression changes in epididymal infiltrating macrophages (SVCs)

tag: diet


title: P5-HF75-W6RS-A

description: Gene expression after Week6


title: P4_LFC_W18_E-A

description: Gene expression after Week18

source_name: LFC_Epididymal SVCs

value: epididymal infiltrating macrophages (SVCs)


title: P5_HF20_W3R2 S_A

description: Gene expression after Week3


title: P5_LFC_W3R2 S_A

description: Gene expression after Week3


title: P5_HFC_Day 10_S

description: Gene expression after 10 Day


title: P4-HFC-W12E-A

description: Gene expression after Week12

source_name: HFC_Epididymal SVCs


title: P4-HF75-W12E-A

description: Gene expression after Week12

source_name: HF75_Epididymal SVCs


title: P4_HF5_W9_E-A

description: Gene expression after Week9

source_name: HF5_Epididymal SVCs


title: P4_HF75_W9_E-A

description: Gene expression after Week9


title: P4-HF20-W12E-A

description: Gene expression after Week12


title: P4_HF20_W18_E-A

description: Gene expression after Week18


title: P4_HFC_W9R3_WE_1

description: Gene expression after Week9


title: P5_LFC_Day 10_S

description: Gene expression after 10 Day


title: P4_HF75_W18_E-A

description: Gene expression after Week18


title: P4_HFC_W18_E-A3

description: Gene expression after Week18


title: P4_HF5_W18_E-A

description: Gene expression after Week18


title: P4_LFC_W9R3_WE_A1

description: Gene expression after Week9


title: P4-HF75-W6RE-A

description: Gene expression after Week6


title: P4-HF20-W6RE-A

description: Gene expression after Week6


title: P5_HF5_W3R2 S_A

description: Gene expression after Week3


title: P4_HF75_W15_E-A

description: Gene expression after Week15


title: P4-LFC-W6RE-A

description: Gene expression after Week6


title: P4_HF20_W3R2_E_A

description: Gene expression after Week3


title: P4 HFC W15-E-A

description: Gene expression after Week15


title: P4 HF5 W15-E-A

description: Gene expression after Week15


title: P4_LFC_EA3

description: Gene expression after Week12


title: P4_LFC_Day 10_E

description: Gene expression after 10 Day


title: P4 LFC W15-E-A

description: Gene expression after Week15


title: P4_Day_14_HFC_E

description: Gene expression after 14 Day


title: P4_HF5_W3R2_E_A

description: Gene expression after Week3


title: P4-HF5-W12E-A

description: Gene expression after Week12


title: P4_HFC_W0_R2_E-A

description: Gene expression after Week0


title: P4_HF20_W9_E-A

description: Gene expression after Week9


title: P4_HFC_Day 10_E

description: Gene expression after 10 Day


title: P4_Day_14_LFC_E

description: Gene expression after 14 Day


title: P5_HF20_W18R1_ED

description: Gene expression after Week18

source_name: HF20_epididymal adipose

treatment_protocol: The mice were kept at 12:12 hr light: dark photoperiod with ad libitum access to food and water. Weaned mice at the age of 3-4 weeks were divided randomly into five groups- (each group contains 30 animals): first group was fed on normal diet (ND) with 10% of calories coming from fat, the second group was HFHSD fed group with increased sucrose and 60% of calories coming from fat (Research diets Inc.USA), and the third, fourth and fifth group of mice were fed on HFHSD with different doses of an ethano-botanical formulation, KAL-1 and we named them as KAL-5 (5µg of KAL-1+ HFHSD), KAL-20 (20µg of KAL-1+ HFHSD) and KAL-75 (75µg of KAL-1+ HFHSD). The daily weight of this aqueous formulation was 700 mg/ml. This dataset consists of gene expression changes in Epididymal Adipose.

