title: Kidney_ClipR-14_rep3

city: Sendai

first: Masayuki

last: Yamamoto

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

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

description:
Gene expression of ClipR-14-treated kidney
ISAM_Kidney_9_3122

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: The data were analyzed and normalized with GeneSpring software (v.11.5). After normalization, the data was baseline transformed to the median of all samples and filtered on expression (20-100 percentile), on flags (detected), on error (CV50%), and stats (One way ANOVA P<0.01) to compare among groups (Sham+Normal as control, Clip, ClipR-14).

label_protocol: 500 ng of total RNA was amplified and labeled using the Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Left Kidney was dissected out. Total RNA of whole kidney was extracted using ISOGEN (Nippon Gene). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Left ureter was obstructed by vascular clip for 2 days (Clip) and removed for 12 days (ClipR-14).

tag: strain background

value: Mixed

value: Male

tag: age

value: 10 weeks

value: ISAM (Epo–/–::3.3K-Epo3'-Tg458)

tag: sample group

value: reversed-UUO (ClipR-14)

value: Kidney


title: slide 4 - Hyp MPTP + aMPT

status: Public on Mar 20 2013

type: RNA

city: Ottawa

first: Jason

middle: T.

last: Popesku

state: ON

address: 20 Marie Curie

department: Biology

country: Canada

institute: University of Ottawa

description:
Sexually mature (mid-May) adult female goldfish received a single injection of MPTP (50 ug/g body weight at 5 uL/g body weight) or 0.6% saline on day 0 and a single injection of alpha-MPT (240 ug/g body weight at 5 uL/g body weight) or 0.6% saline on Day 5.
Hypothalamus tissue was extracted on Day 6.

hyb_protocol: Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)

scan_protocol: Microarrays were scanned at full speed 10 micron resolution using the ScanArray 5000 XL system (Packard Biosciences/PerkinElmer) using both red and blue lasers. Images were obtained with ScanArray Express software using automatic calibration sensitivity varying PMT gain (PMT starting at 65% for Cy5 and 70% for Cy3) with fixed laser power at 80% and the target intensity set for 90%.

data_processing: Microarray images were analyzed using QuantArray (Packard Biosciences/PerkinElmer) and raw signal intensity values were obtained for duplicate spots of genes. Normalization was performed using LOWESS method.

molecule: total RNA

organism: Carassius auratus

source_name: MPTP (50 ug/g) + aMPT (240ug/g)

extract_protocol: Total RNA was isolated with the TRIzol reagent (Invitrogen, Burlington, ON, Canada) as per the manufacturer's protocol. Samples were treated with DNase on-column in an RNeasy Mini Plus kit (Qiagen, Mississauga, ON, Canada). RNA quantity was evaluated using the NanoDrop ND-1000. RNA integrity was evaluated using the BioAnalyzer (Agilent); RIN for each sample was > 8.4.

tag: developmental stage

value: sexually mature (mid-May) adult

tag: gender

value: female

tag: agent

value: MPTP, alpha-MPT

tag: tissue

value: Hypothalamus

source_name: Control

value: saline (control)


title: Unifected B6

city: Cambridge

first: Kirk

last: Jensen

state: MA

address: 77 Massachusetts Ave. Bldg 68-270

country: USA

institute: MIT

description: AA368-uninfected B6

hyb_protocol: Followed Affymetrix instructions.

scan_protocol: Scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. We normalized such that the median intensity value was 500. We then set the minimum intensity to be 50.

label: biotin

organism: Mus musculus

source_name: Uninfected (18hr) Stat6-/- BMDMs

label_protocol: biotin

growth_protocol: BMDMs were plated at 3x10^6 cells per well in 6-well plates. They were generated by incubated bonemarrow cells in 20% L929 medium for 6-7 days before harvesting.

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

treatment_protocol: BMDMs were infected with parasite strains at the indicated Multiplicity of Infection (MOI) for 18 hours before RNA harvesting; the actual MOI of viable parasites after plaque assays for this series of experiments was between 1 and 2.

tag: cell type

value: Bone marrow-derived macrophages (BMDMs)

tag: strain

tag: toxoplasma parasite strain


title: slide 44 - Hyp sulpiride

description: Slide #44

data_processing: Microarray images were analyzed using QuantArray (Packard Biosciences/PerkinElmer) and raw signal intensity values were obtained for duplicate spots of genes. Normalization was performed using LOWESS and GPA methods.

source_name: control

label_protocol: Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)

extract_protocol: RNeasy Mini Plus kit (Qiagen) including optional on-column DNase I treatment. RNA quantity was evaluated using the NanoDrop ND-1000. RNA integrity was evaluated using the BioAnalyzer (Agilent); RIN for each sample was > 8.4.

treatment_protocol:
sexually regressing (mid-june) female adult goldfish received 2 injections at 5 ul/g body weight:
1) 0.1% DMSO in 0.6% saline, and;
2) 0.6% saline
Animals were anaesthetized in MS222 5h post-injection, and tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.

tag: sex

source_name: sulpiride 6 ug/g

treatment_protocol:
sexually regressing (mid-june) female adult goldfish received 2 injections at 5 ul/g body weight:
1) 6 ug/g sulpiride 0.1% DMSO in 0.6% saline, and;
2) 0.6% saline
Animals were anaesthetized in MS222 5h post-injection, and tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.


title: slide 17 - Hyp MPTP + aMPT


title: slide 6 - Hyp sulpiride

description: Slide #6


title: slide 34 - Tel MPTP + aMPT (dye swap)

description:
Sexually mature (mid-May) adult female goldfish received a single injection of MPTP (50 ug/g body weight at 5 uL/g body weight) or 0.6% saline on day 0 and a single injection of alpha-MPT (240 ug/g body weight at 5 uL/g body weight) or 0.6% saline on Day 5.
Telencephalon tissue was extracted on Day 6.

label_protocol:
Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)
This slide is a dye-swap

value: Telencephalon


title: Kidney_ClipR-14_rep2

country: Japan

description:
Gene expression of ClipR-14-treated kidney
ISAM_Kidney_8_3121

tag: genotype/variation


title: slide 43 - Tel MPTP + aMPT


title: slide 48 - Tel MPTP + aMPT


title: Kidney_ClipR-14_rep1

description:
Gene expression of ClipR-14-treated kidney
ISAM_Kidney_7_3123


title: Kidney_Clip_rep3

description:
Gene expression of Clip-treated kidney
ISAM_Kidney_6_2899

value: Unilateral ureteral obstruction (UUO)-treated (Clip)


title: Kidney_Clip_rep1

description:
Gene expression of Clip-treated kidney
ISAM_Kidney_4_1098


title: slide 19 - Tel SCH

description: Slide #19

treatment_protocol:
sexually regressing (mid-june) female adult goldfish received 2 injections at 5 ul/g body weight:
1) 40 ug/g SCH 233090 0.1% DMSO in 0.6% saline, and;
2) 0.6% saline
Animals were anaesthetized in MS222 5h post-injection, and tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.


title: slide 41 - Tel SCH

description: Slide #41


title: Kidney_normal_rep1

description:
Gene expression of normal kidney
ISAM_Kidney_3_2890

value: untreated (normal)


title: Kidney_Clip_rep2

description:
Gene expression of Clip-treated kidney
ISAM_Kidney_5_1099


title: slide 28 - Tel MPTP + aMPT


title: slide 3 - Tel SCH

description: Slide #3


title: slide 30 - Hyp SCH

description: Slide #30


title: non-malignant tissue of patient Nr12, non-smoker with invasive urothelial carcinoma

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

country: Germany

institute: University Heidelberg

description: Expression data from non-malignant tissue of a non-smoker with invasive urothelial carcinoma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133plus2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.

data_processing: The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.

organism: Homo sapiens

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 was extracted using using RNeasy MiniKit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: Informed patients with invasive (pT2-4) or surface (pTa) urological tumours (iU/sU) were enrolled in this study. Patients were divided into three groups according to their smoking habits: current smoker (CS), former smoker (FS, >5 years since smoking cessation) and non-smoker (NS). For each combination of disease and smoking habit two patients were examined. Both tumour tissues (iUC/sUC) and non-tumour adjacent tissues (iUN/sUN) were taken.   Tissues were collected from routine tumour surgery and immediately placed in RNAlater, stored in RNAlater at 4°C over night, snap frozen in liquid nitrogen and stored at –80°C until RNA isolation.

value: urothelial

tag: type

value: non-malignant

tag: smoking habit

value: non-smoker

tag: disease

value: invasive urothelial carcinoma


title: Kidney_Sham_rep2

description:
Gene expression of Sham-treated kidney
ISAM_Kindey_2_3099

value: Mixed

value: Male

value: 10 weeks

value: sham-treated


title: slide 35 - Hyp SCH

description: Slide #35


title: malignant tissue of patient Nr11, smoker with invasive urothelial carcinoma

description: Expression data from malignant tissue of a smoker with invasive urothelial carcinoma

value: malignant

value: smoker


title: non-malignant tissue of patient Nr11, smoker with invasive urothelial carcinoma

description: Expression data from non-malignant tissue of a smoker with invasive urothelial carcinoma


title: malignant tissue of patient Nr12, non-smoker with invasive urothelial carcinoma

description: Expression data from malignant tissue of a non-smoker with invasive urothelial carcinoma


title: Kidney_Sham_rep1

description:
Gene expression of Sham-treated kidney
ISAM_Kidney_1_3065

value: ISAM (Epo–/–::3.3K-Epo3'-Tg458)

value: Kidney


title: slide 16 - Tel Quin

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline, and;
2)  0.6% saline (control) or quinpirole (LY 171555) 2 ug/g in 0.6% saline
Animals were anaesthetized in MS222, and hypothalamus tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #16; dye-swap of slide #24

extract_protocol: RNA was isolated with the TRIzol reagent (Invitrogen, Burlington, ON, Canada) per the manufacturer's protocol.  Samples were treated with DNase on-column in an RNeasy Mini Plus kit (Qiagen, Mississauga, ON, Canada).  RNA quantity was evaluated using the NanoDrop.  RNA integrity was evaluated using the BioAnalyzer (Agilent);   RIN for each sample was > 8.4.

tag: Sexually mature (mid-May) female adult goldfish received 2 injections at 5 uL/g body weight:

tag: 1) 0.1% DMSO in 0.6% saline, and;

tag: 2) 0.6% saline

tag: Telencephalon tissue was extracted 5h post-injection.

