title: Rorc floxed control 2

city: New York

first: Gregory

middle: F

last: Sonnenberg

state: NY

address: 413 East 69th Street, Belfer Research Building 512

institute: Weill Cornell Medical College

data_processing:
Standard protocol; Array was performed at the University of Pennsylvania Microarray core
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

source_name: Rorc floxed control_mesteric lymph node

extract_protocol: Lymph nodes were mechanically disrupted in a cell strainer, cells were sort purified into Trizol.

tag: strain background

tag: genotype/variation

value: Rorc floxed control

tag: treated with

value: tamoxifen for 2 wks

value: mesteric lymph node (LN)

value: CCR6+ innate lymphoid cells (ILCs)


title: 7_pat_rbc_5hrs_narrow cover slip_rpt

status: Public on Feb 15 2016

type: RNA

city: Liverpool

first: Michael

last: Griffiths

address: 8 West Derby Street

country: United Kingdom

institute: Institute of Infection and Global Health, University of Liverpool

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77332.gif

hyb_protocol: not provided

scan_protocol: GenePix Results 3

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: total RNA

organism: Homo sapiens

source_name: Stratagene Human ref. 1 Round Amplification 7ug(input)_4ug(couple)

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Stratagene Universal Human Ref RNA

source_name: 1 round amplification 15ug(input)_7_pat_rbc_5hrs

tag: tissue

value: red blood cells

tag: time

value: 5 h

tag: infection

value: no

tag: individual

tag: disease state

value: PrevHxMal


title: 8_cont_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77347.gif

source_name: 1 round amplification 15ug(input)_8_cont_A4_5hrs

value: yes

value: NoHxMal


title: 4_pat_rbc_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77906.gif

source_name: 1 round amplification 15ug(input)_4_pat_rbc_9hrs

value: 9 h


title: 12_pat_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77314.gif

source_name: 1 round amplification 15ug(input)_12_pat_rbc_5hrs


title: 15_pat_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77322.gif

source_name: 1 round amplification 15ug(input)_15_pat_rbc_5hrs


title: 16_cont_A4_5hrs_wide cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77353.gif

source_name: 1 round amplification 15ug(input)_16_cont_A4_5hrs


title: 8_pat_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77317.gif

source_name: 1 round amplification 15ug(input)_8_pat_A4_5hrs


title: 11_cont_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77340.gif

source_name: 1 round amplification 15ug(input)_11_cont_rbc_5hrs


title: Id2iΔRORγt 1

country: USA

hyb_protocol: Standard protocol; Array was performed at the University of Pennsylvania Microarray core

label: biotin

organism: Mus musculus

source_name: Id2iΔRORγt_mesteric lymph node

tag: cell type


title: Id2iΔRORγt 2

scan_protocol: Standard protocol; Array was performed at the University of Pennsylvania Microarray core


title: 7_cont_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77913.gif

source_name: 1 round amplification 15ug(input)_7_cont_A4_5hrs


title: 15_pat_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77321.gif

source_name: 1 round amplification 15ug(input)_15_pat_A4_5hrs


title: E28_1_LS

type: genomic

city: Tartu

first: Triin

last: Laisk-Podar

address: Puusepa 8

department: Obstetrics and Gynecology

country: Estonia

institute: University of Tartu

description:
Endometrium from patients with endometriosis
SAMPLE 22

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: The raw data were subject to quality control using the standard protocols suggested for the bioconductor R package minfi. Probes containing SNP sites, probes with the detection p-value > 0.01 in more than one sample and probes with the beadcount <3 in at least 5% of the samples were removed using bioconductor champ package. The remaining probes were normalized for adjusting type1 and type2 probes using Beta-Mixture Quantile (BMIQ) normalization method.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Endometrium

label_protocol: According to Illumina protocol

extract_protocol: Genomic DNA was isolated using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instructions

tag: patient id

tag: condition

value: endometriosis

tag: menstrual phase

value: Late secretory

value: endometrium


title: Rorc floxed control 1

label_protocol: Standard protocol; Array was performed at the University of Pennsylvania Microarray core


title: E31_1_LS

description:
Endometrium from patients with endometriosis
SAMPLE 21


title: E30_1_LS

description:
Endometrium from patients with endometriosis
SAMPLE 25


title: E29_1_LS

description:
Endometrium from patients with endometriosis
SAMPLE 20


title: E26_1_LS

description:
Endometrium from patients with endometriosis
SAMPLE 24


title: E19_1_MS_r2

description:
Endometrium from patients with endometriosis
SAMPLE 17

value: Mid secretory


title: E23_1_LS

description:
Endometrium from patients with endometriosis
SAMPLE 18


title: E25_1_LS

description:
Endometrium from patients with endometriosis
SAMPLE 26


title: low capacity runner (lcr), smoke 0428

city: Cambridge

first: Joseph

last: Szustakowski

state: MA

address: 220 Massachusetts Avenue

institute: Novartis Institutes for Biomedical Research

description: N:NIH rats bred for high (HCR) or low intrinsic exercise capacity (LCR) were exposed to cigarette smoke or shame.  After 12 weeks of exposures, lung samples were collected and analyzed for mRNA expression.

hyb_protocol: RNA samples were processed for hybridization on Affymetrix Rat   Genome 230 2.0 array (Affymetrix Inc) gene chip following standard procedures.

data_processing: rma, exponentiated, 2% trimmed mean scaled to 150

organism: Rattus norvegicus

source_name: low capacity runner (lcr), smoke

growth_protocol: age matched, 34 week old, female HCR and LCR rats

extract_protocol: Total RNA was isolated from    ~25 mg of lung tissue using the RNeasy mini RNA isolation kit (QIAGEN)  RNA   content and integrity were assessed using an Agilent 2100 bioanalyzer (Agilent   technologies)

treatment_protocol: rats were exposed to either cigarette smoke or room-air (sham) five days per week

value: lung

tag: strain

tag: age

value: 34 weeks old

tag: gender

value: female


title: E19_1_MS_r1

description:
Endometrium from patients with endometriosis
SAMPLE 16


title: E27_1_LS

description:
Endometrium from patients with endometriosis
SAMPLE 19


title: low capacity runner (lcr), smoke 0424

scan_protocol: RNA samples were processed for hybridization on Affymetrix Rat   Genome 230 2.0 array (Affymetrix Inc) gene chip following standard procedures.


title: low capacity runner (lcr), smoke 0427

label_protocol: RNA samples were processed for hybridization on Affymetrix Rat   Genome 230 2.0 array (Affymetrix Inc) gene chip following standard procedures.


title: E24_1_LS

description:
Endometrium from patients with endometriosis
SAMPLE 23


title: low capacity runner (lcr), smoke 0425


title: low capacity runner (lcr), smoke 0422


title: low capacity runner (lcr), smoke 0426


title: low capacity runner (lcr), smoke 0430


title: low capacity runner (lcr), smoke 0421


title: low capacity runner (lcr), smoke 0431


title: low capacity runner (lcr), smoke 0420


title: low capacity runner (lcr), smoke 0429


title: E22_1_MS

description:
Endometrium from patients with endometriosis
SAMPLE 13


title: low capacity runner (lcr), smoke 0423


title: E17_1_MS

description:
Endometrium from patients with endometriosis
SAMPLE 12


title: Heart, Resected, rep1

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description: Pool of 50 resected ventrical samples, 2 weeks after surgery

hyb_protocol: Arrays (Affymetrix, Santa Clara , CA, USA) were hybridized with 2.7μg of biotinylated target, at  45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: Background subtraction and quantile normalization were performed using the R/Bioconductor package affy, rma method

organism: Danio rerio

source_name: Heart, Resected

label_protocol: 400 ng of total RNA were used to perform target preparation using Message Amp II-biotin Enhanced reagents (Life Technologies).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen). RNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 Bioanalyzer.

value: heart


title: E15_1_MS_r2

description:
Endometrium from patients with endometriosis
SAMPLE 15


title: high capacity runner (hcr), smoke 0412

source_name: high capacity runner (hcr), smoke


title: Heart, Resected, rep3


title: high capacity runner (hcr), smoke 0415


title: E18_1_MS

description:
Endometrium from patients with endometriosis
SAMPLE 11


title: Heart, Control, rep3

description: Pool of 50 control ventrical samples, 2 weeks after surgery

source_name: Heart, Control


title: Heart, Resected, rep4


title: high capacity runner (hcr), smoke 0408


title: Heart, Resected, rep2


title: high capacity runner (hcr), smoke 0416


title: high capacity runner (hcr), smoke 0418


title: Heart, Control, rep4


title: high capacity runner (hcr), smoke 0413


title: Heart, Control, rep2


title: high capacity runner (hcr), smoke 0409


title: E13_1_ES

description:
Endometrium from patients with endometriosis
SAMPLE 3

value: Early secretory


title: high capacity runner (hcr), smoke 0417


title: Heart, Control, rep1


title: high capacity runner (hcr), smoke 0414


title: THP-1_vitC_48h_rep2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
Gene expression of PMA-differentiated vitC-treated-THP-1 cells at 48 h
AA_D2_3

hyb_protocol: 600ng of labeled cRNA were hybridized on Custom Human Whole Genome 8x60K Array 8x60k designed by Genotypic Technology Private Limited (AMADID: 027114)using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned using the Agilent Microarray G2505C scanner (Agilent Technologies)

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106).

growth_protocol: THP-1 cells were maintained in RPMI 1640 in 10% FBS. The cells were passaged at nearly 80% confluency. The experiment was performed at ~99% cell viability as determined by trypan blue exclusion method.

extract_protocol: At respective time-point, the media was removed from the control and vit C-treated flasks. This was immediately followed by addition of TRI reagent and swirling the flasks in order to lyse the adhered cells. The cell lysates were centrifuged at 5000 rpm for 15 min at 4C. The supernatant was used for RNA extraction using bromochloropropane method.Briefly, 1/10th volume of bromochloropropane (Molecular Research Center, USA) was added to the samples and vigorously shaken for 10 sec. The samples were then incubated for 10 min at room temperature (for phase separation). The aqueous phase was separated by centrifuging the samples at 12000 rpm for 15 min at 4°C. The RNA in the aqueous phase was precipitated with 1/100th volume of polyacryl carrier and isopropanol (0.6 volumes, for 30 min), centrifuged (12,000 rpm, 4°C for 15 min) and washed with 75% ethanol and then air-dried. Total RNA was dissolved in 100 μl of DEPC-treated water.

treatment_protocol: Nearly, 8 x 106 THP-1 cells were seeded in T-75 cm2 flasks in RMPI with 10% FBS. The cells were then differentiated with 30 nM PMA for 16-18 h. Following differentiation, the cells were allowed resting for 2-3 h. The cells were then treated with 0.1 mM vitamin C (vitC) and subsequently RNA was isolated from untreated control flasks and vit C treated flasks as 8 h, 24 h, 48 h and 96 h post vit C-addition.