value: epididymal adipose


title: P4_LFC_W3R2_E_A

description: Gene expression after Week3


title: P4-HF5-W6RE-A

description: Gene expression after Week6


title: P4_HF75_W3R_E_A

description: Gene expression after Week3


title: P5_HF75_EA2

description: Gene expression after Week12

source_name: HF75_epididymal adipose


title: P4_HFC_D6_E1

description: Gene expression after 6 Day


title: P4_LFC_W0_R2_E-A

description: Gene expression after Week0


title: P5_HF20_W15_E-A

description: Gene expression after Week15


title: P5_HFC-W12E-A

description: Gene expression after Week12

source_name: HFC_epididymal adipose


title: P4_LFC_D6_E1

description: Gene expression after 6 Day


title: P4_HFC_W3R2_E_A

description: Gene expression after Week3


title: P5_HF75_W18_E-T-A

description: Gene expression after Week18


title: P5_HF5_W18_E(T)-A

description: Gene expression after Week18

source_name: HF5_epididymal adipose


title: P5_HF20_EA2

description: Gene expression after Week12


title: P4-HFC-W6RE-A

description: Gene expression after Week6


title: P5_HF75_W9_E-A

description: Gene expression after Week9


title: P5-HF5-W6RE-A

description: Gene expression after Week6


title: P5_HF75_W15_E-A

description: Gene expression after Week15


title: P5_LFC_W18_E-Ts-A

description: Gene expression after Week18

source_name: LFC_epididymal adipose


title: P5_HF5_W3R2_E-A

description: Gene expression after Week3


title: P5_LFC_EA1

description: Gene expression after Week12


title: P5_HF20_W9_E-A

description: Gene expression after Week9


title: P5-LFC-W6RE-A

description: Gene expression after Week6


title: P5_HF5_W15_E-A

description: Gene expression after Week15


title: P5_HF5_W9_E-A

description: Gene expression after Week9


title: P5_HF5-W12E-A

description: Gene expression after Week12


title: P5_Day_14_HFC_E

description: Gene expression after 14 Day


title: P5_HFC_W15_E-A

description: Gene expression after Week15


title: P5_HFC_W0_R2_E-A

description: Gene expression after Week0


title: P5_HF20_W3R_E-Ts-A

description: Gene expression after Week3


title: P5_LFC_W15_E-A

description: Gene expression after Week15


title: P5-HF20-W6R2E-A4

description: Gene expression after Week6


title: P5_HF75_W3R_E-A

description: Gene expression after Week3


title: P5_LFC_W3R_E-A

description: Gene expression after Week3


title: P5_LFC_W9_E-A

description: Gene expression after Week9


title: P5_HFC_W9_E-A

description: Gene expression after Week9


title: P5_LFC_Day 10_E

description: Gene expression after 10 Day


title: P5_Day_14_LFC_E

description: Gene expression after 14 Day


title: P5_HFC_W3R3_WE_1

description: Gene expression after Week3


title: P5-HFC-W6RE-A

description: Gene expression after Week6


title: P5_HFC_W18_ETA

description: Gene expression after Week18


title: P4_HF75_W18_B-A

description: Gene expression after Week18

source_name: HF75_Brown SVCs

treatment_protocol: The mice were kept at 12:12 hr light: dark photoperiod with ad libitum access to food and water. Weaned mice at the age of 3-4 weeks were divided randomly into five groups- (each group contains 30 animals): first group was fed on normal diet (ND) with 10% of calories coming from fat, the second group was HFHSD fed group with increased sucrose and 60% of calories coming from fat (Research diets Inc.USA), and the third, fourth and fifth group of mice were fed on HFHSD with different doses of an ethano-botanical formulation, KAL-1 and we named them as HF5 (5µg of KAL-1+ HFHSD), HF20 (20µg of KAL-1+ HFHSD) and HF75 (75µg of KAL-1+ HFHSD). The daily weight of this aqueous formulation was 700 mg/ml. This dataset consists of gene expression changes in  brown infiltrating macrophages (SVCs)

