title: wild-type_TM-Fe_60min_3

city: Fukuoka

first: Yasuhiro

last: Fujino

address: Higashiku hakozaki 6-10-1

institute: Kyushu-univ.

description: wild-type strain grown on a TM medium 8 hrs, and removal of Fe 1 hr

hyb_protocol: 3'-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401a520105F GeneChip (Affymetrix, Santa Clara, CA). The array was incubated for 16 h at 50°C in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 20 micro g of herring sperm DNA (Promega), 0.1 mg of bovine serum albumin (BSA), the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix), and then the array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

data_processing: The expression levels were summarized by MAS5 algorithm using Expressino Console Software (Affymetrix, Santa Clara, CA).

organism: Thermus thermophilus HB8

source_name: T. thermophilus HB8, wild-type, TM medium 8 hrs, 1 hr after removal of Fe, biological rep3

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen). The cDNA was fragmented with 1.2 units of DNase I (GE Healthcare Bio-Science Corp.) at 37°C for 10 min, and after inactivation at 98°C for 10 min, the cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturers instructions (Affymetrix).

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TM broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.60).

extract_protocol: Cells were collected from 50 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

treatment_protocol: 600 ppm of silicic acid was added into the medium or removal of iron, and continued cultivation for 60 min.

value: wild-type T. thermophilus HB8

tag: treatment

value: removal of Fe 1hr


title: wild-type_TM+Si_60min_1

status: Public on May 14 2013

type: RNA

country: Japan

description: wild-type strain grown on a TM medium 8 hrs, and addition of 600 ppm SiO2 1 hr

scan_protocol: 3'-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401a520105F GeneChip (Affymetrix, Santa Clara, CA). The array was incubated for 16 h at 50°C in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 20 micro g of herring sperm DNA (Promega), 0.1 mg of bovine serum albumin (BSA), the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix), and then the array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

label: biotin

molecule: total RNA

source_name: T. thermophilus HB8, wild-type, TM medium 8 hrs, 1 hr after addition of 600 ppm SiO2, biological rep1

tag: strain

value: addition of 600 ppm SiO2 1hr


title: wild-type_TM-Fe_60min_1

source_name: T. thermophilus HB8, wild-type, TM medium 8 hrs, 1 hr after removal of Fe, biological rep1


title: ERKO control 1

city: Dublin 2

first: Harry

middle: Myles

last: Harvey

address: York Street

country: Ireland

institute: Royal COllege of Surgeons in Ireland

description: Gene expression data from ERKO mouse livers treated with Oil

hyb_protocol: Microarray facility at the UC-Irvine.

scan_protocol: Microarray facility at the UC-Irvine.

data_processing:
CyberT program was used by the UC-Irvine array facility to identify differences from the various treatments
The array data was analyzed using the bayesian / Cyber-T algorithm. Genes with a bayes p-value of < 0.001, a posterior probability of differential expression (PPDE) > 0.99 and a minimum 2-fold change in expression were considered differentially expressed.

organism: Mus musculus

source_name: Liver, Oil placebo 0.1ml for 3 days

label_protocol: Microarray facility at the UC-Irvine.

growth_protocol: Wild type, ERalpha KO, and membrane ERalpha only mice were ovariectomized, recovered for 1 week, then injected with an ERalpha agonist, PPT 100 micrograms each day for 3 days. The mice were then sacrificed and the livers removed for obtaining RNA

extract_protocol: Snap frozen dissected whole liver was ground to a fine powder and total RNA was extracted and used for qRT-PCR analysis and Affymetrix DNA microarray analysis. cDNA was synthesized using approximately 500ng RNA and Oligo dT primers with the Improm-II reverse transcription system (Promega) for qRT-PCR or converted to cRNA for microarray.  The RNA from three animals was pooled for each treatment type and each mouse type for microarray analysis, the study repeated a second time. For each pooled sample, mouse DNA microarray using the Affymetrix mouse gene 1.0ST chip was run at the Microarray facility at the UC-Irvine. The array data was analyzed using the Cyber T program at a confidence interval of 99.99% and a minimum of a two-fold change was considered significant. The software David (33) was used to determine mRNA targets changed only following PPT treatment in both wild type and MOER mice and not in ERKO.

treatment_protocol: As described immediately above

tag: tissue

value: Liver

tag: genotype/variation

value: ERKO


title: wild-type_TM+Si_60min_2

source_name: T. thermophilus HB8, wild-type, TM medium 8 hrs, 1 hr after addition of 600 ppm SiO2, biological rep2


title: wild-type_TM_60min_1

description: wild-type strain grown on a TM medium 9 hrs

source_name: T. thermophilus HB8, wild-type, TM medium 9 hrs, biological rep1

value: TM medium 1hr


title: MOER control 2

description: Gene expression data from MOER mouse livers treated with Oil

value: MOER


title: wild-type_TM-Fe_60min_2

source_name: T. thermophilus HB8, wild-type, TM medium 8 hrs, 1 hr after removal of Fe, biological rep2


title: Hippocampus, Tg2576-APPSwe mice, 18 month-old, ACE inhibitor-treated-rep2

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description: Gene expression data of hippocampi isolated from 18 month-old Tg2576 (APPSwe-transgenic) AD mice treated for 6 months with the brain-penetrating ACE inhibitor captopril

hyb_protocol: For hybridization, 15 µg of fragmented, biotin-labeled cRNA were incubated with the chip (Mouse Genome MG430 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual.

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

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 600.

source_name: Hippocampi isolated from 18 month-old Tg2576 APPSwe-transgenic mice treated for 6 months with the brain-penetrating ACE inhibitor captopril

label_protocol: Biotin-labeled cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual; Rev.3).

growth_protocol: The study was performed with 18 month-old Tg2576 (APPSwe-transgenic) AD mice treated for six months without or with the brain-penetrating ACE inhibitor, captopril. Mice had free access to food and water, and were fed a standard rodent chow. The treatment group of Tg2576 mice received the centrally active ACE inhibitor, captopril (20 mg/kg/day supplied in drinking water) for 6 months. The control group of Tg2576 mice received drinking water without captopril. At an age of 18 months, hippocampi were isolated from Tg2576 mice treated without or with captopril for six months. As an additional control group, hippocampi were isolated from 12 month-old untreated Tg2576 mice with low Abeta plaque load, reflecting the time point when treatment with captopril was initiated.

extract_protocol: Total hippocampal RNA was isolated with the RNeasy Mini kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: The study was performed with hippocampi isolated from three groups of mice, i.e. (i) untreated 18 month-old Tg2576 (APPSwe-transgenic) AD mice with high Abeta plaque load (APP-18 mo), (ii) 18 month-old Tg2576 (APPSwe-transgenic) AD mice treated for 6 months with the brain-penetrating ACE inhibitor, captopril (20mg/kg/day in drinking water; APP-18mo-ACEI), and (iii) untreated 12 month-old Tg2576 (APPSwe-transgenic) AD mice with low Abeta plaque load (APP-12mo).

value: Hippocampi

tag: Sex

value: male

tag: age

value: 18 months old

tag: genotype/variations

value: Tg2576 APPSwe-transgenic mice


title: wild-type_TM_60min_3

source_name: T. thermophilus HB8, wild-type, TM medium 9 hrs, biological rep3


title: wild-type_TM+Si_60min_3

source_name: T. thermophilus HB8, wild-type, TM medium 8 hrs, 1 hr after addition of 600 ppm SiO2, biological rep3


title: Hippocampus, Tg2576-APPSwe mice, 18 month-old, with high Abeta plaque load-rep2

description: Gene expression data of hippocampi isolated from 18 month-old untreated Tg2576 (APPSwe-transgenic) AD mice with high Abeta plaque load

source_name: Hippocampi isolated from 18 month-old Tg2576 APPSwe-transgenic mice with high Abeta plaque load


title: MOER control 1


title: LVEDV increase between discharge and follow-up patient pool 4

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

hyb_protocol: labeled miRNA was hybridized onto Agilent's Human miRNA Microarrays V3, Release 12.0 (P/N G4471A, AMADID 021827) annotated against the Sanger miRBASE 12.0 database of miRNAs. according to the manufacturer's instructions.

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner

data_processing: The scanned images were analyzed with GenePix Pro 6.0 analysis software using default parameters to obtain background subtracted signal intensities. The data was normalized with quantile method using R Limma package.

organism: Homo sapiens

source_name: LVEDV increase patient pool

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from total RNA of 400µL plasma using Agilent miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions

extract_protocol: mirVana Ambion

tag: sample type

value: plasma

tag: outcome

value: acute myocardial infarction followed by ventricular end diastolic volume increase between discharge and follow-up


title: ERKO experimental 2

description: Gene expression data from ERKO mouse livers treated with PPT

source_name: Liver, PPT (100microgram for 3 days)


title: Wildtype control 1

description: Gene expression data from WildType mouse livers treated with Oil

value: wild type


title: LVEDV increase between discharge and follow-up patient pool 3


title: Hippocampus, Tg2576-APPSwe mice, 12 month-old, with low Abeta plaque load-rep1

description: Gene expression data of hippocampi isolated from 12 month-old untreated Tg2576 (APPSwe-transgenic) AD mice with low Abeta plaque load

source_name: Hippocampi isolated from 12 month-old Tg2576 APPSwe-transgenic mice with low Abeta plaque load

value: 12 months old


title: Wildtype experimental 2

description: Gene expression data from WildType mouse livers treated with PPT


title: wild-type_TM_60min_2

source_name: T. thermophilus HB8, wild-type, TM medium 9 hrs, biological rep2


title: LVEDV increase between discharge and follow-up patient pool 2


title: Hippocampus, Tg2576-APPSwe mice, 18 month-old, ACE inhibitor-treated-rep1


title: ERKO experimental 1


title: Wildtype experimental 1


title: Wildtype control 2


title: Hippocampus, Tg2576-APPSwe mice, 18 month-old, with high Abeta plaque load-rep1


title: ERKO control 2


title: LVEDV increase between discharge and follow-up patient pool 1


title: LVEDV decrease between discharge and follow-up patient pool 3

source_name: LVEDV decrease patient pool

value: acute myocardial infarction followed by ventricular end diastolic volume decrease between discharge and follow-up


title: LVEDV decrease between discharge and follow-up patient pool 2


title: LVEDV decrease between discharge and follow-up patient pool 1


title: LVEDV decrease between discharge and follow-up patient pool 4


title: Treatment with 004 µg/ml VCR for 4h, experiment 3

status: Public on May 13 2013

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

hyb_protocol: GeneChip Fluidics Station 450 was used for washing according to Affymetrix protocol.

scan_protocol: GeneChip Scanner 3000 was used for scanning according to Affymetrix protocol.

data_processing: BRB Array Tools. RMA algorithm.

source_name: TK6, 004 µg/ml VCR, 4h

label_protocol: One Cycle Target Labelling Protocol.

extract_protocol: Extraction was performed using RNeasy Mini Kits.