tag: cell line

value: THP-1 monocytic cell line

tag: protocol

value: differentiated with PMA

tag: treatment

value: vitC


title: high capacity runner (hcr), smoke 0419


title: E7_1_ES

description:
Endometrium from patients with endometriosis
SAMPLE 7


title: low capacity runner (lcr), sham 0443

source_name: low capacity runner (lcr), sham


title: E14_1_MS

description:
Endometrium from patients with endometriosis
SAMPLE 8


title: E21_1_MS

description:
Endometrium from patients with endometriosis
SAMPLE 10


title: E10_1_ES

description:
Endometrium from patients with endometriosis
SAMPLE 6


title: THP-1_vitC_96h_rep1

description:
Gene expression of PMA-differentiated vitC-treated-THP-1 cells at 96 h
D4_AAI


title: E11_1_ES

description:
Endometrium from patients with endometriosis
SAMPLE 4


title: E8_1_ES

description:
Endometrium from patients with endometriosis
SAMPLE 5


title: THP-1_vitC_24h_rep2

description:
Gene expression of PMA-differentiated vitC-treated-THP-1 cells at 24 h
AA_24h_2


title: E12_1_ES

description:
Endometrium from patients with endometriosis
SAMPLE 2


title: THP-1_vitC_96h_rep2

description:
Gene expression of PMA-differentiated vitC-treated-THP-1 cells at 96 h
D4_AAII


title: high capacity runner (hcr), smoke 0410

description: N:NIH rats bred for high (HCR) or low intrinsic exercise capacity (LCR) were exposed to cigarette smoke or shame.  After 12 weeks of exposures, lung samples were collected and analyzed for mRNA expression.


title: THP-1_vitC_8h_rep2

description:
Gene expression of PMA-differentiated vitC-treated-THP-1 cells at 8 h
AA_8h_2

value: 8 h


title: low capacity runner (lcr), sham 0446


title: THP-1_vitC_8h_rep1

description:
Gene expression of PMA-differentiated vitC-treated-THP-1 cells at 8 h
AA_8h_1


title: THP-1_vitC_48h_rep1

description:
Gene expression of PMA-differentiated vitC-treated-THP-1 cells at 48 h
AA_D2_2


title: high capacity runner (hcr), smoke 0411


title: low capacity runner (lcr), sham 0442


title: low capacity runner (lcr), sham 0444


title: THP-1_vitC_8h_rep3

description:
Gene expression of PMA-differentiated vitC-treated-THP-1 cells at 8 h
AA_8h_3


title: THP-1_vitC_24h_rep1

description:
Gene expression of PMA-differentiated vitC-treated-THP-1 cells at 24 h
AA_24h_1


title: E20_1_MS

description:
Endometrium from patients with endometriosis
SAMPLE 9


title: E15_1_MS_r1

description:
Endometrium from patients with endometriosis
SAMPLE 14


title: E9_1_ES

description:
Endometrium from patients with endometriosis
SAMPLE 1


title: low capacity runner (lcr), sham 0441


title: THP-1_UT_96h_rep3

description:
Gene expression of PMA-differentiated untreated-THP-1 cells at 96 h
UT_D4_3

value: control


title: low capacity runner (lcr), sham 0445


title: low capacity runner (lcr), sham 0440


title: high capacity runner (hcr), sham 0432

source_name: high capacity runner (hcr), sham


title: high capacity runner (hcr), sham 0436


title: THP-1_UT_96h_rep2

description:
Gene expression of PMA-differentiated untreated-THP-1 cells at 96 h
UT_D4_2


title: high capacity runner (hcr), sham 0438


title: THP-1_UT_48h_rep2

description:
Gene expression of PMA-differentiated untreated-THP-1 cells at 48 h
UT_D2_3


title: THP-1_UT_24h_rep3

description:
Gene expression of PMA-differentiated untreated-THP-1 cells at 24 h
UT_24h_3


title: high capacity runner (hcr), sham 0434


title: THP-1_UT_8h_rep1

description:
Gene expression of PMA-differentiated untreated-THP-1 cells at 8 h
UT_8h_1


title: THP-1_UT_24h_rep1

description:
Gene expression of PMA-differentiated untreated-THP-1 cells at 24 h
UT_24h_1


title: THP-1_UT_96h_rep1

description:
Gene expression of PMA-differentiated untreated-THP-1 cells at 96 h
UT_D4_1


title: high capacity runner (hcr), sham 0433


title: high capacity runner (hcr), sham  0439


title: THP-1_UT_48h_rep1

description:
Gene expression of PMA-differentiated untreated-THP-1 cells at 48 h
UT_D2_2


title: CRC patient with primary CRC lesions_28

status: Public on Feb 14 2016

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: CRC patient 28 with primary CRC lesions

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

scan_protocol: After hybridization and washing, the slides were scanned using an Agilent scanner (G2505C). Images were extracted using Agilent Feature Extraction software (ver. 10.7.3.1) and Agilent GeneSpring GX software (ver. 10.0.2).

data_processing: Raw data were analyzed using Agilent GeneSpring GX software (ver. 10.0.2).

source_name: CRC patient 28 with primary CRC lesions

label_protocol: Total RNA was dephosphorylated with calf intestine alkaline phosphatase, denatured with dimethyl sulfoxide, and labeled with pCp-Cy3 using T4 RNA ligase using the miRNA Labeling Reagent and Hybridization Kit.

extract_protocol: Total RNA from tissues was isolated using the miRNeasy Mini Kit (QIAGEN) following the manufacturer’s protocol. We quantified the concentrations of all RNA samples using NanoDrop ND-1000 (NanoDrop). Total RNA from cells was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

tag: patient

value: CRC patient 28

value: primary CRC lesions


title: CRC patient with primary CRC lesions_27

description: CRC patient 27 with primary CRC lesions

source_name: CRC patient 27 with primary CRC lesions

value: CRC patient 27


title: THP-1_UT_24h_rep2

description:
Gene expression of PMA-differentiated untreated-THP-1 cells at 24 h
UT_24h_2


title: CRC patient with primary CRC lesions_25

description: CRC patient 25 with primary CRC lesions

source_name: CRC patient 25 with primary CRC lesions

value: CRC patient 25


title: high capacity runner (hcr), sham 0435

description: N:NIH rats bred for high (HCR) or low intrinsic exercise capacity (LCR) were exposed to cigarette smoke or shame.  After 12 weeks of exposures, lung samples were collected and analyzed for mRNA expression.


title: CRC patient with primary CRC lesions_22

description: CRC patient 22 with primary CRC lesions

source_name: CRC patient 22 with primary CRC lesions

value: CRC patient 22


title: CRC patient with primary CRC lesions_26

description: CRC patient 26 with primary CRC lesions

source_name: CRC patient 26 with primary CRC lesions

value: CRC patient 26


title: CRC patient with primary CRC lesions_23

description: CRC patient 23 with primary CRC lesions

source_name: CRC patient 23 with primary CRC lesions

value: CRC patient 23


title: CRC patient with primary CRC lesions_20

description: CRC patient 20 with primary CRC lesions

source_name: CRC patient 20 with primary CRC lesions

value: CRC patient 20


title: CRC patient with primary CRC lesions_19

description: CRC patient 19 with primary CRC lesions

source_name: CRC patient 19 with primary CRC lesions

value: CRC patient 19


title: THP-1_UT_8h_rep2

description:
Gene expression of PMA-differentiated untreated-THP-1 cells at 8 h
UT_8h_2


title: CRC patient with liver metastatic lesions_6

description: CRC patient 06 with liver metastatic lesions

value: CRC patient 06

value: liver metastatic lesions


title: CRC patient with primary CRC lesions_15

description: CRC patient 15 with primary CRC lesions

source_name: CRC patient 15 with primary CRC lesions

value: CRC patient 15


title: CRC patient with primary CRC lesions_17

description: CRC patient 17 with primary CRC lesions

source_name: CRC patient 17 with primary CRC lesions

value: CRC patient 17


title: CRC patient with primary CRC lesions_24

description: CRC patient 24 with primary CRC lesions

source_name: CRC patient 24 with primary CRC lesions

value: CRC patient 24


title: CRC patient with primary CRC lesions_12

description: CRC patient 12 with primary CRC lesions

source_name: CRC patient 12 with primary CRC lesions

value: CRC patient 12


title: CRC patient with primary CRC lesions_18

description: CRC patient 18 with primary CRC lesions

source_name: CRC patient 18 with primary CRC lesions

value: CRC patient 18


title: CRC patient with liver metastatic lesions_8

description: CRC patient 08 with liver metastatic lesions

value: CRC patient 08


title: CRC patient with primary CRC lesions_16

description: CRC patient 16 with primary CRC lesions

source_name: CRC patient 16 with primary CRC lesions

value: CRC patient 16


title: CRC patient with primary CRC lesions_13

description: CRC patient 13 with primary CRC lesions

source_name: CRC patient 13 with primary CRC lesions

value: CRC patient 13

value: primary CRC lesions


title: CRC patient with liver metastatic lesions_7

description: CRC patient 07 with liver metastatic lesions

value: CRC patient 07


title: CRC patient with primary CRC lesions_14

description: CRC patient 14 with primary CRC lesions

source_name: CRC patient 14 with primary CRC lesions

value: CRC patient 14


title: CRC patient with primary CRC lesions_9

description: CRC patient 09 with primary CRC lesions

source_name: CRC patient 09 with primary CRC lesions

value: CRC patient 09


title: CRC patient with primary CRC lesions_11

description: CRC patient 11 with primary CRC lesions

source_name: CRC patient 11 with primary CRC lesions

value: CRC patient 11


title: CRC patient with primary CRC lesions_8

description: CRC patient 08 with primary CRC lesions

source_name: CRC patient 08 with primary CRC lesions


title: CRC patient with liver metastatic lesions_5

description: CRC patient 05 with liver metastatic lesions

value: CRC patient 05


title: CRC patient with liver metastatic lesions_4

description: CRC patient 04 with liver metastatic lesions

value: CRC patient 04


title: CRC patient with primary CRC lesions_10

description: CRC patient 10 with primary CRC lesions

source_name: CRC patient 10 with primary CRC lesions

value: CRC patient 10


title: CRC patient with primary CRC lesions_7

description: CRC patient 07 with primary CRC lesions

source_name: CRC patient 07 with primary CRC lesions


title: CRC patient with liver metastatic lesions_3

description: CRC patient 03 with liver metastatic lesions

value: CRC patient 03

value: liver metastatic lesions


title: CRC patient with liver metastatic lesions_2

description: CRC patient 02 with liver metastatic lesions

value: CRC patient 02


title: CRC patient with primary CRC lesions_6

description: CRC patient 06 with primary CRC lesions

source_name: CRC patient 06 with primary CRC lesions

value: CRC patient 06


title: CRC patient with primary CRC lesions_4

description: CRC patient 04 with primary CRC lesions

source_name: CRC patient 04 with primary CRC lesions


title: CRC patient with primary CRC lesions_3

description: CRC patient 03 with primary CRC lesions

source_name: CRC patient 03 with primary CRC lesions


title: CRC patient with primary CRC lesions_21

description: CRC patient 21 with primary CRC lesions

source_name: CRC patient 21 with primary CRC lesions

value: CRC patient 21


title: CRC patient with primary CRC lesions_2

description: CRC patient 02 with primary CRC lesions

source_name: CRC patient 02 with primary CRC lesions


title: Lung09_(Lung_to_Lymph_node)

status: Public on Feb 13 2016

city: Durham

first: David

last: Hsu

state: NC

address: Rm 2167 CIEMAS Bldg, 101 Science Dr.

department: Institute for Genome Sciences and Policy

institute: Duke University

description: Gene expression data from laser capture microdissected metastatic tumor sample

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133 Plus 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

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

data_processing: The data were analyzed using the open-source R platform with statistical microarray analysis tools compiled by Bioconductor and normalized with Bioconductor's standard RMA analysis methods.

source_name: Lung (primary site) to Lymph node (metastatic site) laser capture microdissected tumor sample

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

extract_protocol: Total RNA from laser capture microdissected adenocarcinoma patient tumor samples was extracted using the Ambion Mirvana totalRNA extraction kit.