value: brown infiltrating macrophages (SVCs)


title: P5-HF75-W6RE-A

description: Gene expression after Week6


title: P4_HF5_W18_B-A

description: Gene expression after Week18

source_name: HF5_Brown SVCs


title: P4_HF5_W15R2_BA

description: Gene expression after Week15


title: P5_HFC_D6_E

description: Gene expression after 6 Day


title: P4-HF5-W12B-A

description: Gene expression after Week12


title: P4_HFC_W18_B-A1

description: Gene expression after Week18

source_name: HFC_Brown SVCs


title: P4_HF20_BA

description: Gene expression after Week12

source_name: HF20_Brown SVCs


title: P5_LFC_W0_R2_E-A

description: Gene expression after Week0


title: P5_HFC_Day 10_E

description: Gene expression after 10 Day


title: P4_LFC_W18R1_BA

description: Gene expression after Week18

source_name: LFC_Brown SVCs


title: P4 HFC W15-B-A

description: Gene expression after Week15


title: P4_LFC_BA1

description: Gene expression after Week12


title: P4_HF75_W9_B-A

description: Gene expression after Week9


title: P4_HFC_W9R3_BAT_A

description: Gene expression after Week9


title: P5_LFC_D6_E

description: Gene expression after 6 Day


title: P4_HF20_W18_B-A

description: Gene expression after Week18

value: High fat+20µg of KAL diet


title: P5_D1_LFC_EA2

description: Gene expression after 1 Day


title: P4_HF75_W15R2_BA

description: Gene expression after Week15

value: High fat+75µg of KAL diet


title: P4_HF5_W9R3_BAT_1

description: Gene expression after Week9

value: High fat+5µg of KAL diet


title: P4_HF20_W9_B-A

description: Gene expression after Week9


title: P4-HF20-W6RB-A

description: Gene expression after Week6


title: P4-HFC-W12B-A

description: Gene expression after Week12

value: High fat diet


title: P4-HF75-W12B-A

description: Gene expression after Week12


title: P4_HFC_W3R2_B_A

description: Gene expression after Week3


title: P4_HF20_W15_B-A

description: Gene expression after Week15


title: P4_HF75_W3R_B_A

description: Gene expression after Week3


title: P4_Day_14_LFC_B

description: Gene expression after 14 Day

value: Low fat diet


title: P4_LFC_W0_R2_B-A

description: Gene expression after Week0


title: P4_HFC_W0_R2_B-A

description: Gene expression after Week0


title: P4_Day_14_HFC_B

description: Gene expression after 14 Day

value: 14 Day


title: P4_HFC_D1_BAT

description: Gene expression after 1 Day


title: P4-HF75-W6RB-A

description: Gene expression after Week6


title: P5_HF5_W18_B-A

description: Gene expression after Week18

source_name: HF5_brown adipose

treatment_protocol: The mice were kept at 12:12 hr light: dark photoperiod with ad libitum access to food and water. Weaned mice at the age of 3-4 weeks were divided randomly into five groups- (each group contains 30 animals): first group was fed on normal diet (ND) with 10% of calories coming from fat, the second group was HFHSD fed group with increased sucrose and 60% of calories coming from fat (Research diets Inc.USA), and the third, fourth and fifth group of mice were fed on HFHSD with different doses of an ethano-botanical formulation, KAL-1 and we named them as KAL-5 (5µg of KAL-1+ HFHSD), KAL-20 (20µg of KAL-1+ HFHSD) and KAL-75 (75µg of KAL-1+ HFHSD). The daily weight of this aqueous formulation was 700 mg/ml. This dataset consists of gene expression changes in Brown Adipose.