tag: cell line

value: 4 µg/ml vincristine

tag: treatment duration


title: Treatment with 001 µg/ml VCR for 4h, experiment 3

source_name: TK6, 001 µg/ml VCR, 4h

value: 1 µg/ml vincristine


title: Treatment with 002 µg/ml VCR for 4h, experiment 3

source_name: TK6, 002 µg/ml VCR, 4h

value: 2 µg/ml vincristine


title: Untreated Control, 24h, VCR experiment 2

source_name: TK6, untreated, 24h


title: Treatment with 004 µg/ml VCR for 24h, experiment 3

source_name: TK6, 004 µg/ml VCR, 24h


title: Treatment with 002 µg/ml VCR for 4h, experiment 2


title: Treatment with 001 µg/ml VCR for 24h, experiment 3

source_name: TK6, 001 µg/ml VCR, 24h


title: Treatment with 004 µg/ml VCR for 4h, experiment 2


title: Untreated Control, 4h, VCR experiment 3

source_name: TK6, untreated, 4h


title: Treatment with 004 µg/ml VCR for 24h, experiment 1


title: Treatment with 001 µg/ml VCR for 4h, experiment 2


title: Treatment with 004 µg/ml VCR for 24h, experiment 2


title: Untreated Control, 4h, VCR experiment 1


title: Treatment with 001 µg/ml VCR for 24h, experiment 2


title: Treatment with 004 µg/ml VCR for 4h, experiment 1


title: Untreated Control, 24h, VCR experiment 1


title: Untreated Control, 4h, VCR experiment 2


title: Untreated Control, 24h, VCR experiment 3


title: Treatment with 002 µg/ml VCR for 24h, experiment 2

source_name: TK6, 002 µg/ml VCR, 24h


title: Treatment with 002 µg/ml VCR for 24h, experiment 1


title: Treatment with 002 µg/ml VCR for 24h, experiment 3


title: Treatment with 001 µg/ml VCR for 24h, experiment 1


title: Treatment with 002 µg/ml VCR for 4h, experiment 1


title: Treatment with 001 µg/ml VCR for 4h, experiment 1


title: Untreated Control, 4h, COL experiment 3


title: Treatment with 004 µg/ml COL for 24h, experiment 3

source_name: TK6, 004 µg/ml COL, 24h

value: 4 µg/ml colcemid


title: Untreated Control, 24h, COL experiment 3


title: Treatment with 002 µg/ml COL for 4h, experiment 3

source_name: TK6, 002 µg/ml COL, 4h

value: 2 µg/ml colcemid


title: Treatment with 004 µg/ml COL for 4h, experiment 3

source_name: TK6, 004 µg/ml COL, 4h


title: Treatment with 002 µg/ml COL for 24h, experiment 3

source_name: TK6, 002 µg/ml COL, 24h


title: Untreated Control, 4h, COL experiment 2


title: Treatment with 001 µg/ml COL for 4h, experiment 3

source_name: TK6, 001 µg/ml COL, 4h

value: 1 µg/ml colcemid


title: Treatment with 004 µg/ml COL for 24h, experiment 2


title: Treatment with 004 µg/ml COL for 4h, experiment 2


title: Treatment with 001 µg/ml COL for 24h, experiment 3

source_name: TK6, 001 µg/ml COL, 24h


title: Treatment with 002 µg/ml COL for 24h, experiment 2


title: cnf1-hlyA1- 2D

city: Bethesda

first: Douglas Scott

last: Merrell

state: MD

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

country: USA

institute: Uniformed Services University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89574.gif

hyb_protocol: not provided

scan_protocol: Scanner model: G2505C

data_processing: VALUE is Log Red/Green

source_name: 850 ng of amplified infected mouse bladder cDNA harvested 24 hours post infection

label_protocol: not provided

extract_protocol: not provided

value: bladder

tag: infection (e. coli genotype)

value: cnf1- hlyA1-

source_name: 850 ng of amplified normal mouse bladder cDNA


title: Untreated Control, 24h, COL experiment 2


title: Untreated Control, 4h, COL experiment 1


title: Treatment with 001 µg/ml COL for 4h, experiment 2


title: Treatment with 001 µg/ml COL for 24h, experiment 2


title: Treatment with 002 µg/ml COL for 4h, experiment 2


title: Untreated Control, 24h, COL experiment 1


title: Treatment with 001 µg/ml COL for 24h, experiment 1


title: Untreated Control, 24h, EMS experiment 3


title: Treatment with 002 µg/ml COL for 4h, experiment 1


title: Treatment with 002 µg/ml COL for 24h, experiment 1


title: Untreated Control, 4h, EMS experiment 3


title: Treatment with 004 µg/ml COL for 4h, experiment 1


title: Treatment with 001 µg/ml COL for 4h, experiment 1


title: cnf1-hlyA1- 1D

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89573.gif


title: cnf1-hlyA1- 4D 4/13/2010

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89578.gif


title: Treatment with 4 mM EMS for 4h, experiment 3

source_name: TK6, 4 mM EMS, 4h

value: 4 mM ethyl methanesulfonate


title: Treatment with 2 mM EMS for 24h, experiment 3

source_name: TK6, 2 mM EMS, 24h

value: 2 mM ethyl methanesulfonate


title: Treatment with 4 mM EMS for 24h, experiment 3

source_name: TK6, 4 mM EMS, 24h


title: Treatment with 1 mM EMS for 24h, experiment 3

source_name: TK6, 1 mM EMS, 24h

value: 1 mM ethyl methanesulfonate


title: cnf1-hlyA1- 5D

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89576.gif


title: Treatment with 1 mM EMS for 4h, experiment 3

source_name: TK6, 1 mM EMS, 4h


title: Treatment with 2 mM EMS for 4h, experiment 3

source_name: TK6, 2 mM EMS, 4h


title: Untreated Control, 24h, EMS experiment 2

source_name: TK6, untreated, 24h


title: Treatment with 4 mM EMS for 24h, experiment 2


title: Untreated Control, 4h, EMS experiment 2

source_name: TK6, untreated, 4h


title: Treatment with 4 mM EMS for 4h, experiment 2


title: Untreated Control, 4h, EMS experiment 1


title: Treatment with 1 mM EMS for 24h, experiment 2


title: Untreated Control, 24h, EMS experiment 1


title: Treatment with 4 mM EMS for 24h, experiment 1


title: Treatment with 2 mM EMS for 4h, experiment 2


title: cnf1-hlyA1- 3D

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89575.gif


title: Treatment with 1 mM EMS for 4h, experiment 2


title: Treatment with 2 mM EMS for 24h, experiment 2


title: cnf1-hlyA1- 7D

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89577.gif


title: Treatment with 4 mM EMS for 4h, experiment 1


title: Treatment with 2 mM EMS for 24h, experiment 1


title: Treatment with 2 mM EMS for 4h, experiment 1


title: Dnup60 Dada2 cells, biological rep3

city: Washington

first: Kristine

last: Willis

state: DC

address: 37 & O Sts. NW

department: Biology

institute: Georgetown University

description: Gene expression data from Dnup60 Dada2 cells grown in rich media to mid-log phase at 30C.

hyb_protocol: Following fragmentation, 5 ug of aRNA were hybridized for 16 hr at 45C on the Yeast Genome 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 within Expression Console 1.1 using Affymetrix default analysis settings and with RMA as the normalization method. Differential expression was assessed using Significance Analysis of Microarray (SAM) with FDR<1% and |fc|>1.5.

organism: Saccharomyces cerevisiae

source_name: cells deleted for NUP60 and ADA2 genes at mid-log phase growth in rich media

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2008-2009, Affymetrix)

growth_protocol: strains were inoculated to 50mL YEPD cultures to equal starting ODs from saturated overnights.  cultures were grown to mid-log phase, collected, washed with chilled water, and stored at -80C before RNA extraction

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, with the following modification for yeast cells: glass beads and Trizol were added to frozen cell pellets, and cells were subjected to bead beating to disrupt the cell wall.  All subsequent steps were carried out according to manufacturer's instructions.

value: MATa his3 leu2 met15 ura3 nup60Δ::KANR ada2Δ::KANR


title: Dnup60 Dada2 cells, biological rep2


title: Dnup60 Dada2 cells, biological rep1


title: Dada2 cells, biological rep1

description: Gene expression data from Dada2 cells grown in rich media to mid-log phase at 30C.

source_name: cells deleted for ADA2 gene at mid-log phase growth in rich media

value: MATa his3 leu2 met15 ura3 ada2Δ::KANR


title: Dnup60 cells, biological rep2

description: Gene expression data from Dnup60 cells grown in rich media to mid-log phase at 30C.

source_name: cells deleted for NUP60 gene at mid-log phase growth in rich media

value: MATa his3 leu2 met15 ura3 nup60Δ::KANR


title: Dnup60 cells, biological rep3


title: wildtype cells, biological rep3

description: Gene expression data from wildtype cells grown in rich media to mid-log phase at 30C.

source_name: wildtype cells at mid-log phase growth in rich media

value: MATa his3 leu2 met15 ura3


title: Dada2 cells, biological rep3


title: Dnup60 cells, biological rep1


title: Dada2 cells, biological rep2


title: Treatment with 1 mM EMS for 24h, experiment 1


title: Untreated Control, 4h, MMS experiment 3


title: Untreated Control, 24h, MMS experiment 3


title: wildtype cells, biological rep2


title: Treatment with 80 µM MMS for 24h, experiment 3

source_name: TK6, 80 µM MMS, 24h

value: 80 µM methyl methanesulfonate


title: wildtype cells, biological rep1


title: Treatment with 80 µM MMS for 4h, experiment 3

source_name: TK6, 80 µM MMS, 4h


title: Treatment with 160 µM MMS for 24h, experiment 3

source_name: TK6, 160 µM MMS, 24h

value: 160 µM methyl methanesulfonate


title: Treatment with 320 µM MMS for 24h, experiment 3

source_name: TK6, 320 µM MMS, 24h

value: 320 µM methyl methanesulfonate


title: Untreated Control, 24h, MMS experiment 2


title: Treatment with 320 µM MMS for 4h, experiment 3

source_name: TK6, 320 µM MMS, 4h


title: IPA_40_1

city: Yokohama

first: Akane

last: Misaizu

address: 1-13-5 Fukuura kanazawa-ku

institute: Kirin Holdings Company, Limited

description:
IPA_005
Gene expression after 3hr incubation in YPD with 40 mg/l IPA

hyb_protocol: The cRNA was subsequently treated with “Gene Expression Hybridization Kit (Agilent Technologies),” followed by the hybridization of the prepared samples to “Yeast (V2) Gene Expression Microarray 8x15K (Agilent Technologies)” for 17 h at 65°C.  The microarray was then washed in “Gene Expression Wash Buffer 1 and 2 (Agilent Technologies)”.

scan_protocol: Slide was scanned using DNA microarray scanner (Model G2565BA, Agilent Technologies).

data_processing:
The data was quantified using software “Feature Extraction ver.9 (Agilent Technologies)”.  The obtained data was analyzed using GeneSpring GX 11 software (Agilent Technologies).
In order to performed inter-array comparison, the 75th percentile signal value was used to normalize the one-color microarray signals.

source_name: IPA_40 g/l

label_protocol: The total RNA was applied for the synthesis of complementary RNA (cRNA), which was labelled with Cyanine3, using “Quick Amp Labeling Kit (Agilent Technologies)”. The procedure was conducted with a systems provided by Agilent Technologies (Santa Clara, CA) according to the manufacture’s instruction.

growth_protocol: The prepared cells were inoculated into 120 ml of fresh media (YPD without isopropanol, and YPD with 40 g/l of isopropanol) in 500-ml Sakaguchi-flasks.