tag: primary tumor site

value: Lung

tag: metastatic tumor site

value: Lymph Node


title: CRC patient with primary CRC lesions_1

description: CRC patient 01 with primary CRC lesions

source_name: CRC patient 01 with primary CRC lesions

value: CRC patient 01

tag: tissue


title: Prostate07_(Prostate_to_Bone)

source_name: Prostate (primary site) to Bone (metastatic site) laser capture microdissected tumor sample

value: Prostate

value: Bone


title: Lung07_(Lung_to_Brain)

source_name: Lung (primary site) to Brain (metastatic site) laser capture microdissected tumor sample

value: Brain


title: Lung10_(Lung_to_Lymph_node)


title: Prostate03_(Prostate_to_Bone)


title: Mother of Patient 2

city: Brasília

first: Rolando

middle: Andre Rios

last: Villacis

state: DF

address: Asa Norte

department: Genetics and Morphology

country: Brazil

institute: University of Brasília - UnB

description: germline alterations

hyb_protocol: Performed following CytoScan Assay User Manual (P/N 703038 Ver.4)

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

data_processing: The data were analyzed with the standard parameters of Chromosome Analysis Suite (ChAS) v3.1 software (Affymetrix)

source_name: Blood

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted from peripheral blood of patients, mother of Patient 2 and four children and from breast tumor tissue (Patient 2) using the standard protocol of Gentra Puregene Blood Kit (Qiagen, Valencia, Ca, USA)

treatment_protocol: Not applicable

value: female


title: Lung05_(Lung_to_Brain)


title: Lung03_(Lung_adenocarcinoma_to_Brain)

source_name: Lung adenocarcinoma (primary site) to Brain (metastatic site) laser capture microdissected tumor sample

value: Lung adenocarcinoma


title: Colon36_(Colorectal_adenocarcinoma_to_Brain)

source_name: Colorectal adenocarcinoma (primary site) to Brain (metastatic site) laser capture microdissected tumor sample

value: Colorectal adenocarcinoma


title: Lung06_(Lung_to_Brain)


title: Prostate04_(Prostate_to_Bone)


title: Prostate05_(Prostate_to_Bone)


title: Lung04_(Lung_adenocarcinoma_to_Brain)


title: Prostate01_(Prostate_to_Bone)


title: Prostate02_(Prostate_to_Bone)


title: Prostate08_(Prostate_to_Bone)


title: Lung08_(Lung_to_Lymph_node)


title: Prostate06_(Prostate_to_Bone)


title: Prostate09_(Prostate_to_Bone)


title: CRC patient with primary CRC lesions_5

description: CRC patient 05 with primary CRC lesions

source_name: CRC patient 05 with primary CRC lesions

value: CRC patient 05

value: primary CRC lesions


title: Breast14_(Breast_mucinous_adenocarcinoma_to_Brain)

source_name: Breast mucinous adenocarcinoma (primary site) to Brain (metastatic site) laser capture microdissected tumor sample

value: Breast mucinous adenocarcinoma


title: Lung02_(Lung_adenocarcinoma_to_Brain)


title: Daughter of Patient 2

description: germline alterations

label_protocol: Performed following CytoScan Assay User Manual (P/N 703038 Ver.4)


title: Breast Cancer of Patient 2

description: somatic alterations

source_name: Breast cancer tissue


title: Colon35_(Colon_adenocarcinoma_to_Brain)

source_name: Colon adenocarcinoma (primary site) to Brain (metastatic site) laser capture microdissected tumor sample

value: Colon adenocarcinoma


title: Colon32_(Colon_to_Liver)

source_name: Colon (primary site) to Liver (metastatic site) laser capture microdissected tumor sample

value: Colon

value: Liver


title: Colon30_(Colon_to_Liver)


title: Colon27_(Colon_to_Liver)


title: Colon34_(Colon_to_Colon,Rectum)

source_name: Colon (primary site) to Colon,Rectum (metastatic site) laser capture microdissected tumor sample

value: Colon, Rectum


title: Colon28_(Colon_to_Liver)


title: Son A of Patient 2

description: germline alterations

value: male


title: Colon23_(Colon_to_Liver)


title: Colon31_(Colon_to_Liver)


title: Colon29_(Colon_to_Liver)


title: Colon33_(Colon_to_Liver)


title: Breast12_(Breast_to_Liver)

source_name: Breast (primary site) to Liver (metastatic site) laser capture microdissected tumor sample

value: Breast


title: Esophogeal01_(Esophageal_adenocarcinoma_to_Brain)

source_name: Esophageal adenocarcinoma (primary site) to Brain (metastatic site) laser capture microdissected tumor sample

value: Esophageal adenocarcinoma


title: Breast13_(Breast_Carcinoma_to_Brain)

source_name: Breast Carcinoma (primary site) to Brain (metastatic site) laser capture microdissected tumor sample

value: Breast carcinoma


title: Colon24_(Colon_to_Liver)


title: Colon21_(Colon_to_Colon,Left)

source_name: Colon (primary site) to Colon,Left (metastatic site) laser capture microdissected tumor sample

value: Colon, left


title: Colon20_(Colon_to_Liver)


title: Breast11_(Breast_to_Liver)


title: Renal06_(Renal_clear_cell_to_Brain)

source_name: Renal clear cell (primary site) to Brain (metastatic site) laser capture microdissected tumor sample

value: Renal clear cell


title: Patient 1

description: germline alterations


title: Son of Patient 1

description: germline alterations


title: Patient 2

description: germline alterations


title: Colon18_(Colon_to_Lung)

source_name: Colon (primary site) to Lung (metastatic site) laser capture microdissected tumor sample

value: Lung


title: Colon22_(Colon_to_Liver)


title: Colon19_(Colon_to_Colon)

source_name: Colon (primary site) to Colon (metastatic site) laser capture microdissected tumor sample


title: Colon17_(Colon_to_Liver)


title: GEJunction02_(GE_Junction_to_Liver)

source_name: GE Junction (primary site) to Liver (metastatic site) laser capture microdissected tumor sample

value: GE junction


title: CRC patient with liver metastatic lesions_1

description: CRC patient 01 with liver metastatic lesions

value: CRC patient 01

value: liver metastatic lesions


title: Colon14_(Colon_to_Liver)


title: Colon11_(Colon_to_Liver)


title: Breast09_(Breast_to_Lymph_node)

source_name: Breast (primary site) to Lymph node (metastatic site) laser capture microdissected tumor sample

value: Lymph Node


title: Colon12_(Colon_to_Liver)


title: Colon13_(Colon_to_Liver)


title: Colon08_(Colon_to_Ovary)

source_name: Colon (primary site) to Ovary (metastatic site) laser capture microdissected tumor sample

value: Ovary


title: Other02_(Adenocarcinoma_possibly_H&N to Cervical_LN)

source_name: Adenocarcinoma possibly H&N (primary site) Cervical LN (metastatic site) laser capture microdissected tumor sample

value: Adenocarcinoma, possibly H&N


title: Breast06_(Breast_to_Lymph_node)


title: Colon16_(Colon_to_Liver)


title: Breast07_(Breast_to_Lymph_node)


title: Breast10_(Breast_to_Lymph_node)


title: Breast08_(Breast_to_Lymph_node)


title: Son B of Patient 2

description: germline alterations

source_name: Blood


title: Ovary12_(Ovary_to_Pelvis)

source_name: Ovary (primary site) to Pelvis (metastatic site) laser capture microdissected tumor sample

value: Pelvis


title: Other01_(Adenocarcinoma_most_likely_GI_to_Femur)

source_name: Adenocarcinoma most likely GI (primary site) to Femur (metastatic site) laser capture microdissected tumor sample

value: Adenocarcinoma, most likely GI

value: Femur


title: Breast05_(Breast_to_Lymph_node)


title: Ovary13_(Ovary_to_Abdominal_wall)

source_name: Ovary (primary site) to Abdominal wall (metastatic site) laser capture microdissected tumor sample

value: Abdominal wall


title: Ovary14_(Ovary_to_Rectum)

source_name: Ovary (primary site) to Rectum (metastatic site) laser capture microdissected tumor sample

value: Rectum


title: Colon07_(Colon_to_Liver)

source_name: Colon (primary site) to Liver (metastatic site) laser capture microdissected tumor sample

value: Colon

value: Liver


title: Colon09_(Colon_to_Liver)


title: Colon10_(Colon_to_Liver)


title: Colon15_(Colon_to_Liver)


title: Ovary11_(Ovary_to_Omentum)

source_name: Ovary (primary site) to Omentum (metastatic site) laser capture microdissected tumor sample

value: Omentum


title: Ovary09_(Ovary_to_Omentum)


title: Ovary10_(Ovary_to_Uterus)

source_name: Ovary (primary site) to Uterus (metastatic site) laser capture microdissected tumor sample

value: Uterus


title: Breast04_(Breast_to_Lymph Node)

value: Breast


title: Breast03_(Breast_to_Liver)

source_name: Breast (primary site) to Liver (metastatic site) laser capture microdissected tumor sample


title: Ovary08_(Ovary_to_Omentum)


title: Breast02_(Breast_to_Chest wall)

source_name: Breast (primary site) to Chest wall (metastatic site) laser capture microdissected tumor sample

value: Chest wall


title: Colon06_(Colon_to_Lung)

value: Lung


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1/5_24h_replicate 3

city: Jinju

first: Dong-hoon

last: Lee

state: Gyeongnam

address: 15 Jinju-daero 816 Beon-gil

department: Convergence Medical Science

country: South Korea

institute: Gyeongsang National University

hyb_protocol: Agilent Gene Expression Hybridization Kit

scan_protocol: GenePix Pro 6.0 software (Axon Instruments, Union City, CA)

data_processing:
Agilent's GeneSpring GX 7.3 software
(Per chip: average or percentile to the normalization of Sikkim Per gene: normalization of Sikkim as an average) divided with the GeneSpring GX intensity values in each column based on the average pack of chips. Then, by dividing each value by the average value for each gene across the sample to obtain a final normalized value.

label_protocol: Agilent Low RNA Input Linear Amplification kit PLUS

growth_protocol: Primary cultures were established using neonatal rat heart tissues collected after anesthetizing the rats, cultures were left to grow for one day on DMEM media then were treated as follow

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

treatment_protocol: Variables of treatment included two time points (6h or 24h) and three reference concentrations (1, 1/5 and 1/25).

tag: developmental stage

value: Neonate

tag: agent

value: diclofenac

tag: reference concentration

tag: time

value: Heart

value: cardiomyocyte


title: Renal05_(Renal_to_Ankle)

source_name: Renal (primary site) to Ankle (metastatic site) laser capture microdissected tumor sample

value: Renal

value: Ankle


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1/25_24h_replicate 1

tag: cell type


title: Breast01_(Breast_to_Chest wall)


title: Colon05_(Colon_to_Lung)

source_name: Colon (primary site) to Lung (metastatic site) laser capture microdissected tumor sample


title: Ovary06_(Ovarian vs Peritoneal_to_Omentum)

source_name: Ovarian vs Peritoneal (primary site) to Omentum (metastatic site) laser capture microdissected tumor sample

value: Ovarian vs Peritoneal


title: Colon04_(Colon_to_Lung)


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1/5_24h_replicate 2


title: GEJunction01_(GE Junction_to_Liver)

source_name: GE Junction (primary site) to Liver (metastatic site) laser capture microdissected tumor sample

value: GE junction


title: Pancreas01_(Pancreas_to_Liver)

source_name: Pancreas (primary site) to Liver (metastatic site) laser capture microdissected tumor sample

value: Pancreas


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1/5_24h_replicate 1


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1/25_24h_replicate 3


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1_24h_replicate 3


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1_24h_replicate 1


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1/25_24h_replicate 2


title: Colon26_(Colon_to_Liver)


title: Colon25_(Colon_to_Lung)