source_name: quinpirole 2 ug/g

tag: 2) quinpirole (LY 171555) 2 ug/g in 0.6% saline


title: malignant tissue of patient Nr10, smoker with invasive urothelial carcinoma


title: non-malignant tissue of patient Nr10, smoker with invasive urothelial carcinoma


title: slide 24 - Tel Quin

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline, and;
2)  0.6% saline (control) or quinpirole (LY 171555) 2 ug/g in 0.6% saline
Animals were anaesthetized in MS222, and hypothalamus tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #24


title: slide 40 - Tel Quin

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline, and;
2)  0.6% saline (control) or quinpirole (LY 171555) 2 ug/g in 0.6% saline
Animals were anaesthetized in MS222, and hypothalamus tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #40


title: non-malignant tissue of patient Nr9, non-smoker with invasive urothelial carcinoma


title: slide 30 - Tel SKF

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline (control) or SKF 38393 40 ug/g in 0.1% DMSO and 0.6% saline, and;
2)  0.6% saline
Animals were anaesthetized in MS222, and telencephalon tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #30

tag: 1) SKF 38393 40 ug/g in 0.1% DMSO and 0.6% saline, and;


title: malignant tissue of patient Nr9, non-smoker with invasive urothelial carcinoma


title: slide 16 - Hyp SCH

description: Slide #16

value: female


title: slide 24 - Hyp SCH

description: Slide #24


title: non-malignant tissue of patient Nr8, former smoker with invasive urothelial carcinoma

description: Expression data from non-malignant tissue of a former smoker with invasive urothelial carcinoma

value: former smoker


title: malignant tissue of patient Nr8, former smoker with invasive urothelial carcinoma

description: Expression data from malignant tissue of a former smoker with invasive urothelial carcinoma


title: NTG 2

city: Glasgow

first: Peter

middle: D.

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

description: Gene expression data from HeLA cells and siHIRA knockdown

hyb_protocol: Subsequent labelling and hybrisation to HG_U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA) using the FL-Ovation cDNA Biotin Module v2.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 running GCOS software.

data_processing: The data were analyzed with RMA (Bioconductor) using Affymetrix default analysis settings and quantile normalisation as normalization method.

molecule: polyA RNA

source_name: HeLa cells nucleofacted with Dharmacon control siRNA

label_protocol: 40ng of RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN, San Carlos, CA).

growth_protocol: Hela cells were nucleofacted with respective siRNAs and RNA was isolated after 72 hours

extract_protocol: RNA was extracted using RNA easy mini kit Cat:74104

treatment_protocol: No treatment other then nucleofaction

value: HeLa


title: slide 47 - Tel SKF

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline (control) or SKF 38393 40 ug/g in 0.1% DMSO and 0.6% saline, and;
2)  0.6% saline
Animals were anaesthetized in MS222, and telencephalon tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #47; dye-swap of slide #30


title: malignant tissue of patient Nr6, non-smoker with superficial urothelial carcinoma

description: Expression data from malignant tissue of a non-smoker with superficial urothelial carcinoma

value: superficial urothelial carcinoma


title: non-malignant tissue of patient Nr7, former smoker with invasive urothelial carcinoma


title: NTG 1

value: nucleofacted with Dharmacon control siRNA


title: NTG 3


title: slide 8 - Tel Quin

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline, and;
2)  0.6% saline (control) or quinpirole (LY 171555) 2 ug/g in 0.6% saline
Animals were anaesthetized in MS222, and hypothalamus tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #8


title: slide 13 - Tel SKF

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline (control) or SKF 38393 40 ug/g in 0.1% DMSO and 0.6% saline, and;
2)  0.6% saline
Animals were anaesthetized in MS222, and telencephalon tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #13


title: non-malignant tissue of patient Nr6, non-smoker with superficial urothelial carcinoma

description: Expression data from non-malignant tissue of a non-smoker with superficial urothelial carcinoma

value: urothelial


title: malignant tissue of patient Nr3, non-smoker with superficial urothelial carcinoma


title: non-malignant tissue of patient Nr5, former smoker with superficial urothelial carcinoma

description: Expression data from non-malignant tissue of a former smoker with superficial urothelial carcinoma

value: non-malignant


title: malignant tissue of patient Nr7, former smoker with invasive urothelial carcinoma


title: siHIRA 1

description: Gene expression data from HeLA cells and NTG control

source_name: HeLa cells nucleofacted with HIRA siRNA

value: nucleofacted with HIRA siRNA


title: Satb1 KO CLP

city: Suita

first: Takafumi

last: Yokota

state: Osaka

address: 2-2 Yamadaoka

department: Hematology & Oncology

institute: Osaka University

description:
CLP sorted from Satb1KO E18.5 fetal liver
AR0943_06

hyb_protocol: 2.0 ug of Cy3-labelled cDNA in a reaction volume of 25 ul containing 1x Agilent blocking agent following the manufacturers instructions.   25 ul of 2x Agilent hybridization buffer was added to the mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.    After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent)  and for 1 minute at 37°C with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (gScale signal).
the gSigEval column shows the results of Signal Evaluation; 2 for transcripts detected,1 for transcripts detected with low level (indicating the signal intensity data might be affected), 0 for transcripts that were not detected.

source_name: Satb1 KO CLP from E18.5 fetal liver

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 6.1ng Total RNA using the Ovation® Pico WTA System V2 (NuGEN) according to the manufacturer's instructions, followed by DNA Clean & Concentrator-25 purification (Zymo Research).    Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using Rneasy Micro Kit(50) (QIAGEN) following the manufacturer's recommendations.

treatment_protocol: Freshly isolated lympho-hematopoietic progenitor cells from fetal liver

tag: strain background

tag: developmental stage

value: fetal liver

value: lympho-hematopoietic progenitor cells

tag: cell subtype

value: Lin- c-kitLo Sca-1Lo IL7Rα+ CLP-enriched cells


title: Satb1 KO LMPP

description:
LMPP sorted from Satb1KO E18.5 fetal liver
AR0943_05

source_name: Satb1 KO LMPP from E18.5 fetal liver

tag: tissue

tag: cell type

value: Lin- c-kitHi Sca-1+ Flt3+LMPP-enriched cells


title: non-malignant tissue of patient Nr4, smoker with superficial urothelial carcinoma

description: Expression data from non-malignant tissue of a smoker with superficial urothelial carcinoma


title: Satb1 KO HSC

description:
HSC sorted from Satb1KO E18.5 fetal liver
AR0943_04

source_name: Satb1 KO HSC from E18.5 fetal liver

value: Lin- c-kitHi Sca-1+ Flt3- HSC-enriched cells


title: siHIRA 3


title: WT CLP

description:
CLP sorted from WT E18.5 fetal liver
AR0943_03

source_name: WT CLP from E18.5 fetal liver

value: wild type


title: malignant tissue of patient Nr5, former smoker with superficial urothelial carcinoma

description: Expression data from malignant tissue of a former smoker with superficial urothelial carcinoma

value: malignant


title: slide 7 - Tel SKF

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline (control) or SKF 38393 40 ug/g in 0.1% DMSO and 0.6% saline, and;
2)  0.6% saline
Animals were anaesthetized in MS222, and telencephalon tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #7


title: malignant tissue of patient Nr2, former smoker with superficial urothelial carcinoma


title: malignant tissue of patient Nr4, smoker with superficial urothelial carcinoma

description: Expression data from malignant tissue of a smoker with superficial urothelial carcinoma

value: smoker


title: meat quality replication 6

city: East Lansing

first: Yuwares

last: Malila

state: Michigan

address: 3340 Anthony Hall

department: Food Science and Human Nutrition

institute: Michigan State University

description: PSE vs normal, turkey breast meat 6, replication 6 of 6

hyb_protocol: Fragmented, Cy3-coupled aRNA was mixed with its Cy5-coupled partner. The mixtures were brought to 110 μL with 68°C SlideHyb 1 (Ambion, Inc.) and incubated at 68°C for 5 min. These dye-coupled mixtures were then hybridized to TSMLO microarrays for 18 h in a GeneTac Hybridization Station (Genomic Solutions, Ann Arbor, MI) using the following conditions: 54°C for 18 h, followed by a medium-stringency wash at 42°C (2X SSC, 0.1% SDS), a high-stringency wash (0.2X SSC, 0.1% SDS) at 22°C, and a wash with post wash buffer (0.2X SSC) at 22°C. Arrays were then rinsed in 2X SSC and Nanopure water, dried by centrifugation at 1000 × g for 5 min.

scan_protocol: The array was scanned with a GenePix 4000B (Molecular Devices, Sunnyvale, CA) scanner. Image analysis was performed using GenePix Pro 6.0, and spot intensities were exported as GPR files.

data_processing: The dye intensity bias was normalized using normexp background correction method (Ritchie et al. 2007). LOESS-normalized data was described as M-value and statistically analyzed with a linear model (Smyth, 2005). Data processing was done in R package (http://www.r-project.org/).

organism: Meleagris gallopavo

source_name: Pectoralis major

label_protocol: Total RNA was amplified using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Inc.) as described in Sporer et al. (2010). Briefly, 2 μg total RNA was primed with T7 Oligo(dT) for 10 min at 70°C then reverse transcribed into cDNA at 42°C for 2 h. Second strand synthesis was performed at 16°C for 2 h. Double-stranded cDNA was purified, and in vitro transcribed at at 37°C for 4 h to sythesize amplified RNA (aRNA). aRNA was purified and quantified using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA). For the dye coupling procedure, 10 μg aRNA was coupled to either Cy3 or Cy5 fluorescent dye (GE Healthcare, Piscataway, NJ) in the dark at room temperature for 1 hour until the reaction was quenched by the addition of 4M hydroxylamine. Dye-coupled aRNA was purified and quantified, then 5 μg was fragmented to 60-200 nucleotide segments using RNA Fragmentation Reagents (Ambion, Inc.) at 70°C for 15 min in preparation for microarray hybridization.

growth_protocol: Growth protocol was described in Chiang et al, 2008. Briefly, 43 birds of RBC2 turkeys were obtained from The Ohio State University. Birds were raised using conventional husbandry practices for commercial turkeys at MSU Poultry farm. Turkeys were harvested at 22 week of age using standard industry practices in the MSU Meat Laboratory. The Pectoralis major muscle (breast meat) was collected and snap frozen in liquid nitrogen and stored at -80C until RNA isolation.