value: Brown Adipose


title: P4_LFC_W9_B-A

description: Gene expression after Week9


title: P4-HFC-W6R2B-A-1

description: Gene expression after Week6


title: P5_HF75_W18_B-A

description: Gene expression after Week18

source_name: HF75_brown adipose


title: P4-HF5-W6RB-A

description: Gene expression after Week6


title: P4_HFC_D6_B2

description: Gene expression after 6 Day

value: 6 Day


title: P5_HF20_W18_B-T-A

description: Gene expression after Week18

source_name: HF20_brown adipose


title: P4_LFC_Day 10_B

description: Gene expression after 10 Day

value: 10 Day


title: P4_Day1_LFB

description: Gene expression after 1 Day

source_name: LFB_Brown SVCs

value: 1 Day


title: P4_HF5_W3_B-A

description: Gene expression after Week3


title: P4_HF20_W3R2_B_A

description: Gene expression after Week3


title: P5_HF5_W15_B(T)-A

description: Gene expression after Week15


title: P5_LFC_D6_BAT

description: Gene expression after 6 Day


title: P5_LFC_W18_B-A

description: Gene expression after Week18

source_name: LFC_brown adipose


title: P5_HFC_W18_B-A

description: Gene expression after Week18

source_name: HFC_brown adipose


title: P4 LFC W15-B-A

description: Gene expression after Week15


title: P5_HF20_W15R2_BA

description: Gene expression after Week15


title: P5_HFC_W15_B-A

description: Gene expression after Week15


title: P5_LFC_W15_B-A

description: Gene expression after Week15


title: P5_HF75_W15_B-A

description: Gene expression after Week15


title: P4_HFC_Day 10_B

description: Gene expression after 10 Day


title: P5_LFC_BA3

description: Gene expression after Week12


title: P4_LFC_W3B_A2

description: Gene expression after Week3


title: P5_HF20_BA

description: Gene expression after Week12


title: P5_HFC_W9_B-A

description: Gene expression after Week9


title: shoot-10 μM DEX- 24 hr - rep2

city: Seoul

first: Eun Kyung

last: Yoon

address: 120 Neungdong-ro Gwangjin-gu

country: South Korea

institute: KonKuk University

description: Sample name: DEX24hr-2

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45°C on Affymetrix ATH1 GeneChip® Arabidopsis Genome Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Microarray Suite version 5.0 (MAS 5.0) algorithm implemented in Affymetrix Expression Console software (version1.1) was used to normalize the raw data. To reduce noise for the significance analysis, probe sets that were called Present by the MAS5 detection call in 100% of the samples were selected.  Highly expressed genes that showed over 1.5-fold difference between the signal values of control and test samples were selected for further study.

organism: Arabidopsis thaliana

source_name: pSHR:SHR-GR in shr-2

label_protocol: Biotinylated cDNA were prepared from 300 ng total RNA (GeneChip® 3’ IVT Express Kit User Manual P/N 702646 Rev. 1, Affymetrix), according to the standard Affymetrix ATH1 microarray instructions.

growth_protocol: Plants were grown on 1/2 MS medium under 16 h light/ 8 h dark cycle at 22°C

extract_protocol: RNeasy plant mini kit (Qiagen), according to manufacturer's instructions

treatment_protocol: 10 μM DEX was applied to the seedlings at 10 DAG (for short treatment) or 9 DAG (for 24hr treatment).

