title: Uninjured_HIF1α_shRNA_Rep2

treatment_protocol: Lentiviral vectors containing MISSION shRNAs for HIF-1α from Sigma were added to eDRGs at DIV4. Spot cultures were then collected at DIV7.


title: Peripheral mononuclear blood cells in patient 29 with Behçet’s disease

status: Public on Jan 21 2016

type: RNA

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description:
Genes expressed in peripheral blood mononuclear cells from patient 29 with Behçet’s disease
BD-29

hyb_protocol: Cy5-labeled cRNAs from the vasculitis patients (1,625 ng) were mixed with the same amount of reverse color Cy3-labeled cRNAs from normal volunteers. Hybridization, rinsing, scanning, and gene analysis were conducted with the Agilent Whole Human Genome Microarray (4x44K G4112F), according to the manufacturer’s protocol.

scan_protocol: The array was scanned using Agilent G2505B DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.1.3.1 and LOWESS background subtraction and dye-normalization were used.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood cells from Behçet’s disease patient 29

label_protocol: Total RNA (500 ng) isolated from the PBMCs of each vasculitis patient was examined along with pooled RNA from normal volunteers. RNA from each patient and the pooled normal RNA were reverse-transcribed with oligo-dT primers containing the T7 RNA polymerase promoter sequence. The resulting cDNA was subjected to in vitro transcription with T7 RNA polymerase for labeling with Cy3 or Cy5 (CyDye, Amersham Pharmacia Biotech).

extract_protocol: RNA was prepared from PBMCs using PAXgene Blood RNA Kit (QIAGEN) according to the manufacturer’s protocol.

tag: age (y)

tag: gender

value: male

tag: disease state

value: Behçet’s disease

tag: cell type

value: peripheral blood cells

source_name: Peripheral mononuclear blood cells from 17 healthy controls

value: 9 females and 7 males

value: healthy controls without any identified diseases


title: 12_HPI_HIF1α_shRNA_Rep2

city: Saint Louis

first: Valeria

last: Cavalli

state: Missouri

address: 660 S. Euclid Ave.

department: Anatomy and Neurobiology

country: USA

institute: Washington University in St. Louis

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Images were quantitated by Illumina Beadscan v3 and imported into Illumina Genome Studio.

label: biotin

organism: Mus musculus

source_name: Embryonic Dorsal Root Ganglia

label_protocol: RNA was linearly amplified using MessageAmp TotalPrep (Life Technologies)

extract_protocol: Total RNA was isolated from samples using the Ambion PureLink Mini Kit as per the manufacturers protocol. RNA was quantified using a Nanodrop 2100 and quality was analyzed using an Agilent Bioanalyzer 2100.

treatment_protocol: Lentiviral vectors containing MISSION shRNAs for HIF-1α from Sigma were added to eDRGs at DIV4. Spot cultures were then axotomized with a blade at DIV7 and collected 12 hours post injury

tag: tissue

value: Embryonic Dorsal Root Ganglia

tag: strain

tag: developmental stage

value: Embryonic day 13


title: Peripheral mononuclear blood cells in patient 27 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 27 with Behçet’s disease
BD-27

source_name: Peripheral blood cells from Behçet’s disease patient 27

value: female


title: 3_HPI_HIF1α_shRNA_Rep1

treatment_protocol: Lentiviral vectors containing MISSION shRNAs for HIF-1α from Sigma were added to eDRGs at DIV4. Spot cultures were then axotomized with a blade at DIV7 and collected 3 hours post injury


title: Peripheral mononuclear blood cells in patient 28 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 28 with Behçet’s disease
BD-28

source_name: Peripheral blood cells from Behçet’s disease patient 28


title: 12_HPI_Control_shRNA_Rep2

treatment_protocol: Lentiviral vectors containing MISSION control shRNAs from Sigma were added to eDRGs at DIV4. Spot cultures were then axotomized with a blade at DIV7 and collected 12 hours post injury


title: 3_HPI_Control_shRNA_Rep2

treatment_protocol: Lentiviral vectors containing MISSION control shRNAs from Sigma were added to eDRGs at DIV4. Spot cultures were then axotomized with a blade at DIV7 and collected 3 hours post injury


title: Peripheral mononuclear blood cells in patient 26 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 26 with Behçet’s disease
BD-26

source_name: Peripheral blood cells from Behçet’s disease patient 26


title: Peripheral mononuclear blood cells in patient 23 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 23 with Behçet’s disease
BD-23

source_name: Peripheral blood cells from Behçet’s disease patient 23


title: Peripheral mononuclear blood cells in patient 22 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 22 with Behçet’s disease
BD-22

source_name: Peripheral blood cells from Behçet’s disease patient 22


title: Peripheral mononuclear blood cells in patient 21 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 21 with Behçet’s disease
BD-21

source_name: Peripheral blood cells from Behçet’s disease patient 21


title: Peripheral mononuclear blood cells in patient 25 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 25 with Behçet’s disease
BD-25

source_name: Peripheral blood cells from Behçet’s disease patient 25


title: Peripheral mononuclear blood cells in patient 19 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 19 with Behçet’s disease
BD-19

source_name: Peripheral blood cells from Behçet’s disease patient 19


title: 12_HPI_HIF1α_shRNA_Rep1


title: Uninjured_HIF1α_Overexpression_Rep1

treatment_protocol: FUGW Lentiviral vectors containing human HIF-1α were added to eDRGs at DIV4. Spot cultures were then collected at DIV7.


title: Peripheral mononuclear blood cells in patient 16 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 16 with Behçet’s disease
BD-16

source_name: Peripheral blood cells from Behçet’s disease patient 16


title: 12_HPI_HIF1α_Overexpression_Rep1

treatment_protocol: FUGW Lentiviral vectors containing human HIF-1α were added to eDRGs at DIV4. Spot cultures were then axotomized with a blade at DIV7 and collected 12 hours post injury.


title: Uninjured_HIF1α_shRNA_Rep1


title: 3_HPI_Control_shRNA_Rep1


title: Peripheral mononuclear blood cells in patient 17 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 17 with Behçet’s disease
BD-17

source_name: Peripheral blood cells from Behçet’s disease patient 17


title: Peripheral mononuclear blood cells in patient 24 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 24 with Behçet’s disease
BD-24

source_name: Peripheral blood cells from Behçet’s disease patient 24


title: Peripheral mononuclear blood cells in patient 14 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 14 with Behçet’s disease
BD-14

source_name: Peripheral blood cells from Behçet’s disease patient 14


title: Peripheral mononuclear blood cells in patient 18 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 18 with Behçet’s disease
BD-18

source_name: Peripheral blood cells from Behçet’s disease patient 18


title: TR_N: XA0572

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

institute: Toray Industries, Inc.

description: miRNA

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing:
Mean and standard deviation (SD) of the 5% trimmed signals of the negative controls were calculated. Signals of miRNAs over mean+2SD of the negative controls were subtracted with the mean of the negative controls. The undetected signal was replaced with the value that was the least signal intensity on each DNA chip minus 0.1 in log2 scale followed by quantile normalization.
R 3.0.2 was used for analysis.

source_name: serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: diagnosis

value: non-cancer

value: serum


title: Peripheral mononuclear blood cells in patient 20 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 20 with Behçet’s disease
BD-20

source_name: Peripheral blood cells from Behçet’s disease patient 20


title: 12_HPI_Control_shRNA_Rep1


title: Peripheral mononuclear blood cells in patient 15 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 15 with Behçet’s disease
BD-15

source_name: Peripheral blood cells from Behçet’s disease patient 15

source_name: Peripheral mononuclear blood cells from 17 healthy controls


title: Uninjured_Control_shRNA_Rep1

source_name: Embryonic Dorsal Root Ganglia

treatment_protocol: Lentiviral vectors containing MISSION control shRNAs from Sigma were added to eDRGs at DIV4. Spot cultures were then collected at DIV7.


title: 3_HPI_HIF1α_Overexpression_Rep1

treatment_protocol: FUGW Lentiviral vectors containing human HIF-1α were added to eDRGs at DIV4. Spot cultures were then axotomized with a blade at DIV7 and collected 3 hours post injury.


title: Peripheral mononuclear blood cells in patient 13 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 13 with Behçet’s disease
BD-13

source_name: Peripheral blood cells from Behçet’s disease patient 13


title: muscle_knockout_contracted_rep7

city: Provo

first: David

middle: M.

last: Thomson

state: Utah

department: PDBIO

institute: Brigham Young University

description: SAMPLE 31

hyb_protocol: 750ug of each aRNA in water (5ul) was suspended in Illumina HYB buffer (10ul) ) and heated to 65C for five minutes, then allowed to cool to room temperature.  The samples were applied to Illumina Mouse Ref-8v2 Expression BeadChips and hybridized at 58C for 16-20 hours at high humidity.  Arrays were washed according to Illumina standard protocol.Immobilized, biotinylated aRNAs were then detected by staining with cy3 Steptavidin (1ug cy3-SA per 1 ml of Illumina “Block E1”) for 10 minutes at room temperature.  Arrays were washed and dried according to Illumina standard protocol.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader.  Laser power and PMT voltage were kept constant for Cy3 scans.  Images were quantitated by Illumina Beadscan, v3.  Quantitated data was imported into Illumina GenomeStudio software.  On-array spot replicates were averaged by GenomeStudio and individual spot probe was reported.

data_processing: Microarray data were analyzed using both the limma (version 3.1) and lumi (version 3.0) R packages in R (version 3.1.2). The data were background subtracted, normalized using Robust Spline Normalization (RSN), and then log2 transformed according to lumi best practices.

label_protocol: RNA transcripts were amplified by T7 linear amplification (MessageAmp TotalPrep amplification kit; Life Technologies).   200 ng of each total cellular RNA sample (11ul) was mixed with an oligo-dT T7 primer (1ul), 10x reaction buffer (2ul), dNTP mix (4ul), Rnase Inhibitor (1ul), and Arrayscript RT enzyme (1ul).  Reverse transcription was carried out for 2 hours at 42C.  After a three minute incubation on ice, the cDNA underwent 2nd strand synthesis by adding water (63ul), 10x 2nd strand buffer (10ul), dNTP mix (4ul), DNA polymerase (2ul) and Rnase H (1ul).  This cocktail was incubated at 16C for 2 hours.  Following a column cleanup using Zymo DNA Clean and Concentrator 5s (Zymo Research) according to protocol, invitro-transcription was carried out by adding 10x T7 reaction buffer (2.5ul), T7 biotin-NTP mix (2.5ul), and T7 RNA polymerase enzyme mix (2.5ul) and incubation at 37C.    The IVT reaction was carried out for 14 hours.  Following reaction termination with water (75ul), the amplified RNAs (aRNA) were cleaned with RNA columns provided in the MessageAmp TotalPrep kit.   The aRNAs were then quantitated on a spectrophotometer, and quality determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer’s recommendations.

extract_protocol: RNA was isolated using TRIZOL followed by cleanup using Quiagen Rneasy columns, following manufacturer directions.

