title: tail-1864

value: tail skin

value: 8 weeks

value: KO

value: no

tag: Sex

value: F


title: pancreatic cancer P12

status: Public on Mar 01 2015

type: RNA

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

country: Japan

institute: Toray Industries, Inc.

description: miRNA profiling

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

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

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

molecule: total RNA

organism: Homo sapiens

source_name: Serum

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

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.). Total RNA was also obtained from the FFPE sections using the Arcturus® Paradise® Extraction and Isolation kit (Life Technologies) in accordance with the manufacturer's instructions.

tag: disease state

value: pancreatic cancer

tag: tissue

value: serum

tag: gender

value: Female

tag: tumor stage

value: cStage IV

tag: age

tag: operability

value: inoperable


title: tail-1779

city: San Francisco

first: David

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

country: USA

institute: UCSF

description: Gene expression data from untreated P56 mouse skin

hyb_protocol: 90 microliters of hybridization sample were incubated in the Affymetrix GeneTitan Hybridization Oven instrument for 16 hours at 48C

scan_protocol: Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the MoGene-1_1-st-v1-96 fluidics script and GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates.  Arrays were scanned in the Affymetrix GeneTitan Multi-Channel (MC) instrument with the AGCC GeneTitan Instrument Control.

data_processing: CEL files were background corrected and normalized with RMA using oligo in R and a custom probe database which avoids SNPs in FVB and Spretus genomes. Data were batch-corrected for plate and genotype and then log2 transformed.

label: biotin

organism: Mus musculus

source_name: tail skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Mice were housed in standard conditions with standard chow and water ad libitum

extract_protocol: Trizol followed by Qiagen RNEasy clean-up

treatment_protocol: Mice were aged to 8 weeks, untreated

tag: plate

value: M


title: FL_Fr.A.4

city: Philadelphia

first: Kyoko

last: Hayakawa

state: PA

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

description: Gene expression of fetal liver Fr.A, replicate 4

hyb_protocol: Follow Agilent 60-mer oligo array hybridization protocol.

scan_protocol: Arrays were scanned by following scanning protocol recommended by Agilent, and spot quantifications were done using feature extraction software

data_processing: data were bakcground corrected using normexp method then loess normalized using bioconduction package limma

source_name: Fetal liver, Fr.A, replicate 4

label_protocol: Amplified RNAs were labeled with cy3 or cy5 dye

extract_protocol: RNA was extracted using the acid phenol method. 100ng of total RNA was used for RNA amplificaiton followingAmbion RNA amplification protocol.

treatment_protocol:
For each bone marrow sort, 16 female BALB/c mice were sacrificed and a single cell suspension was prepared from bone marrow after flushing femur and tibia using a 1ml syringe and a 25 gauge needle.  This generated 1 Fr. A and 1 Fr. B/C sample. Total of 4 sorts
For each fetal liver sort, a BALB/c mouse with embryos at day 16 of gestation was sacrificed, embryos (average of 8) were sacrificed, and a single cell suspension was prepared from liver by gentle dissociation between 2 frosted glass slides.  This generated 1 Fr. A and 1 Fr. B/C sample. Total of 4 sorts.

tag: strain

value: BALB/c

tag: developmental stage

value: Fetus

value: Fetal Liver

source_name: reference

tag: rna source

value: total RNA from six cell lines (R1, RS2, J558, EL4, DN3, and P388d)


title: FL_Fr.B/C.1

description: Gene expression of fetal liver Fr.B/C, replicate 1

source_name: Fetal liver, Fr.B/C, replicate 1


title: WT control B (high light experiment)

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET

description: WTCHLB

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Arabidopsis Genome ATH1 Array were washed and stained in the Affymetrix Fluidics Station 450.

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

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

organism: Solanum tuberosum

source_name: WT control (high light experiment)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Potato plants (Solanum tuberosum cv. Désirée) were grown under sterile conditions in glass bottles containing Murashige and Skoog (MS, Sigma) medium solidified with 0.8% phytoagar (Sigma). Plants were propagated in vitro and grown under 16 h light (50 µmol m-2 s-1cool-white fluorescent illumination)/8 h dark cycles, at 22C. The analysis of physiological and molecular responses of plants to different stress treatments  was conducted on plants transferred to plastic pots containing a mixture of perlite:vermiculite:peat moss (1:1:1), and acclimated for one month under the same light and temperature conditions in which the treatments were applied.

extract_protocol: Total RNA extraction was performed using RNaeasy Mini kit system according to the manufacturer's instructions.

treatment_protocol:
Low temperature: To analyze the effect of low temperature conditions, plants were first grown under long days (16 h light/8 h darkness) with fluorescent illumination (50 µmol m-2 s-1) at 22 ºC. After one month, half of the plants were exposed to 4 ºC under similar light conditions, while the remaining plants were kept at 22 ºC.
High light: The effect of high light stress was evaluated on plants grown first under long day conditions in a growth chamber illuminated with high pressure sodium lamps at 50 µmol m-2 s-1, at 22 ºC. After one month, half of the plants were exposed to 800 µmol m-2 s-1 at 22 ºC, while the remaining plants were kept under 50 µmol m-2 s-1 at 22 ºC.
Drought: for drought stress, plants were grown under natural radiation in a greenhouse in 3 liter pots supplemented with daily irrigation until water soil capacity was saturated. After one month under this condition, irrigation was interrupted for half of the plants while the remaining plants continued with the previous daily irrigation regime.