extract_protocol: Total RNA was isolated from P. major muscle tissue using TRIReagent® Solution (Molecular Research Center, Inc., Cincinnati, OH) according to the manufacturer’s instructions. Integrity of total RNA was determined using Agilent 2100 Bioanalyzer (Santa Clara, CA). The samples with an RNA Integrity Number (RIN) equal or exceeding 8.0 (RIN = 10 is the best) was utilized in further step.

treatment_protocol: Breast meat samples were classified as “normal” or “PSE” based on percent marinade uptake at 24h post-slaughter. Normal meat referred to sample with high marinade uptake; conversely, PSE samples were grouped with low marinade uptake.

tag: meat quality

value: PSE

value: normal


title: siHIRA 2

description: Gene expression data from HeLA cells and siHIRA knockdown


title: siCABIN1 3

source_name: HeLa cells nucleofacted with CABIN1 siRNA

value: nucleofacted with CABIN1 siRNA


title: non-malignant tissue of patient Nr3, non-smoker with superficial urothelial carcinoma

value: non-smoker


title: meat quality replication 5

description: PSE vs normal, turkey breast meat 5, replication 5 of 6


title: siCABIN1 2

value: HeLa


title: meat quality replication 2

description: PSE vs normal, turkey breast meat 2, replication 2 of 6


title: meat quality replication 3

description: PSE vs normal, turkey breast meat 3, replication 3 of 6


title: WT HSC

description:
HSC sorted from WT E18.5 fetal liver
AR0943_01

source_name: WT HSC from E18.5 fetal liver


title: Control knockdown, biological rep1

city: bethesda

first: Lijun

last: Di

address: 41 center dr

institute: NCI

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

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

data_processing: The data were analyzed with Gene Console using Affymetrix default analysis settings. RMA normalization.

source_name: MCF-7 cell with scamble KD for 72 hours

growth_protocol: MCF-7 cells were maintained in regular DMEM supplemented with 10% (v/v) FBS, penicillin-streptomycin (Invitrogen) and insulin.

extract_protocol: Qiagen RNAeasy kit was applied to extract total RNA from MCF-7 cells following manufacturer's manual.

treatment_protocol: CtBP mRNA targetting oligos and the control oligos are from Dharmacon. Dharmafect1 transfection method was applied to introduce gene knockdown oligoes into the cells following manufacturer's manual.

tag: cell line

tag: treatment

value: control KD for 72 hours


title: WT LMPP

description:
LMPP sorted from WT E18.5 fetal liver
AR0943_02

source_name: WT LMPP from E18.5 fetal liver

tag: genotype/variation


title: non-malignant tissue of patient Nr2, former smoker with superficial urothelial carcinoma

description: Expression data from non-malignant tissue of a former smoker with superficial urothelial carcinoma

value: urothelial

tag: type

tag: smoking habit

value: former smoker

value: superficial urothelial carcinoma


title: U87shScramble

status: Public on Mar 19 2013

city: Chicago

first: Ilya

last: Ulasov

address: 5841 S Maryland ave SBRO J339

institute: University of Chicago

description: Lentivirus scramble infected cells upon puromycin selection

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization , the expression of Actin gene was designated as 1,  since it is uniformly presented in glioma samples regardless of the cell origin, grade etc.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: U87 glioma cells, Lentivirus particle from Sigma_shScramble

label_protocol: PCR assays were performed using the Cell Cycle Pathway PCR assay panel (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

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

value: U87 brain tumor cell line

tag: passage

value: control


title: E. faecalis OG1RF exposed to 10μg/mL vancomycin for 60 minutes, replicate 2

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

hyb_protocol: The slides were hybridized to a mixture containing equal amounts of test and reference cDNA for 16 h at 42°C in a MAUI hybridization chamber (BioMicro Systems).  Hybridized slides were washed and scanned using a GenePix scanner (Axon Instruments).

scan_protocol: Hybridized slides were washed and scanned using a GenePix scanner (Axon Instruments, Inc., Union City, CA).

data_processing: Data were analyzed using software available at the J. Craig Venter Institute PFGRC website.  Single-channel images of the slides were loaded into Spotfinder and overlaid.  A spot grid was created according to PFGRC specifications and manually adjusted to fit all spots.  The Microarray Data Analysis System (MIDAS) software was used to normalize the spot intensity data using LOWESS and iterative log mean centering with default setting.  MIDAS also utilized In-Slide Replicate Analysis to average the intensities of the spots that were replicated on the microarray slide.  Spots that were missing or labeled as “bad” during the upstream processes in 50% of the slides were cut off in the output files, which also did not include control spots printed on the slides.   Statistical analysis was carried out with BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P value of 0.001.

organism: Enterococcus faecalis OG1RF

source_name: 10μg/mL vancomycin, 60 minute exposure RNA

label_protocol: Once RNA was purified as described above, cDNA was generated from 2ug RNA per sample as described by the protocol available from the Pathogen Functional Genomics Research Center (PFGRC) using Invitrogen Superscript III Reverse Transcriptase (Invitrogen, Gaithersburg, MD) to increase cDNA yields.  Purified cDNAs were coupled to  Cy3 (experimental samples) or Cy5 (reference cDNA).

growth_protocol: Cells were grown in FMC medium supplemented with 10 mM glucose to OD600 of 0.3 at 37°C.

extract_protocol: RNA was isolated from homogenized E. faecalis cells grown in BHI medium to OD600 of 0.3 with or without exposure to antibiotics by repeated hot acid-phenol: chloroform extractions, and the nucleic acid was precipitated with 1 volume ice-cold isopropanol and one-tenth volume 3M sodium acetate (pH 5) at –20°C overnight.  RNA pellets were resuspended in 80 mL nuclease-free H2O, and treated with DNase I (Ambion) at 37°C for 30 minutes.  RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and 1 mL samples were run on an agarose gel to verify RNA integrity.  The RNA was purified again using the RNeasy mini kit (Qiagen), including a second on-column DNase treatment that was performed as recommended by the supplier.  Final RNA concentrations were determined in triplicate.

treatment_protocol: Upon reaching OD600 = 0.3, cells were treated with 10μg/mL vancomycin for 60 minutes

tag: growth phase

value: 10μg/mL vancomycin

tag: time

value: 60 min

source_name: wild-type mid-log RNA

growth_protocol: Cells were grown in Brain-Heart medium to OD600 of 0.5 at 37°C.

value: reference


title: E. faecalis OG1RF exposed to 10μg/mL vancomycin for 60 minutes, replicate 3


title: siCABIN1 1

description: Gene expression data from HeLA cells and NTG control


title: E. faecalis OG1RF exposed to 10μg/mL vancomycin for 30 minutes, replicate 1

source_name: 10μg/mL vancomycin, 30 minute exposure RNA

treatment_protocol: Upon reaching OD600 = 0.3, cells were treated with 10μg/mL vancomycin for 30 minutes

value: 30 min


title: U87shMMP14

description: Lentivirus MMP14 sh infected cells upon puromycin selection

source_name: U87 glioma cells, Lentivirus particle from Sigma_shMMP14

value: MMP14 knockdown


title: E. faecalis OG1RF exposed to 10μg/mL vancomycin for 60 minutes, replicate 1


title: Control knockdown, biological rep2


title: Control knockdown, biological rep3


title: CtBP knockdown, biological rep3

source_name: MCF-7 cell with CtBP KD for 72 hours

value: CtBP KD for 72 hours


title: meat quality replication 4

description: PSE vs normal, turkey breast meat 4, replication 4 of 6

value: PSE


title: CtBP knockdown, biological rep1


title: malignant tissue of patient Nr1, smoker with superficial urothelial carcinoma

value: malignant

value: smoker

tag: disease


title: E. faecalis OG1RF exposed to 10μg/mL vancomycin for 60 minutes, replicate 4


title: E. faecalis OG1RF exposed to 10μg/mL vancomycin for 30 minutes, replicate 4


title: meat quality replication 1

description: PSE vs normal, turkey breast meat 1, replication 1 of 6

value: normal


title: Whole Fly_Eggless_Infected_Virgin_Rep1

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N Wolfe St.

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

hyb_protocol: Samples were hybridized to Agilent's Drosophila (V2) Gene Expression Microarray (Product # G2519F, Design ID 021791). Hybridization procedure was as described in Agilent's One Color Microarray-Based Gene Expression Analysis Protocol Version 6.5

scan_protocol: Samples scanned using an Axon 4000B scanner and analyzed using Agilent's Feature Extraction Software (V. 10.5.1.1), Grid 021791_D_F_20110615

data_processing: Data were background corrected in R using backgroundCorrect() and the “normexp” method recommended by Ritchie et al. (2007), and then normalized using quantile normalization as recommended by Agilent

organism: Drosophila melanogaster

label_protocol: Samples were labeled using Cy3 and Agilent’s Low Input Quick Amp Labeling kit

growth_protocol: Flies used in this experiment were either egg-producing daughters of a cross between tud1 bw sp/CyO mothers and Canton S fathers or eggless daughters of tud1 bw sp mothers and Canton S fathers. Both egg producing and eggless females had the same genotype (tud1 bw sp/CS), but eggless females lacked a germline due to the maternal effects of the homozygous recessive tudor mutation carried by their mothers. Flies were maintained at 24 degrees Celcius on a 12hr light-dark cycle and allowed ad libidum access to food (8.3% glucose, 8.3% Brewer's yeast, and 1% agar, plus 0.04% phosphoric acid and 0.4% propionic acid)

extract_protocol: Ten hours after infection 25 whole female flies from each treatment were collected on CO2, snap frozen in TRIZOL reagent (Ambion), and placed at 80°C. We extracted RNA from our samples using TRIZOL reagent according to the manufacturer’s protocol.

treatment_protocol: Females were either maintained as virgins or allowed to copulate once with a single male. At 2.5 hours after mating, half of all virgin females and half of all mated females were infected with a gram-negative bacterial pathogen Providencia rettgeri. This same procedure was followed for egg-producing and eggless flies.