tag: strain background

value: FVB

tag: genotype/variation

value: skeletal muscle specific LKB1 knockout

tag: age

value: 4 months

value: gastrocnemius-plantaris-soleus muscle

tag: time point

value: after 15 min of in situ muscle contraction via sciatic nerve stimulation


title: muscle_knockout_contracted_rep5

description: SAMPLE 29


title: Peripheral mononuclear blood cells in patient 11 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 11 with Behçet’s disease
BD-11

source_name: Peripheral blood cells from Behçet’s disease patient 11


title: Peripheral mononuclear blood cells in patient 12 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 12 with Behçet’s disease
BD-12

source_name: Peripheral blood cells from Behçet’s disease patient 12


title: Peripheral mononuclear blood cells in patient 6 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 6 with Behçet’s disease
BD-6

source_name: Peripheral blood cells from Behçet’s disease patient 6


title: Peripheral mononuclear blood cells in patient 7 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 7 with Behçet’s disease
BD-7

source_name: Peripheral blood cells from Behçet’s disease patient 7


title: Mammary Gland Cells from corn oil female offspring rat number 60.5

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

description:
Corn base (as Test)
S12_60.5-CB

data_processing:
TLDA were run in the 7900 HT Sequence Detection system. The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values.
geNorm algortihm was used for the nomalization. It uses the geometric mean of the selected five housekeeping genes: U6 snRNA, snoRNA135, snoRNA202, U87, Y1
Target gene signals normalized to housekeeping genes; Ct_Trans = 2^-deltaCt, where deltaCt = (Ct_Target − min(Ct_Target))], then Ct_Normalized = Ct_Trans / merged_Ct_HKG
All Ct_Normalized based fold-change was calculated in excel
Fold Change worksheet reports test/control (i.e., CB/LB) ratios.

label: FAM

organism: Rattus norvegicus

label_protocol: Individual TaqMan® MicroRNA Assays cards were performed for miRNA profiling following the Manufacturer’s instructions .Reverse transcription was performed from 50ng total RNA per sample using Megaplex™ RT Pools(Applied Biosystems). Then add Megaplex™ PreAmp Primers(Applied Biosystems) for additional assay sensitivity. Quantitative real-time PCR were performed on an AbiPrism 7900 HT cycler (Applied Biosystems) with 1 cycle at 50℃ for 2 minutes and 95℃ for 10 minutes and 40 cycles at 94℃ for 15 seconds and 60℃ for 60 seconds.

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

value: Sprague Dawley

tag: animal id

value: offspring 60.5

tag: fed on

value: corn oil-based high fat diet (male parent)

value: mammary gland cell

tag: sample group

value: Test


title: muscle_knockout_contracted_rep2

description: SAMPLE 26


title: muscle_knockout_contracted_rep3

description: SAMPLE 27


title: muscle_knockout_contracted_rep4

description: SAMPLE 28


title: Peripheral mononuclear blood cells in patient 9 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 9 with Behçet’s disease
BD-9

source_name: Peripheral blood cells from Behçet’s disease patient 9

value: Behçet’s disease

value: peripheral blood cells

value: 9 females and 7 males


title: Peripheral mononuclear blood cells in patient 10 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 10 with Behçet’s disease
BD-10

source_name: Peripheral blood cells from Behçet’s disease patient 10

value: male

value: healthy controls without any identified diseases


title: Mammary Gland Cells from corn oil female offspring rat number 49.2

description:
Corn base (as Test)
S11_49.2-CB

value: female

value: offspring 49.2


title: muscle_knockout_contracted_rep1

description: SAMPLE 25

value: FVB


title: muscle_knockout_rested_rep6

description: SAMPLE 22

value: skeletal muscle specific LKB1 knockout

value: at rest


title: muscle_knockout_rested_rep7

description: SAMPLE 23

value: 4 months

value: gastrocnemius-plantaris-soleus muscle


title: Mammary Gland Cells from corn oil female offspring rat number 41.6

description:
Corn base (as Test)
S10_41.6-CB

value: Sprague Dawley

value: offspring 41.6


title: Mammary Gland Cells from lard female offspring rat number 29.1

description:
Lard base (as control)
S8_29.1-LB

value: offspring 29.1

value: lard-based high fat diet (male parent)

value: Control


title: Peripheral mononuclear blood cells in patient 5 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 5 with Behçet’s disease
BD-5

source_name: Peripheral blood cells from Behçet’s disease patient 5

value: Behçet’s disease


title: muscle_knockout_rested_rep5

description: SAMPLE 21


title: Peripheral mononuclear blood cells in patient 4 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 4 with Behçet’s disease
BD-4

source_name: Peripheral blood cells from Behçet’s disease patient 4

value: peripheral blood cells


title: muscle_knockout_rested_rep4

description: SAMPLE 20


title: muscle_knockout_contracted_rep6

description: SAMPLE 30

value: after 15 min of in situ muscle contraction via sciatic nerve stimulation


title: Peripheral mononuclear blood cells in patient 2 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 2 with Behçet’s disease
BD-2

source_name: Peripheral blood cells from Behçet’s disease patient 2

value: 9 females and 7 males


title: Peripheral mononuclear blood cells in patient 3 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 3 with Behçet’s disease
BD-3

source_name: Peripheral blood cells from Behçet’s disease patient 3

value: male

value: healthy controls without any identified diseases


title: muscle_knockout_rested_rep3

description: SAMPLE 19

value: female


title: Mammary Gland Cells from lard female offspring rat number 25.5

description:
Lard base (as control)
S7_25.5-LB

value: offspring 25.5

value: mammary gland cell


title: Peripheral mononuclear blood cells in patient 1 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 1 with Behçet’s disease
BD-1

source_name: Peripheral blood cells from Behçet’s disease patient 1


title: Peripheral mononuclear blood cells in patient 8 with Behçet’s disease

description:
Genes expressed in peripheral blood mononuclear cells from patient 8 with Behçet’s disease
BD-8

source_name: Peripheral blood cells from Behçet’s disease patient 8


title: muscle_knockout_rested_rep1

description: SAMPLE 17

value: FVB

value: skeletal muscle specific LKB1 knockout

value: at rest


title: muscle_knockout_rested_rep2

description: SAMPLE 18

value: 4 months

value: gastrocnemius-plantaris-soleus muscle


title: Sperm Cells from corn oil fed male rat number 19

description:
Corn base (as Test)
S5_19-CB

source_name: Sperm Cells from corn oil fed male rat

value: Sprague Dawley

value: rat 19

value: corn oil-based high fat diet

value: sperm cell

value: Test


title: Sperm Cells from corn oil fed male rat number 20

description:
Corn base (as Test)
S6_20-CB

value: rat 20


title: Sperm Cells from corn oil fed male rat number 18

description:
Corn base (as Test)
S4_18-CB

value: rat 18


title: Mammary Gland Cells from lard female offspring rat number 31.2

description:
Lard base (as control)
S9_31.2-LB

value: offspring 31.2

value: lard-based high fat diet (male parent)

value: Control


title: Sperm Cells from lard fed male rat number 11

description:
Lard base (as control)
S3_11-LB

source_name: Sperm Cells from lard fed male rat

value: male

value: rat 11

value: lard-based high fat diet


title: Sperm Cells from lard fed male rat number 10

description:
Lard base (as control)
S2_10-LB

value: rat 10


title: muscle_wild-type_contracted_rep7

description: SAMPLE 15

value: FVB

value: wild type

value: female

value: after 15 min of in situ muscle contraction via sciatic nerve stimulation


title: muscle_wild-type_contracted_rep5

description: SAMPLE 13

value: 4 months

value: gastrocnemius-plantaris-soleus muscle


title: muscle_wild-type_contracted_rep4

description: SAMPLE 12


title: muscle_wild-type_contracted_rep6

description: SAMPLE 14


title: muscle_wild-type_contracted_rep2

description: SAMPLE 10


title: muscle_wild-type_contracted_rep3

description: SAMPLE 11


title: muscle_wild-type_contracted_rep1

description: SAMPLE 9


title: Sperm Cells from lard fed male rat number 9

description:
Lard base (as control)
S1_9-LB

value: Sprague Dawley

value: rat 9

value: sperm cell


title: muscle_wild-type_resting_rep5

description: SAMPLE 5

value: at rest


title: muscle_wild-type_resting_rep7

description: SAMPLE 7


title: muscle_wild-type_resting_rep3

description: SAMPLE 3


title: WT amygdala, biological rep2

city: Seoul

first: Sooyoung

last: Chung

address: Ewhayeodae-gil

department: Department of Brain and Cognitive Sciences

country: South Korea

institute: Ewha Womans University

description: Gene expression data from amygdala of WT mice

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

data_processing: The data were analyzed with GCOS software using Affymetrix default analysis settings and normalized by RMA (Robust Multi-array Average) method.

source_name: Amygdala from wild type mice

label_protocol: Affymetrix protocol

growth_protocol: Male IP3K-A KO mice and their wild-type (WT) littermate controls from a C57BL/6N background were used at 10 to 15 weeks old. Mice were housed in temperature (22°C-23°C)- and humidity (50%)-controlled quarters under a 12-hr light/dark photoperiod (lights on at 08:00a.m.) with free access to food and water.

extract_protocol: Total RNA was extracted using RNeasy Mini kits (Qiagen, Valencia, CA) and quality was evaluated with an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: Mice were sacrificed by cervical dislocation between 02:00p.m. and 04:00p.m. Amygdala tissue was rapidly dissected from 1-mm thick slices and frozen in liquid nitrogen.

value: 10-15 weeks

tag: Sex

tag: genotype

value: Wild type


title: muscle_wild-type_resting_rep1

description: SAMPLE 1


title: muscle_wild-type_resting_rep2

description: SAMPLE 2


title: KO amygdala, biological rep2

description: Gene expression data from amygdala of KO mice

source_name: Amygdala from knockout mice

value: IP3K-A KO


title: KO amygdala, biological rep3

value: male


title: dka222_HT

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description:
control
dka222_HT

hyb_protocol: Biotinylated cRNA was hybridized to the Affymetrix array per manufacturer's instructions

scan_protocol: Standard HT TITAN scanning protocol

data_processing: The data were analyzed with Partek Genomics suite 6.6 and  in STATA/SE 11.2.

label: Biotin

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol

growth_protocol: Cerebellar granule neuron progenitors (GNPs) [dka220-222] were obtained from P6 [Cdkn2c-/-, Trp53-/-, Math1-GFP] mouse pups. Spontaneous SHH medulloblastomas [dka204-206] and [blm015-017 or dka050-052] were isolated from [Nestin-Cre;Cdkn2c-/-; Trp53fl/fl] and [Ptch1+/-;Cdkn2c-/-] mice (Uziel et al., 2005, Genes Dev), respectively. Myc or Group3 medulloblastoma [dka201-203] and Myc/ΔPOZ [bvo002-bvo006] were generated by overexpressing Myc in P6-P7 GNPs from [Cdkn2c-/-;Trp53-/-] (Kawauchi et al, 2012, Cancer Cell) and [Trp5Fl/Fl;Miz1ΔPOZ/POZ;Nestin-Cre] mouse pups prior to orthotopic injection into immunocompromised nude mice, respectively. MycVD [bvo017-bvo023] was generated by enforced the expression of MycVD proteins in GNPs, purified from the cerebella of P6-P7 [Cdkn2c-/-;Trp53-/-] or [Cdkn2c-/-, Trp53-/-, Math1-GFP], by retroviral transduction, and implanted the transduced GNPs into the cortices of naïve recipient animals.