tag: cultivar

value: cv. Désirée

tag: genotype/variation

value: wild type

tag: stress condition

value: none (control condition)

value: young leaves


title: CBF1OX control A (high light experiment)

source_name: CBF1OX control (high light experiment)

value: AtCBF1OX transgenic


title: pancreatic cancer P16

description: miRNA profiling

value: Male


title: tail-1771

value: tail skin

value: 8 weeks

value: KO

value: no

value: F


title: pancreatic cancer P10

description: miRNA profiling

value: pancreatic cancer

value: serum

value: pStage IIB

value: operable


title: FL_Fr.A.2

description: Gene expression of fetal liver Fr.A, replicate 2

source_name: Fetal liver, Fr.A, replicate 2

value: BALB/c

value: Fetus

value: Fetal Liver


title: pancreatic cancer P09

description: miRNA profiling

value: Female

value: cStage IV

value: inoperable


title: WT control A (high light experiment)

description: WTCHLA

value: cv. Désirée

value: wild type

value: none (control condition)

value: young leaves


title: tail-1769

value: tail skin

value: 8 weeks

value: KO

value: M


title: pancreatic cancer P08

description: miRNA profiling

value: pancreatic cancer

value: serum

value: Male

value: cStage III


title: tail-1774

value: no


title: pancreatic cancer P11

description: miRNA profiling


title: CBF1OX low temperature B

source_name: CBF1OX low temperature

value: AtCBF1OX transgenic

value: low temperature


title: tail-1765

value: F


title: CBF1OX low temperature A


title: FL_Fr.A.1

description: Gene expression of fetal liver Fr.A, replicate 1

source_name: Fetal liver, Fr.A, replicate 1

value: BALB/c

value: Fetus

value: Fetal Liver

value: total RNA from six cell lines (R1, RS2, J558, EL4, DN3, and P388d)


title: FL_Fr.A.3

description: Gene expression of fetal liver Fr.A, replicate 3

source_name: Fetal liver, Fr.A, replicate 3


title: BM_Fr.B/C.4

description: Gene expression of bone marrow Fr.B/C, replicate 4

source_name: Bone marrow, Fr.B/C, replicate 4

value: Adult

value: Bone Marrow


title: CBF1OX control B (low temperature experiment)

source_name: CBF1OX control (low temperature experiment)

value: cv. Désirée

value: none (control condition)

value: young leaves


title: CBF1OX control A (low temperature experiment)


title: BM_Fr.B/C.3

description: Gene expression of bone marrow Fr.B/C, replicate 3

source_name: Bone marrow, Fr.B/C, replicate 3


title: pancreatic cancer P07

description: miRNA profiling

value: pancreatic cancer

value: pStage IIA

value: operable


title: tail-1742

value: tail skin

value: 8 weeks

value: KO


title: tail-1709

value: no

value: M


title: tail-1706


title: BM_Fr.B/C.1

description: Gene expression of bone marrow Fr.B/C, replicate 1

source_name: Bone marrow, Fr.B/C, replicate 1

value: BALB/c


title: BM_Fr.B/C.2

description: Gene expression of bone marrow Fr.B/C, replicate 2

source_name: Bone marrow, Fr.B/C, replicate 2


title: tail-1701

value: yes


title: tail-1703


title: WT control B (low temperature experiment)

description: WTCLTB

source_name: WT control (low temperature experiment)

value: wild type


title: WT low temperature B

description: WTLTB

source_name: WT low temperature

value: low temperature


title: pancreatic cancer P03

description: miRNA profiling

source_name: Serum

value: serum

value: Male

value: cStage III

value: inoperable


title: BM_Fr.A.3

description: Gene expression of bone marrow Fr.A, replicate 3

source_name: Bone marrow, Fr.A, replicate 3

value: Adult

value: Bone Marrow

value: total RNA from six cell lines (R1, RS2, J558, EL4, DN3, and P388d)


title: pancreatic cancer P04

description: miRNA profiling

value: pancreatic cancer

value: Female

value: cStage IV


title: pancreatic cancer P02

description: miRNA profiling


title: WT low temperature A

description: WTLTA

value: cv. Désirée

value: young leaves


title: BM_Fr.A.2

description: Gene expression of bone marrow Fr.A, replicate 2

source_name: Bone marrow, Fr.A, replicate 2

source_name: reference


title: BM_Fr.A.4

description: Gene expression of bone marrow Fr.A, replicate 4

source_name: Bone marrow, Fr.A, replicate 4


title: WT control A (low temperature experiment)

description: WTCLTA

value: none (control condition)