extract_protocol: The cells were harvested by centrifugation at 3,000 × g for 5 min at 4°C, and the total RNA was extracted using RNeasy Mini kit (QIAGEN GmbH., Hilden, Germany) following the manufacturer's recommendations.

treatment_protocol: Cultivation for 3 h at 30°C with 130-rpm shaking.

tag: isopropanol concentration


title: IPA_40_4

description:
IPA_008
Gene expression after 3hr incubation in YPD with 40 mg/l IPA


title: IPA_40_3

description:
IPA_007
Gene expression after 3hr incubation in YPD with 40 mg/l IPA


title: IPA_40_2

description:
IPA_006
Gene expression after 3hr incubation in YPD with 40 mg/l IPA


title: Treatment with 160 µM MMS for 4h, experiment 3

source_name: TK6, 160 µM MMS, 4h


title: IPA_0_3

description:
IPA_003
Gene expression after 3hr incubation in IPA free YPD

source_name: IPA_0 g/l

value: 0 g/l


title: IPA_0_4

description:
IPA_004
Gene expression after 3hr incubation in IPA free YPD


title: Treatment with 004 µg/ml COL for 24h, experiment 1

source_name: TK6, 004 µg/ml COL, 24h


title: IPA_0_1

description:
IPA_001
Gene expression after 3hr incubation in IPA free YPD


title: Treatment with 160 µM MMS for 24h, experiment 2


title: Treatment with 1 mM EMS for 4h, experiment 1

source_name: TK6, 1 mM EMS, 4h


title: IPA_0_2

description:
IPA_002
Gene expression after 3hr incubation in IPA free YPD


title: Treatment with 320 µM MMS for 24h, experiment 2


title: Naive-3

city: Taipei

first: Kung-Hao

last: Liang

address: Tung Hwa North Road

country: Taiwan

institute: Chang Gung Memorial Hospital

description:
12S219U033
Gene expression data upon transfections.

hyb_protocol: Standard Affymetrix protocol. Affymetrix Human PrimeView arrays were used (Affymetrix, Santa Clara, CA).

scan_protocol: Standard Affymetrix protocol. Fluorescent signal was scanned by GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA) to produce digital images and then converted and summarized to intensity readings per probe sets.

data_processing: The entire set of 18 microarrays were normalized by the RMA algorithm using the RMAExpress software.

source_name: Naive

label_protocol: Standard Affymetrix protocol. An in vitro transcription (IVT) with biotinylated ribonucleotide analog was performed to generate biotin-labeled amplified RNA (aRNA) using the GeneChip 3' IVT Express kit (Affymetrix, Santa Clara, CA). The aRNAs were then purified by magnetic beads and fragmented for the subsequent hybridization according to the manufacturer's protocol.

growth_protocol: Maintained in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% fetal bovine serum and 250 ug of G418 per ml.

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

treatment_protocol: Transfection with null pDR2 vector or pDR2-Alu vector, cultured with Hygromycin selection, then some samples were further cultured without Hygromycin.

tag: cell type

value: human embryonic kidney cells

tag: vector transfection


title: Untreated Control, 4h, MMS experiment 2


title: pDR2-sense-Alu_Hygromycin_added->removed-1

description:
12S219U023
Gene expression data upon transfections.

tag: hygromycin treatment

value: added, then removed


title: Naive-1

description:
12S219U034
Gene expression data upon transfections.


title: pDR2-sense-Alu_Hygromycin_added->removed-2

description:
12S219U019
Gene expression data upon transfections.


title: pDR2-sense-Alu_Hygromycin_added->removed-3

description:
12S219U021
Gene expression data upon transfections.


title: pDR2-sense-Alu_Hygromycin_added-2

description:
12S219U018
Gene expression data upon transfections.

value: added


title: Treatment with 80 µM MMS for 24h, experiment 2


title: Naive-2

description:
12S219U035
Gene expression data upon transfections.


title: pDR2-sense-Alu_Hygromycin_added-1

description:
12S219U022
Gene expression data upon transfections.


title: pDR2-anti-Alu_Hygromycin_added->removed-3

description:
12S219U027
Gene expression data upon transfections.


title: pDR2-sense-Alu_Hygromycin_added-3

description:
12S219U020
Gene expression data upon transfections.


title: pDR2-anti-Alu_Hygromycin_added->removed-2

description:
12S219U025
Gene expression data upon transfections.


title: Treatment with 160 µM MMS for 4h, experiment 2


title: pDR2-anti-Alu_Hygromycin_added->removed-1

description:
12S219U029
Gene expression data upon transfections.


title: pDR2-anti-Alu_Hygromycin_added-1

description:
12S219U028
Gene expression data upon transfections.


title: pDR2-anti-Alu_Hygromycin_added-2

description:
12S219U024
Gene expression data upon transfections.


title: Treatment with 80 µM MMS for 4h, experiment 2


title: Untreated Control, 4h, MMS experiment 1


title: pDR2-2

description:
12S219U038
Gene expression data upon transfections.


title: Untreated Control, 24h, MMS experiment 1

source_name: TK6, untreated, 24h


title: Treatment with 320 µM MMS for 24h, experiment 1


title: Treatment with 320 µM MMS for 4h, experiment 2


title: pDR2-1

description:
12S219U036
Gene expression data upon transfections.


title: Treatment with 320 µM MMS for 4h, experiment 1


title: pDR2-3

description:
12S219U037
Gene expression data upon transfections.


title: pDR2-anti-Alu_Hygromycin_added-3

description:
12S219U026
Gene expression data upon transfections.


title: Treatment with 160 µM MMS for 24h, experiment 1


title: Untreated Control, 24h, FA experiment 3


title: Treatment with 80 µM MMS for 24h, experiment 1


title: Treatment with 160 µM MMS for 4h, experiment 1


title: Untreated Control, 4h, FA experiment 3

source_name: TK6, untreated, 4h


title: Treatment with 80 µM MMS for 4h, experiment 1


title: Treatment with 200 µM FA for 24h, experiment 3

value: 200 µM formaldehyde


title: Treatment with 200 µM FA for 4h, experiment 3

source_name: TK6, 200 µM FA, 4h


title: Treatment with 100 µM FA for 24h, experiment 3

value: 100 µM formaldehyde


title: Treatment with 100 µM FA for 4h, experiment 3

source_name: TK6, 100 µM FA, 4h


title: A6322 iPSC / iGP91-05-1

type: genomic

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

hyb_protocol: Illumina infinium assay

scan_protocol: Illumina HiScan-SQ

data_processing: GenomeStudio version 2011.1, exported Beta values without backround subtraction or normalization.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: X-CGD iPSC derived from reprogrammed CD34+ cells

label_protocol: Illumina infinium assay

growth_protocol: Hematopoietic Stem Cell media, iPSC media

extract_protocol: QIAamp DNA Mini Kit was used for genomic DNA purification,500 ng of genomic DNA (picoGreen-quantified) was bisulfite-converted (EZ DNA methylation kit; Zymo Research)

treatment_protocol: untreated media

value: iPSC


title: A6321 iPSC / iGP91-04-1


title: Treatment with 50 µM FA for 4h, experiment 3

source_name: TK6, 50 µM FA, 4h

value: 50 µM formaldehyde


title: Treatment with 50 µM FA for 24h, experiment 3

source_name: TK6, 50 µM FA, 24h


title: A6320 iPSC / iGP91-03-2


title: A6319 iPSC / iGP91-03-1


title: A6318 ESC / H1

source_name: ESC

value: ESC


title: A6326 PBMC

source_name: Uncultured peripheral blood mononuclear cells

value: PBMC


title: A6324 iPSC / iGP91-05-3


title: A6121 iPSC / iGP91-01


title: A6120 iPSC/ iP47-02

source_name: CGD iPSC from reprogrammed CD34+ cells


title: A6124 Fibroblast / IMR-90

source_name: Fibroblast

value: Fibroblast


title: A6323 iPSC / iGP91-05-2


title: A6116 CD14 / CD14

source_name: Uncultured peripheral blood CD14+ cells


title: A6117 CD34 / CD34-1

source_name: Cultured peripheral blood CD34+ cells


title: Untreated Control, 24h, FA experiment 2


title: A6118 CD34 / CD34-2


title: A6325 iPSC / iGP91-05-4


title: A6122 iPSC / iGP91-02


title: A6158 iPSC / iP47-03


title: A6123 iPSC / iNC-01

source_name: iPSC derived from reprogrammed CD34+ cells


title: A6119 CD34 / CD34-3


title: A6126 ESC / H9


title: A6317 iPSC / iP47-01


title: Treatment with 100 µM FA for 24h, experiment 2


title: Treatment with 200 µM FA for 24h, experiment 2


title: Treatment with 50 µM FA for 24h, experiment 2


title: Treatment with 200 µM FA for 4h, experiment 2


title: Treatment with 100 µM FA for 4h, experiment 2


title: Untreated Control, 4h, FA experiment 2


title: Saliva Twin pair 16 Twin 1

city: Saarbruecken

first: Pavlo

last: Lutsik

institute: Saarland University

description: Saliva spit sample

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD  Methylation Assay protocol.

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

data_processing: GenomeStudio software v2010.3, Methylation module v1.8.5

source_name: Saliva

label_protocol: Standard Infinium HD Methylation Assay protocol

extract_protocol: Genomic DNA was extracted from saliva using the GenElute Mammalian Genomic DNA Miniprep Kit (Sigma-Aldrich, St. Louis, MO, USA) according to the manufacturer’s instructions. The recommended RNase treatment was performed.

treatment_protocol: Saliva DNA was collected from probands using the Oragene DNA Self-collection Kit (DNA Genotek, Ottawa, Canada).

value: saliva

tag: birth weight

value: normal


title: Treatment with 50 µM FA for 4h, experiment 2

tag: treatment


title: Saliva Twin pair 17 Twin 1

description: Saliva spit sample


title: Untreated Control, 24h, FA experiment 1


title: Untreated Control, 4h, FA experiment 1


title: Saliva Twin pair 17 Twin 2

description: Saliva spit sample

value: low


title: Treatment with 200 µM FA for 24h, experiment 1


title: Treatment with 200 µM FA for 4h, experiment 1


title: Saliva Twin pair 14 Twin 2

description: Saliva spit sample


title: Saliva Twin pair 11 Twin 2

description: Saliva spit sample


title: Treatment with 100 µM FA for 24h, experiment 1


title: Saliva Twin pair 15 Twin 2

description: Saliva spit sample


title: Saliva Twin pair 15 Twin 1

description: Saliva spit sample


title: Saliva Twin pair 14 Twin 1

description: Saliva spit sample


title: Saliva Twin pair 16 Twin 2

description: Saliva spit sample


title: Treatment with 100 µM FA for 4h, experiment 1


title: Saliva Twin pair 11 Twin 1

description: Saliva spit sample


title: Saliva Twin pair 7 Twin 2

description: Saliva spit sample


title: Saliva Twin pair 12 Twin 1

description: Saliva spit sample


title: Saliva Twin pair 13 Twin 1

description: Saliva spit sample


title: Saliva Twin pair 8 Twin 1

description: Saliva spit sample


title: Saliva Twin pair 9 Twin 2

description: Saliva spit sample


title: Treatment with 50 µM FA for 24h, experiment 1


title: Treatment with 50 µM FA for 4h, experiment 1


title: Saliva Twin pair 8 Twin 2

description: Saliva spit sample


title: Saliva Twin pair 7 Twin 1

description: Saliva spit sample


title: lungKO_D8_64

city: San Francisco

first: Andrea

middle: J

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

hyb_protocol: Cy3-labelled RNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent UCSF custom 8x15K miRNA arrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent scanner immediately after washing.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.6 (Agilent) using default parameters)

source_name: Lung

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol. Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays

extract_protocol: Samples were homogenized in TRIzol (Life Technologies) and total RNA was extracted and purified from resulting lysates using the PureLink RNA Mini Kit (Life Technologies) according to the manufacturer’s instructions.