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1_24h_replicate 2


title: Raw_Stat3

city: Shanghai

first: Xiaoping

last: Su

address: 800 Xiangyin Road

country: China

institute: National Key Laboratory of Medical Immunology & Institute of Immunology

description: RAW Stat3(2-ΔCt)

data_processing:
Perform initial data analysis using the software supplied with the real-time PCR instrument to obtain raw Cq values (Cp or Ct, depending on PCR instrument).
We recommend performing normalization and further data analysis with the GenEx qPCR analysis software (www.exiqon.com/mirna-pcranalysis) Please refer to our data analysis guide for recommendations.
(1) Calculate the ΔCt for each pathway-focused gene in each treatment group.
ΔCt (group 1) = average Ct – average of HK genes’ Ct for group 1 array
ΔCt (group 2) = average Ct – average of HK genes’ Ct for group 2 array
NOTE: The expression level of the housekeeping genes chosen for normalization in the ΔΔCt method must not be influenced by your experimental conditions. If one or more such genes have been previously identified by independent means and if the PCR Array reproduces those results, use the average of their Ct values in the equation above. If an appropriate housekeeping gene has not been previously identified, use the average Ct value of all five housekeeping genes, but only if the difference in the average values between the two groups to be compared is less than one (1) cycle. Otherwise, simply use zero (0) in the place of the average of HK genes’ Ct for each group to be compared,and rely on the consistency in the quantity and quality of your original input total RNA across your groups to effectively normalize your results.
(2) Calculate the ΔΔCt for each gene across two PCR Arrays (or groups).
ΔΔCt = ΔCt (group 2) - ΔCt (group 1)
Where group 1 is the control and group 2 is the experimental
(3) Calculate the fold-change for each gene from group 1 to group 2 as 2-ΔΔCt.
OPTIONAL: If the fold-change is greater than 1, then the result may be reported as a fold up-regulation. If the fold-change is less than 1, then the negative inverse of the result may be reported as a fold down-regulation.

label: SYBR green

source_name: RAW264.7 cell line

label_protocol: RT-PCR protocol: Expression analysis of miRNAs was used the Exiqon multiplex miRNA arrays according to the manufacturer’s instructions.

growth_protocol: RAW264.7 cells were cultured in DMEM media containing 10% FBS. Cells were maintained at 37℃ and 5% CO2.

extract_protocol: The associated mRNA  was purified using Streptavidin Dynabeads (M-280) and isolated by TRIzol.

treatment_protocol: The probe of mRNA was transfected into RAW264.7 cells to hybridize  mRNA for 24 hours.

tag: cell ine

value: macrophage cells

tag: isolation

value: miRIP

tag: molecule subtype

value: miRNA isolated by Stat3 probe


title: Ovary07_(Ovary_to_Omentum)

value: Ovary

value: Omentum


title: Renal04_(Renal_to_Lung)

source_name: Renal (primary site) to Lung (metastatic site) laser capture microdissected tumor sample


title: Raw_control

description: RAW control(2-ΔCt)

value: miRNA isolated by control probe


title: Rectal01_(Rectal_to_Lung)

source_name: Rectal (primary site) to Lung (metastatic site) laser capture microdissected tumor sample

value: Rectal


title: Lung01_(Lung_to_Kidney)

source_name: Lung (primary site) to Kidney (metastatic site) laser capture microdissected tumor sample

value: Lung

value: Kidney


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1/25_6h_replicate 2

value: Neonate

value: diclofenac


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1/25_6h_replicate 1

value: Heart

value: cardiomyocyte


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1/25_6h_replicate 3


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1/5_6h_replicate 3


title: RalA72L_rep4

description: Gene expression data from cell-lines  transfected with RalA gene

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A Plus 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed using RMA express

source_name: Transfectant cells overexpressing RalA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HEK-HT cells expressing empty vector or RalAQ72L were grown to 90% confluency in DMEM-H containing 10% FBS and 1x penstrep.  When 90% confluency was reached, cells were washed with PBS two times and then grown in DMEM-H without FBS for 48 hours

extract_protocol: Cells were collected and total RNA was isolated using RNAzol B reagent and chloroform.  RNA was precipiated with isoproponal, washed in 75% ethanol, and resuspended in DEPC water.

tag: culture condition

value: penstrep

value: HEK-HT


title: Renal02_(Renal_to_Retroperitoneal)

source_name: Renal (primary site) to Retroperitoneal (metastatic site) laser capture microdissected tumor sample

value: Renal

value: Retroperitoneal


title: RalA72L_rep3


title: Control_rep3

description: Gene expression data from cell-lines not transfected with the RalA gene

source_name: Empty vector control


title: skeletal muscle precursor cells transformed with hTERT and RasG12V_rep2

description: Gene expression data from skeletal muscle precursor cells transformed with hTERT and RasG12V

growth_protocol: Cells were grown in SkBM basal media supplemented with SkGM singlequots (Clonetics) at 37 degrees Celsius and 5% CO2

extract_protocol: Total RNA from was isolated from primary human skeletal myoblasts, primary skeletal muscle cell precursors, and each of these cell lines transformed with hTERT, the early region of SV40 encoding T-Ag and t-Ag, and RasG12V using RNABee (Tel-Test, Friendswood, TX) and then further purified using the RNEasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: HSMMTF-1, -2, -3; and SKBMTF-1, -2, -3 were sequentially selected for 7 to 10 days in medium supplemented with 0.25 µg/mL puromycin (Sigma Chemical Co., St. Louis, MO), 50 µg/mL hygromycin B, 250 µg/mL G418, or 800 µg/mL Zeocin (all from Life Technologies Invitrogen, Carlsbad, CA)

value: Hygromycin, neomycin, puromycin


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1/5_6h_replicate 2


title: Colon03_(Colon_to_Liver)

source_name: Colon (primary site) to Liver (metastatic site) laser capture microdissected tumor sample

value: Colon

value: Liver


title: Control_rep4


title: Colon02_(Colon_to_Liver)


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1_6h_replicate 2


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1_6h_replicate 3


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1/5_6h_replicate 1


title: Control_rep1


title: skeletal muscle precursor cells transformed with hTERT and RasG12V_rep3


title: RalA72L_rep1


title: RalA72L_rep2


title: Ovary03_(Ovary_to_Omentum)

source_name: Ovary (primary site) to Omentum (metastatic site) laser capture microdissected tumor sample

value: Ovary


title: skeletal myoblasts transformed with hTERT and RasG12V_rep3

description: Gene expression data from skeletal myoblasts transformed with hTERT and RasG12V


title: Ovary05_(Ovary_to_Omentum)

value: Omentum


title: skeletal myoblasts transformed with hTERT and RasG12V_rep2


title: Colon01_(Colon_to_Liver)


title: skeletal muscle precursor cells_rep3

description: Gene expression data from skeletal muscle precursor cells

source_name: skeletal muscle precursor cells

value: skeletal muscle precursor cells


title: skeletal myoblasts transformed with hTERT and RasG12V_rep1


title: Rat_cardiomyocyte_diclofenac_reference_concentration_1_6h_replicate 1


title: Ovary02_(Ovary_to_Omentum)


title: Rat_cardiomyocyte_non-treated_replicate 2

value: control


title: breast tumor sample, patient 100202

status: Public on Feb 12 2016

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description: invasive breast cancer sample with unknown status of hormone receptors

hyb_protocol: Unhybridized oligos were washed away and hybridized oligos were enriched by PCR and hybridized to Sentrix Array Matrix Universal Probe Set 7A, 1536 Bead Types.

scan_protocol: Imaging was performed in the Bead Array Reader.

data_processing:
The raw data was processed by the BeadStudio Methylation Module to generate Beta values.
Raw data was lost, and therefore not included in the GEO submission.

label: Cy5 and Cy3

source_name: genomic DNA from breast tumor sample, patient 100202

label_protocol: Bisulfite conversion was performed on 500 ng of extracted DNA using EZ DNA Methylation kit (Cat # D5001, Zymo Research, Irvine, CA) according to the manufacturer’s instructions. As the result of conversion, unmethylated cytosine residues were converted to uracils. The converted DNA was eluted in 10 µl M-Elution buffer provided in the kit. DNA methylation assays were performed using 5 µl bisulfite converted DNA in Illumina’s GoldenGate Assay for Methylation as per Illumina’s protocol. The converted DNA was biotinylated and the Allele Specific Oligos were added (for methylated and unmethylated sequence).

extract_protocol: DNA extraction was performed by adding to each core 100 µl Xylene. After the incubation with gentle shaking for 5 minutes, supernatant was removed by centrifugation at 14,000 g to remove the paraffin. The process was repeated two more times. The tissue was then weighted and 2-4 mg tissue was used for DNA extraction using Gentra Puregene kit (QIAGEN). All tissues were homogenized after adding Cell Lysis solution, Proteinase K and overnight incubation. The extracted DNA was measured by NanoDrop and normalized at 50 ng/µl concentration.

tag: gender

value: Female

value: invasive breast cancer

tag: hormone receptor status (presence or absence of er and pr) # 1 means either er+ or pr+ (er+pr+, er+pr- or er-pr+) 0 means negative for both (er-pr-)

value: unknown


title: skeletal muscle precursor cells_rep1


title: skeletal muscle precursor cells_rep2


title: breast tumor sample, patient 101063

source_name: genomic DNA from breast tumor sample, patient 101063


title: breast tumor sample, patient 100098

source_name: genomic DNA from breast tumor sample, patient 100098


title: breast tumor sample, patient 100276

source_name: genomic DNA from breast tumor sample, patient 100276


title: Renal03_(Renal_to_Retroperitoneal)


title: Rat_cardiomyocyte_non-treated_replicate 1

value: Neonate


title: skeletal myoblasts_rep1

description: Gene expression data from skeletal myoblasts

source_name: skeletal myoblasts

value: skeletal myoblasts


title: breast tumor sample, patient 101300

description: hormone receptor positive invasive breast cancer sample

source_name: genomic DNA from breast tumor sample, patient 101300


title: breast tumor sample, patient 101199

source_name: genomic DNA from breast tumor sample, patient 101199


title: skeletal myoblasts_rep2


title: Ovary01_(Ovary_to_Omentum)


title: breast tumor sample, patient 101116

source_name: genomic DNA from breast tumor sample, patient 101116


title: breast tumor sample, patient 101175

source_name: genomic DNA from breast tumor sample, patient 101175


title: breast tumor sample, patient 101038

source_name: genomic DNA from breast tumor sample, patient 101038


title: skeletal myoblasts_rep3


title: breast tumor sample, patient 101024

description: hormone receptor negative invasive breast cancer sample

source_name: genomic DNA from breast tumor sample, patient 101024


title: breast tumor sample, patient 101012

source_name: genomic DNA from breast tumor sample, patient 101012


title: breast tumor sample, patient 100118

source_name: genomic DNA from breast tumor sample, patient 100118


title: Renal01_(Renal_to_Adrenal)

source_name: Renal (primary site) to Adrenal (metastatic site) laser capture microdissected tumor sample