title: pancreatic cancer P06

description: miRNA profiling


title: pancreatic cancer P05

description: miRNA profiling


title: pancreatic cancer P01

description: miRNA profiling


title: tail-1690

source_name: tail skin

value: tail skin

value: 8 weeks

value: KO

value: no

value: M


title: tail-1689


title: tail-1692

value: F


title: WT drought A

description: WTDA

source_name: WT drought

value: wild type

value: drought


title: BM_Fr.A.1

description: Gene expression of bone marrow Fr.A, replicate 1

source_name: Bone marrow, Fr.A, replicate 1

value: BALB/c

value: Adult


title: sdg8_pC_pL_rep3

city: New York

first: Ying

last: Li

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

hyb_protocol: 8 μg of cRNA was used to hybridize the GeneChip Arabidopsis ATH1 genome array (from Affymetrix) at 42°C for 16 hours. Following the hybridization, the chips had been washed and stained by following Affymetrix protocol.

scan_protocol: The microarrays were scanned using a GeneChip Scanner (Affymetrix).

data_processing: The raw CEL files were normalized using MAS5 package in the R environment (http://www.r-project.org/). A low expression level cutoff of 40 was applied to remove probes with extremely low expression level across all conditions, while most (21553/22810) probes were kept for the following statistical tests. A three-way ANOVA was performed to dissect the gene expression variation as caused by genotype, light, carbon, genotype×light, genotype×carbon, light×carbon, and three way interaction genotype×light×carbon in R. The raw p-value from the ANOVA was then adjusted for multi-testing error with FDR correction in R. The FDR adjusted p-value was then used to select probes that are significantly affected by single factors, a binary interaction of two factors, or an interaction of all three factors using an FDR cutoff 0.05. Only unambiguous probes mapped to single gene were used.

label: Biotin

organism: Arabidopsis thaliana

source_name: Shoots, treated with carbonhydrate and light

label_protocol: The Affymetrix one-cycle cDNA synthesis kit was used to synthesize double stranded cDNA from 1μg of total RNA. The cDNA was cleaned using the GeneChip Sample Cleanup Module (Affymetrix#900371) and followed by Biotin-labeling of the cRNA using the 3’ amplification reagent for IVT labeling (Affymetrix). The concentration and quality of cRNA was checked through an A260/280 nm by using the nanodrop.

growth_protocol: WT and sdg8-5 (previously named cli186) seeds were surface sterilized and imbibed in darkness for 2 days. Plants were then grown hydroponically inside a sterile Phytatray (Sigma-Aldrich, St. Louis, MO, USA) on liquid Basal MS medium (GIBCO Formula# 97-5068EC) supplemented with 1% sucrose and 2 mM KNO3 at a pH of 5.7. The phytatrays were kept under white light (50 uE m-2s-1) in long-day cycle (16h Light/8h Dark) at 220C for 3 weeks (when they start flowering).

extract_protocol: Shoots were flash-frozen in liquid nitrogen for RNA extraction. RNA (3 sets of biological replicates) was isolated using RNeasy plant mini-kit (Cat# 74904) from Qiagen.

treatment_protocol: After 3 weeks, the plants were starved in liquid basal MS medium (GIBCO Formula# 97-5068EC) supplemented with 0% sucrose and 2 mM KNO3 at a pH of 5.7 and the phytatrays were covered with aluminum foil (for light starvation) for 24 hours. Plants were then treated with +/- 1% Sucrose and +/- Light (70 uEin m-2s-1) for 2 hours.

tag: genotype

tag: treatment

value: 1% sucrose, 70 uE light


title: WT control B (drought experiment)

description: WTCDB

source_name: WT control (drought experiment)


title: WT drought B

description: WTDB


title: tail-1687


title: tail-1688


title: tail-1679


title: WT control A (drought experiment)

description: WTCDA


title: tail-1677


title: WT_pC_pL_rep3

value: WT


title: sdg8_mC_mL_rep3

source_name: Shoots, untreated

value: 0% sucrose, dark


title: sdg8_mC_pL_rep2

source_name: Shoots, treated with light

value: 0% sucrose, 70 uE light


title: WT_pC_mL_rep3

source_name: Shoots, treated with carbonhydrate

value: 1% sucrose, dark


title: tail-1665


title: tail-1664


title: sdg8_pC_mL_rep3


title: L-540_Givinostat 100 nM+Sorafenib 5µM_24hrs, 4A

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software.

source_name: L-540, Givinostat + Sorafenib, 24hrs

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

growth_protocol: The Hodgkin lymphoma cell line L-540 was obtained from the DSMZ (Braunschweig, Germany, EU). Cells were routinely maintained in RPMI medium 1640 (Lonza, Basel, Switzerland) supplemented with 20% FBS (Lonza) and 2 mM glutamine (Lonza). Cells were maintained at 37°C in a water-saturated atmosphere of 5% CO2 in air.