treatment_protocol: Biologic quadruplicate samples obtained from wild type and Klf15–/– mice treated with dex (2.5 mg/kg) or vehicle for 4 and 8 hours were used for microarrays analysis

tag: genotype

value: KO

value: Dexamethesone

tag: time

tag: strain

value: 6-8 weeks


title: lungKO_D8_63


title: Saliva Twin pair 6 Twin 2

description: Saliva spit sample

tag: tissue


title: Saliva Twin pair 9 Twin 1

description: Saliva spit sample


title: lungKO_D8_61

tag: age


title: Saliva Twin pair 13 Twin 2

description: Saliva spit sample


title: Saliva Twin pair 12 Twin 2

description: Saliva spit sample


title: Saliva Twin pair 10 Twin 1

description: Saliva spit sample


title: lungKO_D4_58


title: lungKO_D4_57


title: lungKO_D8_62


title: Saliva Twin pair 6 Twin 1

description: Saliva spit sample


title: lungKO_D4_59


title: lungWT_D8_56

value: WT


title: lungWT_D8_55


title: Saliva Twin pair 2 Twin 2

description: Saliva spit sample


title: Saliva Twin pair 5 Twin 2

description: Saliva spit sample


title: Saliva Twin pair 10 Twin 2

description: Saliva spit sample


title: lungWT_D4_51


title: Saliva Twin pair 4 Twin 2

description: Saliva spit sample


title: lungWT_D8_54


title: lungWT_D4_52


title: lungKO_V8_47

value: Saline


title: Saliva Twin pair 4 Twin 1

description: Saliva spit sample


title: lungKO_V8_46


title: lungWT_D4_49


title: Saliva Twin pair 5 Twin 1

description: Saliva spit sample


title: lungKO_V8_48


title: Saliva Twin pair 2 Twin 1

description: Saliva spit sample


title: lungKO_V4_43


title: Saliva Twin pair 1 Twin 2

description: Saliva spit sample


title: Saliva Twin pair 3 Twin 2

description: Saliva spit sample


title: lungKO_V4_44


title: Untreated_plants_rep4

status: Public on May 12 2013

city: Rehovot

first: Noam

last: Leviatan

department: Plant Sciences

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Whole-transcript double stranded target assay protocol, without amplification. GeneChips were washed and stained on the Affymetrix Fluidics Station 450 using Affymetrix protocol FS450_0001.

scan_protocol: Genechip Scanner 3000 7G

data_processing: Data analysis was done using Matlab and Perl

organism: Arabidopsis thaliana

source_name: aerial parts, untreated

growth_protocol: Arabidopsis thaliana (Columbia ecotype) plants were grown in Petri dishes (25 plants per dish) on Murashige and Skoog germination medium, containing 0.8% agar and 3% sucrose for 2 weeks under long day conditions (16h light/8 h dark) at 22°C

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: For cold treatment, the Petri dishes with the plants were transfered to 4°C for 24h under long day conditions. In order to keep variation between treatment and control to a minimum, cold treatment was started at 11am under light and continued for 24h before harvesting the aerial parts of plants from both groups

value: aerial

value: two weeks

tag: ecotype


title: 24-h_cold-treated_plants_rep3

source_name: aerial parts, cold treated, 24-h

label_protocol: Whole-transcript double stranded target assay protocol, without amplification


title: Untreated_plants_rep3


title: 24-h_cold-treated_plants_rep2


title: 24-h_cold-treated_plants_rep1


title: 24-h_cold-treated_plants_rep4


title: Untreated_plants_rep2


title: lungKO_D4_60


title: lungKO_V8_45


title: Saliva Twin pair 3 Twin 1

description: Saliva spit sample


title: lungWT_V8_38


title: lungWT_V4_34


title: lungKO_V4_41


title: lungWT_V8_37


title: lungWT_V4_36


title: lungWT_V4_33


title: lungWT_V8_39


title: Saliva Twin pair 1 Twin 1

description: Saliva spit sample


title: HUVEC GA13 SI.1

status: Public on May 11 2013

city: New Haven

first: hyung

last: chun

state: CT

address: 300 George St Room 770H

department: Internal Medicine

institute: Yale University

hyb_protocol: Samples were hybridized onto beadchips according to gene expression profiling protocol from Illumina.

scan_protocol: The Illumina BeadArray Reader and BeadScan software were used to scan and extract raw intensity values.

data_processing: Background subtraction and quantile normalization were performed.

source_name: HUVEC

label_protocol: Samples were labeled according to gene expression profiling protocol from Illumina

growth_protocol: HUVECs grown in EGM-2 (Lonza)

extract_protocol: Qiagen miRNeasy per manufacturer's protocol

treatment_protocol: Transfected with siRNAs (Stealth siRNA, Invitrogen) for 72 hours

value: HUVEC

tag: genotype/variation


title: lungWT_V4_35


title: HUVEC GA13 SI.2


title: HUVEC MEF2 A/C SI.2


title: Untreated_plants_rep1


title: HUVEC MEF2 A/C SI.1


title: PC12_+NGF_6h

city: Roma

first: Sergio

last: Nasi

state: Italia

address: P.le A. Moro 5

department: IBPM - Sapienza Università di Roma

country: Italy

institute: CNR - Consiglio Nazionale delle Ricerche

hyb_protocol: Hy5™‐labeled samples and Hy3™‐labelled reference RNA sample were mixed pair‐wise and hybridized to the miRCURY™ LNA Array version 11.0 – miRBASE version 12.0 (Exiqon, Denmark). The hybridization was carried out as recommended by the vendor.

scan_protocol: Scanned on a Perkin Elmer ScanArray Express scanner. Images were analysed by the GenePix Pro 6.0 program.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Rattus norvegicus

source_name: PC12 cells treated with NGF for 6h

label_protocol: 5 μg RNA from each sample were labelled with Hy5™ (treated) and Hy3™ (control) fluorescent label respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: PC12 cells were cultured in RPMI medium containing 10% horse serum and 5% foetal bovine serum in a CO2 humidified incubator at 37°C.

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

treatment_protocol: PC12 cells were treated with with  100ng/ml  NGF  for  1h in complete medium

source_name: PC12 untreated cells


title: PC12_+NGF_240h

source_name: PC12 cells treated with NGF for 240h


title: PC12_+NGF_3h

source_name: PC12 cells treated with NGF for 3h


title: PC12_+NGF_24h

source_name: PC12 cells treated with NGF for 24h


title: PC12_NGF_24h_deprivation

source_name: PC12 differentiated cells (+NGF 240h) after 24h of NGF deprivation

treatment_protocol: For  NGF  deprivation, PC12 terminally differentiated cells  were  washed three  times  with  PBS  and  one  time  with  serum  free  medium.  Subsequently, cells were placed in serum-free media without NGF for 24h.

treatment_protocol: PC12 cells treated with NGF for 240h


title: PC12_+NGF_1h

source_name: PC12 cells treated with NGF for 1h


title: lungWT_D4_50


title: toe3 Deletion

city: Calgary

first: Gordon

last: Chua

state: Alberta

address: 2500 University Drive NW

department: Biological Sciences

country: Canada

institute: University of Calgary

description: untreated strains

hyb_protocol: Hybridization was performed according to the manufactruer's instruction (Agilent Technology). Microarray was washed in 6X SSPE/0.005% sodium N-lauroylsarcosine at room temperature for 5 min followed by a second wash in pre-heated 42°C 0.6X SSPE for 2 min.

scan_protocol: Microarrays were scanned on an GenePix 4200A instrument with GenePix 3.0 software

data_processing: The raw data was lowess normalized and the average log2 ratios with the corresponding t-test p values from the dye-swap experiments were obtained using the R Bioconductor Limma package.

organism: Schizosaccharomyces pombe

source_name: toe3 deletion strain

label_protocol: 2 ug of mRNA were converted into cDNA using 140 nmol of Oligo-dT(25) anchored primer (Sigma), 20 nmol of aminoallyl dUTP dNTP (Sigma) mixture, and 200 units of SuperScript II reverse transcriptase (Invitrogen). 1 ug of cDNA each from overexpression or del

growth_protocol: S. pombe yeast cells were inoculated in YES+ALU media and cultured for 20-24hr.

extract_protocol: Total RNA was extracted using hot phenol-chloroform method, followed by mRNA isolation using gravity-flow Oligo-dT cellulose beads.

value: strain 972

value: toe3 deletion strain

source_name: wild type strain

value: wild type strain


title: Wild Type +/- Chlorpromazine Replicate 2

growth_protocol: S. pombe yeast cells were inoculated in YES+ALU media and cultured for 20-24hr. The ch2 sample was exposed to 300 µg/ml chlorpromazine for 1.5 hours of that time.

value: 300 µg/ml chlorpromazine for 1.5 hours


title: Wild Type +/- Chlorpromazine Replicate 1

growth_protocol: S. pombe yeast cells were inoculated in YES+ALU media and cultured for 20-24hr. The ch1 sample was exposed to 300 µg/ml chlorpromazine for 1.5 hours of that time.


title: toe2 Deletion Replicate 2

description: untreated strains

source_name: toe2 deletion strain

value: toe2 deletion strain


title: toe1 Deletion Replicate 2

description: untreated strains

source_name: toe1 deletion strain

value: toe1 deletion strain


title: HMLE/Gcnt2

city: New York

first: Yongzhong

last: Zhao

state: New York

address: 1470 Madison Avenue btw. 101st and 102nd Streets

department: Genetics

institute: Mount Sinai Medical Center

description:
Human mammary epithelial cell HMLE stably transfected with Gcnt2 gene.
mRNA

hyb_protocol: Hybridization reagents were mixed with 750 ng of labeled RNA, and the mixture was hybridized overnight at 58 ºC to HumanRef-8 v3.0 Expression BeadChips™ array (Illumina®).

scan_protocol: Following washing and staining with Cy3 dye-labeled streptavidin, BeadChips™ (Illumina®) were imaged using the BeadArray Reader (Illumina®).

data_processing: Data was acquired with GenomeStudio™ software (version 2010.1, Illumina®), and then processed for background-correction, variance-stabilizing transformation, and then robust splines-normalization between arrays using the lumi Bioconductor package (version 1.14) for R language (version 2.11.1) with default settings.

source_name: HMLE transfected with Gcnt2

label_protocol: Illumina® TotalPrep RNA Amplification kit (Ambion®) was used to convert 500 ng of RNA to cDNA which was then transcribed in vitro to generate biotin-labeled RNA.