extract_protocol: Trizol

treatment_protocol: Tumor cells were dissociated and purified by percoll-gradient before RNA extraction.

tag: class genotype

tag: cell/tissue type


title: dka204_HT

description:
medulloblastoma model
dka204_HT

source_name: SHH medulloblastoma

value: Cdkn2c-/-; Trp53Fl/Fl;Nestin-Cre

value: SHH medulloblastoma


title: WT amygdala, biological rep1


title: dka203_HT

description:
medulloblastoma model
dka203_HT

source_name: Myc tumor

value: Trp53-/-;Cdkn2c-/- GNPs infected with Myc-RFP

value: Myc- tumor


title: muscle_wild-type_resting_rep6

description: SAMPLE 6

value: FVB

value: wild type

tag: gender


title: dka201_HT

description:
medulloblastoma model
dka201_HT


title: dka221_HT

description:
control
dka221_HT

source_name: Cerebellar granule neuron progenitors (GNPs)


title: dka205_HT

description:
medulloblastoma model
dka205_HT


title: muscle_wild-type_resting_rep4

description: SAMPLE 4

value: female


title: dka202_HT

description:
medulloblastoma model
dka202_HT


title: KO amygdala, biological rep1


title: bvo023

description:
medulloblastoma model
bvo023

source_name: MycVD tumor

value: Trp53-/-;Cdkn2c-/- GNPs infected with MycVD-RFP

value: Myc VD- tumor


title: WT amygdala, biological rep3


title: dka206_HT

description:
medulloblastoma model
dka206_HT


title: bvo022

description:
medulloblastoma model
bvo022


title: bvo021

description:
medulloblastoma model
bvo021


title: bvo019

description:
medulloblastoma model
bvo019

value: Math1-GFP;Trp53-/-;Cdkn2c-/- GNPs infected with MycVD-RFP


title: bvo018

description:
medulloblastoma model
bvo018


title: bvo006

description:
medulloblastoma model
bvo006

source_name: Myc/ΔPOZ tumor

value: Trp53Fl/Fl;Miz1ΔPOZ/POZ;Nestin-Cre GNPs infected with Myc-RFP

value: Myc/ΔPOZ tumor


title: bvo020

description:
medulloblastoma model
bvo020


title: bvo017

description:
medulloblastoma model
bvo017


title: blm017_13655 (dka052, Ptch;Cdkn2c_45672)

description:
medulloblastoma model
blm017_13655


title: dka220_HT

description:
control
dka220_HT

value: Cerebellar granule neuron progenitors (GNPs)


title: blm015 (dka050, Ptch;Cdkn2c_45672)

description:
medulloblastoma model
blm015


title: bvo003

description:
medulloblastoma model
bvo003


title: bvo002

description:
medulloblastoma model
bvo002


title: blm016 (dka051, Ptch;Cdkn2c_45672)

description:
medulloblastoma model
blm016


title: bvo005

description:
medulloblastoma model
bvo005


title: Wild-type-4

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

description: Wild-type cells treated with vehicle (Ethanol) for 1 hour. Biological replicate 4.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Custom Yeast Oligo Microarrays (G2509F) for 17 hours at 65°C in a rotating Robbins Model 400 hybridization oven (Robbins Scientific) and an Agilent Rotator Rack.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then a 10 seconds Acetonitrile Wash (Agilent) followed by a 30 seconds Stabilization and Drying Solution wash (Agilent).

scan_protocol: Slides were scanned immediately after washing using a GenePix 4200A (Molecular Devices) using only the cy3 channel, scanning each each array individually (scan area 2088 x 3112 pixels). Scan resolution 10 µm, lines to average= 1, focus position 0µm. Laser set at 100% and PMT between 280 and 380 according to strength of the individual array.

data_processing: The scanned images were analyzed with GenePix 6.0 (Molecular Devices) using default parameters to obtain background subtracted. Features flagged in GenePix as absent or non-uniform outliers were excluded. A normalization factor was applied to each array so that the mean intensity of each array equals 1900.

organism: Saccharomyces cerevisiae

source_name: wild-type yeast, treated with vehicle (ethanol)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis Protocol version 5.7 (Agilent) according to the manufacturer's instructions, except using half of the reagents amount in step 2, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All strains were grown in YPD and treated with PC(O-16:0/2:0) (Enzo Life Sciences, BML-L100) at (40 μM) for 1 hour.

extract_protocol: Total RNA was isolated using TRI reagent (Sigma) as per the manufacturer’s protocol, followed by RNAeasy column purification (QIAGEN)

treatment_protocol: Wild-type cells were treated with vehicle (Ethanol) or 40 μM PC(O-16:0/2:0) (Enzo Life Sciences, BML-L100) for 1 hour.


title: bvo004

description:
medulloblastoma model
bvo004


title: PC(O-16:0/2:0)-treated wild-type-1

description: Wild-type cells treated with 40μM PC(O-16:0/2:0) for 1 hour. Biological replicate 1

source_name: wild-type yeast treated with PC(O-16:0/2:0)


title: PC(O-16:0/2:0)-treated wild-type-4

description: Wild-type cells treated with 40μM PC(O-16:0/2:0) for 1 hour. Biological replicate 4


title: PC(O-16:0/2:0)-treated wild-type-3

description: Wild-type cells treated with 40μM PC(O-16:0/2:0) for 1 hour. Biological replicate 3


title: Wild-type-2

description: Wild-type cells treated with vehicle (Ethanol) for 1 hour. Biological replicate 2.


title: PC(O-16:0/2:0)-treated wild-type-2

description: Wild-type cells treated with 40μM PC(O-16:0/2:0) for 1 hour. Biological replicate 2


title: DM1 rep2

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

hyb_protocol: Following fragmentation, 4.7 μg of cDNAs were hybridized for 16 hours at 45oC, 60 rpm on GeneChip® Human Exon 1.0 ST arrays. The chips were then washed and stained in the GeneChip® Fluidics Station 450.

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G. Raw data were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.1

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

source_name: Myotonic Dystrophy type 1

label_protocol: Biotinylated cDNA targets were prepared from 250 ng of total RNA using  Ambion WT Expression Kit (Cat # 4411974) and  Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations

extract_protocol: Total RNA from heart samples was extracted by Trizol

value: heart

tag: disease state

value: Myotonic Dystrophy type 1


title: CTL rep3

source_name: Control

tag: tissue

value: Control


title: CTL rep2


title: DM1 rep3


title: Wild-type-1

description: Wild-type cells treated with vehicle (Ethanol) for 1 hour. Biological replicate 1.

tag: strain


title: HUVEC_6h

city: Toyama

first: yukihiro

last: furusawa

address: Kurokawa

institute: Toyama Prefectural University

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

scan_protocol: GeneChips were scanned using the  Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: HUVEC were cultured in Humedia EB-2 (Wako)

extract_protocol: QIAGEN Rneasy mini kit

treatment_protocol: Cells were irradiated with X-ray (2.5 Gy) followed by RNA extraction

tag: cell type

value: HUVEC

tag: stress

value: Irradiated

tag: time (culture)


title: DM1 rep1


title: HUVEC_0h

value: Untreated


title: HUVEC_24h


title: CTL rep1


title: HUVEC_12h


title: NCH421k_4Days_rep2

city: Heidelberg

first: Emma

last: Phillips

address: In Neuenheimer Feld 580

department: Brain Tumor Translational Targets

country: Germany

institute: DKFZ

hyb_protocol: The Quick Amp labelling Kit (Agilent Technologies) was used. Briefly, RNA was fragmented by incubation at 60°C for 30 minutes and 2× Hi-RPM Hybridization Buffer was added. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G25505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Agilent Feature Extraction Software (v9.1) was used for background subtraction and LOWESS normalization.

source_name: GSCs NCH421k transduction with shNT for 4 days

label_protocol: The Quick Amp labelling Kit (Agilent Technologies) was used. Briefly, 200 ng of total RNA were primed with 0.8 µl of 100 µM T7 DNA primer at 65°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of T7 RNA plymerase blend, and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3/Cy5-label

growth_protocol: The GSC lines NCH421k and NCH644 were derived from primary GBM patients who underwent surgical resection according to the research proposals approved by the Institutional Review Board at the Medical Faculty of Heidelberg. Tissues were enzymatically dissociated and cells were cultivated as floating neurospheres in serum-free DMEM/F-12 medium, supplemented with 20 % BIT-admixture (Pelo Biotech, Planegg, Germany) and basal fibroblast growth factor (Biomol, Hamburg, Germany) and epidermal growth factor (Life Technologies, Hamburg, Germany) at 20 ng/ml each. Genotypic and phenotypic studies have been carried out in previous investigations. Passaging and seeding was carried out by dissociation with accutase (Sigma-Aldrich, Munich, Germany).

extract_protocol: RNA was extracted from cells using the RNAeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol and examined for integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: GSCs were seeded at a density of 50000 cells per ml and transduced with a multiplicity of infection (MOI) of 5. plko.1 TurboGFP containing lentivirus was used to estimate transduction efficiency via FACS. Experiments were discarded if <70 % of cells were green.

tag: cell line

tag: transduction

value: shNT for 4 days

source_name: GSCs NCH421k transduction with shPRKCI for 4 days

tag: tranduction

value: shPRKCI for 4 days


title: NCH644_4Days_rep3

source_name: GSCs NCH644 transduction with shNT for 4 days

source_name: GSCs NCH644 transduction with shPRKCI for 4 days


title: Adult Muscle Stem Cells Replicate#1

status: Public on Jan 20 2016

city: La Jolla

first: Francesca

last: Boscolo

state: CA

address: 9500 Gilman Drive

department: Reproductive Medicine

institute: UCSD

description: 2 months old

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

source_name: Mouse Muscle

label_protocol: Biotinylated cRNA were prepared with the Illumina Total Prep RNA Amplification Kit by Ambion

growth_protocol: RNA was extracted with mirVana miRNA Isolation Kit by Ambion. Quality control was performed with Agilent Bioanalyser.

extract_protocol: Followed manufacturer Instructionsfor mRNA isolation

tag: mouse strain

value: Adult Muscle Stem Cells


title: Fetal Muscle Stem Cells Replicate#1

description: Embryonic day 16.5

value: Fetal Muscle Stem Cells


title: Fetal Muscle Stem Cells Replicate#2

description: Embryonic day 16.5


title: NCH421k_4Days_rep1


title: Neonatal Muscle Stem Cells Replicate#1

description: 7 days post birth

value: Neonatal Muscle Stem Cells


title: Adult Muscle Stem Cells Replicate#3

description: 2 months old


title: Fetal Muscle Stem Cells Replicate#3

description: Embryonic day 16.5


title: Neonatal Muscle Stem Cells Replicate#3

description: 7 days post birth


title: Neonatal Muscle Stem Cells Replicate#2

description: 7 days post birth


title: Adult Muscle Stem Cells Replicate#2

description: 2 months old


title: Fshr mutant/Lhr null rep4

city: London

first: Ariel

last: Poliandri

state: London

address: WHRI, Charterhouse Sq.