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

treatment_protocol:
0x10^6 L-540 cells were seeded in 75 cm2 flask and, after 24 hrs, cells were treated with 100 nM Givinostat (Italfarmaco SpA, Milan, Italy, EU) and/or 5 µM sorafenib (Bayer, Berlin,
Germany, EU) in culture medium for 24 hours. At the end of treatment, cells were collected and RNA was extracted.

tag: cell line

tag: tissue derivation

value: Hodgkin lymphoma

value: Givinostat + Sorafenib

tag: drug concentration

tag: time of exposure


title: sdg8_pC_pL_rep2


title: tail-1628

tag: tissue

value: tail skin

tag: Sex


title: sdg8_mC_pL_rep3


title: WT_mC_mL_rep3


title: L-540_Givinostat 100 nM+Sorafenib 5µM_24hrs, 4B


title: L-540_Sorafenib 5µM_24hrs, 3B

source_name: L-540, Sorafenib, 24hrs

value: Sorafenib

value: 5 µM


title: L-540_Givinostat 100 nM+Sorafenib 5µM_24hrs, 4C


title: WT_mC_pL_rep3


title: L-540_Sorafenib 5µM_24hrs, 3C


title: sdg8_pC_mL_rep2


title: L-540_Sorafenib 5µM_24hrs, 3A


title: L-540_Givinostat 100 nM_24hrs, 2C

source_name: L-540, Givinostat, 24hrs

value: Givinostat


title: tail-1624

tag: age

value: 8 weeks

value: KO

value: no

value: M


title: tail-1655


title: L-540_Givinostat 100 nM_24hrs, 2B


title: tail-1641

value: F


title: sdg8_mC_mL_rep2


title: WT_pC_pL_rep2


title: L-540_Givinostat 100 nM_24hrs, 2A


title: L-540_CTRL_24hrs, 1C

source_name: L-540, CTRL, 24hrs

value: CTRL


title: tail-1616


title: tail-1617


title: WT_mC_mL_rep2


title: tail-1619


title: WT_mC_pL_rep2


title: tail-1623


title: WT_pC_mL_rep2


title: tail-1608


title: L-540_CTRL_24hrs, 1A


title: tail-1586


title: tail-1587


title: HDLM-2_Givinostat 100 nM+Sorafenib 5µM_24hrs, 4B

source_name: HDLM-2, Givinostat + Sorafenib, 24hr

growth_protocol: The Hodgkin lymphoma cell line HDLM-2 was obtained from the DSMZ (Braunschweig, Germany, EU). Cells were routinely maintained in RPMI medium 1640 (Lonza, Basel, Switzerland) supplemented with 20% FBS (Lonza) and 2 mM glutamine (Lonza). Cells were maintained at 37°C in a water-saturated atmosphere of 5% CO2 in air.

treatment_protocol:
10x10^6 HDLM-2 cells were seeded in 75 cm2 flask and, after 24 hrs, cells were treated with 100 nM Givinostat (Italfarmaco SpA, Milan, Italy, EU) and/or 5 µM sorafenib (Bayer, Berlin,
Germany, EU) in culture medium for 24 hours. At the end of treatment, cells were collected and RNA was extracted.


title: L-540_CTRL_24hrs, 1B


title: tail-1604


title: sdg8_mC_pL_rep1


title: HDLM-2_Givinostat 100 nM+Sorafenib 5µM_24hrs, 4C


title: sdg8_pC_mL_rep1


title: WT_pC_pL_rep1

value: 1% sucrose, 70 uE light


title: sdg8_pC_pL_rep1


title: HDLM-2_Sorafenib 5µM_24hrs, 3C

source_name: HDLM-2, Sorafenib, 24hr


title: tail-1578


title: tail-1582


title: sdg8_mC_mL_rep1


title: HDLM-2_Givinostat 100 nM+Sorafenib 5µM_24hrs, 4A


title: WT_mC_pL_rep1

value: WT


title: HDLM-2_Sorafenib 5µM_24hrs, 3B


title: tail-1564


title: tail-1565


title: HDLM-2_Sorafenib 5µM_24hrs, 3A


title: WT_pC_mL_rep1


title: WT_mC_mL_rep1

value: 0% sucrose, dark


title: tail-1560


title: HDLM-2_Givinostat 100 nM_24hrs, 2C

source_name: HDLM-2, Givinostat, 24hr


title: HINAE cell_IRF10_polyIC2

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

description: Total RNA was extracted from HINAE cells using the RNeasy Micro Kit plus. RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the double-strand synthesis.  double-strand cDNA was converted and labeled into cRNA with Cy3. Cy3-labeld cRNA was purified using the RNeasy mini kit. Following cleanup, fragmentation of the cRNA for target preparation was done according to the Agilent Low input QuickAmp Labeling kit one-color protocol. After hybridization cocktails preparation, the Agilent 8x15k custom oligo DNA microarray was hybridized with the fragmented labelled cRNA for 16 h at 65℃ as described in the Agilent Low input QuickAmp Labeling kit one-color protocol. Oligo DNA microarray, bound to Cy3-labeled cRNA, were processed using the Genepix pro v6.0 and scanned with a Axon Genepix4000B scanner

hyb_protocol: After hybridization cocktails preparation, the Agilent 8x15k oligo DNA microarray was hybridized with the fragmented labelled cRNA for 16 h at 65℃ as described in the Agilent's manuals.