value: SHR induction by DEX

tag: time

value: 24 hr

value: whole shoot


title: shoot-10 μM DEX- 12 hr - rep2

description: Sample name: DEX12hr-2

value: 12 hr


title: shoot-10 μM DEX- 3 hr - rep2

description: Sample name: DEX3hr-2

value: 3 hr


title: shoot-10 μM DEX- 24 hr - rep1

description: Sample name: DEX24hr-1


title: shoot-10 μM DEX- 6 hr - rep2

description: Sample name: DEX6hr-2

value: 6 hr


title: P5_HF5_W9_B-A

description: Gene expression after Week9


title: P5_HFC-W12B-A

description: Gene expression after Week12


title: shoot-10 μM DEX- 3 hr - rep1

description: Sample name: DEX3hr-1


title: P5-HF5-W6RB-A

description: Gene expression after Week6


title: P5-HFC-W6RB-A

description: Gene expression after Week6


title: shoot-10 μM DEX- 0 hr - rep2

description: Sample name: Control-2

value: control

value: 0 hr


title: P5-HF75-W6RB-A

description: Gene expression after Week6

value: High fat+75µg of KAL diet


title: P5_LFC_W9R3_BAT_A1

description: Gene expression after Week9


title: shoot-10 μM DEX- 6 hr - rep1

description: Sample name: DEX6hr-1


title: CD19-CreDPB B220- (B-ALL)_E0782

city: London

first: Rodney

middle: P.

last: DeKoter

state: Ontario

address: 1151 Richmond Street

department: Microbiology & Immunology

institute: University of Western Ontario

description: mouse exon 1.0

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: GeneChip Scanner 3000 (Affymetrix).

data_processing:
Batch effect was removed using ComBat. Data were analyzed using Partek Genomics Suite.
probe group file: MoEx-1 0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.mps

source_name: CD19-CreDPB B220- (B-ALL)

label_protocol: RNA was processed using the WT terminal labeling and hybridization kit (Affymetrix, Santa Clara, CA)

growth_protocol: B cells (B220+) or leukemia cells (B220-) were sorted from the spleen of mice aged 11-18 weeks

extract_protocol: Total RNA was prepared from single cell suspensions using Trizol reagent (Life Technologies)

treatment_protocol: not applicable

value: 11-18 weeks

value: Spleen

value: Leukemia cells


title: P5_HF20_W9_B-A

description: Gene expression after Week9

value: High fat+20µg of KAL diet


title: CD19-CreDPB B220- (B-ALL)_E0668

description: mouse exon 1.0


title: CD19-CreDPB B220- (B-ALL)_E0783

description: mouse exon 1.0


title: shoot-10 μM DEX- 0 hr - rep1

description: Sample name: Control-1


title: CD19-CreDPB B220+ (B cell)_E0760

description: mouse exon 1.0

source_name: CD19-CreDPB B220+ (B cell)