tag: egg-producing or eggless

value: Eggless

tag: mating status

value: Virgin

tag: infection status

value: Infected


title: Whole Fly_Eggless_Infected_Mated_Rep1

value: Mated


title: non-malignant tissue of patient Nr1, smoker with superficial urothelial carcinoma

description: Expression data from non-malignant tissue of a smoker with superficial urothelial carcinoma

value: urothelial

value: non-malignant

value: superficial urothelial carcinoma


title: E. faecalis OG1RF exposed to 10μg/mL vancomycin for 30 minutes, replicate 3

value: 10μg/mL vancomycin


title: E. faecalis OG1RF exposed to 10μg/mL vancomycin for 30 minutes, replicate 2


title: E. faecalis OG1RF control replicate 3

source_name: Control OD600 = 0.3 RNA

value: control


title: E. faecalis OG1RF control replicate 4

value: reference


title: Whole Fly_Eggless_Infected_Virgin_Rep3


title: CtBP knockdown, biological rep2


title: Whole Fly_Eggless_Uninfected_Mated_Rep3

value: Uninfected


title: Whole Fly_Eggless_Uninfected_Mated_Rep2


title: E. faecalis OG1RF control replicate 2


title: Whole Fly_Wildtype_Infected_Mated_Rep3

value: Egg-Producing


title: Whole Fly_Eggless_Uninfected_Mated_Rep1


title: Whole Fly_Wildtype_Infected_Mated_Rep1


title: Whole Fly_Eggless_Uninfected_Virgin_Rep2


title: E. faecalis OG1RF control replicate 1


title: Whole Fly_Wildtype_Infected_Virgin_Rep3


title: Whole Fly_Wildtype_Uninfected_Mated_Rep3


title: Whole Fly_Eggless_Infected_Mated_Rep2


title: Whole Fly_Eggless_Infected_Mated_Rep3


title: Whole Fly_Wildtype_Infected_Virgin_Rep2


title: Whole Fly_Wildtype_Uninfected_Virgin_Rep2


title: Whole Fly_Eggless_Uninfected_Virgin_Rep1


title: Whole Fly_Wildtype_Infected_Virgin_Rep1


title: cHL diseased node NS7

city: Brisbane

first: Kimberley

last: Jones

state: QLD

address: 300 Herston Road

country: Australia

institute: Queensland Institute of Medical Research

hyb_protocol: Labelled RNA was hybridised using agilent miRNA complete labelling and Hyb kit

scan_protocol: Scanned using Agilent Technologies Scanner G2505C US80603148

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) to obtain background subtracted and spatially detrended. Processed Signal intensities Non-uniform outliers were excluded.

label: Cyanine 3-pcp

source_name: cHL diseased node

label_protocol: 100ng RNA were labelled with Cyanine-3cpc using the agilent miRNA complete labelling and Hyb kit

extract_protocol: RNA was extracted using using RecoverAll™ Total Nucleic Acid Isolation kit (Ambion) as per manufacturer's instructions

treatment_protocol: Formalin-fixed paraffin-embedded tissue

value: Formalin-fixed Paraffin-embedded cHL diseased node

tag: histology

value: Nodular Sclerosing cHL


title: cHL diseased node MC6

value: Mixed Cellularity cHL


title: cHL diseased node MC7


title: Whole Fly_Wildtype_Infected_Mated_Rep2


title: cHL diseased node MC4


title: Non-malignant Lymph Node LN8

source_name: lymph node

value: Formalin-fixed Paraffin-embedded lymph nodes


title: Whole Fly_Eggless_Infected_Virgin_Rep2


title: Whole Fly_Eggless_Uninfected_Virgin_Rep3


title: cHL diseased node NS1


title: cHL diseased node NS3


title: cHL diseased node NS5


title: cHL diseased node NS6


title: Whole Fly_Wildtype_Uninfected_Virgin_Rep1


title: Whole Fly_Wildtype_Uninfected_Mated_Rep1


title: Whole Fly_Wildtype_Uninfected_Mated_Rep2


title: cHL diseased node NS9


title: cHL diseased node NS8


title: cHL diseased node MC3


title: cHL diseased node MC1


title: cHL diseased node MC2


title: cHL diseased node NS2


title: Non-malignant Lymph Node LN7


title: Non-malignant Lymph Node LN6


title: Non-malignant Lymph Node LN2


title: Whole Fly_Wildtype_Uninfected_Virgin_Rep3


title: Non-malignant Lymph Node LN5


title: Non-malignant Lymph Node LN4


title: Non-malignant Lymph Node LN3


title: Non-malignant Lymph Node LN1


title: rvpm low stretch high shortening rep3

city: Charlottesville

first: Charles

last: Haggart

state: VA

address: 415 Lane Road

department: Biomedical Engineering

institute: University of Virginia

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained per the appropriate Affymetrix user manual (3' IVT Express Kit User Manual).

scan_protocol: GeneChips were scanned per the appropriate Affymetrix user manual (Expression Wash, Stain and Scan User Manual for Cartridge Arrays, www.affymetrix.com).

data_processing: The CEL files for each of 12 microarrays were read into R using the Bioconductor ReadAffy function. The Robust Multichip Average (RMA) algorithm was then used within R to normalize expression values across all probesets and microarrays. Finally, the spike-in controls were removed from the raw dataset (reduced probesets from 31,099 to 31,042) and a script was written to remove probesets whose expression was very low across at least 2 microarrays in each of the four experimental groups (reduced probesets from 31,042 to 16,391). Specifically, if the log2-transformed expression for a probeset was less than log2(50) on at least two microarrays within one or more mechanical groups, the probeset was removed from additional analysis. The resulting log2-transformed expression values are included in the Matrix tab of this spreadsheet.  Filtered results are provided as a supplementary file on the Series record.

organism: Rattus norvegicus

source_name: right ventricular papillary muscle, low mean stretch, high cyclic shortening, 12hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (3' IVT Express Kit User Manual, www.affymetrix.com).

growth_protocol: Each muscle was dissected from the right ventricle of an adult male LBNF rat and carefully hung in a sterilized muscle culture bath. Each muscle was bathed in well oxygenated, supplemented Medium 199 and stimulated to contract with a 2-4V biopolar square wave at 1Hz. At the beginning of the 12 hour culture period, each muscle was incrementally stretched from slack to a pre-defined length to establish a baseline low or high mean stretch. A muscle-specific computer-generated waveform was then initiated to impose a low or high percentage of cyclic shortening, as defined by the mechanical group design. The culture media was maintainted at 37°C and exchanged for fresh media at the 6 hour time point. Mechanical stretch and shortening were monitored at 0, 3, 6, 9, and 12 hours to ensure accurate and precise mechanical control throughout the study.

extract_protocol: While frozen in liquid nitrogen, each muscle was mechanically homogenized via pulverization with a pyrogen-free pestle with a hard polymeric head followed by Trizol incubation and mechanical shearing by drawing the Trizol-tissue cocktail through a 25 gauge needle three times. Glycogen was added to each sample, and Trizol extraction was conducted according to the manufacturer's instructions, including the addition of DNase I treatment. Each sample concentration was measured twice and DNAse free water added to ensure a 100 ng total RNA sample in total volume of 3μl.

treatment_protocol: After 12 hours of mechanically controlled muscle culture, the electrical stimulus and mechanical shortening were terminated and each muscle was carefully removed from the culture system, placed into a pyrogen free tube, flash frozen in liquid nitrogen, and stored at -80°C until further processing.

tag: strain

tag: gender

value: male

tag: age

tag: weight


title: CAF4_ongel_rep2

city: London

first: Fernando

last: Calvo

address: 44 Lincoln's Inn Fields

department: London Research Institute

institute: Cancer Research UK

description:
murine fibroblasts from mammary carcinoma (MMTV-PyMT model), E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 16

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Carcinoma-associated mammary fibroblasts, E6 immortalized, cultured on gel 72h

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

growth_protocol: Cells were isolated from the defined tissues, immortalized using hpvE6 and seeded on a Matrigel:Collagen I deformable matrix and cultured for 72h on 10%FBS DMEM

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

treatment_protocol: No treatment

tag: background strain

value: FVB/N

tag: tumour stage

value: Carcinoma


title: rvpm low stretch high shortening rep2


title: CAF4_ongel_rep1

description:
murine fibroblasts from mammary carcinoma (MMTV-PyMT model), E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 15


title: rvpm low stretch high shortening rep1


title: CAF2_ongel_rep2

description:
murine fibroblasts from mammary carcinoma (MMTV-PyMT model), E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 12


title: rvpm high stretch low shortening rep3

source_name: right ventricular papillary muscle, high mean stretch, low cyclic shortening, 12hr


title: RAS 2

description: Gene expression data from IMR90 cells and RASG12V-transduced cells

source_name: IMR90 cells transfected with RAS retrovirus

growth_protocol: IMR90 cell lines were cultured according to ATCC guidelines in low oxygen (2%). Fibroblasts were cultured in Dulbecco's modified Eagle's medium supplemented with 20% fetal bovine serum.

treatment_protocol: Retroviral-mediated gene transfer was performed using Phoenix packaging cells (Dr. Gary Nolan, Stanford University). Phoenix cells were transfected using Polyethylenimine (PEI) (Linear MW 25,000) (Polysciences, Inc. Warrington, PA). To one milliliter of serum free DMEM, 16 μg of retroviral plasmid DNA and 2 μg of a plasmid encoding vesicular stomatitis virus glycoprotein G (VSV-G) and 38 μg of PEI were added. This solution was briefly vortexed, left to sit for 10 minutes and then added to Phoenix Cells. Twenty-four hours later, media was changed on Phoenix cells. At 48 hours post transfection, virus-containing medium was collected, supplemented with 8μg/ml of polybrene (Sigma), and incubated with the target cells at 37°C for 24 hours. A second round of infection was performed on the same target cells. Fibroblasts were drug selected and kept in drug for duration of experiments. Lentivirus-mediated gene transfer was performed as described in the Virapower kit (Invitrogen) using 293FT cells to make infectious virus and the transfection protocol described above.