scan_protocol: Oligo DNA microarray, bound to Cy3-labeled cRNA, were processed using the Genepix pro v6.0. and scanned with a Genepix4000B (Axon, USA). Scanner setting was a 5μm resolution using a PMT setting of 600 and a laser power of 100 percents.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent, USA) using default parameters (protocol GE1-v5_95 and Grid: 025875_D_F_20091023) to obtain background subtracted and spatially detrended Processed Signal intensities (raw values). GeneSpring GX v11.0 calculated normalized values that the log summarized values from the baseline transformed by control samples after corrected the average of a 75th percentile values of the arrays in the experiments.

organism: Paralichthys olivaceus

source_name: HINAE cell, IRF10_2, polyIC, 48h

label_protocol: Conversion of double stranded cDNA into Cy3-labeled cRNA was accomplished using the Low input QuickAmp Labeling kit one-color (Agilent, USA) according to the manufacturer’s instructions

growth_protocol: Cells were maintained using 24-well plate with L-15 medium supplemented 10 % fetal bovin serum, 100 UI/ml penicillin and 100 μg/ml streptomycin

extract_protocol: Total RNA was extracted from HINAE cells using RNeasy micro kit plus according to the manufacturer’s instructions (Qiagen, Germany)

treatment_protocol: After transfection using the 7.2nM pcDNA3.1-IRF10 plasmid and the 1μg/ml poly I:C with lipofectamine2000 (Invitrogen, USA), HINAE cell was cultured for 48 h

tag: hinae cell

value: Japanese flounder embryonic cell

source_name: average of control group


title: tail-1541

source_name: tail skin

tag: plate


title: HINAE cell_IRF10_polyIC1

source_name: HINAE cell, IRF10_1, polyIC, 48h


title: HINAE cell_vector_polyIC2

source_name: HINAE cell, vector2, polyIC, 48h

treatment_protocol: After transfection using the 7.2nM pcDNA3.1 plasmid and the 1μg/ml poly I:C with lipofectamine2000 (Invitrogen, USA), HINAE cell was cultured for 48 h


title: tail-1537


title: tail-1536


title: HDLM-2_Givinostat 100 nM_24hrs, 2B


title: HINAE cell_vector_polyIC1

source_name: HINAE cell, vector1, polyIC, 48h


title: HINAE cell_IRF10_polyIC3

source_name: HINAE cell, IRF10_3, polyIC, 48h


title: HDLM-2_CTRL_24hrs, 1C

source_name: HDLM-2, CTRL, 24hr


title: tail-1534


title: HINAE cell_vector_polyIC3

source_name: HINAE cell, vector3, polyIC, 48h


title: HINAE cell_polyIC2

source_name: HINAE cell, polyIC2, 48h

treatment_protocol: After transfection using the 1μg/ml poly I:C with lipofectamine2000 (Invitrogen, USA), HINAE cell was cultured for 48 h


title: HDLM-2_CTRL_24hrs, 1A


title: HDLM-2_Givinostat 100 nM_24hrs, 2A


title: ATAD3A knockdown-rep 3

city: AUGUSTA

first: yong

last: teng

institute: GRU

description:
mRNA expression levels between the ATAD3A knockdown and control cells.
shATAD3A-3

hyb_protocol: Following labeling, aRNAs were hybridized for 16 hr at 45C on Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Intensities of arrays have been quantile-normalized using Partek Genomic Suite (v6.6).  Differential expressions were calculated using ANOVA of Partek package.

source_name: MDA-MB-231 ATAD3A knockdown cells

label_protocol: Biotinylated aRNAs were prepared according to the standard Affymetrix protocol from 250 ng total RNA using The 3' IVT Expression Kit (Affymetrix).

growth_protocol: MDA-MB-231 cells were purchased from the American Type Culture Collection (Rockville, MD) and maintained in RPMI 1640 medium supplemented with 10% FBS and 1% P/S.

extract_protocol: Total RNA including small RNA was extracted using Qiagen miRNeasy Mini kit (Qiagen, CA) according to manufacturer’s instructions and then evaluated using an Agilent® 2100 Bioanalyzer.

treatment_protocol: To generate ATAD3A stable knockdown MDA-MB-231 cells, the pLKO.1 lentiviral vectors harboring shRNAs targeting ATAD3A or GFP were obtained from Open Biosystems (Huntsville, AL, USA) and used for cell transfection and infection. In this assay the shGFP lentiviral vector was used as a control. Virally infected cells were selected in a medium containing 1.0 μg/ml puromycin (Sigma, NY) for 2 weeks and the knockdown effects were determined by realtime RT-PCR and Western blot. Then the RNA used in this analysis were extracted from the knockdown cells and its control cells using extract protocol.