department: Endocrinology

country: United Kingdom

institute: Queen Mary University

description: Group 3 replicate 4

hyb_protocol: Labelled RNA strands were hybridized in an overnight reaction to the bead on a BeadChip containing the complementary gene-specific sequence

scan_protocol: The BeadChip was imaged with Illumina HiScan

data_processing: Data was processed using Illumina GenomeStudio version 1.7.0 and quantile normalised

source_name: Mouse testis

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

growth_protocol: Mice were kept under, and in accordance with, a Project License issued by the United Kingdom Home Office. Food and water were provided ad libitum.

extract_protocol: RNA was extracted using Trizol followed by clean up with Qiage RNeasy MinElute Cleanup Kit

treatment_protocol: Samples were collected from 12 week old mice.

tag: age

value: 12 weeks old

value: FVB/N x C57/BL6 cross

tag: genotype/variation

value: Fshr mutant/Lhr null


title: Fshr mutant/Lhr null rep2

description: Group 3 replicate 2


title: Wild type rep 4

description: Group 1 replicate 4

value: Wild type


title: Fshr mutant rep 4

description: Group 2 replicate 4

value: Fshr mutant


title: Fshr mutant rep 1

description: Group 2 replicate 1


title: Lhr null rep4

description: Group 4 replicate 4

value: Lhr null


title: Fshr mutant/Lhr null rep3

description: Group 3 replicate 3


title: Fshr mutant/Lhr null rep1

description: Group 3 replicate 1


title: Wild type rep 3

description: Group 1 replicate 3


title: Lhr null rep3

description: Group 4 replicate 3


title: Fshr mutant rep 3

description: Group 2 replicate 3


title: Fshr mutant/Lhr null rep5

description: Group 3 replicate 5


title: sample_278

city: Durham

first: Ephraim

last: Tsalik

state: NC

address: 315 Trent Dr., Hanes House Rm 157, Box 102359

department: Center for Applied Genomics and Precision Medicine

institute: Duke University

hyb_protocol: Next, 11ug of purified cRNA is fragmented using a 5X fragmentation buffer, then a hybridization cocktail is prepared and added to the fragmentation product using the Hybridization, Wash and Stain kit (Affymetrix), applied to arrays, and incubated at 45°C for 16 hours.

scan_protocol: Affymetrix GeneChip Scanner

data_processing: Expression Console

source_name: blood

label_protocol: Total RNA is converted into double stranded cDNA via reverse transcription (RT) using an oligo-d(T) primer-adaptor. During this RT step, four peptide nucleic acid (PNA) oligomers that bind portions of the alpha and beta hemoglobin transcripts are added to prevent transcription of globin mRNAs.  The cDNA is then converted to dsDNA using T4 DNA polymerase.  The resulting dsDNA is purified to remove unincorporated nucleotides, salts, enzymes and inorganic phosphates.  This is used as a template for in vitro transcription using T7 RNA polymerase and biotinylated ribonucleotides. The resulting cRNA is purified and quantitated using spectrophotometry.  Globin reduction in the cRNA is verified using an Agilent Bioanalyzer.

extract_protocol: RNA isolation was performed from blood collected in PAXgene Blood RNA Tubes using the PAXgene 96 Blood RNA Kit (QIAgen).  Briefly, blood was pelleted, washed, resuspended, and incubated in optimized buffers with Proteinase K.  The lysate was applied to a filter plate and centrifuged to remove any residual cell debris.  Ethanol was added to the flow-through to provide appropriate binding conditions for the RNA.  The lysate was then applied to an RNA plate where the RNA selectively binds to membrane.  Residual DNA was removed through a DNase digestion on the membrane and any remaining contaminants were washed away.  High-quality RNA was then eluted in nuclease-free water.

tag: replicates

tag: batch

value: bacterial


title: Wild type rep 1

description: Group 1 replicate 1


title: Lhr null rep5

description: Group 4 replicate 5


title: sample_277

value: viral


title: sample_279


title: Lhr null rep2

description: Group 4 replicate 2


title: Fshr mutant rep 2

description: Group 2 replicate 2


title: sample_280

value: non-infectious illness


title: Lhr null rep1

description: Group 4 replicate 1


title: sample_275


title: sample_276


title: sample_274


title: sample_272


title: sample_271


title: sample_270


title: sample_273


title: sample_268


title: sample_267


title: Wild type rep 2

description: Group 1 replicate 2


title: sample_266


title: sample_264


title: sample_260


title: sample_257


title: sample_262


title: sample_250


title: sample_263


title: sample_265


title: sample_261


title: sample_258


title: sample_255


title: sample_251


title: sample_253


title: sample_242


title: Wild-type-3

description: Wild-type cells treated with vehicle (Ethanol) for 1 hour. Biological replicate 3.


title: sample_243


title: sample_245


title: sample_252


title: sample_247


title: sample_241


title: sample_256


title: sample_244


title: sample_248


title: sample_249


title: sample_254


title: sample_239


title: sample_240


title: sample_237


title: sample_236


title: sample_238


title: sample_246


title: sample_231


title: sample_233


title: sample_226


title: sample_235


title: sample_230


title: sample_224


title: sample_223


title: sample_228


title: sample_229


title: sample_234


title: sample_218


title: sample_225


title: sample_232


title: sample_222


title: sample_217


title: sample_214


title: sample_227


title: sample_219


title: sample_213


title: sample_216


title: sample_221


title: sample_206


title: sample_215


title: sample_220


title: sample_209


title: sample_200


title: sample_199


title: sample_210


title: sample_205


title: sample_207


title: sample_197


title: sample_212


title: sample_198


title: sample_208


title: sample_203


title: sample_202


title: sample_204


title: sample_193


title: sample_196


title: sample_195


title: sample_191


title: sample_201


title: sample_187


title: sample_189


title: sample_192


title: sample_182


title: sample_177


title: sample_178


title: sample_183


title: sample_181


title: sample_174


title: sample_194


title: sample_184


title: sample_176


title: sample_173


title: sample_188


title: sample_179


title: sample_172


title: sample_190


title: sample_175


title: sample_180


title: sample_169


title: sample_185


title: sample_171


title: sample_164


title: sample_163


title: sample_166


title: sample_269


title: sample_168


title: sample_170


title: sample_165


title: sample_161


title: sample_159


title: sample_157


title: sample_158


title: sample_156


title: sample_154


title: sample_152


title: sample_146


title: sample_150


title: sample_151


title: sample_145


title: sample_155


title: sample_144


title: sample_160


title: sample_148


title: sample_147


title: sample_186


title: sample_149


title: sample_162


title: sample_143


title: sample_142


title: sample_141


title: sample_153


title: sample_140


title: sample_137


title: sample_139


title: sample_259


title: sample_138


title: sample_133


title: sample_135


title: sample_136


title: sample_132


title: sample_211


title: sample_134


title: sample_131


title: sample_123


title: sample_125


title: sample_129


title: sample_124


title: sample_121


title: sample_114


title: sample_115


title: sample_127


title: sample_122


title: sample_108


title: sample_117


title: sample_130


title: sample_128


title: sample_106


title: sample_107


title: sample_111


title: sample_118


title: sample_113


title: sample_112


title: sample_103


title: sample_109


title: sample_110


title: sample_104


title: sample_116


title: sample_126


title: sample_120


title: sample_119


title: sample_105


title: sample_102


title: sample_99


title: sample_101


title: sample_96


title: sample_95


title: sample_79


title: sample_85


title: sample_90


title: sample_78


title: sample_84


title: sample_89


title: sample_88


title: sample_94


title: sample_100


title: sample_91


title: sample_87


title: sample_93


title: sample_92


title: sample_82


title: sample_86


title: sample_76


title: sample_97


title: sample_73


title: sample_167


title: sample_75


title: sample_81


title: sample_83


title: sample_77


title: sample_74


title: sample_80


title: sample_98


title: sample_71


title: sample_72


title: sample_61


title: sample_62


title: sample_56


title: sample_65


title: sample_67


title: sample_59


title: sample_53


title: sample_64


title: sample_54


title: sample_69


title: sample_55


title: sample_57


title: sample_63


title: sample_49


title: sample_51


title: sample_60


title: sample_70


title: sample_47


title: sample_52


title: sample_45


title: sample_46


title: sample_44


title: sample_58


title: sample_50


title: sample_66


title: sample_68


title: sample_43


title: sample_41


title: sample_42


title: sample_48


title: sample_36


title: sample_33


title: sample_37


title: sample_32


title: sample_27


title: sample_31


title: sample_23


title: sample_39


title: sample_35


title: sample_26


title: sample_18


title: sample_30


title: sample_34


title: sample_24


title: sample_28


title: sample_17


title: sample_21


title: sample_29


title: sample_14


title: sample_38


title: sample_20


title: sample_15


title: Hexafluoro rep3

city: Atlanta

first: Jack

middle: L

last: Arbiser

state: GA

address: 101 Woodruff Circle WMB 5309

department: Dermatology

institute: Emory School of Medicine

description: replicate 3

data_processing: The data were normalised using quantile normalization in Illumina Genome Studio 2011.1

source_name: A375 melanoma

label_protocol: biotin labeling

extract_protocol: RNA extraction protocol as per Qiagen Rneasy kit.

value: Male


title: sample_16


title: sample_25


title: sample_22


title: sample_40


title: sample_19


title: sample_13


title: sample_12


title: Vehicle Control rep3

description: replicate 3


title: sample_8


title: X4904_VFC

city: Tampa

first: Feng

last: Cheng

state: FL

address: 12901 Bruce B Downs Blvd MDC 30

department: Department of Pharmaceutical Science

institute: University of South Florida

hyb_protocol: Microarrays were hybridized at 45 °C for 16–24 hours, washed and stained using an Affymetrix FS450 fluidics station, according to manufacturer recommendations. Microarrays were scanned on a GeneChip Scanner 3000 and visually inspected for hybridization artefacts. Exon chip analysis was performed using Affymetrix Power Tools 1.12.0. Probe level data was summarized into probe set level data using the Robust Multichip Average (RMA) background correction algorithm in combination with an R-script. The raw image files (.DAT files) were analyzed using Affymetrix GeneChip Operating Software to generate CEL files.