value: B cells, leukemic


title: shoot-10 μM DEX- 12 hr - rep1

description: Sample name: DEX12hr-1


title: P5-HF20-W6R2B-A5

description: Gene expression after Week6

value: Brown Adipose


title: P5_HF75_W9_B-A

description: Gene expression after Week9


title: CD19-CreDPB B220+ (B cell)_E0669

description: mouse exon 1.0


title: P5-LFC-W6RB-A

description: Gene expression after Week6

value: Low fat diet


title: Control DB_E0667

description: mouse exon 1.0

source_name: Control DB

value: B cells, control


title: P5_HF75_W3R2 B_A

description: Gene expression after Week3


title: Control DB_E0761

description: mouse exon 1.0


title: P5_HFC_W3R3_BAT_1

description: Gene expression after Week3

value: High fat diet


title: Control DB_E0762

description: mouse exon 1.0


title: P5_HF20_W3R3_BAT_A

description: Gene expression after Week3


title: P5_LFC_W3R3_BAT_1

description: Gene expression after Week3


title: P5_HF5_W3R2 B_A

description: Gene expression after Week3

value: High fat+5µg of KAL diet


title: P5_Day_14_LFC_B

description: Gene expression after 14 Day

value: 14 Day


title: P5_Day_14_HFC_B

description: Gene expression after 14 Day


title: P5_LFC_D6_B1

description: Gene expression after 6 Day

value: 6 Day


title: P5_HFC_W0_R2_B-A

description: Gene expression after Week0


title: P5_HFC_D6_B1

description: Gene expression after 6 Day


title: P5_HF75-W12B-A

description: Gene expression after Week12


title: P5_LFC_Day 10_B

description: Gene expression after 10 Day

value: 10 Day


title: P5_LFC_W0_R2_B-A5

description: Gene expression after Week0


title: P5_HF5-W12B-A

description: Gene expression after Week12


title: P5_HFC_Day 10_BAT

description: Gene expression after 10 Day


title: Melanoma cell line M050829, siEZH2 transfected, biol Rep 2

city: Zurich

first: Daniel

last: Zingg

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

hyb_protocol: According to Human Gene 2.1 ST Array (902136, Affymetrix) protocol and GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Scanned with a GeneChip Scanner 7G (Affymetrix)

data_processing: Differential gene expression was determined by R package limma (Smyth, G. K. limma: Linear Models for Microarray Data. Statistics for Biology and Health 5, 397–420 (2005))

source_name: Melanoma cell line transfected for 72h

label_protocol: According to MessageAmp II-Biotin Enhanced aRNA Amplification Kit (AM1791, Life Technologies)

extract_protocol: According to RNeasy Mini Kit (74104, Qiagen)

tag: transfection

value: Subcutaneous melanoma metastasis


title: Melanoma cell line M050829, siEZH2 transfected, biol Rep 3


title: genomic DNA peripheral blood DNA p2F12

type: genomic

first: James

middle: M

last: Flanagan

state: London

address: Hammersmith Hospital, Du Cane Rd

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College London

description: normal blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2
The in vitro methylated control samples IVM100 and IVM0 could not be pre-processed with the actual samples, but they are represented in Matrix_raw_signal.txt (linked as supplementary file on Series record).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: peripheral blood DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA samples were extracted from buffy coats using DNA Blood Mini Kits (Qiagen, Crawley, UK) according to standard instructions

value: Female

tag: sample type

value: peripheral blood DNA

tag: disease state

value: normal

tag: duplicate

tag: plate

tag: row

value: F

tag: col

tag: ChIP

tag: label

tag: agegap

tag: agebloodtaken

tag: round

tag: subjectid for matching


title: genomic DNA peripheral blood DNA p2C12

description: normal blood sample

tag: gender

value: C


title: genomic DNA peripheral blood DNA p2E12

description: normal blood sample

value: E


title: genomic DNA peripheral blood DNA p2G11

description: normal blood sample

value: G


title: Melanoma cell line M050829, siEZH2 transfected, biol Rep 1

tag: cell line

tag: tissue


title: genomic DNA peripheral blood DNA p2H11

description: normal blood sample

value: H


title: Melanoma cell line M050829, siControl transfected, biol Rep 3

value: siControl


title: genomic DNA peripheral blood DNA p2B12

description: normal blood sample

value: B


title: genomic DNA peripheral blood DNA p2F11

description: normal blood sample


title: genomic DNA peripheral blood DNA p2A12

description: normal blood sample

value: A


title: Melanoma cell line M050829, siControl transfected, biol Rep 2


title: brain-oxBS-2

first: Dario

last: Beraldi

address: Robinson Way

institute: Cambridge Research Institute

description: Commercial sample: amsbio ltd. Catalogue number: D1234039-DC, Lot No: A807003

hyb_protocol: Standard protocol for 450K Illumina array

data_processing:
idat files generated by Illumina GenomeStudio Software
Beta values and detection pvalues obtained with the R/Bioconductor package minfi.