value: invasive breast cancer cell line MDA-MB-231

tag: passage

value: passage 2, puromycin resistant

value: ATAD3A knockdown


title: tail-1493

value: tail skin


title: tail-1509


title: ATAD3A knockdown-rep 2

description:
mRNA expression levels between the ATAD3A knockdown and control cells.
shATAD3A-2


title: HINAE cell_IRF10_3

source_name: HINAE cell, IRF10_3, 48h

treatment_protocol: After transfection using the 7.2nM pcDNA3.1-IRF10 plasmid with lipofectamine2000 (Invitrogen, USA), HINAE cell was cultured for 48 h


title: tail-1487

description: Gene expression data from untreated P56 mouse skin


title: ATAD3A knockdown-rep 1

description:
mRNA expression levels between the ATAD3A knockdown and control cells.
shATAD3A-1


title: tail-1478


title: liver tissue MCD 4

first: Satoshi

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: liver tissue

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Mice were fed either a normal diet or a MCD(methionine-and choline-deficient) diet for 23 weeks.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: No treatment was performed.

value: liver

tag: diet

value: methionine-and choline-deficient diet for 23 weeks


title: liver tissue control4

value: normal


title: HDLM-2_CTRL_24hrs, 1B

value: Hodgkin lymphoma


title: HINAE cell_IRF10_2

source_name: HINAE cell, IRF10_2, 48h


title: tail-1506

value: 8 weeks

value: KO


title: HINAE cell_IRF10_1

source_name: HINAE cell, IRF10_1, 48h


title: knockdown control-rep 3

description:
mRNA expression levels between the ATAD3A knockdown and control cells.
shGFP-3

source_name: MDA-MB-231 knockdown control cells

value: control


title: tail-1479

value: no

value: M


title: liver tissue control3


title: liver tissue MCD 3


title: HINAE cell_polyIC1

source_name: HINAE cell, polyIC1, 48h


title: knockdown control-rep 2

description:
mRNA expression levels between the ATAD3A knockdown and control cells.
shGFP-2


title: tail-1474

value: F


title: HINAE cell_vector2

source_name: HINAE cell, vector2, 48h

treatment_protocol: After transfection using the 7.2nM pcDNA3.1 plasmid with lipofectamine2000 (Invitrogen, USA), HINAE cell was cultured for 48 h


title: HINAE cell_vector1

source_name: HINAE cell, vector1, 48h

source_name: average of control group


title: tail-1470

source_name: tail skin


title: knockdown control-rep 1

description:
mRNA expression levels between the ATAD3A knockdown and control cells.
shGFP-1


title: tail-1452


title: liver tissue MCD 1


title: tail-1467


title: liver tissue control1


title: liver tissue MCD+metformin4

growth_protocol: Each mouse was fed MCD(methionine-and choline-deficient) diet.

treatment_protocol: The metformin-treated group was treated with metformin 2.4mg/day in drinking water for 15 weeks.

tag: mouse model

value: NASH


title: liver tissue MCD 2


title: HINAE cell_vector3

source_name: HINAE cell, vector3, 48h


title: VL1 96h 670DAP

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
P-VL1-670-96h
cDNA labelling from VL1 strain after 96h growing in 670 g/L DAP

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing:
Raw image quantization with background subtracted and Median Absolute Desviation normalization of each duplicate.
Value was the result of the local background sustraction to the raw data. In Processed data, we normalized all individual replicates data using ArrayStat software (Median Absolute Deviation)

organism: Saccharomyces cerevisiae

source_name: VL1 strain after 96 h growing in 670 mg/L DAP

label_protocol: cDNA was synthetized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labelling

growth_protocol: The commercial S. cerevisiae wine yeasts strains, QA23, Uvaferm CEG and Zimaflore VL1 were obtained from the market as active dried yeasts. Each one of the commercial yeast strains was rehydrated according to the manufacturer’s instructions (in water with 50 g/L of glucose, at 37C, for 30 min) and inoculated in synthetic grape juice media at a cell count of 10^6 CFU/mL. Model solutions based on the chemically defined grape juice medium (GJM) formulated by Henschke and Jiranek (1993) were used, with some modifications. An equimolecular mixture of glucose and fructose (100:100 g/L) was used as carbon and energy source, and the yeast assimilable nitrogen (YAN) was supplied as di-ammonium phosphate (DAP) as sole nitrogen source to facilitate monitoring nitrogen consumption profile. Two extreme initial concentrations were used: 67 mg/L, a low nitrogen condition (LN) or 10-fold higher, 670 mg/L, a high nitrogen condition (HN)

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

tag: strain

tag: initial dap concentration

value: 670 mg/L; high nitrogen condition (HN)


title: HINAE cell_control2

description: Total RNA was extracted from HINAE cells using the RNeasy Micro Kit plus. RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the double-strand synthesis.  double-strand cDNA was converted and labeled into cRNA with Cy3. Cy3-labeled cRNA was purified using the RNeasy mini kit. Following cleanup, fragmentation of the cRNA for target preparation was done according to the Agilent Low input QuickAmp Labeling kit one-color protocol. After hybridization cocktails preparation, the Agilent 8x15k custom oligo DNA microarray was hybridized with the fragmented labelled cRNA for 16 h at 65℃ as described in the Agilent Low input QuickAmp Labeling kit one-color protocol. Oligo DNA microarray, bound to Cy3-labeled cRNA, were processed using the Genepix pro v6.0 and scanned with a Axon Genepix4000B scanner

hyb_protocol: After hybridization cocktails preparation, the Agilent 8x15k oligo DNA microarray was hybridized with the fragmented labeled cRNA for 16 h at 65℃ as described in the Agilent's manuals.