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing:
Partek Genomics Suite version 6.7 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction, quantile normalization, mean probe set summarization, and log2 transformation. Only high-quality core probe sets, as defined by Affymetrix, were included because theyalways have reliable annotations from RefSeq (www.ncbi.nlm.nih.gov) or Ensembl (www.ensembl.org). It is noted that thedatasets were annotated according to the UCSC human genome hg19 reference sequence (http://genome.ucsc.edu/cgi-bin/hgGateway).Besides,105,271 core probes (within 62,448 prob sets) contained common SNPswas removed because SNP-containing probe sets may lead to reduced signal intensity and result in spurious results. These probes were defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is basedon the dbSNPdatabase (version 129, April 2008) andSNPinprobe_1.0 database. Removal of SNP-affected probes was accomplished in Partek program.Probe sets and gene intensities was summarized only on those probes not affected by SNPs.Finally, a total of 17,565 genes (transcript clusters) were surveyed for downstream analysis.
probe group file: HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label_protocol: Exon array hybridizations were performed at the Yale Center for Genome Analysis and at Gene Logic Inc. (Gaithersburg, MD). Reverse transcription (RT) was performed to generate cDNA from total RNA using RT primers designed using an oligonucleotide matching algorithm. For the selective cDNA synthesis, the Ambion WT Expression kit (Ambion) was used in combination with the GenechipWT Terminal Labeling and Controls Kit (Affymetrix) for target preparation, according to manufacturer recommendations. PolyA controls were added to the input RNA to measure efficiency of target amplification. Fragmented and labelled second cycle cDNA (5.5 μg) was added to a hybridization cocktail prior to loading of 200 μl onto individual Affymetrix Human Exon 1.0 ST arrays.

growth_protocol: not applicable

extract_protocol: A bead mill homogenizer (Bullet Blender, Next Advance) was used to lyse the pulverized tissue. Each pulverized tissue sample was transferred to a chilled safe-lock microcentrifuge tube (Eppendorf). A mass of chilled stainless steel beads (Next Advance, cat# SSB14B) equal to the mass of the tissue was added to the tube. Two volumes of Buffer RLT (Qiagen) were added to the tissue and beads. Samples were mixed in the Bullet Blender for 1 min at a speed of six. Samples were visually inspected to confirm desired homogenization and then incubated at 37 °C for five min. Buffer RLT was added up to 0.6 ml, and samples were mixed in the Bullet Blender for 1 min. Total RNA was extracted using a non-phenolic procedure (RNeasy Plus Mini Kit, Qiagen), followed by DNase treatment (TURBO DNase, Ambion) as per manufacturers’ instructions. Optical density values of extracted RNA were measured using a NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RNA integrity number (RIN) was determined for each sample using Bioanalyzer RNA 6000 Nano Kit or Bioanalyzer RNA 6000 Pico Kit (Agilent), depending upon the total amount of RNA.

treatment_protocol: This study was conducted using postmortem human brain specimens from tissue collections at the Department of Neurobiology at Yale University School of Medicine and the Clinical Brain Disorders Branch of the National Institute of Mental Health. Additional specimens were procured from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM), the Brain and Tissue Bank for Developmental Disorders at the University of Maryland, the Birth Defects Research Laboratory at the University of Washington, Advanced Bioscience Resources Inc. and the MRC-Wellcome Trust Human Developmental Biology Resource at the Institute of Human Genetics, University of Newcastle, UK. Tissue was collected after obtaining parental or next of kin consent and with approval by the institutional review boards at the Yale University School of Medicine, the National Institutes of Health, and at each institution from which tissue specimens were obtained. Specimens range in age from 5.7 post-conceptual weeks (PCW) to over 80 years. Of 57 post-mortem brain specimens included in this study, 24 were obtained with either left or right hemisphere, and 33 were obtained with both hemispheres. Embryonic and fetal age was extrapolated based on the date of the mother’s last menstruation, characteristics of the fetus noted upon ultrasonographic scanning, foot length of the fetus, and visual inspection.

tag: braincode

tag: region

value: VFC

tag: disease status

value: DS

tag: Sex

value: M

tag: Stage

tag: postmortem interval

tag: race

value: AA

tag: rna integrity number


title: sample_9


title: sample_7


title: Honokiol DCA rep2

description: replicate 2

tag: gender

tag: strain


title: X4904_DFC

value: DFC


title: sample_3


title: sample_1


title: Honokiol DCA rep1

description: replicate 1

tag: cell line


title: Honokiol DCA rep3

description: replicate 3


title: sample_2


title: Vehicle Control rep1

description: replicate 1


title: X5005_ITC

value: ITC

value: F

value: CC


title: Vehicle Control rep2

description: replicate 2


title: X5005_CBC

value: CBC


title: X4904_ITC


title: X4904_OFC

value: OFC


title: sample_6


title: X5005_V1C


title: sample_10


title: sample_4


title: X5005_VFC


title: X5005_HIP

value: HIP


title: Hexafluoro rep2

description: replicate 2


title: Hexafluoro rep1

description: replicate 1


title: X5005_DFC


title: sample_11


title: sample_5


title: X5005_OFC


title: X707_V1C


title: X707_CBC


title: X1276_DFC


title: X1276_CBC


title: X5301_ITC


title: X1276_V1C


title: X5301_CBC


title: X1267_CBC


title: X1267_V1C


title: X707_DFC


title: X5277_DFC


title: X5277_OFC


title: X5301_VFC


title: X1267_FC

value: FC


title: X5301_OFC


title: X5301_DFC


title: X1948_CBC


title: X2135_CBC


title: X1276_VFC


title: X170_V1C


title: X170_CBC


title: X170_ITC


title: X1948_V1C


title: X170_S1C


title: X5277_VFC


title: X170_STC

value: STC


title: X170_IPC

value: IPC


title: X2135_V1C


title: X170_MFC

value: MFC


title: X5301_HIP


title: X170_VFC


title: X170_OFC


title: X170_DFC


title: X1273_V1C


title: X1282_HIP


title: X1273_FC


title: X1282_OFC


title: X1218_FC


title: X1089_V1C


title: X1282_CBC


title: X1282_V1C


title: X1282_VFC


title: X1282_DFC


title: X1218_V1C


title: HSB183_VFC_L

value: CTL


title: HSB183_ITC_L


title: HSB126_CBC_L


title: X1282_ITC


title: HSB126_ITC_L


title: HSB126_VFC_L


title: HSB183_OFC_L


title: X1152_FC


title: HSB142_V1C_L


title: HSB126_HIP_R


title: HSB126_OFC_L


title: X1273_CBC


title: HSB142_DFC_L


title: HSB126_DFC_L


title: HSB183_DFC_L


title: HSB105_DFC_L


title: HSB105_OFC_L


title: K3.4

city: Newcastle Upon Tyne

first: Olaf

last: Heidenreich

address: Brewery Lane

department: Wolfson Childhood Cancer Research Centre

institute: Newcastle University

description: replicate 4

data_processing: The data were normalised using robust spline with R Biconductor package Lumi

molecule: polyA RNA

growth_protocol: NGP cells were obtained from Northern Institute for Cancer Research bank of authenticated cell lines. Post-authentication passages were limited to 30 for experimental procedures (<6 Months) before replacing with lower passage number stocks. NGP cells were seeded at 6 x 10^5 cells per well of a 6-well plate 24hrs before treatment.

extract_protocol: RNA extraction was carried out using RNeasy Plus Mini Kit (Qiagen). Concentration and quality of mRNA were determined using  Agilent RNA 6000 nano kit on an Agilent 2100 Bioanalyzer (RNA integrity numbers > 9)

treatment_protocol: NGP cells were treated for 4 hours with 0.5% DMSO (solvent control), RG7388 (75nM) + GSK2830371 (2.5µM) before cell harvesting and total RNA extraction. Four independent biological repeats were performed.

value: NGP

tag: tumour of origin

value: Neuroblastoma


title: HSB105_VFC_L

value: VFC


title: HSB119_V1C_L

value: M


title: HSB119_VFC_L

value: AA


title: HSB174_V1C_L


title: HSB173_CBC_L


title: HSB119_CBC_L


title: HSB174_DFC_L

value: DFC


title: HSB119_DFC_L


title: HSB173_HIP_L


title: HSB172_V1C_L

value: H


title: K3.2

description: replicate 2


title: K2.3

description: replicate 3


title: K1.4

description: replicate 4

source_name: DMSO rep4


title: K2.2

description: replicate 2


title: HSB173_ITC_L

value: ITC

value: F


title: HSB174_CBC_L

value: CBC


title: HSB172_CBC_L


title: K3.3

description: replicate 3


title: K2.4

description: replicate 4


title: K1.3

description: replicate 3

source_name: DMSO rep3


title: HSB143_DFC_L

value: CC


title: K1.2

description: replicate 2

source_name: DMSO rep2


title: K2.1

description: replicate 1


title: K1.1

description: replicate 1

source_name: DMSO rep1


title: non_involved_lung_tissue_patient_284

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

data_processing: Primary microarray data were collected using BeadStudio v3 software package. The two datasets of 206 and 78 samples were processed independently using log2 transformation and robust spline normalization, implemented in the lumi package (Du, 2008) of the R/Bioconductor project. Then, the two sets were combined using the ComBat adjustment method (Johnson, 2007) implemented in the sva R package (Leek, 2012). Probes that were not annotated and those with a detection P value < 0.01 in fewer than 10% of samples were filtered out. Finally, when multiple probes mapped to the same transcript, we included only the one with the highest detection rate, defined as the percentage of samples in which the probe had detection P values < 0.01.

source_name: Non-involved (apparently normal) lung parenchyma

label_protocol: RNA was reverse transcribed, labeled with biotin and amplified overnight using the Illumina TotalPrep RNA Amplification Kit (Life Technologies).

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: male

tag: age at diagnosis (years)

tag: clinical stage

tag: smoking status

value: smoker

tag: tissue


title: K3.1

description: replicate 1


title: non_involved_lung_tissue_patient_282

tag: batch

value: Non-involved (apparently normal) lung parenchyma


title: HSB122_V1C_L

tag: braincode

tag: age


title: non_involved_lung_tissue_patient_281


title: non_involved_lung_tissue_patient_283


title: HSB143_OFC_L

tag: region

value: OFC

tag: disease status


title: HSB171_ITC_L

tag: Sex

tag: Stage


title: HSB171_STC_L

value: STC

tag: postmortem interval

tag: race


title: HSB171_CBC_L

value: CTL

tag: rna integrity number


title: HSB171_V1C_L


title: HSB171_S1C_L


title: HSB171_IPC_L

value: IPC


title: HSB171_OFC_L


title: HSB171_MFC_L

value: MFC


title: non_involved_lung_tissue_patient_276

tag: gender


title: non_involved_lung_tissue_patient_277


title: non_involved_lung_tissue_patient_279


title: non_involved_lung_tissue_patient_275

value: female


title: non_involved_lung_tissue_patient_278


title: HSB171_VFC_L

value: VFC

value: M


title: non_involved_lung_tissue_patient_280


title: HSB171_DFC_L

value: DFC

value: AA


title: non_involved_lung_tissue_patient_274


title: non_involved_lung_tissue_patient_273


title: non_involved_lung_tissue_patient_269


title: HSB131_CBC_L


title: non_involved_lung_tissue_patient_268


title: non_involved_lung_tissue_patient_270


title: HSB142_CBC_L


title: non_involved_lung_tissue_patient_272


title: non_involved_lung_tissue_patient_267


title: non_involved_lung_tissue_patient_271


title: HSB131_HIP_L

value: HIP


title: HSB131_V1C_L

value: F


title: HSB131_ITC_L

value: ITC


title: HSB131_VFC_L

value: CC


title: non_involved_lung_tissue_patient_266

value: male


title: HSB131_DFC_L


title: HSB132_CBC_L

value: CBC


title: HSB131_OFC_L


title: non_involved_lung_tissue_patient_263

value: smoker

value: Non-involved (apparently normal) lung parenchyma


title: non_involved_lung_tissue_patient_262


title: non_involved_lung_tissue_patient_264


title: HSB159_V1C_L


title: HSB132_DFC_L


title: HSB100_V1C_L


title: non_involved_lung_tissue_patient_265


title: non_involved_lung_tissue_patient_259


title: non_involved_lung_tissue_patient_261


title: HSB97_DFC_L


title: HSB173_VFC_L


title: HSB132_V1C_L


title: non_involved_lung_tissue_patient_260


title: NRCC, FSTL1 knockdown, biological rep2

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

country: China

institute: Second Military Medical University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA,US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA,US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US)followed the manufacturer’s instructions.