tag: cell line

tag: genotype/variation

value: transfected with RAS retrovirus


title: RAS 4


title: rvpm high stretch low shortening rep1


title: rvpm high stretch high shortening rep2

source_name: right ventricular papillary muscle, high mean stretch, high cyclic shortening, 12hr


title: CAF1_ongel_rep1

description:
murine fibroblasts from mammary carcinoma (MMTV-PyMT model), E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 9


title: RAS 3


title: rvpm high stretch low shortening rep2


title: CAF3_ongel_rep1

description:
murine fibroblasts from mammary carcinoma (MMTV-PyMT model), E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 13


title: rvpm low stretch low shortening rep2

source_name: right ventricular papillary muscle, low mean stretch, low cyclic shortening, 12hr


title: rvpm low stretch low shortening rep3


title: CAF3_ongel_rep2

description:
murine fibroblasts from mammary carcinoma (MMTV-PyMT model), E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 14


title: CAF1_ongel_rep2

description:
murine fibroblasts from mammary carcinoma (MMTV-PyMT model), E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 10


title: miR-145, replicate 1

first: Tai-Chung

last: Huang

address: 733 N Broadway BRB R560

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

hyb_protocol: input: all, for each sample, 55 degree of celcius, 20 rpm, 20 hr

scan_protocol: Agilent Technologies Scanner G2505C US22502585

data_processing:
R-LIMMA package, normalization method: Quantile, thr probe with the highest p value (i.e. least significant) was chosen to represent the gene
log2FC_matrix_miRNA.txt: systematic name (SystematicName), normalized log2 expression fold change miR-145/control (logFC), normalized overall average expression level (AveExpr), t value of T test (t), p value before multiple comparison correction (P.Value), p value after Benjamini-Hochberg test (adj.P.Value), B value of B test (B)

label_protocol: input 150 ng for each sample, dye conc. 2.1-4.4 ng/ul

growth_protocol: Mia-PaCa2 cells were grown in the DMEM culture media containing10% FBS and 1% penicillin-streptomycin

extract_protocol: 48 hr after transfection, QIAGEN Rneasy was used for total RNA extraction

treatment_protocol: 50 nM miR-145 mimics or control RNA (both from Dharmacon) was transfected into Mia-PaCa2 cells

tag: transfection

value: miR-145 mimics


title: miR-145, replicate 2


title: CAF2_ongel_rep1

description:
murine fibroblasts from mammary carcinoma (MMTV-PyMT model), E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 11


title: RAS 1


title: CONTROL 4

description: Gene expression data from IMR90 cells and control-transduced cells

source_name: IMR90 cells transfected with Control retrovirus

value: transfected with Control retrovirus


title: rvpm high stretch high shortening rep3


title: rvpm high stretch high shortening rep1


title: Control, replicate 2

value: control scramble RNA


title: AdAF1_ongel_rep2

description:
murine fibroblasts from mammary adenoma (MMTV-PyMT model), E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 8

source_name: Adenoma-associated mammary fibroblasts, E6 immortalized, cultured on gel 72h

value: Adenoma


title: rvpm low stretch low shortening rep1


title: Control, replicate 1


title: CONTROL 3


title: AKT 4

description: Gene expression data from IMR90 cells and mAKT1-transduced cells

source_name: IMR90 cells transfected with AKT retrovirus

value: transfected with AKT retrovirus


title: AdAF1_ongel_rep1

description:
murine fibroblasts from mammary adenoma (MMTV-PyMT model), E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 7


title: NF3_ongel_rep2

description:
murine fibroblasts from normal mammary gland, E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 4

source_name: Normal mammary fibroblasts, E6 immortalized, cultured on gel 72h

value: Normal


title: CONTROL 2


title: CONTROL 1


title: AKT 1


title: Rv1 shSiah2 rep2

city: Oxford

first: Natasha

last: Sahgal

address: Old Road Campus

department: Ludwig Institute of Cancer Research

institute: University of Oxford

description: replicate 2

data_processing: The data was background corrected, filtered for p < 0.01 and normalised using the vsn package in R

source_name: CWR22Rv1 prostate cancer cells expressing Siah2 shRNA

growth_protocol: Cells were grown in RPMI1640 medium supplemented with 10% FBS, antiboitics, and 1 ug/ml of puromycin

extract_protocol: Total RNA was extracted using GeneElute Mammalian Total RNA Miniprep Kit

tag: treatment


title: HpAF1_ongel_rep1

description:
murine fibroblasts from mammary hyperplasia (MMTV-PyMT model), E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 5

source_name: Hyperplasia-associated mammary fibroblasts, E6 immortalized, cultured on gel 72h

value: Hyperplasia


title: AKT 2


title: AKT 3


title: NF3_ongel_rep1

description:
murine fibroblasts from normal mammary gland, E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 3


title: miR-145-Cy5/Control-Cy3, replicate 2

hyb_protocol: input 0.85 ug for each sample, 65 degree of celcius, 10 rpm, 17 hr

data_processing:
R-LIMMA package, normalization within sample: Loess, normalization between samples: Scale, thr probe with the highest p value (i.e. least significant) was chosen to represent the gene
log2FC_matrix.txt: gene symbol (SYMBOL), gene name (GENENAME), normalized log2 expression fold change miR-145/control (log2FC), normalized expression fold change miR-145/control (FC), normalized overall average expression level (AveExpr), t value of T test (t), p value before multiple comparison correction (P.Value), p value after Benjamini-Hochberg test (adj.P.Value), B value of B test (B)

source_name: Metastatic pancreatic cancer cells

label_protocol: input 0.4 ug for each sample, dye conc. 4.44-6.03 ug/ul, dye activity 15-20

value: control


title: Control-Cy5/miR-145-Cy3, replicate 1


title: HpAF1_ongel_rep2

description:
murine fibroblasts from mammary hyperplasia (MMTV-PyMT model), E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 6


title: miR-145-Cy5/Control-Cy3, replicate 1


title: Rv1 pLKO.1 rep1

description: replicate 1

source_name: CWR22Rv1 prostate cancer cells expressing control pLKO.1 vector

value: pLKO


title: Control-Cy5/miR-145-Cy3, replicate 2


title: Rv1 pLKO.1 rep2

description: replicate 2


title: Rv1 shSiah2 rep1

description: replicate 1


title: NF2_ongel_rep1

description:
murine fibroblasts from normal mammary gland, E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 1


title: NF2_ongel_rep2

description:
murine fibroblasts from normal mammary gland, E6 immortalized, cultured on Matrigel:collagen matrix for 72h before RNA extraction
SAMPLE 2


title: Liver wild (s) 5 RT2006W26

status: Public on Mar 18 2013

city: West Vancouver

first: Samantha

middle: Louise

last: White

state: BC

address: 4160 Marine Drive

department: CAER

institute: Fisheries and Oceans Canada

description:
LWS3626
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

hyb_protocol: Hybridisation was performed following the procedures outlined in the Agilent Low Input Quick Amp protocol www.genomics.agilent.com (publication no. G4140-90052).

scan_protocol: Fluorescent images were collected at 5µm resolution using the ScanArray express scanner (Perkin Elmer). The same laser power (90%) and photomultiplier values (PMT) were used for all slides (Cy3 - 85 and Cy5 - 70). Fluorescence intensities were extracted using Imagene version 9.0 software (BioDiscovery).

data_processing: Data transformation (raw data converted to a threshold value of 1.0 and log2 transformed, LOWESS normalised and baseline transformed to the median of all samples) and analysis were performed in GeneSpring version 12.0 software (Agilent).

organism: Oncorhynchus mykiss

source_name: Liver, wild size-matched, pool

label_protocol: Reverse transcription (100ng of total RNA) and labelling were performed as per the Agilent Low Input Quick Amp protocol www.genomics.agilent.com (publication no. G4140-90052).

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) as per the manufacturer's protocol. Tissue homogenisation was by pellet pestal (Kontes).

value: Pennask Lake

tag: tissue

value: liver

tag: genotype

value: wild

tag: match to domesticated

value: size

tag: year reared

tag: sample type

value: reference pool

source_name: Liver, wild size-matched, individual 5

tag: individual


title: Liver hybrid 1 RT2007H32

description:
LWD3232
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild-domesticated, individual 1

value: wild-domesticated


title: Liver domesticated 3 RT2007D22

description:
LD3422
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, domesticated, individual 3

value: domesticated


title: Liver hybrid 6 RT2007H2

description:
LWD3702
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild-domesticated, individual 6


title: Liver wild (a) 5 RT2007W15

description:
LW3615
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild age-matched, individual 5

value: age


title: Liver hybrid 3 RT2007H19

description:
LWD3419
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild-domesticated, individual 3


title: Liver domesticated 4 RT2007D18

description:
LD3518
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, domesticated, individual 4


title: Liver hybrid 2 RT2007H27

description:
LWD3327
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild-domesticated, individual 2


title: Liver wild (s) 6 RT2006W25

description:
LWS3725
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild size-matched, individual 6


title: Liver domesticated 5 RT2007D5

description:
LD3605
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, domesticated, individual 5


title: Liver domesticated 1 RT2007D31

description:
LD3231
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, domesticated, individual 1


title: Liver hybrid 5 RT2007H6

description:
LWD3606
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild-domesticated, individual 5


title: Liver wild (a) 6 RT2007W4

description:
LW3704
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild age-matched, individual 6


title: Liver wild (s) 2 RT2006W58

description:
LWS3358
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild size-matched, individual 2


title: Liver hybrid 4 RT2007H14

description:
LWD3514
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild-domesticated, individual 4


title: Liver domesticated 6 RT2007D18

description:
LD3701
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, domesticated, individual 6


title: Liver wild (s) 1 RT2006W73

description:
LWS3273
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild size-matched, pool

source_name: Liver, wild size-matched, individual 1


title: Liver domesticated 2 RT2007D26

description:
LD3326
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, domesticated, individual 2


title: Liver wild (s) 3 RT2006W50

description:
LWS3450
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild size-matched, individual 3


title: Liver wild (s) 4 RT2006W33

description:
LWS3533
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild size-matched, individual 4


title: Liver wild (a) 3 RT2007W25

description:
LW3425
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild age-matched, individual 3


title: Liver wild (a) 4 RT2007W21

description:
LW3521
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild age-matched, individual 4


title: Liver wild (a) 1 RT2007W14

description:
LW3214
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild age-matched, individual 1


title: Liver wild (a) 2 RT2007W33

description:
LW3333
The strain of domesticated rainbow trout used in this study has a greatly enhanced growth-rate (approximately 5-fold greater) compared to the wild strain.

source_name: Liver, wild age-matched, individual 2


title: LC705_24h_sample3

city: Helsinki

first: Matti

last: Kankainen

address: PL0056 (Viikinkaari 5)

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

description: Primary macrophages stimulated with Lactobacillus rhamnosus LC705 24h, third pool of macrophages from six healthy humans

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using Affymetrix scanning protocol.

data_processing: Raw data was processed with R/Bioconductor. Signal intensities were calculated with the 'rma' function using default parameters, including quantile normalization and log2 transformation. For summarizing the expression data, we used custom chip definition files (Custom CDF, v. 11) based on Ensembl gene annotation rather than Affymetrix annotation (Dai et al., PMID: 16284200).