source_name: HINAE cell, control2, 48h

growth_protocol: Cells were maintained in 24-well plate with L-15 medium supplemented 10 % fetal bovin serum, 100 UI/ml penicillin and 100 μg/ml streptomycin

treatment_protocol: After transfection using the vehicles and Lipofectamine2000 (Invitrogen, USA), HINAE cell was cultured for 48 h (control)

value: Japanese flounder embryonic cell


title: HINAE cell_control1

source_name: HINAE cell, control1, 48h


title: VL1 24h 670DAP

description:
P-VL1-670-24h
cDNA labelling from VL1 strain after 24h growing in 670 g/L DAP

source_name: VL1 strain after 24 h growing in 670 mg/L DAP


title: liver tissue MCD4


title: liver tissue MCD+metformin3

value: treated with metformin 2.4mg/day in drinking water for 15 weeks


title: liver tissue control2


title: VL1 12h 670DAP

description:
P-VL1-670-12h
cDNA labelling from VL1 strain after 12h growing in 670 g/L DAP

source_name: VL1 strain after 12 h growing in 670 mg/L DAP


title: VL1 96h 67DAP

description:
P-VL1-67-96h
cDNA labelling from VL1 strain after 96h growing in 67 g/L DAP

source_name: VL1 strain after 96 h growing in 67 mg/L DAP

value: 67 mg/L; low nitrogen condition (LN)


title: VL1 24h 67DAP

description:
P-VL1-67-24h
cDNA labelling from VL1 strain after 24h growing in 67 g/L DAP

source_name: VL1 strain after 24 h growing in 67 mg/L DAP


title: liver tissue MCD3

source_name: liver tissue


title: tail-1445


title: liver tissue MCD+metformin2


title: tail-1438


title: tail-1448


title: tail-1437


title: tail-1436


title: VL1 PI

description:
P-VL1-PI
cDNA labelling from VL1 strain preinoculum

source_name: VL1 strain preinoculum rehidrated


title: QA23 96h 670DAP

description:
P-QA23-670-96h
cDNA labelling from QA23 strain after 96h growing in 670 g/L DAP

source_name: QA23 strain after 96 h growing in 670 mg/L DAP


title: VL1 12h 67DAP

description:
P-VL1-67-12h
cDNA labelling from VL1 strain after 12h growing in 67 g/L DAP

source_name: VL1 strain after 12 h growing in 67 mg/L DAP


title: liver tissue MCD+metformin1


title: liver tissue MCD1


title: tail-1427


title: tail-1421


title: liver tissue MCD2


title: tail-1439


title: QA23 96h 67DAP

description:
P-QA23-67-96h
cDNA labelling from QA23 strain after 96h growing in 67 g/L DAP

source_name: QA23 strain after 96 h growing in 67 mg/L DAP


title: tail-1418


title: QA23 12h 670DAP

description:
P-QA23-670-12h
cDNA labelling from QA23 strain after 12h growing in 670 g/L DAP

source_name: QA23 strain after 12 h growing in 670 mg/L DAP


title: QA23 36h 670DAP

description:
P-QA23-670-36h
cDNA labelling from QA23 strain after 36h growing in 670 g/L DAP

source_name: QA23 strain after 36 h growing in 670 mg/L DAP


title: QA23 24h 670DAP

description:
P-QA23-670-24h
cDNA labelling from QA23 strain after 24h growing in 670 g/L DAP

source_name: QA23 strain after 24 h growing in 670 mg/L DAP


title: QA23 36h 67DAP

description:
P-QA23-67-36h
cDNA labelling from QA23 strain after 36h growing in 67 g/L DAP

source_name: QA23 strain after 36 h growing in 67 mg/L DAP


title: QA23 24h 67DAP

description:
P-QA23-67-24h
cDNA labelling from QA23 strain after 24h growing in 67 g/L DAP

source_name: QA23 strain after 24 h growing in 67 mg/L DAP


title: tail-1409

description: Gene expression data from untreated P56 mouse skin

source_name: tail skin


title: tail-1412


title: QA23 12h 67DAP

description:
P-QA23-67-12h
cDNA labelling from QA23 strain after 12h growing in 67 g/L DAP

source_name: QA23 strain after 12 h growing in 67 mg/L DAP


title: tail-1414


title: tail-1417


title: tail-1402


title: tail-1407


title: tail-1400


title: QA23 PI

description:
P-QA23-PI
cDNA labelling from QA23 strain preinoculum

source_name: QA23 strain preinoculum rehidrated


title: tail-1399


title: CEG 36h 670DAP

description:
P-CEG-670-36h
cDNA labelling from CEG strain after 36h growing in 670 g/L DAP

source_name: CEG strain after 36 h growing in 670 mg/L DAP

value: CEG


title: CEG 96h 670DAP

description:
P-CEG-670-96h
cDNA labelling from CEG strain after 96h growing in 670 g/L DAP

source_name: CEG strain after 96 h growing in 670 mg/L DAP


title: SiO2NPs_6.0µg/cm²_rep biol2_rep tech2 [US11183901_252665217057_S01_GE1_1100_Jul11_1_3]

city: Bagnols sur Cèze

first: Odette

last: Prat

address: Site de Marcoule

department: Life Science

country: France

institute: CEA

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665217057
Block: 3

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µL of 2X Gex Hybridization Buffer Hi-RPM was added to the fragmentation mixture and hybridized to Human V2 4x44K oligo microarrays (Agilent) for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent), then dried at ambiant atmosphere.