scan_protocol: Microarrays were scanned by Affymetrix GeneChip® Scanner 3000.

data_processing: Raw intesities were preprocessed by MAS5 integrated in Expression Console with default parameters.

source_name: NRCC_FSTL1 knockdown

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT.Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: FSTL1 gene was stably knocked down in Chinese renal cell carcinoma(RCC) cell lines,termed as NRCC,by transduced with retrovirus containing shRNA targeted to FSTL1.NRCC-shRNA-1,NRCC-shRNA-2 and NRCC-shsiscramble cells were cultivated under the same cell culture condition.

extract_protocol: Trizol extraction of total RNA of NRCC-shFSTL1-1,NRCC-shFSTL1-2,NRCC-shsiscramble  was performed according to the manufacturer's instructions.

tag: cell line

value: NRCC

tag: cell type

value: Clear cell renal cell carcinoma (ccRCC) cell line

tag: transfected with

value: shFSTL1-2-constructed vector


title: non_involved_lung_tissue_patient_256

tag: age at diagnosis (years)

tag: clinical stage


title: non_involved_lung_tissue_patient_255

tag: smoking status

tag: tissue


title: NRCC, FSTL1 knockdown, biological rep1

value: shFSTL1-1-constructed vector


title: non_involved_lung_tissue_patient_254

tag: batch


title: HSB100_DFC_L

tag: braincode

value: CTL

tag: age


title: HSB122_CBC_L

tag: region

tag: disease status


title: non_involved_lung_tissue_patient_252


title: NRCC, FSTL1 shsiscramble, biological rep1

source_name: NRCC_FSTL1 shsiscramble

value: scambled control-constructed vector


title: non_involved_lung_tissue_patient_258

value: female


title: non_involved_lung_tissue_patient_253


title: SJHYPER153

first: William

last: Evans

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences

description: processed signal intensity

hyb_protocol: hybridization was done at 56 degrees Celsius for 16 hours followed by washing on an HS Pro instrument from Tecan.

scan_protocol: Scanning was performed using an Agilent G2505B scanning system

data_processing: raw counts were processed using the limma package(version 3.6.9) from Bioconductor

source_name: Leukemia cells

label_protocol: miRCURY Power labeling kit used according to manufacturer's (Exiqon) instructions