source_name: Cerebellum, male

growth_protocol: n/a (fresh tissue)

extract_protocol: n/a (commercial sample)

treatment_protocol: No treatment

value: Cerebellum

value: Male

tag: age

value: oxBS


title: genomic DNA peripheral blood DNA p2D12

description: normal blood sample

value: D


title: brain-oxBS-1

scan_protocol: Standard protocol for 450K Illumina array


title: brain-BS-3

label_protocol: Standard protocol for 450K Illumina array

value: BS


title: genomic DNA peripheral blood DNA p2C11

description: normal blood sample


title: genomic DNA peripheral blood DNA p2F10

description: normal blood sample


title: genomic DNA peripheral blood DNA p2E11

description: normal blood sample


title: genomic DNA peripheral blood DNA p2E10

description: normal blood sample


title: Melanoma cell line M010817, siEZH2 transfected, biol Rep 3

tag: transfection

value: Subcutaneous melanoma metastasis


title: genomic DNA peripheral blood DNA p2D11

description: normal blood sample

value: Female

tag: sample type


title: genomic DNA peripheral blood DNA p2A11

description: normal blood sample

value: peripheral blood DNA

tag: disease state


title: brain-oxBS-4


title: genomic DNA peripheral blood DNA p2H10

description: normal blood sample

value: normal

tag: duplicate


title: brain-oxBS-3


title: genomic DNA peripheral blood DNA p2D10

description: normal blood sample

tag: plate


title: genomic DNA peripheral blood DNA p2B11

description: normal blood sample

tag: row


title: Melanoma cell line M010817, siControl transfected, biol Rep 3


title: Melanoma cell line M010817, siEZH2 transfected, biol Rep 1


title: Melanoma cell line M010817, siControl transfected, biol Rep 2


title: Melanoma cell line M010817, siControl transfected, biol Rep 1


title: genomic DNA peripheral blood DNA p2C10

description: normal blood sample

tag: col


title: genomic DNA peripheral blood DNA p2B10

description: normal blood sample

tag: ChIP


title: Embryo 18.5

city: Brussels

first: Kurt

last: Jacobs

address: Laarbeeklaan 103

department: Faculty of Medicine and Pharmacy

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

description:
Embryo 18 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.

hyb_protocol: After ethanol precipitation, samples were dissolved in hybridization mix at 75°C for 10 minutes, and incubated overnight at 47°C on the arrays in closed incubation chambers with 50% formamide. The slides were washed 10min in 2xSSC/0.05% Tween20, 10 min 1xSSC, 5min 0.1%SSC at 60°C and 1min in 0.1%SSC at RT

scan_protocol: Agilent dual laser DNA microarray scanner G2566AA was used for scanning the arrays, data was stored as .TIFF files

data_processing: .TIFF files were imported in, and processed by, BlueFuse Multi 3.1.

source_name: Embryo culture

label_protocol: Labelling was done following standard 24sure v3 protocol. In brief, samples were mixed with 5µl of random primers and denaturated for 5min at 94°C. Afterwards, samples were mixed with 12µl of Cy3/Cy5 labelling master mix and incubated at 37°C for 4 hours.

extract_protocol: Extraction was done following standard 24sure v3 protocol. In brief, 2.5µl extraction buffer and 5µl extraction cocktail were added per sample, followed by 10min incubation at 75°C and 4min at 95°C.

tag: cell type

value: Single Blastomere

source_name: female/male reference

tag: sample

value: reference


title: Embryo 18.6

description:
Embryo 18 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 18.4

description:
Embryo 18 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 18.3

description:
Embryo 18 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 18.7

description:
Embryo 18 cell 7
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 18.2

description:
Embryo 18 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 18.1

description:
Embryo 18 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Melanoma cell line M050829, siControl transfected, biol Rep 1


title: Embryo 17.7

description:
Embryo 17 cell 7
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 17.6

description:
Embryo 17 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: brain-BS-4


title: genomic DNA peripheral blood DNA p2A10

description: normal blood sample

tag: label

tag: agegap

tag: agebloodtaken


title: Embryo 17.4

description:
Embryo 17 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 17.5

description:
Embryo 17 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2G9

description: normal blood sample

tag: gender

tag: round

tag: subjectid for matching


title: genomic DNA peripheral blood DNA p2F9

description: normal blood sample

value: F


title: Embryo 17.2

description:
Embryo 17 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Melanoma cell line M010817, siEZH2 transfected, biol Rep 2