extract_protocol: Total RNA was isolated using Purelink™ RNA isolation kit (Invitrogen®) as per the manufacturer's recommended protocol. RNA quantity and quality were assessed on a Bioanalyzer™ 2100 instrument (Agilent®). The RNA preparations had 260 nm/280 nm absorbance ratios in the 1.9-2.0 range, 260 nm/230 nm absorbance ratios >1.8, and RNA integrity numbers >7.

value: HMLE

value: mammary epithelial cells

tag: stable transfection


title: HMLE/Foxq1

description:
Human mammary epithelial cell HMLE stably transfected with Foxq1 gene.
mRNA

source_name: HMLE transfected with Foxq1

tag: cell line


title: toe2 Deletion Replicate 1

description: untreated strains


title: toe1 Deletion Replicate 1

description: untreated strains


title: toe3-HA Overexpression chIP-chip

description: untreated strains

data_processing: The raw data was normalized using global linear normalization and significant spots were selected with chIPOTle.

source_name: toe3 HA tagged overexpression strain with antibody

label_protocol: The linker-ligated DNA was PCR-amplified by adding 15 µl of labeling mix (2 µl aa-dUTP dNTP mix containing 5 mM each dATP, dCTP and dGTP, 3 mM dTTP, and 2 mM aminoallyl-dUTP (Sigma)), 1.25 µl 40 µM Oligo #1 (5’-GCGGTGACCCGGGAGATCTGAATTC-3’), and 5 and 0.001 units of GoTaq DNA polymerase (Promega) and Pfu Turbo DNA polymerase (Stratagene), respectively, and using the following program: one cycle of 55°C (4 min); 72°C (5 min); 95°C (2 min) and 30 cycles of 95°C (30 sec); 55°C (30 sec); 72°C (1 min), followed by a final extension at 72°C (4 min). Equal amounts of PCR product (3-5 mg) from immunoprecipitated and corresponding input samples were coupled to Cy3 and Cy5 dyes (GE Healthcare), and combined for QIAquick purification (QIAGEN).

growth_protocol: S. pombe yeast cells were inoculated in EMM+AL minimal media with no thiamine and cultured for 20-24hr.

extract_protocol: Cells were fixed and quenched in 1% formaldehyde and 125 mM glycine, respectively followed by 30 minute room temperature agitation and lysis by bead-beating. The cell lysate was sonicated to generate 100 bp – 1 kb DNA fragments. The chromatin-bound transcription factor was immunoprecipitated with 100–200 µl of Dynabeads® conjugated with sheep anti-mouse IgG (Invitrogen) and 5 µg of anti-HA F-7 antibody (Santa Cruz Biotechnology). Both immunoprecipitated and input cell lysates were incubated at 65°C overnight to reverse the DNA-protein cross-linking, and DNA was then extracted by phenol-chloroform. Blunt ends were generated in the entire immunoprecipitate and input DNA samples with 1 unit of T4 DNA Polymerase (Invitrogen), and 200 pmol of annealed linker (linker generated with Oligo #1: 5’-GCGGTGACCCGGGAGATCTGAATTC-3’ and Oligo #2: 5’-GAATTCAGATC-3’) was ligated with 1000 units of T4 DNA Ligase (NEB).

value: strain MBY1343 (ura4-D18)

tag: antibody

value: anti-HA F-7 antibody, Santa Cruz Biotechnology, lot E0610, catalogue sc-7392


title: PRDM5 KO cells 2

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

hyb_protocol: Standard Affymetrics protocol

scan_protocol: Standard scan protocol

data_processing: raw data were imported in Bioconductor using oneChannelGUI package and normalized with RMA

source_name: embryos

growth_protocol: Prdm5+/LacZ mice were intercrossed and pregnant females sacrificed at 13.5 days after the observation of a vaginal plug.  Uterus were harvested and embryos were dissected by mechanical disruption as well as trypsin digestion. Single cells suspensions were plated and maintained in complete media containing DMEM, 10% FBS, 1% Pen/strep.  Cells from different clones were genotyped and 3 littermate pairs of wild type and LacZ/LacZ MEFs (files named as KO) were harvested at passage 3 for RNA isolation.  RNA was isolated with RNAeasy mini kit (QIAGEN) and labelled cDNA was obtained by Affymetrix 3' IVT kit according to manufacturer recommendation.  Labeled cDNA was hybridized on Gene1.0ST arrays according to manufacturer recommendations.

value: PRDM5 KO


title: toe1 Deletion +/- Chlorpromazine Replicate 1


title: toe1-HA Overexpression chIP-chip

description: untreated strains

source_name: toe1 HA tagged overexpression strain with antibody


title: PRDM5 KO cells 1

label_protocol: cDNA was obtained by Affymetrix 3' IVT kit according to manufacturer recommendation.

extract_protocol: RNA was isolated with RNAeasy mini kit (QIAGEN)


title: wt cells 1

value: wt


title: PRDM5 KO cells 3


title: toe1 Deletion versus Wild Type + Chlorpromazine Replicate 2

growth_protocol: S. pombe yeast cells were inoculated in YES+ALU media and cultured for 20-24hr. Both samples were exposed to 300 µg/ml chlorpromazine for 1.5 hours of that time.


title: wt cells 2


title: toe2-HA Overexpression chIP-chip

description: untreated strains

source_name: toe2 HA tagged overexpression strain with antibody


title: toe1 Deletion +/- Chlorpromazine Replicate 2


title: wt cells 3


title: TetON-Oct4 animal +DOX, replica 2

first: Andrey

last: Kuzmichev

state: Maryland

address: 35, Lincoln Drive

institute: NINDS/NIH

description: Gene expression in ileum of TetON-Oct4 animal +DOX, replica 2

hyb_protocol: Cy3-labelled cRNA (1.65 ug) was hybridized to Agilent whole mouse genome (4 X 44K) oligo microarray (G4122F) at 65C for 17 h at 10 rpm using 2x Gex HI-RPM hybridization buffer.

scan_protocol: After washes, slides were scanned  on the Agilent DNA Microarray Scanner (G2565) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT XDR Hi: 100%, Lo: 10%)

data_processing:
The scanned images were analyzed with Feature Extraction 9.1 Software (Agilent). Extracted signal intensities were analysed using GeneSpring 7.3.1 software and the datasets were normalized using standard Agilent FE Import 1-color settings.
Data were normalized in two batches.  Both Matrix files are available as supplementary files on the Series record.

source_name: Adult intestine (ileum) of TetON-Oct4 animal +DOX, replica 2

label_protocol: cDNA and Cy3-labelled cRNA were prepared using Agilent Low RNA input linear amplification kit plus according to munufacturer's instructions.

extract_protocol: Mice were sacrificed by CO2 asfyxiation, intestines (ileum part) were removed, cleaned, chopped into small pieces and frozen at -80C. RNA was isolated using Trizol, quantified using NanoDrop spectrophotometer and quality-cotrolled using Agilent Bioanalyzer.

treatment_protocol: 6-8 week mice of indicated above genotypes were treated with 2 mg/ml DOX in drinking water containing 1% sucrose for 2 days or were left untreated.

value: adult intestine (ileum)


title: toe2 Overexpression Replicate 2

description: untreated strains

source_name: empty vector

label_protocol: 2 ug of mRNA were converted into cDNA using 140 nmol of Oligo-dT(25) anchored primer (Sigma), 20 nmol of aminoallyl dUTP dNTP (Sigma) mixture, and 200 units of SuperScript II reverse transcriptase (Invitrogen). 1 ug of cDNA each from overexpression or deletion strain and empty vector control strain was labeled with Cy3 or Cy5 (GE Healthcare) and were combined for QIAquick purification (QIAGEN).

value: empty vector

source_name: toe2 HA tagged overexpression

value: toe2 HA tagged overexpression


title: TetON-Sox2 animal +DOX, replica 2

description: Gene expression in ileum of TetON-Sox2 animal +DOX, replica 2

source_name: Adult intestine (ileum) of TetON-Sox2 animal +DOX, replica 2


title: toe3 Overexpression Replicate 1

description: untreated strains

source_name: toe3 HA tagged overexpression

value: toe3 HA tagged overexpression


title: SUM159/LacZ

description:
Breast cancer cell line SUM159 stably transfected with Lac Z gene as a control.
mRNA

source_name: SUM159 transfected with LacZ

value: breast cancer cells

value: LacZ


title: TetON-Oct4 animal +DOX, replica 1

description: Gene expression in ileum of TetON-Oct4 animal +DOX, replica 1

source_name: Adult intestine (ileum) of TetON-Oct4 animal +DOX, replica 1


title: toe3 Overexpression Replicate 2

description: untreated strains


title: SUM159/IRX5

description:
Breast cancer cell line SUM159 stably transfected with IRX5 gene.
mRNA

source_name: SUM159 transfected with IRX5


title: TetON-Sox2 animal +DOX, replica 1

description: Gene expression in ileum of TetON-Sox2 animal +DOX, replica 1

source_name: Adult intestine (ileum) of TetON-Sox2 animal +DOX, replica 1


title: toe2 Overexpression Replicate 1

description: untreated strains


title: TetON-Sox2 animal -DOX, replica 2

description: Gene expression in ileum of TetON-Sox2 animal -DOX, replica 2

source_name: Adult intestine (ileum) of TetON-Sox2 animal -DOX, replica 2


description: Gene expression in ileum of TetON-Oct4 X TetON-Sox2 animal +DOX, replica 1

source_name: Adult intestine (ileum) of TetON-Oct4 X TetON-Sox2 animal +DOX, replica 1

value: TetON-Sox2 X TetON-Oct4


title: HMLE/LacZ

description:
Human mammary epithelial cell HMLE stably transfected with Lac Z gene as a control.
mRNA

source_name: HMLE transfected with LacZ


title: SUM1315

description:
Basal-like breast cancer cell line.
mRNA

value: basal-like breast cancer cells


title: TetON-Sox2 animal -DOX, replica 1

description: Gene expression in ileum of TetON-Sox2 animal -DOX, replica 1

source_name: Adult intestine (ileum) of TetON-Sox2 animal -DOX, replica 1


title: toe1 Overexpression Replicate 1

description: untreated strains

source_name: toe1 HA tagged overexpression

value: toe1 HA tagged overexpression


title: rtTA animal +DOX, replica 2

description: Gene expression in ileum of rtTA animal +DOX, replica 2

source_name: Adult intestine (ileum) of rtTA animal +DOX, replica 2

value: rtTA controls (no TetOP-Sox2 transgene)


title: toe1 Overexpression Replicate 2

description: untreated strains


title: SUM159


title: MDA-MB231


title: rtTA animal +DOX, replica 1

description: Gene expression in ileum of rtTA animal +DOX, replica 1

source_name: Adult intestine (ileum) of rtTA animal +DOX, replica 1


description: Gene expression in ileum of TetON-Oct4 X TetON-Sox2 animal +DOX, replica 2

source_name: Adult intestine (ileum) of TetON-Oct4 X TetON-Sox2 animal +DOX, replica 2


title: NPYR treated 4V

city: Chengdu, Sichuan

first: Lingxia

last: Xie

address: South Renmin Road Section 3 NO.20

department: OB & GY

country: China

institute: Sichuan University

description: Gene expression data from NPYR-treated Id-shRNA H8 cells.