value: Adrenal


title: breast tumor sample, patient 101002

source_name: genomic DNA from breast tumor sample, patient 101002


title: breast tumor sample, patient 101010

source_name: genomic DNA from breast tumor sample, patient 101010


title: breast tumor sample, patient 100940

source_name: genomic DNA from breast tumor sample, patient 100940


title: breast tumor sample, patient 100969

source_name: genomic DNA from breast tumor sample, patient 100969


title: breast tumor sample, patient 100878

source_name: genomic DNA from breast tumor sample, patient 100878


title: breast tumor sample, patient 100818

source_name: genomic DNA from breast tumor sample, patient 100818


title: breast tumor sample, patient 100781

source_name: genomic DNA from breast tumor sample, patient 100781


title: breast tumor sample, patient 100902

source_name: genomic DNA from breast tumor sample, patient 100902


title: breast tumor sample, patient 100772

source_name: genomic DNA from breast tumor sample, patient 100772


title: breast tumor sample, patient 100734

source_name: genomic DNA from breast tumor sample, patient 100734


title: breast tumor sample, patient 100748

source_name: genomic DNA from breast tumor sample, patient 100748


title: breast tumor sample, patient 100639

source_name: genomic DNA from breast tumor sample, patient 100639


title: breast tumor sample, patient 100658

source_name: genomic DNA from breast tumor sample, patient 100658


title: breast tumor sample, patient 100580

source_name: genomic DNA from breast tumor sample, patient 100580


title: breast tumor sample, patient 100540

source_name: genomic DNA from breast tumor sample, patient 100540


title: breast tumor sample, patient 100684

source_name: genomic DNA from breast tumor sample, patient 100684


title: breast tumor sample, patient 100551

source_name: genomic DNA from breast tumor sample, patient 100551


title: breast tumor sample, patient 100559

source_name: genomic DNA from breast tumor sample, patient 100559


title: breast tumor sample, patient 100429

source_name: genomic DNA from breast tumor sample, patient 100429


title: breast tumor sample, patient 100492

source_name: genomic DNA from breast tumor sample, patient 100492


title: breast tumor sample, patient 100504

source_name: genomic DNA from breast tumor sample, patient 100504


title: breast tumor sample, patient 100493

source_name: genomic DNA from breast tumor sample, patient 100493


title: breast tumor sample, patient 100446

source_name: genomic DNA from breast tumor sample, patient 100446


title: breast tumor sample, patient 100416

source_name: genomic DNA from breast tumor sample, patient 100416


title: skeletal muscle precursor cells transformed with hTERT and RasG12V_rep1


title: Control_rep2

source_name: Empty vector control

value: penstrep

tag: cell line


title: breast tumor sample, patient 100399

source_name: genomic DNA from breast tumor sample, patient 100399


title: breast tumor sample, patient 100339

source_name: genomic DNA from breast tumor sample, patient 100339


title: breast tumor sample, patient 100360

source_name: genomic DNA from breast tumor sample, patient 100360


title: breast tumor sample, patient 100334

source_name: genomic DNA from breast tumor sample, patient 100334


title: breast tumor sample, patient 100320

source_name: genomic DNA from breast tumor sample, patient 100320


title: breast tumor sample, patient 100337

source_name: genomic DNA from breast tumor sample, patient 100337


title: breast tumor sample, patient 100313

source_name: genomic DNA from breast tumor sample, patient 100313


title: breast tumor sample, patient 100318

source_name: genomic DNA from breast tumor sample, patient 100318


title: breast tumor sample, patient 100235

source_name: genomic DNA from breast tumor sample, patient 100235


title: breast tumor sample, patient 100212

source_name: genomic DNA from breast tumor sample, patient 100212


title: breast tumor sample, patient 100269

source_name: genomic DNA from breast tumor sample, patient 100269


title: breast tumor sample, patient 100505

source_name: genomic DNA from breast tumor sample, patient 100505


title: breast tumor sample, patient 100072

source_name: genomic DNA from breast tumor sample, patient 100072


title: breast tumor sample, patient 100077

source_name: genomic DNA from breast tumor sample, patient 100077


title: breast tumor sample, patient 100078

source_name: genomic DNA from breast tumor sample, patient 100078


title: breast tumor sample, patient 100080

source_name: genomic DNA from breast tumor sample, patient 100080


title: breast tumor sample, patient 100094

source_name: genomic DNA from breast tumor sample, patient 100094


title: breast tumor sample, patient 100092

source_name: genomic DNA from breast tumor sample, patient 100092


title: breast tumor sample, patient 100120

source_name: genomic DNA from breast tumor sample, patient 100120


title: breast tumor sample, patient 100099

source_name: genomic DNA from breast tumor sample, patient 100099


title: breast tumor sample, patient 100121

source_name: genomic DNA from breast tumor sample, patient 100121


title: breast tumor sample, patient 100152

source_name: genomic DNA from breast tumor sample, patient 100152


title: breast tumor sample, patient 100160

source_name: genomic DNA from breast tumor sample, patient 100160


title: breast tumor sample, patient 100174

source_name: genomic DNA from breast tumor sample, patient 100174


title: breast tumor sample, patient 100122

source_name: genomic DNA from breast tumor sample, patient 100122


title: breast tumor sample, patient 100137

source_name: genomic DNA from breast tumor sample, patient 100137


title: breast tumor sample, patient 100183

source_name: genomic DNA from breast tumor sample, patient 100183


title: breast tumor sample, patient 100185

source_name: genomic DNA from breast tumor sample, patient 100185


title: breast tumor sample, patient 100168

source_name: genomic DNA from breast tumor sample, patient 100168


title: breast tumor sample, patient 100059

source_name: genomic DNA from breast tumor sample, patient 100059


title: breast tumor sample, patient 100048

source_name: genomic DNA from breast tumor sample, patient 100048


title: breast tumor sample, patient 100402

source_name: genomic DNA from breast tumor sample, patient 100402


title: breast tumor sample, patient 100061

source_name: genomic DNA from breast tumor sample, patient 100061


title: breast tumor sample, patient 100300

source_name: genomic DNA from breast tumor sample, patient 100300


title: breast tumor sample, patient 100189

source_name: genomic DNA from breast tumor sample, patient 100189


title: breast tumor sample, patient 100267

source_name: genomic DNA from breast tumor sample, patient 100267


title: breast tumor sample, patient 100060

source_name: genomic DNA from breast tumor sample, patient 100060


title: breast tumor sample, patient 100047

source_name: genomic DNA from breast tumor sample, patient 100047


title: breast tumor sample, patient 100046

source_name: genomic DNA from breast tumor sample, patient 100046


title: breast tumor sample, patient 100039

source_name: genomic DNA from breast tumor sample, patient 100039


title: breast tumor sample, patient 100032

source_name: genomic DNA from breast tumor sample, patient 100032


title: breast tumor sample, patient 100043

source_name: genomic DNA from breast tumor sample, patient 100043


title: breast tumor sample, patient 100482

source_name: genomic DNA from breast tumor sample, patient 100482


title: TRB2_(wheat)

city: Changchun

first: Huakun

last: Zhang

state: Jilin

address: Renmin Street

institute: Northeast Normal University

hyb_protocol: 10 cycles of 2 mixes/cycle with Wash Buffer A at 30°C; 4 cycles of 15 mixes/cycle with Wash Buffer B at 50°C; Stain the probe array for 300 seconds in Streptavidin Solution Mix at 35°C;10 cycles of 4 mixes/cycle with Wash Buffer A at 30°C; Stain the probe array for 300 seconds in Antibody Solution Mix at 35°C;Stain the probe array for 300 seconds in SAPE Solution Mix at 35°C;15 cycles of 4 mixes/cycle with Wash Buffer A at 35°C. The holding temperature is 25°C

scan_protocol: 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. ⇒ The Scanner dialog box appears with a drop-down list of experiments that have not been run. 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.3. By default, for the Agilent® GeneArray® Scanner only, after selecting the experiment the number  is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required. 4. Once the experiment has been selected, click the Start button. ⇒ A dialog box prompts you to load a sample into the scanner. 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam. Pixel value = 3 µm Wavelength = 570 nm If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed. 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode. 7. Click OK in the Start Scanner dialog box. ⇒ The scanner begins scanning the probe array and acquiring data. When Scan in Progress is Selected from the View menu, the probe array image appears on the screen as the scan progresses.

data_processing: The raw CEL data were normalized with the robust multichip averagemethod using the R software limma package. Genes that were differentially expressed among genotypes were identified by performing thet-moderated test ebayes (Smyth, 2004), and the raw P values were adjusted for multiple testing effects by the Benjamini and Yekutieli method (false discovery rate, or FDR< 0.05). The present or absent calls of eachprobe set were determined by the MAS5 method using R software.Differently expressed genes that did not show present calls in all threebiological replications of at least one genotype were excluded from further analysis (Aprile et al., 2009). In total, 24,494 and 26,197 genes were detected as expressed in the leaf and young-inflorescence tissues, respectively.

organism: Triticum aestivum

source_name: TRB_3-wk old_leaf

label_protocol: 1. RNA Extraction 2. Random priming cDNA synthesis 3. RNA degradation with NaOH 4. cDNA column purification 5. cDNA fragmentation and terminal labeling with biotinylated GeneChip® DNA Labeling Reagent

growth_protocol: All plants were grown in chambers under controlled conditions at 24/18℃ day/night of 16-h daylength

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) and purified through RNeasy Mini Spin Columns (Qiagen, Shanhai, China). The integrity of RNA was Total RNA was extracted using Trizol reagent (Invitrogen) and purified through RNeasy Mini Spin Columns (Qiagen, Shanhai, China). The integrity of RNA was determined with an Agilent Bioanalyser2100 Eukaryote Total RNA Nano Series II system (Santa Clara, California, USA). The second leaf of three-leaf-stage seedlings was the source tissue for all RNA isolations.

treatment_protocol: No special treatment

tag: genotype/variation

value: synthetic allotetraploid wheat (AT2)

tag: age/developmental stage

value: 3-week old

value: leaf


title: TRS1_(wheat)

source_name: TRS_booting stage_young-inflorescence

value: booting stage

value: young-inflorescence


title: Control_Sample 2

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

description: Gene expression data from cultured human mesenchymal stem cells

hyb_protocol: Hybridization and staining to the HumanHT-12 v4 Expression BeadChip (Illumina, San Diego, CA) was performed using 750ng of biotin-antisense RNA (aRNA) product following protocols outlined in the Whole-Genome Gene Expression Direct Hybridization Assay Guide.

scan_protocol: Scanning of the BeadChip was performed using the iScan Microarray Scanner (Illumina, San Diego, CA).

data_processing: Gene expression data were imported into Illumina’s Genome Studio. They were imported with cubic spline normalization. Quality control was performed in Genome Studio. The Partek Report Plug-in from Illumina’s Genome Studio was used to export the gene expression data for import into Partek’s Genomics Suite (version 6.14.0828).

label_protocol: RNA was then amplified and labeled using the TargetAmp-Nano Labeling Kit (Epicenter, Madison, WI) which enables amplification and target preparation compatible with the Direct Hybridization Assay (Illumina, San Diego, CA). Amplification was performed with 500 ng of total RNA input following procedures described in the TargetAmp-Nano Labeling Kit user guide.

growth_protocol: Human umbilical cord derived MSCs (CPJ45) were isolated and characterized in our laboratory . MSCs were seeded onto 0.1% gelatin-coated culture plates and propagated in the growth medium containing high glucose DMEM, supplemented with 10% of fetal bovine serum, and 5.6% of antibiotic solution (0.1% gentamicin, 0.2% streptomycin, and 0.12% penicillin). Cells were incubated at 37°C in an atmosphere of 5% CO2 in a humidified incubator.

extract_protocol: RNA was isolated from frozen cell pellets using the E.Z.N.A. Total RNA Kit I (Omega, Norcross, GA).  RNA was purified using spin cartridge technology, quantified (Nanodrop 8000, Thermo Scientific), and stored at -80°C.

treatment_protocol: MSCs (1×106 cells) were cultured in 75 cm2 flasks in GM overnight. Cells were treated with 0 nM, 100 nM and 500 nM of JQ1 for 24h.