source_name: Primary macrophage, stimulated with LC705, 24h

label_protocol: For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA).

growth_protocol: Human monocytes were isolated from peripheral blood mononuclear cells of healthy blood donors (Finnish Red Cross Blood Transfusion Service, Helsinki, Finland) by adhesion. Macrophages were differentiated from monocytes for 7 d by culturing in serum-free macrophage medium (Gibco Invitrogen, Grand Island, NY, USA), and supplemented with 10 ng/ml of GM-CSF (Shering-Plough, Innishannon, Ireland). L. rhamnosus GG (ATCC 53103) and LC705 (DSM 7061) were grown in de Man, Rogosa and Sharpe (MRS) medium to late logarithmic growth phase by passaging three times. The number of bacteria was counted in a Petroff Hausser chamber.

extract_protocol: Total RNA was isolated by using Trizol (Invitrogen, Carlsbad, CA, USA) and RNeasy Midi Kit (Qiagen, Hilden, Germany) according to the manufactirer's instructions.

treatment_protocol: L. rhamnosus GG and LC705 from late logarithmic growth phase were resuspended in RPMI-1640 (Sigma-Aldrich, St. Louis, MO, USA) with 0.6 ug/ml penicillin and 60 ug/ml streptomycin at a ratio of 1 bacteria to 1 macrophage (1:1). Macrophages were stimulated at +37˚C in 5% CO2 with RPMI medium only, or with bacteria for 6 h and 24 h. After stimulations, the cells were washed, and immediately lyzed for RNA isolation.

tag: time point

value: 24 hrs

tag: probiotic

value: Lactobacillus rhamnosus LC705

tag: cell type

value: Primary macrophage

tag: macrophage pool

value: pool 3, individuals number 13-18


title: LC705_24h_sample2

description: Primary macrophages stimulated with Lactobacillus rhamnosus LC705 24h, second pool of macrophages from six healthy humans

value: pool 2, individuals number 7-12


title: LGG_24h_sample2

description: Primary macrophages stimulated with Lactobacillus rhamnosus GG 24h, second pool of macrophages from six healthy humans

source_name: Primary macrophage, stimulated with LGG, 24h

value: Lactobacillus rhamnosus GG


title: LC705_24h_sample1

description: Primary macrophages stimulated with Lactobacillus rhamnosus LC705 24h, first pool of macrophages from six healthy humans

value: pool 1, individuals number 1-6


title: LGG_24h_sample3

description: Primary macrophages stimulated with Lactobacillus rhamnosus GG 24h, third pool of macrophages from six healthy humans


title: LC705_6h_sample3

description: Primary macrophages stimulated with Lactobacillus rhamnosus LC705 6h, third pool of macrophages from six healthy humans

source_name: Primary macrophage, stimulated with LC705, 6h

value: 6 hrs


title: LC705_6h_sample2

description: Primary macrophages stimulated with Lactobacillus rhamnosus LC705 6h, second pool of macrophages from six healthy humans


title: LGG_6h_sample3

description: Primary macrophages stimulated with Lactobacillus rhamnosus GG 6h, third pool of macrophages from six healthy humans

source_name: Primary macrophage, stimulated with LGG, 6h


title: Control_24h_sample3

description: Primary macrophages stimulated with control medium 24h, third pool of macrophages from six healthy humans

source_name: Primary macrophage, unstimulated, 24h


title: Control_24h_sample2

description: Primary macrophages stimulated with control medium 24h, second pool of macrophages from six healthy humans


title: LGG_6h_sample1

description: Primary macrophages stimulated with Lactobacillus rhamnosus GG 6h, first pool of macrophages from six healthy humans


title: iPS cell line rep3

city: Beijing

first: Tao

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

country: China

institute: National Institute Of Biological Sciences, Beijing (NIBS)

hyb_protocol: Hybridization, wash and Stain Kit(Affymetrix.Inc)

scan_protocol: GeneChip® Scanner 3000 7G 3000 (Affymetrix.Inc)

data_processing: The raw image files were processed by Bioconductor “Affy” and “vsn” package, the intensity of probes in arrays passed quality control were calculated and normalized for expression value.

source_name: iPS cell line

label_protocol: WT Terminal Labeling Kit (Affymetrix.Inc)

growth_protocol: The iPS cells were cultured on mitomycin C treated MEFs in ES medium containing DMEM medium (Gibco Invitrogen, Carlsbad, CA) supplemented with 15% (v/v) fetal bovine serum (FBS), 1 mM L-glutamine, 0.1 mM mercaptoethanol, 1% nonessential amino acid stock, and 1000 U/ml LIF. The TSKM 2nd induction cells were deriven from TSKM iPS mice and cultured with Feeder Medium for 3 passages. On passages 4 the culture were changed to ES Medium with doxycycline for 3 days.

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

treatment_protocol: The cells were cultured until the appropriate stage. The culture medium were threw out and washed with PBS. The cells were  centrifuge dissociated by 0.05% trypsin EDTA.The ESCs were added 2-folds-volume ESM and dissociated to single cells. The cell suspension were plated in new dished for 0.5hr(37℃) to clear away the feeder cells. The supernatant supension were further collected carefully and centrifuged for RNA extraction. The fibroblasts were centrifuged to collect the cells and treated with centrifuge centrifuged and treated with Trizol (Invirtrogen).

value: Tet1 Sox2 Klf4 and c-Myc inducted iPS cells (derived driven from TSKM 2nd reprogramming system with full pluripotency)

tag: stage or passages

tag: strain


title: LC705_6h_sample1

description: Primary macrophages stimulated with Lactobacillus rhamnosus LC705 6h, first pool of macrophages from six healthy humans


title: Control_24h_sample1

description: Primary macrophages stimulated with control medium 24h, first pool of macrophages from six healthy humans


title: LGG_6h_sample2

description: Primary macrophages stimulated with Lactobacillus rhamnosus GG 6h, second pool of macrophages from six healthy humans


title: Control_6h_sample1

description: Primary macrophages stimulated with control medium 6h, first pool of macrophages from six healthy humans

source_name: Primary macrophage, unstimulated, 6h


title: iPS cell line rep2


title: JURKAT_shSTAT1#3_dup2

city: Boston

first: Takaomi

last: Sanda

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

hyb_protocol: Standard Affymetrix 3' array hybridyzation protocol.

scan_protocol: Standard Affymetrix confocal laser scanner protocol.

data_processing: The data was normalized and analyzed by dChip software.

label: Biotin

source_name: T-ALL cell line, shSTAT1

label_protocol: Standard Affymetrix biotin label protocol.

growth_protocol: JURKAT cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol: After 72 hours of infection, total RNA was harvested by Trizol, followed by a column purification using the RNeasy Mini kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: JURKAT cells were infected with lentivirus encoding shRNA. The infected cells were selected by puromycin.

value: Jurkat

value: T-ALL cell line

tag: shRNA


title: JURKAT_shSTAT1#2_dup1

tag: cell line


title: Control_6h_sample2

description: Primary macrophages stimulated with control medium 6h, second pool of macrophages from six healthy humans


title: Control_6h_sample3

description: Primary macrophages stimulated with control medium 6h, third pool of macrophages from six healthy humans


title: LGG_24h_sample1

description: Primary macrophages stimulated with Lactobacillus rhamnosus GG 24h, first pool of macrophages from six healthy humans


title: JURKAT_shSTAT1#2_dup2


title: JURKAT_shSTAT1#3_dup1


title: iPS cell line rep1


title: JURKAT_shTYK2#3_dup2

source_name: T-ALL cell line, shTYK2


title: JURKAT_shTYK2#2_dup1


title: Day_9

type: genomic

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII and MspI signals are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167). After intra-array normalization each channel was centered by subtracting background noise (2.5 median absolute deviations from the median of the random probes’ log2 signal for that channel) from its log2-transformed signal intensities. The HpaII/MspI (unmethylated/reference) ratio was then determined for each probe set on array.

molecule: genomic DNA

source_name: reprogrammed somatic cells

label_protocol: Random 9-mers pre-labeled with either Cy3 or Cy5

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

value: in vitro reprogrammed somatic cells

tag: restriction enzyme

value: MspI

value: day 9

value: HpaII


title: TSKM-3D cells (intermediate stage) rep1

source_name: TSKM-3D cells (intermediate stage)

value: TSKM-iPS mouse derived fibroblast cells (3-days induced)

value: p4  supply with doxycycline for 3 days


title: fibroblast cell line rep1

source_name: fibroblast cell line

value: TSKM-iPS mouse derived fibroblast


title: Day_0

value: day 0


title: JURKAT_shGFP_dup2

source_name: T-ALL cell line, shGFP control

value: shGFP


title: fibroblast cell line rep2


title: JURKAT_shLuc_dup2

source_name: T-ALL cell line, shLuc control

value: shLuc


title: JURKAT_shTYK2#3_dup1


title: fibroblast cell line rep3


title: strain B6 PAM stimulations at 2 hours, repeat 1

status: Public on Mar 17 2013

city: Tel-Aviv

first: Irit

last: Gat Viks

address: Department of Cell Research and Immunology

department: Cell Research and Immunology

country: Israel

institute: Tel-Aviv University

hyb_protocol: Standard Affymetrix protocols for mouse ht arrays

data_processing: RMA algorithm was applied using the ExpressionFileCreator procedure (version 11) in the GenePattern software (http://genepattern.broadinstitute.org/gp).