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US)

source_name: Id-1 shRNA-transfected H8 cells, NPYR transformed

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

growth_protocol: The HPV16 immortalized but not transformed human cervical epithelial cell line H8 was originated from the Institute of Virology of Chinese Academy of Medical Sciences and is a generous gift by Professor Yong Zhao, Department of Pathology of Chongqing Medical University. H8 cells cannot form tumor in nude mice or colony in soft agar. Both H8 and shRNA H8 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) (Gibco/BRL) supplemented with 100 μg/mL of streptomycin, 100U/mL of penicillin and 10% heat-inactivated fetal bovine serum (FBS) (Invitrogen Corporation, Carlsbad, CA, USA). The cultures were maintained in a humidified 5% CO2 incubator at 37 ºC. The medium was changed three times a week.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life Technologies, Carlsbad, CA, US) following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: NPYR (Sigma Chemical Co., St. Louis, MO, USA) was used to induce malignant transformation. In order to determine the dosage of NPYR to be used in the transformation assay, a preliminary cytotoxic test was performed as reported before 20. Generally, cells were seeded at a density of 1x10^5 cells in 5 mL of culture mediums per 60 mm dish (three dishes per group). After 3 or 4 days, when cells were in log growth phase, the cells were fed with 5 mL of fresh media and exposed to different concentrations of NPYR for 24 hours. Cells were counted and cytotoxicity was determined by comparing viable cell numbers in exposed cultures to that of untreated controls. A dose of 80 μM NPYR that killed approximately 50% of cells was used for transformation assays following the procedure described in a previous report. Exponentially growing H8 cells were plated at a density of 1x10^5 cells per 60-mm dish and incubated for 24 hour. The cells were exposed to NPYR for 48 hours, followed by culture in fresh medium for another 48 hours. This treatment cycle was repeated for 7 times followed by a subsequent incubation in fresh medium for 3 to 4 weeks before further experiments.

value: HPV-immortalized cervical epithelial cells

tag: shRNA

value: N-nitrosopyrrolidine (NPYR)


title: Multiciliated cell_control_rep1

city: Shanghai

first: Lei

last: Wang

address: Room 408, Building 1 225 South Chong Qing Road

institute: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: Gene expression data of kidney multiciliated cells from embryos injected with control morpholino.

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 (P/N 00-00212, Affymetrix).

data_processing: The data were analyzed with Command Console Software 3.1 using Affymetrix default analysis settings. Primary data was normalized by GeneSpring Software 11.0 (Agilent) using MAS5.0 as normalization method.

organism: Danio rerio

source_name: Multiciliated cell from embryos injected with control morpholino

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).

growth_protocol: Zebrafish embryos were raised under 28.5 degrees.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. 100 ng total RNA was amplified using Ovation RNA Amplification System.

treatment_protocol: Tissue block containing the kidney was dissected from 3 days post fertilization Tg(cmyb:EGFP) embryos, digested with 0.25% trypsin (Invitrogen) for 1hour and filtered through 40 um cell strainer (BD Falcon). 20000 GFP+ cells were sorted out using FACS Aria flow cytometer (BD) and used for RNA extraction.

tag: strain/background

value: AB

value: kidney multiciliated cells

tag: developmental stage

value: 3 days post fertilization embryo

tag: morpholino

value: control


title: NPYR treated 3V

description: Gene expression data from NPYR-treated Id-shRNA control H8 cells.

source_name: shRNA control-transfected H8 cells, NPYR transformed

tag: cell type


title: Id-1-shRNA H8

description: Gene expression data from Id-shRNA H8 cells.

source_name: Id-1 shRNA-transfected H8 cells, untreated


title: Id-1-shRNA control H8

description: Gene expression data from Id-shRNA control H8 cells.

source_name: shRNA control-transfected H8 cells, untreated


title: Multiciliated cell_miR-34B morphants_rep1

description: Gene expression data of kidney multiciliated cells from embryos injected with miR-34b morpholino.

source_name: Multiciliated cell from embryos injected with miR-34b morpholino


title: Multiciliated cell_miR-34B morphants_rep2


title: Multiciliated cell_control_rep2


title: toe1 Deletion versus Wild Type + Chlorpromazine Replicate 1

source_name: toe1 deletion strain

value: strain 972

value: toe1 deletion strain

value: 300 µg/ml chlorpromazine for 1.5 hours

source_name: wild type strain

value: wild type strain


title: miRNA at Day2, dish A

status: Public on May 10 2013

city: Cambridge

first: Di

last: Wu

state: MA

address: Statistics Department, Science Center, 1 Oxford Street

institute: Di Wu

description: miRNA expression data from Mouse embryonic fibroblast (MEF) cells at day 2 after deletion of Dicer

hyb_protocol: The RNA was hybridized to GeneChip miRNA 1.0 microarrays (Affymetrix Inc., Santa Clara, USA) as per the Genisphere manual. Labeled samples were hybridized to the arrays at 48°C for 16 hours and then washed and stained with a Steptavidin-PE solution prior to imaging

scan_protocol: Array images were scanned using Genepix.

data_processing:
The Affymetrix miRNA 1.0 microarray contains perfect match probes (PM) only.
The raw CEL microarray files were read using the ReadAffy function in the Affy package. RMA probe set summarized value. The normalized data is from robust Normexp-by-control background correction, cyclicloess normalization and RMA summarization). The version 2.15.1 of R was used.

source_name: MEF at day 2 after deletion of Dicer

label_protocol: The RNA was labeled using the FlashTag Biotin RNA Labeling Kit (Genisphere LLC, Hatfield, USA). 500 ng of RNA was poly-A tailed and a proprietary biotin-labeled dendramer molecule was joined to the 3’ end using DNA ligase.

growth_protocol: Dicer(flox/flox) x Cre/Esr1 MEFs have been reported previously (Gantier et al. 2011; Gantier et al. 2012). MEFs were cultured in complete Dulbecco’s modified Eagle medium (DMEM) (Invitrogen Corporation, Carlsbad, USA) supplemented with 10% sterile fetal bovine serum (ICPBio Ltd, Auckland, New Zealand) and 1X antibiotic/antimycotic (referred to as complete DMEM). OHT (Sigma Aldrich, St. Louis, USA) was resuspended in 0.5 ml of 100% ethanol (resulting in stock solution at 25 mM) kept at -80°C.

extract_protocol: Total RNA containing small RNAs was purified from cultured MEFs using the mirVana miRNA Isolation Kit (Applied Biosystems, Foster City, USA),

treatment_protocol: Prior to cell treatment, the stock solution was first diluted to 2.5 mM in 100% ethanol before being diluted further to the final concentration of 500 nM in complete DMEM. The cells were incubated overnight with 500 nM OHT before being rinsed with fresh complete DMEM the next day (day 1).

tag: strain background

value: C57BL/6-129 mixed

value: Dicer(flox/flox) x Cre/Esr1

value: Mouse embryonic fibroblast (MEF) cells

tag: days after dicer deletion

value: 2 days

tag: culture dish as biological replicates

value: dish A


title: Notch1 T-ALL MycGFP positive replicate 2

first: Bryan

last: King

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

description: Murine T-ALL

hyb_protocol: 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using Genespring GX program. No further adjustments were made to the data in the table.

source_name: Notch1-deltaE+, CD25+, mycGFP+ splenocytes, 4 weeks post transplant

label_protocol: 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2

extract_protocol: Qiagen RNEasy Plus mini Kit  was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems

treatment_protocol: Total mononuclear cells were isolated from congenic recipients and sorted on the basis of mCherry, GFP

value: Spleen

value: 12 weeks

tag: genotype

value: Notch1[delta]E mycGFP


title: miRNA at Day3, dish A

description: miRNA expression data from Mouse embryonic fibroblast (MEF) cells at day 3 after deletion of Dicer

source_name: MEF at day 3 after deletion of Dicer

value: 3 days


title: miRNA at Day2, dish C

value: dish C


title: miRNA at Day4, dish B

description: miRNA expression data from Mouse embryonic fibroblast (MEF) cells at day 4 after deletion of Dicer

source_name: MEF at day 4 after deletion of Dicer

value: 4 days

value: dish B


title: Notch1 T-ALL MycGFP positive replicate 3

description: Murine T-ALL

tag: strain


title: miRNA at Day2, dish B


title: miRNA at Day3, dish B


title: miRNA at Day4, dish A


title: Notch1 T-ALL MycGFP positive replicate 1

description: Murine T-ALL

tag: tissue


title: miRNA at Day3, dish C


title: embryo at E10.5 of WT

city: Toyama

first: Seiji

last: Yamamoto

state: Toayma

address: 2630 Sugitani

department: Department of Pathology

institute: University of Toyama

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were checked with Affymetrix GeneChip Command Console Software, analyzed with Expression Console using default analysis settings and global scaling as normalization method.

label: Biotin

source_name: embryo at E10.5 of WT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA .

growth_protocol: Plugged day was counted embryonic day 0.5. In E10.5, embryos were extracted total RNA.

extract_protocol: Total RNA was extracted using RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: Qiazol extraction of total RNA was performed according to the manufacturer's instructions.

value: brain


title: Notch1 T-ALL MycGFP negative replicate 3

description: Murine T-ALL

source_name: Notch1-deltaE+, CD25+, mycGFP- splenocytes 4 weeks post-transplant

tag: age


title: miRNA at Day4, dish C


title: Notch1 T-ALL MycGFP negative replicate 1

description: Murine T-ALL


title: Notch1 T-ALL MycGFP negative replicate 2

description: Murine T-ALL


title: embryo at E10.5 of KO

source_name: embryo at E10.5 of KO


title: Osteoblasts cultured with CD34+ cells

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description: Osteoblasts co-cultured with CD34+ cells

hyb_protocol: Fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix HGU-133Plus2 arrays. GeneChips were washed and stained using Hybridization, Wash, and Stain Kit for 3’IVT Arrays.

scan_protocol: GeneChip were scanned using GeneChip Scanner 3000 7G System.

data_processing: The GeneChip-Operating-Software (GCOS) absolute analysis algorithm (MAS5) was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.

source_name: Human Osteoblasts from trabecular bone

label_protocol: Biotinylated cRNA were prepared according to the standard  3’IVT Express Kit protocol from 500ng of  total RNA. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

growth_protocol: Human CD34+ cells were purified from umbilical cord blood (UCB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material, as previously described (Salati S. Stem Cells 2008). After purification, CD34+ cells were seeded in 24-well plates at 5x105 cells/mL in Iscove’s modified Dulbecco’s medium (IMDM) (GIBCO, Grand Island, NY, USA) containing 20% Human Serum (Bio-Whittaker, Walkersville, MD, USA), SCF (50 ng/ml), FLT3LG (50 ng/ml), TPO (20ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from R&D Systems, Minneapolis, MN, USA). Human osteoblasts (OBs) were directly isolated from the trabecular bone harvested from the inner portion of the tibia plateau of 16 patients undergoing total knee replacement for osteoarthritis (mean ± SD age 70 ± 8.2 years) as previously reported (Lisignoli G., J Cell Physiol. 2006). The bone chips were fed with medium twice a week. After 2 weeks, they were removed and the OBs were allowed to grow until confluent and analyzed at the first and second passages.

extract_protocol: Total cellular RNA was extracted after 48 hours of treatment from 0.3x106 cells of each sample using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer.