tag: source

value: bone marrow


title: SJBALL119

description: processed signal intensity


title: SJHYPO145

description: processed signal intensity


title: SJBALL118

description: processed signal intensity


title: non_involved_lung_tissue_patient_251


title: non_involved_lung_tissue_patient_250


title: non_involved_lung_tissue_patient_249


title: SJHYPER149

description: processed signal intensity


title: SJHYPER150

description: processed signal intensity


title: SJTALL222

description: processed signal intensity


title: SJBALL117

description: processed signal intensity


title: SJETV113

description: processed signal intensity


title: SJERG022

description: processed signal intensity


title: non_involved_lung_tissue_patient_257


title: SJHYPER147

description: processed signal intensity


title: SJHYPO143

description: processed signal intensity


title: SJETV111

description: processed signal intensity


title: SJHYPER146

description: processed signal intensity


title: non_involved_lung_tissue_patient_245


title: non_involved_lung_tissue_patient_246


title: non_involved_lung_tissue_patient_247


title: non_involved_lung_tissue_patient_248


title: non_involved_lung_tissue_patient_243


title: non_involved_lung_tissue_patient_240


title: SJBALL115

description: processed signal intensity


title: non_involved_lung_tissue_patient_239


title: non_involved_lung_tissue_patient_242


title: non_involved_lung_tissue_patient_238


title: non_involved_lung_tissue_patient_244


title: non_involved_lung_tissue_patient_237


title: non_involved_lung_tissue_patient_241


title: SJE2A035

description: processed signal intensity


title: SJHYPER143

description: processed signal intensity


title: SJBALL114

description: processed signal intensity


title: non_involved_lung_tissue_patient_236


title: non_involved_lung_tissue_patient_235


title: SJHYPER141

description: processed signal intensity


title: SJTALL085

description: processed signal intensity


title: SJTALL087

description: processed signal intensity


title: SJHYPO142

description: processed signal intensity


title: SJHYPO141

description: processed signal intensity


title: non_involved_lung_tissue_patient_231


title: non_involved_lung_tissue_patient_232


title: non_involved_lung_tissue_patient_233


title: non_involved_lung_tissue_patient_234


title: SJTALL084

description: processed signal intensity


title: SJHYPER137

description: processed signal intensity


title: SJETV102

description: processed signal intensity


title: SJERG020

description: processed signal intensity


title: SJETV104

description: processed signal intensity


title: SJETV103

description: processed signal intensity


title: SJDOWN014

description: processed signal intensity


title: non_involved_lung_tissue_patient_230


title: SJDOWN013

description: processed signal intensity


title: non_involved_lung_tissue_patient_229


title: non_involved_lung_tissue_patient_226


title: non_involved_lung_tissue_patient_225


title: non_involved_lung_tissue_patient_227


title: non_involved_lung_tissue_patient_228


title: non_involved_lung_tissue_patient_224


title: non_involved_lung_tissue_patient_222


title: non_involved_lung_tissue_patient_219


title: non_involved_lung_tissue_patient_223


title: non_involved_lung_tissue_patient_220


title: SJBALL107

description: processed signal intensity


title: SJMLL033

description: processed signal intensity


title: SJHYPER126

description: processed signal intensity


title: SJBALL211

description: processed signal intensity


title: SJBALL102

description: processed signal intensity


title: SJBALL101

description: processed signal intensity


title: non_involved_lung_tissue_patient_218


title: SJINF020

description: processed signal intensity


title: non_involved_lung_tissue_patient_217


title: SJETV096

description: processed signal intensity


title: SJTALL035

description: processed signal intensity


title: non_involved_lung_tissue_patient_221


title: non_involved_lung_tissue_patient_215


title: non_involved_lung_tissue_patient_211


title: non_involved_lung_tissue_patient_213


title: SJMLL004

description: processed signal intensity


title: non_involved_lung_tissue_patient_212


title: non_involved_lung_tissue_patient_214


title: SJHYPER121

description: processed signal intensity


title: SJMLL032

description: processed signal intensity


title: SJHYPER120

description: processed signal intensity


title: SJERG016

description: processed signal intensity


title: non_involved_lung_tissue_patient_216


title: SJERG015

description: processed signal intensity


title: SJTALL010

description: processed signal intensity


title: SJHYPER119

description: processed signal intensity


title: non_involved_lung_tissue_patient_210


title: SJBALL095

description: processed signal intensity


title: SJBALL098

description: processed signal intensity


title: non_involved_lung_tissue_patient_209


title: non_involved_lung_tissue_patient_205


title: non_involved_lung_tissue_patient_204


title: non_involved_lung_tissue_patient_202

value: non-smoker


title: HSB126_V1C_L

tag: Sex

tag: Stage

tag: postmortem interval


title: non_involved_lung_tissue_patient_206

tag: gender


title: non_involved_lung_tissue_patient_201


title: non_involved_lung_tissue_patient_208


title: non_involved_lung_tissue_patient_207


title: SJHYPER113

description: processed signal intensity


title: non_involved_lung_tissue_patient_203


title: SJTALL034

description: processed signal intensity


title: SJBALL094

description: processed signal intensity


title: non_involved_lung_tissue_patient_198


title: non_involved_lung_tissue_patient_197


title: non_involved_lung_tissue_patient_199


title: SJE2A026

description: processed signal intensity


title: SJBALL097

description: processed signal intensity


title: SJHYPER112

description: processed signal intensity


title: non_involved_lung_tissue_patient_200


title: non_involved_lung_tissue_patient_195


title: SJPHALL023

description: processed signal intensity


title: SJHYPER116

description: processed signal intensity


title: SJETV090

description: processed signal intensity


title: non_involved_lung_tissue_patient_191


title: SJHYPER111

description: processed signal intensity


title: SJE2A025

description: processed signal intensity


title: non_involved_lung_tissue_patient_193


title: non_involved_lung_tissue_patient_194


title: SJHYPER106

description: processed signal intensity


title: SJHYPER108

description: processed signal intensity


title: non_involved_lung_tissue_patient_190


title: non_involved_lung_tissue_patient_187


title: non_involved_lung_tissue_patient_192


title: non_involved_lung_tissue_patient_196


title: non_involved_lung_tissue_patient_189


title: non_involved_lung_tissue_patient_188


title: SJBALL160

description: processed signal intensity


title: SJETV087

description: processed signal intensity


title: SJETV086

description: processed signal intensity


title: SJBALL092

description: processed signal intensity


title: SJHYPER103

description: processed signal intensity


title: SJETV085

description: processed signal intensity


title: SJTALL030

description: processed signal intensity


title: non_involved_lung_tissue_patient_186


title: non_involved_lung_tissue_patient_184


title: SJETV084

description: processed signal intensity


title: non_involved_lung_tissue_patient_185


title: non_involved_lung_tissue_patient_182


title: SJETV083

description: processed signal intensity


title: SJDOWN010

description: processed signal intensity


title: SJHYPER101

description: processed signal intensity


title: non_involved_lung_tissue_patient_183


title: SJBALL090

description: processed signal intensity


title: non_involved_lung_tissue_patient_180


title: non_involved_lung_tissue_patient_181


title: SJHYPER100

description: processed signal intensity


title: SJBALL089

description: processed signal intensity


title: non_involved_lung_tissue_patient_179


title: non_involved_lung_tissue_patient_176


title: non_involved_lung_tissue_patient_177


title: SJBALL099

description: processed signal intensity


title: SJBALL085

description: processed signal intensity


title: SJMLL029

description: processed signal intensity


title: SJBALL083

description: processed signal intensity


title: non_involved_lung_tissue_patient_173


title: SJERG014

description: processed signal intensity


title: non_involved_lung_tissue_patient_174


title: SJHYPO124

description: processed signal intensity


title: non_involved_lung_tissue_patient_175


title: non_involved_lung_tissue_patient_172


title: SJTALL027

description: processed signal intensity


title: non_involved_lung_tissue_patient_178


title: non_involved_lung_tissue_patient_171


title: non_involved_lung_tissue_patient_168


title: non_involved_lung_tissue_patient_167


title: non_involved_lung_tissue_patient_170


title: SJETV076

description: processed signal intensity


title: SJTALL025

description: processed signal intensity


title: non_involved_lung_tissue_patient_169


title: non_involved_lung_tissue_patient_166


title: non_involved_lung_tissue_patient_165


title: SJBALL082

description: processed signal intensity


title: SJHYPER096

description: processed signal intensity


title: SJERG013

description: processed signal intensity


title: SJHYPER091

description: processed signal intensity


title: non_involved_lung_tissue_patient_164


title: SJTALL024

description: processed signal intensity


title: non_involved_lung_tissue_patient_162


title: SJTALL005

description: processed signal intensity


title: non_involved_lung_tissue_patient_163


title: non_involved_lung_tissue_patient_161


title: SJETV070

description: processed signal intensity


title: SJBALL210

description: processed signal intensity


title: non_involved_lung_tissue_patient_158


title: non_involved_lung_tissue_patient_160


title: SJHYPER198

description: processed signal intensity


title: SJHYPO123

description: processed signal intensity


title: non_involved_lung_tissue_patient_159


title: SJHYPER023

description: processed signal intensity


title: SJETV028

description: processed signal intensity


title: SJTALL040

description: processed signal intensity


title: non_involved_lung_tissue_patient_152


title: non_involved_lung_tissue_patient_157


title: SJTALL081

description: processed signal intensity


title: non_involved_lung_tissue_patient_156


title: non_involved_lung_tissue_patient_155


title: SJE2A009

description: processed signal intensity


title: non_involved_lung_tissue_patient_153


title: SJBALL014

description: processed signal intensity


title: SJETV025

description: processed signal intensity


title: non_involved_lung_tissue_patient_151


title: non_involved_lung_tissue_patient_150


title: non_involved_lung_tissue_patient_148


title: SJETV068

description: processed signal intensity


title: SJHYPO122

description: processed signal intensity


title: SJHYPER095

description: processed signal intensity


title: non_involved_lung_tissue_patient_146


title: SJTALL023

description: processed signal intensity


title: non_involved_lung_tissue_patient_147


title: SJBALL209

description: processed signal intensity


title: SJBALL207

description: processed signal intensity


title: SJETV024

description: processed signal intensity


title: SJBALL206

description: processed signal intensity


title: SJETV023

description: processed signal intensity


title: SJTALL080

description: processed signal intensity


title: SJERG030

description: processed signal intensity


title: SJBALL205

description: processed signal intensity


title: non_involved_lung_tissue_patient_149


title: non_involved_lung_tissue_patient_143


title: SJETV064

description: processed signal intensity


title: non_involved_lung_tissue_patient_141


title: SJETV022

description: processed signal intensity


title: non_involved_lung_tissue_patient_139


title: SJHYPER018

description: processed signal intensity


title: SJHYPER080

description: processed signal intensity


title: SJMLL024

description: processed signal intensity


title: non_involved_lung_tissue_patient_140


title: SJTALL079

description: processed signal intensity


title: non_involved_lung_tissue_patient_142


title: non_involved_lung_tissue_patient_136


title: non_involved_lung_tissue_patient_133


title: non_involved_lung_tissue_patient_144


title: SJBALL200

description: processed signal intensity


title: non_involved_lung_tissue_patient_138


title: non_involved_lung_tissue_patient_135


title: non_involved_lung_tissue_patient_134


title: non_involved_lung_tissue_patient_137


title: SJPHALL010

description: processed signal intensity


title: non_involved_lung_tissue_patient_131


title: non_involved_lung_tissue_patient_154


title: SJETV057

description: processed signal intensity


title: SJETV014

description: processed signal intensity


title: SJMLL003

description: processed signal intensity


title: SJHYPER069

description: processed signal intensity


title: non_involved_lung_tissue_patient_127


title: SJBALL022430

description: processed signal intensity


title: SJBALL197

description: processed signal intensity


title: non_involved_lung_tissue_patient_132


title: non_involved_lung_tissue_patient_145


title: non_involved_lung_tissue_patient_125


title: non_involved_lung_tissue_patient_128


title: BT549_siJun_TNF_rep2

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description:
CZ18_SiJun_TNF_C07.CEL
Gene expression in si_c-Jun/TNF-treated cells.
Replicate 2 of 3.

hyb_protocol: Hybridization to Human Gene 1.1 ST array plates was carried out overnight with biotin-labeled cRNA according to the Affymetrix protocol.

scan_protocol: Array plates were scanned using a GeneTitan scanner.

data_processing: Preprocessing in Affymetrix Expression Console (v. 1.1) using the following methods: Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.

source_name: BT549 cells, c-Jun knockdown, 72h, TNF

label_protocol: Total RNA was converted to sense strand cDNA using Ambion WT Expression kit. For fragmentation and labeling, GeneChip WT Target Labeling kit was used.

growth_protocol: The human breast cancer cell line BT549 was maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen) at 37°C, under a humidified atmosphere of 5% carbon dioxide.

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

treatment_protocol: BT549 cells were transfected with a control siRNA or with the pool of siRNAs targeting c-Jun for 72 hours, followed by treatment with or without TNFalpha for 6 hours, and then cells were harvested and total RNA was extracted.

tag: cell line

value: breast cancer cell line

tag: sirna

value: siJun

tag: treatment

value: TNFalpha


title: non_involved_lung_tissue_patient_121

tag: age at diagnosis (years)


title: BT549_siJun_TNF_rep3

description:
CZ24_16_2nd_D09.CEL
Gene expression in si_c-Jun/TNF-treated cells.
Replicate 3 of 3.

tag: cell type


title: non_involved_lung_tissue_patient_118

tag: clinical stage

tag: smoking status


title: non_involved_lung_tissue_patient_117

tag: batch

tag: tissue


title: non_involved_lung_tissue_patient_119


title: non_involved_lung_tissue_patient_124


title: non_involved_lung_tissue_patient_122


title: BT549_siJun_rep1

description:
CZ13_SiJun_C_C05.CEL
Gene expression in si_c-Jun-treated cells.
Replicate 1 of 3.

source_name: BT549 cells, c-Jun knockdown, 72h, vehicle

value: vehicle


title: BT549_siJun_rep3

description:
CZ15_SiJun_C_D05.CEL
Gene expression in si_c-Jun-treated cells.
Replicate 3 of 3.


title: non_involved_lung_tissue_patient_123

value: male


title: non_involved_lung_tissue_patient_126


title: non_involved_lung_tissue_patient_120


title: non_involved_lung_tissue_patient_116


title: BT549_sicontrol_TNF_rep3

description:
CZ06_Sictrl_TNF_B07.CEL
Gene expression in si_control/TNF-treated cells.
Replicate 3 of 3.

source_name: BT549 cells, siControl, 72h, TNF

value: siControl


title: non_involved_lung_tissue_patient_115

value: smoker


title: BT549_siJun_rep2

description:
CZ14_SiJun_C_H05.CEL
Gene expression in si_c-Jun-treated cells.
Replicate 2 of 3.


title: SJHYPO21982

description: processed signal intensity


title: BT549_sicontrol_rep2

description:
CZ02_Sictrl_C_E07.CEL
Gene expression in si_control-treated cells.
Replicate 2 of 3.

source_name: BT549 cells, siControl, 72h, vehicle


title: BT549_sicontrol_TNF_rep1

description:
CZ04_Sictrl_TNF_F09.CEL
Gene expression in si_control/TNF-treated cells.
Replicate 1 of 3.


title: non_involved_lung_tissue_patient_110

value: Non-involved (apparently normal) lung parenchyma


title: non_involved_lung_tissue_patient_130


title: SJETV021981

description: processed signal intensity


title: BT549_sicontrol_TNF_rep2

description:
CZ05_Sictrl_TNF_G07.CEL
Gene expression in si_control/TNF-treated cells.
Replicate 2 of 3.


title: non_involved_lung_tissue_patient_113


title: non_involved_lung_tissue_patient_114


title: SJETV021980

description: processed signal intensity


title: SJE2A067

description: processed signal intensity


title: SJTALL022066

description: processed signal intensity


title: non_involved_lung_tissue_patient_112


title: BT549_sicontrol_rep1

description:
CZ01_Sictrl_C_A07.CEL
Gene expression in si_control-treated cells.
Replicate 1 of 3.


title: non_involved_lung_tissue_patient_111


title: BT549_sicontrol_rep3

description:
CZ03_Sictrl_c_B05.CEL
Gene expression in si_control-treated cells.
Replicate 3 of 3.


title: SJINF22043

description: processed signal intensity


title: SJTALL022067

description: processed signal intensity


title: SJETV022041

description: processed signal intensity


title: non_involved_lung_tissue_patient_109


title: non_involved_lung_tissue_patient_108


title: non_involved_lung_tissue_patient_105


title: non_involved_lung_tissue_patient_107


title: non_involved_lung_tissue_patient_106


title: non_involved_lung_tissue_patient_103


title: non_involved_lung_tissue_patient_104


title: non_involved_lung_tissue_patient_102


title: SJTALL022065

description: processed signal intensity


title: non_involved_lung_tissue_patient_101


title: non_involved_lung_tissue_patient_129


title: SJTALL022062

description: processed signal intensity


title: SJTALL022063

description: processed signal intensity


title: SJHYPER021974

description: processed signal intensity


title: SJETV021977

description: processed signal intensity


title: SJBALL021973

description: processed signal intensity


title: SJBALL21971

description: processed signal intensity


title: SJETV021972

description: processed signal intensity


title: SJTALL022061

description: processed signal intensity


title: non_involved_lung_tissue_patient_95


title: non_involved_lung_tissue_patient_97


title: SJBALL255

description: processed signal intensity


title: non_involved_lung_tissue_patient_93


title: non_involved_lung_tissue_patient_94


title: SJTALL022060

description: processed signal intensity


title: non_involved_lung_tissue_patient_91


title: non_involved_lung_tissue_patient_100


title: non_involved_lung_tissue_patient_99


title: non_involved_lung_tissue_patient_88


title: non_involved_lung_tissue_patient_87


title: non_involved_lung_tissue_patient_96


title: non_involved_lung_tissue_patient_98


title: non_involved_lung_tissue_patient_85


title: non_involved_lung_tissue_patient_83


title: non_involved_lung_tissue_patient_92


title: non_involved_lung_tissue_patient_86


title: non_involved_lung_tissue_patient_90


title: non_involved_lung_tissue_patient_84


title: non_involved_lung_tissue_patient_89


title: non_involved_lung_tissue_patient_82


title: SJETV021969

description: processed signal intensity


title: SJBALL21968

description: processed signal intensity


title: non_involved_lung_tissue_patient_79


title: SJHYPER021970

description: processed signal intensity


title: SJBALL022035

description: processed signal intensity


title: non_involved_lung_tissue_patient_73


title: non_involved_lung_tissue_patient_75


title: non_involved_lung_tissue_patient_77


title: SJHYPER021966

description: processed signal intensity


title: SJETV021967

description: processed signal intensity


title: non_involved_lung_tissue_patient_76


title: non_involved_lung_tissue_patient_80


title: SJHYPER022034

description: processed signal intensity


title: BT549_siJun_TNF_rep1

description:
CZ16_SiJun_TNF_A09.CEL
Gene expression in si_c-Jun/TNF-treated cells.
Replicate 1 of 3.