tag: treatment

value: 0 nM JQ1 (Control)


title: TRB3_(wheat)


title: TDB2_(wheat)

source_name: TDB_3-wk old_leaf


title: MSC_Treated with 100nm JQ1_Replicate 1

description: Gene expression data from cultured human mesenchymal stem cells treated with 100 nM JQ1

source_name: MSC_Treated with 100nm JQ1

value: Human umbilical cord derived MSCs (CPJ45)

value: 100 nM JQ1


title: MSC_Treated with 100nm JQ1_Replicate 2


title: MSC_Treated with 500nm JQ1_Replicate 2

description: Gene expression data from cultured human mesenchymal stem cells treated with 500 nM JQ1

source_name: MSC_Treated with 500nm JQ1

value: 500 nM JQ1


title: TRS2_(wheat)


title: TDS3_(wheat)

source_name: TDS_booting stage_young-inflorescence


title: TDS2_(wheat)


title: TDB3_(wheat)


title: MSC_Treated with 500nm JQ1_Replicate 1


title: MS1_(wheat)

source_name: MS_booting stage_young-inflorescence


title: Control_Sample 1


title: MB2_(wheat)

source_name: MB_3-wk old_leaf


title: MS2_(wheat)


title: MS3_(wheat)


title: TDS1_(wheat)


title: Ovary04_(Ovary_to_Omentum)

source_name: Ovary (primary site) to Omentum (metastatic site) laser capture microdissected tumor sample

tag: primary tumor site

value: Ovary

tag: metastatic tumor site

value: Omentum


title: TRB1_(wheat)

tag: tissue


title: LU8S1_(wheat)

source_name: LU8S_booting stage_young-inflorescence


title: MB3_(wheat)


title: LU8S2_(wheat)


title: TRS3_(wheat)


title: MB1_(wheat)


title: breast tumor sample, patient 100855

source_name: genomic DNA from breast tumor sample, patient 100855

value: Female

value: invasive breast cancer


title: TDB1_(wheat)


title: LU8B3_(wheat)

source_name: LU8B_3-wk old_leaf


title: LU8S3_(wheat)


title: LU8B1_(wheat)


title: LU7B2_(wheat)

source_name: LU7B_3-wk old_leaf


title: iHeps_Hnf1a transduced, +small molecules, 2

first: Kyungtae

last: Lim

address: Tennis Court Road

department: The Wellcome Trust/Cancer Research UK Gurdon Institute

institute: University of Cambridge

description:
Induced hepatocyte-like cells, directly converted from MEFs by the defined sets of transcription factors; Hnf1a, cultured in the presence of small molecules.
Epithelial colonies appeared after 5 weeks post-transduction and established as expandable iHep lines with several passaging.

hyb_protocol: The fragmented cRNA was hybridized to Affymetrix GeneChip arrays for 16 h. The Chips were washed and stained using an Affymetrix Fluidics Station.

scan_protocol: Fluorescence was detected using the Affymetrix Imaging Station.

data_processing: Raw data were background-corrected and subsequently normalized using Partek Express Affymetrix Edition under the Robust Microarray Analysis (RMA) algorithm.

label: Biotin

source_name: iHeps, Hnf1a-transduced in the presence of small molecules, p16

label_protocol: 100 ng of total RNA undergoes reverse transcription to synthesize first-strand cDNA. This cDNA is then converted into a double-stranded DNA template for transcription. In vitro transcription synthesizes aRNA and incorporates a biotin-congugated nucleotide.

growth_protocol: All iHep lines were cultured in standard Hep medium: DMEM/F-12 supplemented with 10% FBS (Biowest), 0.1 μM dexamethasone (Sigma), 10 mMnicotinamide (Sigma), 1% ITS (insulin-transferrin-selenium) premix (Gibco), and penicillin/streptomycin/glutamine (Invitrogen), 10 ng/ml fibroblast growth factor 4 (Peprotech) and both hepatocyte growth factor (Peprotech) and epidermal growth factor (Peprotech) at a final concentration of 20 ng/ml on Type I collagen-coated dish (Sigma)

extract_protocol: Total RNA was prepared from MEFs, iHeps and primary hepatocytes using the RNeasy Mini Kit (Qiagen)

treatment_protocol: Fibroblasts were transduced with replication-defective retroviral particles coding for the defined sets of hepatic transcription factors in the presence or absence of c-Myc, and Klf4. After 48 h, the transduced fibroblasts were cultured in standard Hep medium.

value: induced hepatocyte-like cells

tag: transcription factors

tag: small molecules

value: present


title: Primary Hepatocytes, 1

description: Primary hepatocytes were isolated from liver tissue of 8- to 10-week-old male C57/B6 mice by collagenase perfusion method, and then cultured in Hep medium.

source_name: Primary isolated hepatocytes

tag: strain

tag: age

value: 8-10 weeks

tag: Sex

value: male

value: control hepatocytes


title: LU7B1_(wheat)

value: synthetic allotetraploid wheat (AT2)

value: 3-week old


title: LU7B3_(wheat)

value: leaf


title: iHeps_Hnf1a transduced, -small molecules, 1

description:
Induced hepatocyte-like cells, directly converted from MEFs by the defined sets of transcription factors; Hnf1a, cultured in the absence of small molecules.
Epithelial colonies appeared after 5 weeks post-transduction and established as expandable iHep lines with several passaging, and then further cultured without small molecules.

source_name: iHeps, Hnf1a-transduced in the absence of small molecules, p21

tag: cell type

value: absent


title: LU7S1_(wheat)

source_name: LU7S_booting stage_young-inflorescence

value: booting stage

value: young-inflorescence


title: LU7S2_(wheat)


title: Primary Hepatocytes, 2


title: LU6S2_(wheat)

source_name: LU6S_booting stage_young-inflorescence


title: LU8B2_(wheat)


title: LU7S3_(wheat)


title: LU6B3_(wheat)

source_name: LU6B_3-wk old_leaf


title: iHeps_Hnf1a transduced, -small molecules, 2


title: iHeps_Hnf1a transduced, +small molecules, 1


title: LU6S3_(wheat)


title: MEFs, 1

description:
Mouse embryonic fibroblasts after removing the head and all internal organs.
MEFs are mesenchymal cells showing flat and elongated morphology.

source_name: Primary isolated mouse embryonic fibroblasts

value: embryos at embryonic day (E)13.5

value: mouse embryonic fibroblasts


title: LU6S1_(wheat)


title: LU6B2_(wheat)


title: LU5S3_(wheat)

source_name: LU5S_booting stage_young-inflorescence


title: LU6B1_(wheat)


title: LU5S2_(wheat)


title: LU5B3_(wheat)

source_name: LU5B_3-wk old_leaf


title: LU5B2_(wheat)


title: LU5B1_(wheat)


title: US2_(wheat)

source_name: US_booting stage_young-inflorescence


title: LU5S1_(wheat)


title: US1_(wheat)


title: 10-017B_BPE

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
WGA2-amplified DNA
10-017B_benign prostate epithelium (BPE)

hyb_protocol: Cy3 and Cy5 probes were combined and hybridized to Agilent 2x400K SurePrint G3 CGH Microarrays and washed following the manufacturer’s specifications.

scan_protocol: Fluorescent array images were collected using the Agilent DNA microarray scanner G2505C and Agilent Feature Extraction software.

data_processing: Agilent Feature Extraction software version 10.7.3.1 was used to grid and extract the data using the CGH_107_Sep09 protocol with default settings. Feature Extraction Grid_GenomicBuild was hg18:NCBI36:Mar2006. Control probes were removed, duplicate probes averaged, and log2 ratios defined as gProcessedSignal/rProcessedSignal.

label_protocol: Two micrograms of either WGA2-amplified DNA or genomic DNA from each sample was labeled by random priming using the Agilent Genomic DNA Enzymatic Labeling Kit (Cy3-dUTP.)  A pool of reference normal male DNA (Promega) was labeled with Cy5-dUTP following manufacturer's suggest protocols

extract_protocol:
tissue: A pool of reference normal male DNA (Promega, Part No. G1471)
Promega reference DNA

extract_protocol:
tissue: Twenty fresh-frozen prostate adenocarcinomas and adjacent benign tissue were obtained from Baylor College of Medicine and the University of Washington under approval from their respective Institutional Review Boards. Fifteen samples had a combined Gleason score (GS) of 7 and five had a GS>7.  To obtain tumor epithelium and tumor stroma, laser capture microdissection was performed. In brief, frozen sections (7 µM) were cut from OCT embedded snap-frozen prostate tissue into PAP-membrane slides. Approximately 4000 cells were microdissected from four spatially and histologically-defined cell compartments: prostate cancer epithelium (CPE), benign prostate epithelium (BPE), prostate cancer-adjacent stroma (CAS), benign prostate epithelium-adjacent stroma (BAS).  For CAS, we specifically captured stromal fibroblasts adjacent (<1 mm away) to neoplastic epithelium and avoided foci of inflammatory cells. The corresponding benign cells for each case were microdissected from separate blocks identified as containing no adenocarcinoma cells (first choice) or, from non-neoplastic tissues at a distance >1mm from the cancer. Digital photos were taken of tissue sections before, during, and after LCM and assessed to confirm the cell type-specificity of the captured cells.
Genomic DNA was extracted from microdissected tissue using the QIAamp DNA micro kit (Qiagen, Inc.) according to the manufacturer’s instructions, except that the samples were incubated in RLT buffer with proteinase K overnight at 56ºC before DNA extraction. DNA concentrations were measured by Quant-iT™ dsDNA HS Assay Kit and read on a Qubit™ Fluorometer (Invitrogen).  Aliquots of extracted DNA (10 ng) were amplified to yield sufficient DNA for aCGH using random fragmentation whole genome amplification following the manufacturer's instructions (WGA2, Sigma-Aldrich).

tag: sample type

value: BPE

value: Ep

tag: cancer (ca) benign (b)

value: B

tag: patient


title: 10-016D_BAS

description:
WGA2-amplified DNA
10-016D_benign prostate epithelium-adjacent stroma (BAS)

source_name: A pool of reference normal male DNA (Promega, Part No. G1471)

tag: gender

value: BAS

value: St


title: UB1_(wheat)

source_name: UB_3-wk old_leaf


title: UB3_(wheat)


title: US3_(wheat)


title: LS1_(wheat)

source_name: LS_booting stage_young-inflorescence


title: UB2_(wheat)


title: 10-017A_CPE

description:
WGA2-amplified DNA
10-017A_prostate cancer epithelium (CPE)

value: CPE

value: Ca


title: LS3_(wheat)


title: 10-011E_CPE

description:
WGA2-amplified DNA
10-011E_prostate cancer epithelium (CPE)

value: male


title: 10-017B_BAS

description:
WGA2-amplified DNA
10-017B_benign prostate epithelium-adjacent stroma (BAS)


title: LB3_(wheat)

source_name: LB_3-wk old_leaf


title: 10-016D_BPE

description:
WGA2-amplified DNA
10-016D_benign prostate epithelium (BPE)


title: LB2_(wheat)


title: 10-016E_CAS

description:
WGA2-amplified DNA
10-016E_prostate cancer-adjacent stroma (CAS)

value: CAS


title: 10-016E_CPE

description:
WGA2-amplified DNA
10-016E_prostate cancer epithelium (CPE)


title: 10-008D_BAS

description:
WGA2-amplified DNA
10-008D_benign prostate epithelium-adjacent stroma (BAS)


title: LS2_(wheat)

value: synthetic allotetraploid wheat (AT2)


title: RBD-Mutant 2

city: London

first: Esther

last: Castellano

state: London

address: 44 Lincoln's Inn Fields

institute: The Crick Institute

description: SAMPLE 5

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was added on microarray slide for 17 hours at 65 C at 10 rpm using the Hybridization Oven kit procedure provided by Agilent Technologies. After hybridization, the slides were then washed per Agilent’s SSPE wash protocol, dried, and scanned

scan_protocol: scanned at 5 µm resolution with a G2505C DNA microarray scanner (Agilent Technologies, Palo Alto, CA). Data were then extracted from images by the Feature Extraction software version 10.5.1.1, protocol GE1_105_Jan09 (Agilent Technologies, Palo Alto, CA).