tag: cell line

tag: tissue


title: genomic DNA peripheral blood DNA p2E9

description: normal blood sample

tag: sample type

value: E


title: genomic DNA peripheral blood DNA p2G10

description: normal blood sample

tag: disease state

value: G


title: Embryo 17.1

description:
Embryo 17 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 17.3

description:
Embryo 17 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2D9

description: normal blood sample

tag: duplicate


title: brain-BS-2

tag: age


title: genomic DNA peripheral blood DNA p2B9

description: normal blood sample

tag: plate

tag: row


title: Embryo 16.4

description:
Embryo 16 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 16.3

description:
Embryo 16 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2H8

description: normal blood sample

value: H

tag: col

tag: ChIP


title: genomic DNA peripheral blood DNA p2C9

description: normal blood sample

value: C


title: Embryo 16.6

description:
Embryo 16 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.

tag: cell type

tag: sample


title: Embryo 16.2

description:
Embryo 16 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 16.1

description:
Embryo 16 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2H9

description: normal blood sample

tag: label

tag: agegap


title: Embryo 15.7

description:
Embryo 15 cell 7
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2E8

description: normal blood sample

tag: gender

tag: agebloodtaken


title: genomic DNA peripheral blood DNA p2G8

description: normal blood sample

tag: round

tag: subjectid for matching


title: Embryo 16.5

description:
Embryo 16 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: brain-BS-1

description: Commercial sample: amsbio ltd. Catalogue number: D1234039-DC, Lot No: A807003

tag: tissue


title: genomic DNA peripheral blood DNA p2F8

description: normal blood sample

tag: sample type


title: Embryo 15.6

description:
Embryo 15 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 15.5

description:
Embryo 15 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2A9

description: normal blood sample

tag: disease state

value: A


title: Embryo 15.4

description:
Embryo 15 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2D8

description: normal blood sample

tag: duplicate


title: genomic DNA peripheral blood DNA p2F7

description: normal blood sample


title: Embryo 15.3

description:
Embryo 15 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 15.2

description:
Embryo 15 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2B8

description: normal blood sample

value: B


title: Embryo 14.5

description:
Embryo 14 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 15.1

description:
Embryo 15 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 14.4

description:
Embryo 14 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 14.2

description:
Embryo 14 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2C7

description: normal blood sample


title: Embryo 14.6

description:
Embryo 14 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2H7

description: normal blood sample


title: Embryo 13.5

description:
Embryo 13 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2B7

description: normal blood sample


title: Embryo 14.1

description:
Embryo 14 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2A7

description: normal blood sample


title: genomic DNA peripheral blood DNA p2D7

description: normal blood sample


title: Embryo 14.3

description:
Embryo 14 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 13.4

description:
Embryo 13 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 13.3

description:
Embryo 13 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2E6

description: normal blood sample


title: genomic DNA peripheral blood DNA p2F6

description: normal blood sample


title: Embryo 13.2

description:
Embryo 13 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2A8

description: normal blood sample


title: Embryo 13.1

description:
Embryo 13 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 12.6

description:
Embryo 12 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2E7

description: normal blood sample


title: genomic DNA peripheral blood DNA p2G6

description: normal blood sample


title: genomic DNA peripheral blood DNA p2C8

description: normal blood sample


title: Embryo 12.5

description:
Embryo 12 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2H6

description: normal blood sample


title: genomic DNA peripheral blood DNA p2C6

description: normal blood sample


title: genomic DNA peripheral blood DNA p2A6

description: normal blood sample


title: genomic DNA peripheral blood DNA p2E5

description: normal blood sample


title: genomic DNA peripheral blood DNA p2B6

description: normal blood sample


title: genomic DNA peripheral blood DNA p2D6

description: normal blood sample


title: genomic DNA peripheral blood DNA p2G7

description: normal blood sample