treatment_protocol: 24h after isolation, CD34+ cells were seeded directly onto semiconfluent OB monolayers at a final density of 7x103 cell/cm2 in 6-well plates. Cultures were maintained for 2 weeks in medium consisting of a 1:1 mix of IMDM and DMEM/F12 (Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12, both Celbio, Italy) supplemented with 20% FBS (Lonza, Italy), SCF 5ng/mL, FLT3LG 5ng/mL, TPO 2ng/mL, IL-3 1ng/mL and IL-6 1ng/mL (all R&D Systems, Minneapolis, MN, USA), streptomicin 100μg/mL, penicillin 100 μg/mL e L-glutamine 2mM (all purchased from Celbio, Italy). In order to better assess erythroid and megakaryocytic differentiation, cells were cultured in serum free medium consisting of a 1:1 mix of of IMDM and DMEM/F12 supplemented with 20% BIT (StemCell Technologies, Vancouver, Canada), SCF 5ng/mL, FLT3LG 5ng/mL, TPO 1ng/mL, IL-6 1ng/mL (all R&D Systems, Minneapolis, MN, USA), streptomicin 100μg/mL, penicillin 100 μg/mL e L-glutamine 2mM (all Celbio, Italy). Cells were harvested by trypsinization and vigorous pipetting on days 3, 7, 10 and 14 of co-culture.

value: trabecular bone

value: Osteoblasts

tag: culture condition

value: co-cultured with CD34+ cells

tag: time


title: shScr Replicate 3

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

hyb_protocol: The  amplified, biotin-labeled antisense RNA (aRNA) was purified and quality  was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano  kit. 750 ng of aRNA in 5 ul was mixed with 10 ul of hybridization  reagents and heated at 65C for 10min. After cooled to room temperature,  total 15 ul of the hyb solution was applied to Illumina MouseRef-8 v2  chip. The chip was incubated for about 18 hours at 58C.

scan_protocol: After washing  and staining with streptavidin-Cy3, the chip was scanned using Illumina  BeadArray Reader. The scanning was done using standard DirectHyb Gene  Expression protocol with the following settings: Factor=1, PMT=587,  Filter=100%.

data_processing: The raw data was extracted using Illumina BeadStudio  software without normalization. Raw data was imported into Partek genomic suite.

source_name: LNCaP Cells

label_protocol: ~500 ng of total RNA was used to prepare biotin-labeled RNA using Ambion Illumina TotalPrep RNA Amplification Kit (Cat# AMIL1791,  Applied Biosystems, Foster City, CA).  Briefly, 500 ng of total RNA was used to synthesize the first strand of  cDNA using ArrayScript reverse transcriptase and an oligo(dT) primer  bearing a T7 promoter. The single-stranded cDNA was then converted into  a double-stranded DNA (dsDNA) by DNA polymerase^ I in the presence of  /E. coli/ RNase H and DNA ligase. After column purification, the dsDNA  was served as a template for in vitro transcription in a reaction  containing biotin-labeled UTP, unlabeled NTPs and T7 RNA Polymerase.

growth_protocol: LNCaP cells are growing logarithmically in RPMI with 10% fetal bovine serum.

extract_protocol: RNA is extracted using Rneasy per protocol. RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit (Agilent Technologies Inc., Palo Alto, CA).

treatment_protocol: LNCaP cells infected in triplicate with three different shRNA lentiviruses, Two pLKO.1 constructs against ETV1 (ETV1sh1: TRCN0000013923, targeting GTGGGAGTAATCTAAACATTT in 39 UTR; and ETV1sh2: TRCN0000013925, targeting CGACCCAGTGTATGAACACAA in exon 7) were purchased from Open Biosystems and pLKO.1 shScr (targeting CCTAAGGTTAAGTCGCCCTCG) was purchased from Addgene. Three days after infection, RNA was harvested for expression profiling.

value: LNCaP

tag: transfected

value: pLKO.1 shScr


title: ETV1sh2 Replicate 1

tag: cell line


title: Osteoblasts

description: Osteoblasts maintaned in normal culture conditions

value: normal culture conditions


title: ETV1sh2 Replicate 2


title: ETV1sh2 Replicate 3


title: ETV1sh1 Replicate 2


title: ETV1sh1 Replicate 1


title: ETV1sh1 Replicate 3


title: CD34+ cells in liquid culture

description: CD34+ cells in liquid culture

source_name: Cord Blood CD34+ cells

value: Cord Blood

value: CD34+ cells

value: liquid culture


title: CD34+ cells cultured with Osteoblasts

description: CD34+ cells co-cultured with osteoblasts

value: co-cultured with osteoblasts


title: shScr Replicate 2


title: Pten f/f;ERG (Pb-Cre Pos;Pten f/f;R26-ERG/ERG) Rep4

source_name: Mouse Prostate

label_protocol: ~500 ng of^ total RNA was used to prepare biotin-labeled RNA using Ambion Illumina TotalPrep RNA Amplification Kit (Cat# AMIL1791,  Applied Biosystems, Foster City, CA).  Briefly, 500 ng of total RNA was used to synthesize the first strand of  cDNA using ArrayScript reverse transcriptase and an oligo(dT) primer  bearing a T7 promoter. The single-stranded cDNA was then converted into  a double-stranded DNA (dsDNA) by DNA polymerase^ I in the presence of  /E. coli/ RNase H and DNA ligase. After column purification, the dsDNA  was served as a template for in vitro transcription in a reaction  containing biotin-labeled UTP, unlabeled NTPs and T7 RNA Polymerase.

treatment_protocol: Mice were either castrated or left intact and RNA was isolated 3 days after castration.

tag: organ

value: Prostate

value: Pten f/f;ERG

tag: androgen

value: Ventral Lobe


title: Pten f/f (Pb-Cre Pos;Pten f/f) Rep3

value: Pten f/f


title: Pten f/f;ERG (Pb-Cre Pos;Pten f/f;R26-ERG/ERG) Rep1


title: Pten f/f;ERG (Pb-Cre Pos;Pten f/f;R26-ERG/ERG) Rep3


title: Pten f/f (Pb-Cre Pos;Pten f/f) Rep1


title: ERG (Pb-Cre Pos;R26-ERG/ERG) Rep2

value: ERG


title: Pten f/f (Pb-Cre Pos;Pten f/f) Rep4


title: CAF-LM DGOct10--730-2010--D5T

city: L'Hospitalet de Llobregat

first: david

middle: g

last: mollevi

address: Av Gran Via 197-203

country: Spain

institute: IDIBELL

hyb_protocol: Samples were hybridized with GeneChip Human Gene1.0 ST Arrays (Affymetrix) and scanned at the IRB Microarray Core Facility.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: We used RMA background correction, quantile normalization and RMA summarization

source_name: carcinoma-associated fibroblast liver metastasis

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: We obtained fibroblast cultures from fresh surgical specimen ressected from patients with primary colorectal carcinoma: normal colonic fibroblasts (NCF=9) from the normal colonic mucosa at least 5-10cm from the surgical margin, carcinoma-associated fibroblasts from the primary tumor (CAF-PT=14) and carcinoma-associated fibroblasts (CAF-LM=11) from fresh surgical specimens of liver metastases. All samples were collected under the supervision of the Ethics Committee of the Hospital Universitari de Bellvitge. To establish primary cultures, firstly we homogenated surgical specimens with Collagenase IV and Dispase in a MACS separation unit (Milteny Biotech, Auburn, CA, USA), depleted homogenates from epithelial cells using anti-EPCAM Dynabeads (Invitrogen) and positively selected fibroblasts using anti-fibroblasts microbeads (Milteny Biotech, Auburn, CA, USA). Cells were then cultured in DMEMF12+10%FBS (Gibco) with added penicillin/streptomycin.

extract_protocol: Total RNA was isolated from fresh cells using Qiagen Rneasy mini kit

tag: disease state

value: primary colorectal carcinoma

value: colorectal cancer LIVER MET

tag: Stage

tag: gender

value: MALE


title: Pten f/f;ERG (Pb-Cre Pos;Pten f/f;R26-ERG/ERG) Rep2


title: Pten f/f (Pb-Cre Pos;Pten f/f) Rep2


title: ERG (Pb-Cre Pos;R26-ERG/ERG) Rep3


title: ERG (Pb-Cre Pos;R26-ERG/ERG) Rep1


title: shScr Replicate 1


title: WT (Pb-Cre neg;R26-ERG/ERG) Rep3

value: WT (Cre negative)


title: WT (Pb-Cre neg;R26-ERG/ERG) Rep2


title: WT (Pb-Cre neg;R26-ERG/ERG) Rep1


title: Sox2cond/cond;aP0CREiresGFP  rep6

city: Bethesda

first: Whitney

middle: E

last: Heavner

address: Building 35 Rm 2B-203

department: NINDS

institute: National Institutes of Health

description:
BCP23.6
mutant replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: The filtered (reduced) data set was generated, in which any transcript that was not detected in at least 5% of the samples was removed. Also, The quantile distribution is estimated from the project samples, and after normalizing each sample's quantile distribution to the overall quantile distribution, negative values in the quantile distribution of the individual sample were censored (assigned as 1) , or 'scrunched'  to the range 1-2.  The scrunch procedure is a simple transformation of the form:  x_transformed =  {(x-min(x)) / (2 – min(x)) + 1, x < 2}, x  >= 2 where x is the signal value of any particular gene/probe ID for any particular specimen.

label_protocol: 500ng of RNA from each sample was amplified and biotin-labeled using an Ambion Illumina TotalPrep RNA Amplification kit.

growth_protocol: embryos

extract_protocol: RNA was purified using an Ambion Rnaqueous kit following the manufacturer's instructions.

treatment_protocol: genetic knockout

tag: genotype/variation

value: whole embyronic eye


title: Sox2cond/cond;aP0CREiresGFP  rep3

description:
BCP31.7
mutant replicate 3

tag: strain background


title: Sox2cond/cond;aP0CREiresGFP  rep4

description:
BCP33.4
mutant replicate 4


title: wild-type control rep6

description:
BCP23.7
replicate 6

source_name: wild-type control

value: wild type


title: Sox2cond/cond;aP0CREiresGFP  rep5

description:
BCP23.5
mutant replicate 5


title: wild-type control rep2

description:
CP121.5
replicate 2


title: Sox2cond/cond;aP0CREiresGFP  rep2

description:
CP121.2
mutant replicate 2


title: wild-type control rep3

description:
BCP31.10
replicate 3


title: wild-type control rep5

description:
BCP23.2
replicate 5


title: Donor II monocytes and monocyte-derived macrophages

city: Baltimore

first: Kenneth

middle: W

last: Witwer

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

description: Dye-swap analysis comparing miRNA profiles of human monocytes and monocyte-derived macrophages

hyb_protocol: For each donor, dye-swap array hybridizations were performed with monocyte and macrophage RNA using NCode Human miRNA microarrays (V3). Note that arrays for Donors I and II were performed several months prior to the arrays for Donor III; this was done to assess reproducibility of results. The NCode V3 slide includes probes to over 700 human miRNA targets and additional small RNA sequences reportedly identified by the manufacturer through next generation sequencing. Three replicates of each probe are printed on each slide. Arrays were maintained at 52 degrees C overnight in Maui mixer stations and covered with Maui chamber slips (Type 'SL', Biomicrosystems) for hybridization solution recirculation.