data_processing: The expression data was log2 transformed and quantile normalised (normalizeBetweenArrays function, method=quantile from Limma, Bioconcductor). Control probes were removed prior to normalisation. Genotype dependent transcriptional changes were identified by linear model.

source_name: MEFs without RAS binding to p110a

label_protocol: 1ug of total RNA and Cy3-labeled CTP fluorescent dyes were used to generate fluorescent cRNA with One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling) v5.7 (Agilent Technologies, Palo Alto, CA).

growth_protocol: MEFs were grown on DMEM media supplemented with 10% FBS and antibiotics and kept at 10% CO2. On the day of the experiment media was replaced with FBS-free DMEM and left over night. Samples were then collected.

extract_protocol: RNAsy Kit (Qiagen)

tag: strain source

tag: cell line

value: Inmortalized mouse embrionic fibroblasts

value: RBD-Mutant

tag: clone id

value: Clone 2


title: WT 3

description: SAMPLE 3

source_name: MEFs with RAS binding to p110a

tag: genotype/variation

value: wild type

value: Clone 1+2


title: 10-011F_BPE

description:
WGA2-amplified DNA
10-011F_benign prostate epithelium (BPE)


title: 10-009B_CPE

description:
WGA2-amplified DNA
10-009B_prostate cancer epithelium (CPE)


title: 10-009D_BAS

description:
WGA2-amplified DNA
10-009D_benign prostate epithelium-adjacent stroma (BAS)


title: 10-011E_CAS

description:
WGA2-amplified DNA
10-011E_prostate cancer-adjacent stroma (CAS)


title: LB1_(wheat)

tag: age/developmental stage

value: 3-week old

value: leaf


title: RBD-Mutant 1

description: SAMPLE 4

value: Clone 1


title: 10-009B_CAS

description:
WGA2-amplified DNA
10-009B_prostate cancer-adjacent stroma (CAS)


title: RBD-Mutant mix 3

description: SAMPLE 6


title: 10-008A_CPE

description:
WGA2-amplified DNA
10-008A_prostate cancer epithelium (CPE)

value: Ep


title: 10-011F_BAS

description:
WGA2-amplified DNA
10-011F_benign prostate epithelium-adjacent stroma (BAS)

value: B


title: WT 2

description: SAMPLE 2


title: 10-009D_BPE

description:
WGA2-amplified DNA
10-009D_benign prostate epithelium (BPE)

value: BPE


title: 10-008A_CAS

description:
WGA2-amplified DNA
10-008A_prostate cancer-adjacent stroma (CAS)

value: St


title: WT 1

description: SAMPLE 1


title: 10-008D_BPE

description:
WGA2-amplified DNA
10-008D_benign prostate epithelium (BPE)


title: 10-004D_CPE

description:
WGA2-amplified DNA
10-004D_prostate cancer epithelium (CPE)

value: CPE


title: 10-004D_BPE

description:
WGA2-amplified DNA
10-004D_benign prostate epithelium (BPE)


title: 10-004D_CAS

description:
WGA2-amplified DNA
10-004D_prostate cancer-adjacent stroma (CAS)

value: Ca


title: 06-066B_CAS

description:
WGA2-amplified DNA
06-066B_prostate cancer-adjacent stroma (CAS)

value: male


title: 10-004D_BAS

description:
WGA2-amplified DNA
10-004D_benign prostate epithelium-adjacent stroma (BAS)

value: BAS


title: 06-066B_CPE

description:
WGA2-amplified DNA
06-066B_prostate cancer epithelium (CPE)


title: 06-066C_BAS

description:
WGA2-amplified DNA
06-066C_benign prostate epithelium-adjacent stroma (BAS)


title: 00-081E_BPE

description:
WGA2-amplified DNA
00-081E_benign prostate epithelium (BPE)


title: 01-127F_CAS

description:
WGA2-amplified DNA
01-127F_prostate cancer-adjacent stroma (CAS)

value: CAS


title: 01-127F_CPE

description:
WGA2-amplified DNA
01-127F_prostate cancer epithelium (CPE)


title: 00-081B_CAS

description:
WGA2-amplified DNA
00-081B_prostate cancer-adjacent stroma (CAS)


title: 01-127C_BAS

description:
WGA2-amplified DNA
01-127C_benign prostate epithelium-adjacent stroma (BAS)


title: 01-127C_BPE

description:
WGA2-amplified DNA
01-127C_benign prostate epithelium (BPE)


title: 00-084E_CAS

description:
WGA2-amplified DNA
00-084E_prostate cancer-adjacent stroma (CAS)


title: 56465_CPE

description:
WGA2-amplified DNA
56465_prostate cancer epithelium (CPE)


title: 06-066C_BPE

description:
WGA2-amplified DNA
06-066C_benign prostate epithelium (BPE)


title: 00-084E_CPE

description:
WGA2-amplified DNA
00-084E_prostate cancer epithelium (CPE)


title: 00-081B_CPE

description:
WGA2-amplified DNA
00-081B_prostate cancer epithelium (CPE)


title: 00-084D_BPE

description:
WGA2-amplified DNA
00-084D_benign prostate epithelium (BPE)


title: 64819_CAS

description:
WGA2-amplified DNA
64819_prostate cancer-adjacent stroma (CAS)


title: 58754_CPE2

description:
WGA2-amplified DNA
58754_prostate cancer epithelium (CPE)


title: 64817_BPE

description:
WGA2-amplified DNA
64817_benign prostate epithelium (BPE)


title: 55840_CAS

description:
WGA2-amplified DNA
55840_prostate cancer-adjacent stroma (CAS)


title: 56462_BPE

description:
WGA2-amplified DNA
56462_benign prostate epithelium (BPE)


title: 00-084D_BAS

description:
WGA2-amplified DNA
00-084D_benign prostate epithelium-adjacent stroma (BAS)


title: 56465_CAS

description:
WGA2-amplified DNA
56465_prostate cancer-adjacent stroma (CAS)


title: 64819_CPE

description:
WGA2-amplified DNA
64819_prostate cancer epithelium (CPE)


title: 64817_BAS

description:
WGA2-amplified DNA
64817_benign prostate epithelium-adjacent stroma (BAS)


title: 00-081E_BAS

description:
WGA2-amplified DNA
00-081E_benign prostate epithelium-adjacent stroma (BAS)


title: 55840_CPE

description:
WGA2-amplified DNA
55840_prostate cancer epithelium (CPE)


title: 54371_CAS

description:
WGA2-amplified DNA
54371_prostate cancer-adjacent stroma (CAS)


title: 58756_BPE2

description:
WGA2-amplified DNA
58756_benign prostate epithelium (BPE)


title: 58754_CAS2

description:
WGA2-amplified DNA
58754_prostate cancer-adjacent stroma (CAS)


title: 56462_BAS

description:
WGA2-amplified DNA
56462_benign prostate epithelium-adjacent stroma (BAS)


title: 55841_BAS

description:
WGA2-amplified DNA
55841_benign prostate epithelium-adjacent stroma (BAS)


title: 54371_CPE

description:
WGA2-amplified DNA
54371_prostate cancer epithelium (CPE)


title: 58484_BAS

description:
WGA2-amplified DNA
58484_benign prostate epithelium-adjacent stroma (BAS)


title: 54373_BPE

description:
WGA2-amplified DNA
54373_benign prostate epithelium (BPE)


title: 58756_BAS2

description:
WGA2-amplified DNA
58756_benign prostate epithelium-adjacent stroma (BAS)


title: 64589_CPE

description:
WGA2-amplified DNA
64589_prostate cancer epithelium (CPE)


title: 58487_CAS

description:
WGA2-amplified DNA
58487_prostate cancer-adjacent stroma (CAS)


title: 58487_CPE

description:
WGA2-amplified DNA
58487_prostate cancer epithelium (CPE)


title: 58484_BPE

description:
WGA2-amplified DNA
58484_benign prostate epithelium (BPE)


title: 64975_CPE

description:
WGA2-amplified DNA
64975_prostate cancer epithelium (CPE)


title: 64973_BPE

description:
WGA2-amplified DNA
64973_benign prostate epithelium (BPE)


title: 69657_BPE

description:
WGA2-amplified DNA
69657_benign prostate epithelium (BPE)


title: 60800_BPE

description:
WGA2-amplified DNA
60800_benign prostate epithelium (BPE)


title: 60799_CPE

description:
WGA2-amplified DNA
60799_prostate cancer epithelium (CPE)


title: 69654_CPE

description:
WGA2-amplified DNA
69654_prostate cancer epithelium (CPE)


title: 54373_BAS

description:
WGA2-amplified DNA
54373_benign prostate epithelium-adjacent stroma (BAS)


title: 10-017A_CAS

description:
WGA2-amplified DNA
10-017A_prostate cancer-adjacent stroma (CAS)


title: 69657_BAS

description:
WGA2-amplified DNA
69657_benign prostate epithelium-adjacent stroma (BAS)


title: 69654_CAS

description:
WGA2-amplified DNA
69654_prostate cancer-adjacent stroma (CAS)


title: 6005_NAF

description: 6005_benign/normal associated fibroblasts (NAF)

extract_protocol:
tissue: For the preparation of cancer-associated fibroblasts (CAF) and benign/normal associated fibroblasts (NAF), de-identified prostate tissue samples were collected at Vanderbilt University under local IRB approval through the NCI-funded Cooperative Human Tissue Network. CAF and NAF were isolated from cancer and normal tissue respectively, as previously described (PMID:11719442). CAF activity was validated using a tissue recombination bioassay in which CAF or NAF were recombined with initiated reporter epithelium (BPH-1) and grafted to the renal capsule of severe combined immunodeficient (SCID) mice. Cells were classified as CAF if they demonstrated the ability to induce tumorigenesis (defined grossly and histologically) in the epithelial cells under these conditions. Cells from benign sources were also checked to confirm that they did not induce tumor growth.
Genomic DNA was extracted from cells using the QIAamp DNA mini kit (Qiagen, Inc.) according to the manufacturer’s instructions.

value: NAF


title: Genomic DNA from adult human whole blood [9985131146_R04C02]

city: Kansas City

first: Devin

middle: Charles

last: Koestler

state: KS

address: 3901 Rainbow Blvd.

department: Biostatistics

institute: University of Kansas Medical Center

description:
X9985131146_R04C02
DNA methylation profiling of adult human whole blood (WB)
SAMPLE 18

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

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

data_processing: Unmethylated and methylated signal intensities were generated using the publicly available, minfi Bioconductor package.  Data processing of these data was also carried out using the minfi Bioconductor package and included: background subtraction and normalization utilizing the various internal controls present on the Illumina Infinium Methylation450 BeadChip and Subset quantile within array-normalization (SWAN) to adjust the beta-values of type 2 design probes into a statistical distribution characteristic of type 1 probes.