source_name: B6 PAM stimulations at 2 hrs

growth_protocol: mouse primary BMDCs (Gat-Viks et al. 2012)

extract_protocol: miRNEASY (QIAGEN) as recommended by manufactor

tag: age

value: 12 weeks

value: primary bone marrow dendritic cell


title: TSKM-3D cells (intermediate stage) rep3


title: Day_6

value: day 6


title: strain B6 poly IC stimulations at 2 hours, repeat 1

scan_protocol: Standard Affymetrix protocols for mouse ht arrays

source_name: B6 poly IC stimulations at 2 hrs


title: TSKM-3D cells (intermediate stage) rep2


title: JURKAT_shLuc_dup1


title: iPSC

value: iPSC


title: strain D2 PAM stimulations at 2 hours, repeat 1

source_name: D2 PAM stimulations at 2 hrs

label_protocol: Standard Affymetrix protocols for mouse ht arrays


title: JURKAT_shGFP_dup1


title: JURKAT_shTYK2#2_dup2


title: Day_3

value: day 3


title: strain D2 poly IC stimulations at 2 hours, repeat 1

source_name: D2 poly IC stimulations at 2 hrs


title: strain D2 PAM stimulations at 6 hours

source_name: D2 PAM stimulations at 6 hrs


title: strain BXD28 LPS stimulations at 6 hours, repeat 2

source_name: BXD28 LPS stimulations at 6 hrs


title: strain BXD40 LPS stimulations at 6 hours, repeat 2

source_name: BXD40 LPS stimulations at 6 hrs


title: strain B6 PAM stimulations at 6 hours

source_name: B6 PAM stimulations at 6 hrs


title: strain D2 poly IC stimulations at 6 hours

source_name: D2 poly IC stimulations at 6 hrs


title: strain D2 no stimulations repeat 2

source_name: D2 no stimulations


title: strain BXD5 LPS stimulations at 6 hours, repeat 2

source_name: BXD5 LPS stimulations at 6 hrs


title: strain D2 LPS stimulations at 2 hours, repeat 1

source_name: D2 LPS stimulations at 2 hrs


title: strain BXD40 LPS stimulations at 6 hours, repeat 1


title: strain BXD16 LPS stimulations at 6 hours, repeat 1

source_name: BXD16 LPS stimulations at 6 hrs


title: strain B6 LPS stimulations at 2 hours, repeat 1

source_name: B6 LPS stimulations at 2 hrs


title: strain B6 no stimulations repeat 2

source_name: B6 no stimulations


title: DMSO

city: Berkeley

first: Wenjun

last: Shao

state: CA

address: 2151 Berkeley Way

department: Molecular and Cell Biology

institute: University of California

description: cDNA

hyb_protocol: Slides were hybridized using Nimblegen's standard protocol.

scan_protocol: Nimblegen slides were scanned on an Axon Gene Pix 4200A scanner with 100% gain

data_processing: Slides were analyzed with Nimblescan, with no local alignment and a border value of -1. Data from potentially cross-hybridizing probes (matching at 50 or more of 60 nucleotides to a second location in the genome) was removed.

label: Alexa 555

organism: Shewanella oneidensis MR-1

source_name: MR-1 grown in minimal lactate medium anaerobically with dimethyl sulfoxide as the electron acceptor

label_protocol: First-strand cDNA was synthesized with random hexamer primers using SuperScript indirect cDNA labeling system (Invitrogen); the reaction buffer was supplemented with actinomycin D to inhibit second-strand synthesis.  First-strand cDNA was labeled with Alexa 555.  About 2 ug of labeled first-strand cDNA was hybridized to the array. For the genomic control, we used DNA from cells in stationary phase to minimize copy number variation across the chromosome.  Genomic DNA was extracted using the DNeasy blood tissue kit (Qiagen) and labeled with Nimblegen's comparative genomic hybridization protocol. Briefly, genomic DNA was sonicated to 200-1000 bp and amplified using Klenow fragment and Cy3-labeled random nonamer primers.

growth_protocol: MR1 were grown at 30oC anaerobially till mid exponential phase

extract_protocol: Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 oC in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyzer; only samples with an RNA integrity number of around 8 or better were used.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads coated with oligonucleotides that hybridize to ribosomal RNA.

treatment_protocol: Bacteria were harvested at OD600nm~0.4 by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes

tag: treatment

tag: media

value: 20 mM D,L-lactate, 30 mM PIPES, salts (1.5 g/L NH4Cl, 0.1 g/L KCl, 1.75 g/L NaCl, 0.61 g/L MgCl2.6H20, 0.6 g/L NaH2PO4, Wolfe's vitamins, and Wolfe's minerals, at pH 7; 20mM dimethyl sulfoxide


title: strain D2 no stimulations repeat 1


title: Genomic

source_name: MR-1 grown in rich LB medium

growth_protocol: MR1 were grown at 30oC aerobically till stationary phase

treatment_protocol: Bacteria were harvested at OD600nm~4.0 by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes

value: grown in rich LB medium

value: Luria-Bertani broth (LB)


title: strain BXD16 LPS stimulations at 6 hours, repeat 2


title: strain BXD14 LPS stimulations at 6 hours, repeat 1

source_name: BXD14 LPS stimulations at 6 hrs


title: FE

description: cDNA

source_name: MR-1 grown in minimal lactate medium anaerobically with iron (III) citrate as the electron acceptor

value: 20 mM D,L-lactate, 30 mM PIPES, salts (1.5 g/L NH4Cl, 0.1 g/L KCl, 1.75 g/L NaCl, 0.61 g/L MgCl2.6H20, 0.6 g/L NaH2PO4, Wolfe's vitamins, and Wolfe's minerals, at pH 7; 10mM iron (III) citrate


title: HS

description: cDNA

source_name: MR-1 heat shocked for 10 minutes at 42 oC.

growth_protocol: MR1 were grown at 30oC aerobically till mid exponential phase

treatment_protocol: Bacteria were obtained at OD600nm~0.7 and incubated at 42oC for 10min, then harvested by centrifuging cultures for 10 minutes at 10,000 g at 4oC in RNAse free 50ml polypropylene tubes

value: heat shocked for 10 minutes at 42 oC in LB medium


title: strain BXD14 LPS stimulations at 6 hours, repeat 2


title: strain BXD5 LPS stimulations at 6 hours, repeat 1


title: strain BXD2 LPS stimulations at 6 hours, repeat 2

source_name: BXD2 LPS stimulations at 6 hrs


title: strain BXD2 LPS stimulations at 6 hours, repeat 1


title: strain B6 LPS stimulations at 6 hours, repeat 1

source_name: B6 LPS stimulations at 6 hrs


title: Total mammary epithelial cells_nulliparous_biological replicate 4

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidiscs protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affzmetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader

data_processing: Arrays were normalized and probeset-level expression values were calculated with R/Bioconductor's (v2.15) 'affy' package using the justRMA() function.

source_name: 4th mammary glands from 5 virgin mice

label_protocol: 100ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: Mice were maintained according to the national guidelines.

extract_protocol: The 4th mammary glands from parous and age-matched virgin control mice were collected, digested to single cells and enriched for mammary epithelial cells.

treatment_protocol: Mice were mated when 42 days old, allowed to undergo normal pregnancy, and 21 and 28 days were allocated for lactation and mammary gland involution, respectively.

tag: reproductive history

value: Age-matched virgins


title: Total mammary epithelial cells_nulliparous_biological replicate 1


title: Luminal CD24+High Sca1+_nulliparous_biological replicate 3

description: 10000 cells

label_protocol: total RNA from FACS sorted cells (2000 or 10000 depending on sample) was amplified using the NuGEN Ovation Pico WTA System (NuGEN # 3300). 3ug of the the resulting SPIA amplified cDNA was processed with the NuGEN WT-Ovation Exon Module. 5.5ug of the resulting ssDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

extract_protocol: The 4th mammary glands from parous and age-matched virgin control mice were collected, digested to single cells and FACS-sorted into distinct mammary cell subpopulations.

treatment_protocol: Mice were mated when 42 days old, allowed to undergo normal pregnancy and 21 and 40 days were allocated for lactation and mammary gland involution, respectively.

value: Luminal CD24+High Sca1+_nulliparous

tag: biological replicate


title: Total mammary epithelial cells_parous_biological replicate 2

source_name: 4th mammary glands from 5 parous mice

value: Total mammary epithelial cells_parous

value: Parous


title: Basal CD24+Low Sca1- CD49fHigh_nulliparous_biological replicate 2

description: 2000 cells


title: Basal CD24+Low Sca1- CD49fHigh_nulliparous_biological replicate 3

description: 2000 cells


title: Total mammary epithelial cells_nulliparous_biological replicate 3


title: Basal CD24+Low Sca1- CD49fHigh_nulliparous_biological replicate 1

description: 2000 cells


title: Total mammary epithelial cells_parous_biological replicate 4


title: Total mammary epithelial cells_parous_biological replicate 3


title: Basal CD24+Low Sca1- CD49fLow_nulliparous_biological replicate 2

description: 10000 cells


title: Total mammary epithelial cells_parous_biological replicate 1


title: Basal CD24+Low Sca1- CD49fLow_nulliparous_biological replicate 1

description: 10000 cells


title: strain B6 LPS stimulations at 6 hours, repeat 2


title: Basal CD24+Low Sca1- CD49fLow_nulliparous_biological replicate 3

description: 10000 cells


title: Total mammary epithelial cells_nulliparous_biological replicate 2


title: strain D2 LPS stimulations at 6 hours, repeat 1

source_name: D2 LPS stimulations at 6 hrs


title: LB

description: cDNA

treatment_protocol: Bacteria were harvested at OD600nm~0.7 by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes


title: Epithelial cells_nulliparous_biological replicate 2

description: 10000 cells

value: Epithelial cells_nulliparous


title: Luminal CD24+High Sca1+_nulliparous_biological replicate 2

description: 10000 cells


title: Luminal CD24+High Sca1-_nulliparous_biological replicate 2

description: 10000 cells

value: Luminal CD24+High Sca1-_nulliparous


title: strain B6 poly IC stimulations at 6 hours

source_name: B6 poly IC stimulations at 6 hrs


title: Luminal CD24+High Sca1+_nulliparous_biological replicate 1

description: 10000 cells


title: Luminal CD24+High Sca1-_nulliparous_biological replicate 3

description: 10000 cells


title: Epithelial cells_nulliparous_biological replicate 3

description: 10000 cells


title: Luminal CD24+High Sca1-_nulliparous_biological replicate 1

description: 10000 cells


title: Epithelial cells_nulliparous_biological replicate 1

description: 10000 cells


title: Stromal cells_nulliparous_biological replicate 2

description: 10000 cells

value: Stromal cells_nulliparous


title: Luminal CD24+High Sca1+_parous_biological replicate 2

description: 10000 cells

value: Luminal CD24+High Sca1+_parous


title: VA-ES-BJ_Trail

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

description:
Gene expression data from VA-ES-BJ cells treated with Trail
total RNA (>200 nt)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit..

scan_protocol: Arrays were scanned in the Affymetrix GeneChip Scanner 3000 with G7 update.