scan_protocol: Following 15 minute washes in each of the following solutions, pre-warmed to 55 degrees C--2X SSC, 0.2% SDS; 2X SSC; 0.2X SSC--slides were scanned with an Axon scanner (3000B) controlled by GenePix Pro software. Slides were kept immersed in 0.2x SSC until scanning to avoid unecessary exposure to atmospheric ozone.

data_processing: Intensity values were log2 transformed and loaded into BRBArray-Tools software.  Background correction of median signal intensity was performed, and data were filtered for a minimum spot size of 80 and an intensity value of 100 or greater. Normalization was conducted by median centering (lowess normalization was performed separately, and results were not substantially different--not shown). Results for human miRNAs were processed further, while array results for hypothetical RNA species and other small RNAs were discarded. For each donor, results of on-array triplicates and dye swaps were averaged, requiring present calls for at least five of six total replicates for at least two of three donors for inclusion of the respective miRNA in further analysis.

source_name: Donor II monocytes

label_protocol: One microgram aliquots of each RNA sample were polyA tailed and labeled with Alexa fluor dendrimers AF3 or AF5 (fluorescing in the green and red channels, respectively), using the NCode Rapid miRNA Labeling System (Invitrogen) per manufacturer's protocol.

growth_protocol: CD14+ monocytes were isolated from total PBMCs using anti-CD14 beads (Dynal). For monocyte-derived macrophages, total PBMCs were plated at 10^7 cells per well in 6-well plates and differentiated for seven days under mammalian culture conditions in medium containing 20% human serum and M-CSF (R&D), with half re-feeding at day 4.

extract_protocol: Total RNA was extracted using the Trizol Reagent (Life Technologies) RNA extraction protocol.

treatment_protocol: CD14+ monocytes were compared with 7-day monocyte-derived macrophages.

tag: cell type

value: monocytes

tag: selection

value: Immunoselection by CD14

source_name: Donor II macrophages

value: monocyte-derived macrophages

tag: growth condition

value: Differentiated for seven days from total PBMC in 20% human serum and in presence of M-CSF


title: Sox2cond/cond;aP0CREiresGFP  rep1

description:
C96.2
mutant replicate1


title: wild-type control rep1

description:
C96.5
replicate 1


title: white adipose_HFD F0_9months_mix4

city: Wuhan

first: Ling

last: Zheng

email: lzheng@whu.edu.cn, ywding0628@gmail.com

address: Wuhan University

department: College of Life Science

institute: Wuhan University

description:
9FF0
Mixed 4 samples.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned using BeadArray Reader, and raw intensities were extracted and background-corrected using Illumina BeadStudio Amplification.

data_processing: The intensity data were normalized using the average normalization algorithm (GenomeStudio (V2010.2), Gene Expression Module (v1.8.0)).

source_name: white adipose, HFD, fed for 9 months, F0 generation

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Mice were fed with normal chow or a high fat diet (60% Kcal fat).

extract_protocol: Total RNA was extracted with RNAiso Plus (Takara Biotechnology Co., Dalian, China).

tag: strain

value: female

value: 9 months

tag: generation

tag: treatment

value: high fat diet

value: white adipose tissue


title: Donor I monocytes and monocyte-derived macrophages

source_name: Donor I monocytes

source_name: Donor I macrophages


title: white adipose_normal chow_9months_mix3

description:
9FNC
Mixed 3 samples.

source_name: white adipose, normal chow, fed for 9 months

tag: age

value: normal chow

tag: tissue


title: Donor III monocytes and monocyte-derived macrophages

source_name: Donor III monocytes

source_name: Donor III macrophages


title: Non-smoker female, NSCLC, aCGH [PAT3N]

city: Daejeon

first: Sanghyuk

last: Lee

address: 125 Gwahak-ro

department: KOBIC

country: South Korea

institute: KRIBB

hyb_protocol: Hybridization was performed using Oligo aCGH Hybridization Kit at 65℃ and 20 rpm for 40 hours, enclosed in Agilent SureHyb-enabled hybridization chambers

scan_protocol: Images were scanned on the Agilent G2505 C Scanner and quantified using the Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: human genomic female DNA: Promega G1521

label_protocol: 3 µg of gDNA were digested each  0.5 µl of AluⅠ(10U/ µl) and RsaⅠ(10U/µl) restriction enzyme at 37°C for 120 min, 65°C for 20 min then fluorescent labeled at 37°C for 120 min, 65°C for 10 min in Exo-Klenow Fragment enzyme and 2.5mM each dNTP with 1.0mM Cyanine 3-dUTP and 1.0mM Cyanine 5-dUTP

extract_protocol: genomic DNA prep: Standard protocol by phenol extraction

tag: reference

value: pooled female genomic DNA

source_name: Non-smoker female, NSCLC

tag: disease

value: Adenocarcinoma, NSCLC

tag: patient

tag: tissue type

value: normal

value: IB

value: 53 years

tag: smoker

value: non-smoker


title: AGS-003-004-010-008 Arm2

city: Durham

first: Irina

middle: Yurievna

last: Tcherepanova

state: NC

address: 4233 Technology Drive

department: REsearch and Development

institute: Argos Therapeutics Inc.

description: RNA amplified using old protocol from sample 010-008

hyb_protocol: hybridization was performed according to standard Agilent procedures for 4X44K array. The arrays were custom made (Agilent) using probes generated for RCC genelist (Agilent) to correspond to 5' end, middle and 3' end of each transcript.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_95) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: RCC tumor_Arm2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from total or amplified RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and quality was checked using Bioanalyzer 2100.

extract_protocol:
RNA was extracted from homogenate made in RLT buffer using Qiagen Rneasy mini kit according to manufacturers instructions. The RNA was eluted in water. After verification of its integrity on denaturing agarose gel,  Total RCC RNA, were amplified according to the following procedure (Harris et al 2005) via cDNA intermediate.

Arm 2 [original amplification protocol]: Briefly, 2 μg of RNA 64T + oligo primer and 2 µM Capswitch RNA block primer 2 μM final concentration each were mixed in 40 µl total volume reaction.  Primers were allowed to annealed to the RNA templates at 72C for 2 min prior to addition of 16 µl 5X First Strand Buffer, 8 µl 100 mM DTT, 8 µl 10 mM dNTPs and 8 µl Superscript II Reverse Transcriptase (200 U/μl; Invitrogen).  Reverse transcription was carried out for 1 hour at 42C.  20 µl of the reverse transcription reaction was added to a mixture containing 819 µl water, 105 µl 10X Advantage 2  PCR Buffer, 21 µl 10 mM dNTPs, 42 µl 10 µM 64T + oligo primer, and 21 µl 20 uM of Capswitch primer (5’ – TAATACG ACTCACTATAGGGAGGAAGCAGTGGTAACAACGCAGAG T – 3’) instead of Capswitch primer. Advantage 2 Polymerase (Clonetech).  100 µl of PCR reaction mix were aliquotted into 10 PCR tubes and PCR was carried out using the following program:  95C 1 min then 20 cycles of 95C 5 s, 65C 5 s, 68C 6 min 4 º C hold.  All amplified cDNAs were purified over Qiagen PCR purification column and eluted in water. For the generation of RNA, in vitro transcription was carried out from using AmpliCap™ T7 High Yield Message Maker Kit from Epicentre Biotechnologies as per the manufacturer’s instructions

Arm 5 [improved amplification protocol] utilized a different PCR enzyme Fast Start High Fidelity enzyme (Roche) at the PCR step and a new primer. The conditions were as follows: 8 μg RNA with annealed primers in a 40 µl reaction. After annealing to each 20 µl of RNA solution  16 µl 5X First Strand Buffer, 8 µl 100 mM DTT, 8 µl 10 mM dNTPs and 8 µl Superscript II Reverse Transcriptase (200 U/μl; Invitrogen) were added and volume adjusted with water to 80 µl. The first strand synthesis was carried out at 45oC for one hour. 4 µl of each RT reaction was taken into 100 uL PCR reaction (multiple reactions were set, depending on the cDNA amount needed) containing FSFH reaction buffer with MgCl2, 4 µl of μM 10  64T+ oligo, 2 μM of 20 Powerswitch T7 primer, 2 µl of PCR nucleodide mix (10 mM each) and 2 µl of FSHF enzyme and 21 µl 20 µM T7 Powerswitch primer (5’-GAATTTAATACG ACTCACTATAGG TAGGAAGCAGTGGTAACAACGCAGAG T – 3’) instead of Capswitch primer. PCR was carried out using the following program:  95C  for 5 min followed by 10 cycles 95C 30 s, 65C 30s and 67C 6 min, then 10 cycles of 95C 30 s, 65C 30 s, 67C 6 min with 5 s increase each cycle, followed by 67C hold for 7 min and 4C hold. All amplified cDNAs were purified over Qiagen PCR purification column and eluted in water. For the generation of RNA, in vitro transcription was carried out using AmpliScribe™ T7-Flash™ Transcription Kit from Epicentre Biotechnologies as per the manufacturer’s instructions to generate uncapped RNA.  The uncapped RNAs were then post-transcriptionally capped using Epicentre Biotechnologies’ ScriptCap™ m7G Capping System in conjunction with ScriptCap™ 2'-O-Methyltransferase to generate type I 5’ end cap structure.
The cDNA was then in vitro transcribed and RNA capped. The final in vitro transcribed RNA was purified using Qiagen RNeasy Maxi column according to manufacturing instructions for RNA cleanup and eluted in water. individual aliquots of total and amplified RNA were stored in liquid nitrogen.

treatment_protocol: RCC tumor tissue was cut into 5 mm cubes and placed into RNAlater stabilizing solution at a bedside. The stabilized tumor tissue was stored refrigerated. Tumor tissue was homogenized using Pro homogenizer fitted with a steel blade in the RLT solution (Qiagen, RNeasy kit)

value: renal cell carcinoma (RCC) tumor

tag: rna amplification protocol

value: Arm2 [original protocol]

tag: molecule subtype

value: amplified RNA


title: AGS-003-004-010-003 Arm2 Rep

description: RNA amplified using old protocol from sample 010-003, technical replicate


title: AGS-003-004-010-008

description: starting RNA for amplification sample 010-008

source_name: RCC tumor

value: total RNA


title: Non-smoker female, NSCLC, aCGH [PAT4T]

value: tumor

tag: Stage

value: IA

tag: gender

value: 60 years


title: AGS-003-004-010-008 Arm5

description: RNA amplified using new protocol from sample 010-008

source_name: RCC tumor_Arm5

value: Arm5 [improved protocol]


title: AGS-003-004-010-007 Arm2

description: RNA amplified using old protocol from sample 010-007


title: AGS-003-004-010-003 Arm2

description: RNA amplified using old protocol from sample 010-003


title: AGS-003-004-010-003 Arm5

description: RNA amplified using new protocol from sample 010-003


title: AGS-003-004-010-007 Arm5 Rep

description: RNA amplified using new protocol from sample 010-007, technical replicate


title: AGS-003-004-010-007

description: starting RNA for amplification Sample 010-007

source_name: RCC tumor_starting RNA


title: AGS-003-004-010-007 Arm5

description: RNA amplified using new protocol from sample 010-007


title: wild-type control rep4

description:
BCP33.5
replicate 4

tag: strain background

tag: genotype/variation

value: wild type

value: whole embyronic eye