title: non_involved_lung_tissue_patient_78


title: SJTALL022058

description: processed signal intensity


title: SJBALL022052

description: processed signal intensity


title: non_involved_lung_tissue_patient_70


title: non_involved_lung_tissue_patient_72


title: non_involved_lung_tissue_patient_71


title: non_involved_lung_tissue_patient_74


title: non_involved_lung_tissue_patient_65


title: non_involved_lung_tissue_patient_66


title: non_involved_lung_tissue_patient_81


title: non_involved_lung_tissue_patient_67


title: non_involved_lung_tissue_patient_64


title: non_involved_lung_tissue_patient_69


title: SJETV021963

description: processed signal intensity


title: SJBALL21964

description: processed signal intensity


title: SJHYPER022032

description: processed signal intensity


title: SJBALL247

description: processed signal intensity


title: SJHYPER022039

description: processed signal intensity


title: SJMLL022031

description: processed signal intensity


title: SJINF075

description: processed signal intensity


title: non_involved_lung_tissue_patient_68


title: non_involved_lung_tissue_patient_63


title: SJBALL022029

description: processed signal intensity


title: non_involved_lung_tissue_patient_55


title: SJBALL022051

description: processed signal intensity


title: non_involved_lung_tissue_patient_56


title: non_involved_lung_tissue_patient_60


title: non_involved_lung_tissue_patient_57


title: non_involved_lung_tissue_patient_54


title: non_involved_lung_tissue_patient_53


title: non_involved_lung_tissue_patient_61


title: non_involved_lung_tissue_patient_58


title: non_involved_lung_tissue_patient_49


title: non_involved_lung_tissue_patient_62


title: SJBALL243

description: processed signal intensity


title: non_involved_lung_tissue_patient_51


title: non_involved_lung_tissue_patient_46


title: non_involved_lung_tissue_patient_59


title: non_involved_lung_tissue_patient_50


title: non_involved_lung_tissue_patient_48


title: non_involved_lung_tissue_patient_47


title: non_involved_lung_tissue_patient_45


title: non_involved_lung_tissue_patient_52


title: non_involved_lung_tissue_patient_43


title: SJHYPER022027

description: processed signal intensity


title: SJTALL022056

description: processed signal intensity


title: non_involved_lung_tissue_patient_42


title: non_involved_lung_tissue_patient_41


title: SJETV22026

description: processed signal intensity


title: SJHYPER21961

description: processed signal intensity


title: SJE2A066

description: processed signal intensity


title: SJMLL22028

description: processed signal intensity


title: non_involved_lung_tissue_patient_44


title: non_involved_lung_tissue_patient_38


title: non_involved_lung_tissue_patient_40


title: SJBALL021960

description: processed signal intensity


title: non_involved_lung_tissue_patient_39


title: non_involved_lung_tissue_patient_37


title: non_involved_lung_tissue_patient_36


title: non_involved_lung_tissue_patient_35


title: SJETV021959

description: processed signal intensity


title: SJTALL022055

description: processed signal intensity


title: SJBALL010

description: processed signal intensity


title: non_involved_lung_tissue_patient_34


title: SJETV21956

description: processed signal intensity


title: SJBALL021958

description: processed signal intensity


title: non_involved_lung_tissue_patient_33


title: SJTALL021920

description: processed signal intensity


title: SJHYPER021957

description: processed signal intensity


title: non_involved_lung_tissue_patient_30


title: non_involved_lung_tissue_patient_22


title: non_involved_lung_tissue_patient_23


title: non_involved_lung_tissue_patient_28


title: non_involved_lung_tissue_patient_32


title: non_involved_lung_tissue_patient_31


title: non_involved_lung_tissue_patient_17


title: non_involved_lung_tissue_patient_29


title: non_involved_lung_tissue_patient_14


title: non_involved_lung_tissue_patient_20


title: non_involved_lung_tissue_patient_13


title: non_involved_lung_tissue_patient_26


title: non_involved_lung_tissue_patient_25


title: non_involved_lung_tissue_patient_24


title: SJBALL239

description: processed signal intensity


title: non_involved_lung_tissue_patient_21


title: SJBALL021955

description: processed signal intensity


title: SJETV021953

description: processed signal intensity


title: SJHYPER21954

description: processed signal intensity


title: SJETV021952

description: processed signal intensity


title: non_involved_lung_tissue_patient_11


title: non_involved_lung_tissue_patient_12


title: non_involved_lung_tissue_patient_27


title: non_involved_lung_tissue_patient_18


title: non_involved_lung_tissue_patient_7


title: non_involved_lung_tissue_patient_5


title: non_involved_lung_tissue_patient_4


title: SJHYPER021950

description: processed signal intensity


title: non_involved_lung_tissue_patient_19


title: SJETV022023

description: processed signal intensity


title: SJTALL021919

description: processed signal intensity


title: SJBALL021901

description: processed signal intensity


title: SJHYPER021951

description: processed signal intensity


title: non_involved_lung_tissue_patient_10


title: non_involved_lung_tissue_patient_16


title: non_involved_lung_tissue_patient_8


title: non_involved_lung_tissue_patient_6


title: non_involved_lung_tissue_patient_15


title: non_involved_lung_tissue_patient_9


title: non_involved_lung_tissue_patient_1


title: non_involved_lung_tissue_patient_3


title: non_involved_lung_tissue_patient_2


title: goiter-DL-G-1 [B10]

city: Beijing

first: Yanqiong

last: Zhang

address: No 16, Nanxiaojie, Dongzhimennei

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

hyb_protocol: ROA2.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: ROA2.1arrays were scanned by Agilent Microarray Scanner( G2505C ) 0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: Wistar rats, male and female equally, 160~180g, were fed in the condition of 18~22℃ and kept at the humidity of 50~60%. Animals could eat and drink freely.

extract_protocol: RNA extraction by Trizol Reagent (invitrogen #15596-026). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: Except the rats in control and model groups, the three other groups, which were established as goiter model, were administered appropriate medication  at the dose of 1mL/100g for 28 consecutive days. After all animals sacrificed, thyroids were removed and then put in Trizol for microarray experiments.

tag: strain background

value: Wistar

tag: weight

value: Male

tag: mouse group

value: goiter model group

tag: intragastric administration

value: Haizao Yuhu decotion lacking Radix Glycyrrhiza

value: thyroid  tissue

tag: treatment outcome

value: higher thyroid volumes and relative thyroid weight in DL-S than in normal control ,as same as model.


title: SJPHALL027

description: processed signal intensity

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

tag: source


title: SJETV021949

description: processed signal intensity


title: SJTALL021918

description: processed signal intensity


title: F06_d31_CM

city: Ann Arbor

first: Guihua

last: Jiang

state: MI

address: 109 Zina Pitcher PL

department: Surgery

institute: University of Michigan

description: Cardiomyocytes

data_processing:
Matrix non-normalized template reports the CT values generated from SDS2.4 Using Automatic baseline and manual threshold of .2
Matrix normalized template reports deltaCt values, for target transcripts, calculated as the difference to the average housekeeping genes(ACTB, B2M, GAPDH, RPLRO)
Fold Change worsheet reports the ratio between samples (2^-(deltadeltaCt))
CT Values Matrix non-normalized template

label: SYBR Green

source_name: Differentiated from iPS

label_protocol: SYBR Green

growth_protocol: Normal tissue culture condition with correspondent medium

extract_protocol: MagMAX-96 Total RNA Isolation Kit (Life technologies)  & MAG MAX Express (Applied Biosystems). RNA quantity and quality were determined spectrophotometrically, using a Nano Drop 2000( Thermoscientific)

value: Cardiomyocytes

tag: sample type

value: 31-day old cardiomyocytes


title: F06_iPS_P4

description: iPS

source_name: re-programed from fibroblast

value: iPS


title: SJTALL021917

description: processed signal intensity

value: bone marrow


title: SJBALL021947

description: processed signal intensity


title: SJETV021948

description: processed signal intensity


title: SJETV022049

description: processed signal intensity


title: SJHYPER021946

description: processed signal intensity


title: SJINF074

description: processed signal intensity


title: SJBALL022020

description: processed signal intensity


title: SJETV022019

description: processed signal intensity


title: F17_iPS_P23

description: iPS


title: F17_d31_CM

description: Cardiomyocytes


title: F06_P4

description: Fibroblast

source_name: New born foreskin

value: Fibroblast


title: goiter-control-1 [B4]

tag: Sex

value: normal saline

value: higher thyroid volumes and relative thyroid weight in model than in normal control


title: goiter-DL-G-1 [B9]


title: goiter-DL-G-1 [G10]

value: Female


title: goiter-Haizao Yuhu decotion-1 [G6]

source_name: goiter-Haizao Yuhu decotion-1

value: Haizao Yuhu decotion

value: thyroid volumes and relative thyroid weight were reduced by HYD


title: goiter-Haizao Yuhu decotion-1 [G5]


title: goiter-DL-S-1 [B8]

value: Haizao Yuhu decotion lacking Sargassum fusiforme


title: goiter-DL-S-1 [B7]

value: Wistar


title: SJHYPER022017

description: processed signal intensity


title: goiter-control-1 [B3]

value: Male


title: healthy control-1 [B2]

source_name: healthy control-1

value: control group

value: normal


title: healthy control-1 [B1]

value: thyroid  tissue


title: goiter-control-1 [G4]

value: goiter model group


title: goiter-Haizao Yuhu decotion-1 [B6]


title: F12_P2

description: Fibroblast


title: F12_iPS_P3

description: iPS


title: SJE2A065

description: processed signal intensity


title: goiter-DL-S-1 [G7]

value: higher thyroid volumes and relative thyroid weight in DL-S than in normal control ,as same as model.


title: SJBALL021944

description: processed signal intensity


title: HAF03_P2

description: amniocytes

source_name: Human Amniotic Fluid

value: amniocytes


title: SJTALL011

description: processed signal intensity


title: F17_P1

description: Fibroblast


title: F12_d31_CM

description: Cardiomyocytes

value: Cardiomyocytes

value: 31-day old cardiomyocytes


title: HAF03_d31_CM

description: Cardiomyocytes


title: SJTALL021916

description: processed signal intensity

value: bone marrow


title: SJETV021942

description: processed signal intensity


title: SJETV022015

description: processed signal intensity


title: SJHYPER022016

description: processed signal intensity


title: SJBALL021941

description: processed signal intensity


title: HAF03_iPS_P25

description: iPS

source_name: re-programed from amniocytes

value: iPS


title: SJMLL021940

description: processed signal intensity


title: SJETV021939

description: processed signal intensity


title: SJETV021945

description: processed signal intensity


title: SJTALL021915

description: processed signal intensity


title: SJBALL231

description: processed signal intensity


title: SJTALL021914

description: processed signal intensity


title: healthy control-1 [G1]

value: normal saline