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling to a target intensity of 1000 as normalization method.

source_name: epithelioid sarcoma VA-ES-BJ cells

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix 3'IVT protocol starting from 4-5 µg total RNA.

growth_protocol: Rhabdomyosarcoma (A-204) and leiomyosarcoma (SK-LMS-1) and epithelioid cell sarcoma (VA-ES-BJ) cells were maintained in modified Eagle's medium (MEM) and NEAA (non-essential amino acids) + 10% FBS (foetal bovine serum) supplemented with 1% penicillin (100 U/ml) and streptomycin (100 μg/ ml), 1% sodium pyruvate and 1% L-glutamine. The cells were cultured in a humidified atmosphere with 5% CO2 at 37°C .

extract_protocol: RNA isolation from cell lines was performed using standard acid guanidinium thiocyanate-phenolchloroform extraction procedure. Total-RNA concentration and purity of total RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).

treatment_protocol: For every drug experiment, 80 µl of 3.125 × 106 cells/ml were placed in 6-well plates containing the medium. After 24 hours, the medium was replaced and the drugs were added to each well. The cultivated soft tissue sarcoma cells were incubated with TRD (250 μmol/l) and/or TRAIL (50 ng/ml) for 6 hours.

value: epithelioid sarcoma VA-ES-BJ cells

tag: agent

value: Trail


title: Basal CD24+Low Sca1- CD49fLow_parous_biological replicate 3

description: 10000 cells

value: Basal CD24+Low Sca1- CD49fLow_parous


title: Basal CD24+Low Sca1- CD49fLow_parous_biological replicate 2

description: 10000 cells


title: VA-ES-BJ_Control

description:
Gene expression data from VA-ES-BJ cells, untreated
total RNA (>200 nt)

value: untreated


title: Stromal cells_nulliparous_biological replicate 1

description: 10000 cells


title: Stromal cells_nulliparous_biological replicate 3

description: 10000 cells


title: Luminal CD24+High Sca1+_parous_biological replicate 1

description: 10000 cells


title: Luminal CD24+High Sca1+_parous_biological replicate 3

description: 10000 cells


title: Basal CD24+Low Sca1- CD49fHigh_parous_biological replicate 2

description: 2000 cells; One replicate was excluded because it did not hybridize properly.

value: Basal CD24+Low Sca1- CD49fHigh_parous


title: Basal CD24+Low Sca1- CD49fHigh_parous_biological replicate 3

description: 2000 cells


title: Luminal CD24+High Sca1-_parous_biological replicate 2

description: 10000 cells

value: Luminal CD24+High Sca1-_parous


title: Epithelial cells_parous_biological replicate 1

description: 10000 cells

value: Epithelial cells_parous


title: SK-LMS-1_Trail

description:
Gene expression data from SK-LMS-1 cells treated with Trail
total RNA (>200 nt)

source_name: leiomyosarcoma SK-LMS-1 cells

value: leiomyosarcoma SK-LMS-1 cells


title: VA-ES-BJ_TRD

description:
Gene expression data from VA-ES-BJ cells treated with Taurolidine
total RNA (>200 nt)

value: Taurolidine


title: VA-ES-BJ_T+T

description:
Gene expression data from VA-ES-BJ cells treated with Trail and Taurolidine
total RNA (>200 nt)

value: Trail and Taurolidine


title: Luminal CD24+High Sca1-_parous_biological replicate 1

description: 10000 cells


title: Epithelial cells_parous_biological replicate 3

description: 10000 cells


title: SK-LMS-1_TRD

description:
Gene expression data from SK-LMS-1 cells treated with Taurolidine
total RNA (>200 nt)


title: SK-LMS-1_T+T

description:
Gene expression data from SK-LMS-1 cells treated with Trail and Taurolidine
total RNA (>200 nt)


title: strain BXD28 LPS stimulations at 6 hours, repeat 1

source_name: BXD28 LPS stimulations at 6 hrs

value: 12 weeks

value: primary bone marrow dendritic cell


title: A-204_Trail

description:
Gene expression data from A-204 cells treated with Trail
total RNA (>200 nt)

source_name: rhabdomyosacrcoma A-204 cells

value: rhabdomyosacrcoma A-204 cells


title: Basal CD24+Low Sca1- CD49fLow_parous_biological replicate 1

description: 10000 cells

value: Parous


title: Luminal CD24+High Sca1-_parous_biological replicate 3

description: 10000 cells


title: A-204_TRD

description:
Gene expression data from A-204 cells treated with Taurolidine
total RNA (>200 nt)


title: strain B6 no stimulations repeat 1


title: Epithelial cells_parous_biological replicate 2

description: 10000 cells


title: Stromal cells_parous_biological replicate 3

description: 10000 cells

value: Stromal cells_parous


title: Stromal cells_parous_biological replicate 1

description: 10000 cells


title: Stromal cells_parous_biological replicate 2

description: 10000 cells


title: HUVEC_Flow 10_with stent_rep2

status: Public on Mar 16 2013

city: Milan

first: Jonica

last: Campolo

state: Milan

address: Piazza Ospedale Maggiore 3

department: CardioThoraco and Vascular, Niguarda Hospital

country: Italy

institute: CNR Institute of Clinical Phisiology

description: Gene expression data from HUVEC at 10 dyne/cm2 in presence of stent

hyb_protocol: Performed by Cogentech Service

scan_protocol: Performed by Cogentech Service

data_processing: Data Analysis Software: Partek Genomic Suite 6.5; Processing Algorithm: RMA; Probeset Summarization: Median Polish

source_name: HUVEC, 10 dyne/cm2, presence of stent

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol by Cogentech Service

growth_protocol: Primary HUVEC were isolated from human cords and grown in ECGM medium (Promocell) in an incubator at 37 ºC. Every 2 days media culture was changed, until the confluence. HUVECs between 2nd and 5th passage were used for bioreactor experiments.

extract_protocol: Rneasy Micro QIAGEN extraction kit

treatment_protocol: Cells were exposed at different flow in absence or presence of stent procedure in bioreactor for 24 hours. Endothelial cells were washed with PBS and trypsinised. Viable cells were finally collected in RNA later solution (Qiagen) and frozen at -80°.

value: Human Umbelical Vein Endothelial Cell

tag: stress

value: 10 dyne/cm2

tag: stent

value: presence


title: A-204_T+T

description:
Gene expression data from A-204 cells treated with Trail and Taurolidine
total RNA (>200 nt)


title: HUVEC_Flow 5_no stent_rep2

description: Gene expression data from HUVEC at 5 dyne/cm2 in absence of stent

source_name: HUVEC, 5 dyne/cm2, absence of stent

value: 5 dyne/cm2

value: absence


title: HUVEC_Flow 10_no stent_rep2

description: Gene expression data from HUVEC at 10 dyne/cm2 in absence of stent

source_name: HUVEC, 10 dyne/cm2, absence of stent


title: HUVEC_Flow 10_with stent_rep1


title: HUVEC_Flow 1_no stent_rep2

description: Gene expression data from HUVEC at 1 dyne/cm2 in absence of stent

source_name: HUVEC, 1 dyne/cm2, absence of stent

value: 1 dyne/cm2


title: HUVEC_Flow 10_no stent_rep1


title: HUVEC_Flow 5_no stent_rep1


title: HUVEC_Flow 1_with stent_rep1

description: Gene expression data from HUVEC at 1 dyne/cm2 in presence of stent

source_name: HUVEC, 1 dyne/cm2, presence of stent


title: HUVEC_Flow 0_no stent_rep1

description: Gene expression data from HUVEC at 0 dyne/cm2 in absence of stent

source_name: HUVEC, 0 dyne/cm2, absence of stent

value: 0 dyne/cm2


title: HUVEC_Flow 1_no stent_rep1


title: HUVEC_Flow 0_no stent_rep2


title: HUVEC_Flow 1_with stent_rep2


title: A-204_Control

description:
Gene expression data from A-204 cells, untreated
total RNA (>200 nt)

value: untreated


title: sjnb6

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol

value: Neuroblastoma cell


title: sjnb1


title: sknbe

source_name: sknbe

value: sknbe


title: uhgnp

source_name: uhgnp

value: uhgnp


title: tr14


title: lan5


title: SK-LMS-1_Control

description:
Gene expression data from SK-LMS-1 cells, untreated
total RNA (>200 nt)

value: leiomyosarcoma SK-LMS-1 cells


title: lan1


title: Against CDK8 and CDK19 rep3

city: San Diego

first: Taiki

last: Tsutsui

state: California

address: 9500 Gilman Dr

department: CMM

institute: UCSD

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA using GeneSpring software. Base line was created as median of all sample.

source_name: Against CDK8 and CDK19 double transfected cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: HeLa S3 cells were seeded on 6-well plate at 4 x 104 cells per well in 2ml antibiotic free DMEM medium before 24hr transfection.

extract_protocol: RNA was prepared using RNeazy column (QIAGEN).

treatment_protocol: We transfect two siRNA against CDK8 and CDK19 at a same time using Lipofectamine 2000 (invitrogen) according to its manual and siRNA final concentration in the medium was 10nM each. After culturing for 48hr, transfection medium was changed to fresh antibiotic containing medium. Then the cells were incubated for additional 12hr

value: HeLa s3


title: sjnb8


title: Against CDK8 and CDK19 rep2


title: sjnb10


title: chp134


title: smskcnr

source_name: smskcnr

value: smskcnr


title: sgs1△ control, repeat 3

city: Taipei

first: SHIN YEN

last: CHONG

address: No. 1, Sec. 4, Roosevelt Road,

department: Institute of Food Science and Technology

country: Taiwan

institute: National Taiwan University

description:
S3_H009
Sgs1

hyb_protocol: The hybridization protocol was provided by the Phalanx Biotech Group (see http://www.onearray.com/ for protocols).

scan_protocol: The scan protocol was provided by the Phalanx Biotech Group (see http://www.onearray.com/ for protocols), and .gpr files were provided.

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. Data were analyzed and calibrated by Rosetta Resolver software. The normalized intensity is the mean of the normalized data after median normalization.

organism: Saccharomyces cerevisiae

source_name: sgs1△, control

label_protocol: The label protocol was provided by the Phalanx Biotech Group (see http://www.onearray.com/ for protocols).

extract_protocol: Total RNA were extracted following the hot-phenol process (Collart and Oliviero, 2001) and converted into cDNA.

tag: genotype/variation

value: sgs1 deletion (MATα his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 trp1∆::HPH sgs1∆::kanMX4 pRS414-GAL1-HO-TRP1)

value: trp d.o medium

tag: treatment duration

value: 4 hrs

tag: treatment protocol

value: Cells were grown in trp d.o medium 4h at 30˚C with 0.2% v/v DMSO.


title: imr32

tag: cell type


title: n206