source_name: Adult human whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using QIAGEN Dneasy blood and tissue kit according to standard instructions

treatment_protocol: Leukocyte subtypes were purified via magnetic activated cell sorting (MACS) using kits from Miltenyi Biotec; venous whole blood was collected into Heparin

tag: cd4+ t cell (%)

tag: cd8+ t cell (%)

tag: b cell (%)

tag: natural killer cell (%)

tag: monocyte (%)

tag: granulocyte (%)


title: 6006_CAF

description: 6006_cancer-associated fibroblasts (CAF)

value: CAF


title: 60800_BAS

description:
WGA2-amplified DNA
60800_benign prostate epithelium-adjacent stroma (BAS)


title: Genomic DNA from adult human whole blood [9985131146_R03C01]

description:
X9985131146_R03C01
DNA methylation profiling of adult human whole blood (WB)
SAMPLE 17


title: 64973_BAS

description:
WGA2-amplified DNA
64973_benign prostate epithelium-adjacent stroma (BAS)


title: Genomic DNA from adult human whole blood [9985131146_R01C01]

description:
X9985131146_R01C01
DNA methylation profiling of adult human whole blood (WB)
SAMPLE 16


title: 64586_BPE

description:
WGA2-amplified DNA
64586_benign prostate epithelium (BPE)


title: 5906_CAF

description: 5906_cancer-associated fibroblasts (CAF)


title: 64975_CAS

description:
WGA2-amplified DNA
64975_prostate cancer-adjacent stroma (CAS)


title: Genomic DNA from adult human whole blood [9985131137_R02C02]

description:
X9985131137_R02C02
DNA methylation profiling of adult human whole blood (WB)
SAMPLE 13


title: Genomic DNA from a reconstructed mixture of purified human leukocytes  [9985131145_R06C02]

description:
X9985131145_R06C02
DNA methylation profiling across mixture of white blood cell (WBC) types
SAMPLE 8

source_name: Reconstructed mixture of purified human leukocytes


title: Genomic DNA from adult human whole blood [9985131137_R05C01]

description:
X9985131137_R05C01
DNA methylation profiling of adult human whole blood (WB)
SAMPLE 14


title: Genomic DNA from adult human whole blood [9985131145_R04C01]

description:
X9985131145_R04C01
DNA methylation profiling of adult human whole blood (WB)
SAMPLE 15


title: Genomic DNA from a reconstructed mixture of purified human leukocytes  [9985131146_R01C02]

description:
X9985131146_R01C02
DNA methylation profiling across mixture of white blood cell (WBC) types
SAMPLE 9


title: BY-P41K- Rpb7 growth in YPAD until OD reached 1 sample 2

city: Singapore

first: Zilong

last: Qiu

address: 62 Nanyang Drive

department: School of Chemical & Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

description: Gene expression  in YPAD until OD reached 1

hyb_protocol: Gene Expression Hybridization Kit (5188-5242), Lot: 0006279504

scan_protocol: After hybridization, the microarray slide was washed in gene expression wash buffer 1 for one minute at room temperature and another minute in gene expression wash buffer 2 at 37oC before scanning on Agilent High Resolution Microarray Scanner (C-model).

data_processing: Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1).

label: cyanine 3-CTP

organism: Saccharomyces cerevisiae

source_name: growth in YPAD until OD reached 1

label_protocol: Low Input Quick Amp Labeling Kit (Agilent: 5190-2331), Lot: 0006208922

extract_protocol: Total cellular RNAs were extracted from both the mutant and the control using RNeasy® Mini Kit and RNase-Free DNase Set (Qiagen,Hilden, Germany)

treatment_protocol: There are two conditions: i) when cells reached early exponential phase (OD600 ~1.0) in YPAD; ii) after 12h VHG fermentation.

value: BY-P41K- Rpb7

tag: treatment


title: BY-P41K- Rpb7 growth in YPAD until OD reached 1 sample 1


title: Genomic DNA from a reconstructed mixture of purified human leukocytes  [9985131146_R05C01]

description:
X9985131146_R05C01
DNA methylation profiling across mixture of white blood cell (WBC) types
SAMPLE 6


title: Genomic DNA from a reconstructed mixture of purified human leukocytes  [9985131145_R05C01]

description:
X9985131145_R05C01
DNA methylation profiling across mixture of white blood cell (WBC) types
SAMPLE 3


title: M1 after 12h VHG fermentation sample 2

description: Gene expression after 12h VHG fermentation

source_name: 12h VHG fermentation

value: 12h VHG fermentation


title: BY-P41K- Rpb7 after 12h VHG fermentation sample 2


title: M1 growth in YPAD until OD reached 1 sample 1


title: 60799_CAS

description:
WGA2-amplified DNA
60799_prostate cancer-adjacent stroma (CAS)

tag: cell type


title: M1 after 12h VHG fermentation sample 1


title: 5905_NAF

description: 5905_benign/normal associated fibroblasts (NAF)

tag: sample type


title: Genomic DNA from a reconstructed mixture of purified human leukocytes  [9985131137_R04C01]

description:
X9985131137_R04C01
DNA methylation profiling across mixture of white blood cell (WBC) types
SAMPLE 10


title: M1 growth in YPAD until OD reached 1 sample 2


title: 64589_CAS

description:
WGA2-amplified DNA
64589_prostate cancer-adjacent stroma (CAS)

tag: cancer (ca) benign (b)


title: Genomic DNA from a reconstructed mixture of purified human leukocytes  [9985131146_R06C01]

description:
X9985131146_R06C01
DNA methylation profiling across mixture of white blood cell (WBC) types
SAMPLE 7


title: Genomic DNA from a reconstructed mixture of purified human leukocytes  [9985131145_R02C01]

description:
X9985131145_R02C01
DNA methylation profiling across mixture of white blood cell (WBC) types
SAMPLE 2


title: BY-P41K- Rpb7 after 12h VHG fermentation sample 1


title: Genomic DNA from a reconstructed mixture of purified human leukocytes  [9985131146_R03C02]

description:
X9985131146_R03C02
DNA methylation profiling across mixture of white blood cell (WBC) types
SAMPLE 12


title: HEPG2 Sup 2

city: Tel-Hashomer

first: Sharon

last: Moshitch-Moshkovitz

address: Laboratory wing

department: Cancer Research Center

country: Israel

institute: Sheba Medical Center

hyb_protocol: Affymetrix 3' IVT labeling protocol  https://www.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf

data_processing: RMA

source_name: HEPG2 cell line

label_protocol: Affymetrix biotin labeling_ wt kit  (Affymetrix)

growth_protocol: HepG2 cells were grown in DMEM medium

extract_protocol: Total RNA was extracted from cell lysate using  Perfect Pure RNA cultured cell kit (5Prime). Total RNA was subjected to two rounds of polyA enrichment (GenElute mRNA miniprep Kit, Sigma). Intact mRNA was subjected to immunodepletion with anti m1A antibody (Sup) and compared to input (original) control.

treatment_protocol: cells were harvested in Cell lysis solution (5Prime)

tag: immunodepletion

value: immunodepleted


title: Genomic DNA from a reconstructed mixture of purified human leukocytes  [9985131146_R02C01]

description:
X9985131146_R02C01
DNA methylation profiling across mixture of white blood cell (WBC) types
SAMPLE 4


title: 132 haim-rep3

status: Public on Feb 11 2016

first: Weihua

last: Tang

address: 300 Fenglin Rd

institute: Shanghai Inst. Plant Phys. & Eco.

description: Gene expression data from infecting hyphae for maize stalk

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

data_processing: The data were analyzed with software R, the RMA package

organism: Fusarium graminearum

source_name: infecting hyphae of F.graminearum for maize stalk

growth_protocol: Fusarium graminearum hyphae infecting maize stalk

extract_protocol: Picopure RNA isolation kit (Acturus) was used for trace RNA extraction

treatment_protocol: The maize tissue was fixed and paraffin embedded. Then Laser capture microdissection was used for material collection

tag: time point (hours after inoculation)


title: HEPG2 input 2

scan_protocol: Affymetrix 3' IVT labeling protocol  https://www.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf

value: not treated


title: 144 haim-rep2


title: 132 haim-rep2


title: HEPG2 Sup 1


title: BS1418_NAF

description: BS1418_benign/normal associated fibroblasts (NAF)

hyb_protocol: Standard Illumina Infinium HD protocol

scan_protocol: Standard Illumina Infinium HD protocol

data_processing: Intensity data were extracted in Genome studio version 1.9.4

label: c-bio; a-DNP

label_protocol: Standard Illumina Infinium HD protocol

tag: gender

tag: patient


title: 132 haim-rep1


title: 64586_BAS

description:
WGA2-amplified DNA
64586_benign prostate epithelium-adjacent stroma (BAS)


title: 108 haim-rep1


title: Genomic DNA from a reconstructed mixture of purified human leukocytes  [9985131137_R06C02]

description:
X9985131137_R06C02
DNA methylation profiling across mixture of white blood cell (WBC) types
SAMPLE 11


title: 72 haim-rep1


title: 72 haim-rep2


title: 144 haim-rep1


title: 48 haim-rep2


title: 108 haim-rep2


title: Genomic DNA from a reconstructed mixture of purified human leukocytes  [9985131137_R04C02]

description:
X9985131137_R04C02
DNA methylation profiling across mixture of white blood cell (WBC) types
SAMPLE 5


title: 36 haim-rep2


title: HEPG2 input 1

tag: cell line


title: 36 haim-rep3


title: 48 haim-rep1


title: 36 haim-rep1


title: 18 haim-rep2


title: VA145_NAF

description: VA145_benign/normal associated fibroblasts (NAF)


title: 18 haim-rep1


title: VA145_CAF

description: VA145_cancer-associated fibroblasts (CAF)


title: BS1418_CAF

description: BS1418_cancer-associated fibroblasts (CAF)


title: 72 haim-rep3


title: 12 haim-rep3


title: 12 haim-rep1


title: 447 (10014479)

city: Hoesholm

first: Anker

last: Hansen

address: Venlighedsvej 1

country: Denmark

institute: Medical Prognosis Institute A/S

description: FFPE

hyb_protocol: Affymetrix standardized protocol for U133p2 array

data_processing: R, affypackage, justRMA

source_name: NSCLC

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol

tag: Stage

value: Stage 1A

tag: tissue

value: NSCLC


title: 459 (10014592)

description: FFPE

scan_protocol: Affymetrix standardized protocol for U133p2 array


title: 307 (10013076)

description: FFPE


title: 469 (10014691)

description: FFPE


title: 464 (10014646)

description: FFPE


title: 288 (10012888)

description: FFPE


title: 12 haim-rep2


title: Genomic DNA from a reconstructed mixture of purified human leukocytes  [9985131145_R03C02]

description:
X9985131145_R03C02
DNA methylation profiling across mixture of white blood cell (WBC) types
SAMPLE 1

tag: cd4+ t cell (%)


title: 253 (10012536)

description: FFPE


title: 10-751B_NAF

description: 10-751B_benign/normal associated fibroblasts (NAF)


title: 460 (10014608)

description: FFPE


title: 268 (10012680)

description: FFPE


title: 281 (10012819)

description: FFPE


title: 168 (10011683)

description: FFPE


title: 120 (10011201)

description: FFPE


title: 164 (10011645)

description: FFPE


title: 245 (10012451)

description: FFPE


title: HepG2 _24h_Verte_3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: HCC cells treated with Verteporfin

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Hugene-2_0-st-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: HCC cell line

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

growth_protocol: HepG2 cells were cultured in RPMI at 37°C in a 5% CO2 atmosphere.

extract_protocol: total RNA was extracted using the NucleoSpin RNA II kit (Machery-Nagel, Düren, Germany) according to the manufacturer's protocol

treatment_protocol: HepG2 cells were treated with DMSO (control) or Verteporfin (0.75 µM) for 24 hours followed by RNA isolation

value: Verteporfin


title: 118 (10011188)

description: FFPE


title: 109 (10011096)

description: FFPE


title: 222 (10012222)

description: FFPE


title: 013 (10010136)

description: FFPE


title: HepG2 _24h_Verte_2

description: HCC cells treated with Verteporfin


title: 004 (10010044)

description: FFPE


title: HepG2 _24h_DMSO_2

description: HCC cells treated with DMSO

value: DMSO


title: 206 (20082062)

description: FreshFrozen