scan_protocol: Microarrays were scanned immediately after washing on the Agilent Scanner using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction software (Agilent technologies) using one-color treatment to obtain background subtracted and spatially detrended Processed Signal intensities.  Non-uniform outliers were excluded. Data were statistically analyzed with Genespring GX11 software (Agilent technologies).

source_name: A549 exposed to 6.0µg/cm² SiO2NPs, 24h

label_protocol: RNA samples were amplified and labeled with cyanine-3 fluorophore using a Low Input Quick Amp Labeling Kit (Agilent), according to the supplier’s protocol. The efficiency of fluorescent labelling was controlled by UV spectroscopy (Nanodrop 1000).

growth_protocol: A549 cells (ATCC, Manassas, VA, US) were cultured in DMEM/F12 medium supplemented with 10% FCS (LGC Standards, Middlesex, UK) and penicillin/streptomycin (100 U/mL, 100 µg/mL) in a humidified incubator at 37 °C, and 5% CO2. Cells were used between passages 20 to 40. Cells were passed twice a week and the medium was changed three times per week, keeping confluence below 80%.

extract_protocol: Total RNAs were extracted using the RNeasy Mini Kit (Qiagen). RNAs were quantified with the NanoDrop 1000 spectrophotometer and their qualities were assessed with the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: For microarray experiments, the A549 cells were seeded in 6-well plates to collect sufficient amounts of RNA. Three different cultures were exposed to five concentrations of SiO2 NPs (0.1, 1.0, 1.5, 3.0 and 6.0 µg/cm²) and serum-free medium (control cells) for 24h, and exposed to two concentrations of SiO2 NPs (3.0 and 6.0 µg/cm²) for 72h. Each condition of exposure to NPs was compared with control cells.

value: Lung

tag: cell type

value: Alveolar epithelium


title: tail-1390

value: tail skin


title: SiO2NPs_6.0µg/cm²_rep biol2_rep tech2 [US11183901_252665217679_S01_GE1_1100_Jul11_1_4]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665217679
Block: 4

source_name: A549 exposed to 6.0µg/cm² SiO2NPs, 72h


title: SiO2NPs_6.0µg/cm²_rep biol1_rep tech1 [US11183901_252665217056_S01_GE1_1100_Jul11_1_3]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665217056
Block: 3


title: SiO2NPs_6.0µg/cm²_rep biol3_rep tech3 [US11183901_252665217680_S01_GE1_1100_Jul11_1_3]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665217680
Block: 3


title: CEG 96h 67DAP

description:
P-CEG-67-96h
cDNA labelling from CEG strain after 96h growing in 67 g/L DAP

source_name: CEG strain after 96 h growing in 67 mg/L DAP


title: SiO2NPs_3.0µg/cm²_rep biol2_rep tech2 [US11183901_252665217680_S01_GE1_1100_Jul11_1_1]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665217680
Block: 1

source_name: A549 exposed to 3.0µg/cm² SiO2NPs, 72h


title: SiO2NPs_6.0µg/cm²_rep biol1_rep tech1 [US11183901_252665217060_S01_GE1_1100_Jul11_1_4]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665217060
Block: 4


title: SiO2NPs_3.0µg/cm²_rep biol3_rep tech3 [US11183901_252665217680_S01_GE1_1100_Jul11_1_2]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665217680
Block: 2


title: tail-1382


title: CEG 36h 67DAP

description:
P-CEG-67-36h
cDNA labelling from CEG strain after 36h growing in 67 g/L DAP

source_name: CEG strain after 36 h growing in 67 mg/L DAP


title: SiO2NPs_6.0µg/cm²_rep biol3_rep tech3 [US11183901_252665217058_S01_GE1_1100_Jul11_1_3]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665217058
Block: 3


title: SiO2NPs_3.0µg/cm²_rep biol1_rep tech1 [US11183901_252665217059_S01_GE1_1100_Jul11_1_4]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665217059
Block: 4


title: CEG 24h 670DAP

description:
P-CEG-670-24h
cDNA labelling from CEG strain after 24h growing in 670 g/L DAP

source_name: CEG strain after 24 h growing in 670 mg/L DAP


title: CEG 12h 670DAP

description:
P-CEG-670-12h
cDNA labelling from CEG strain after 12h growing in 670 g/L DAP

source_name: CEG strain after 12 h growing in 670 mg/L DAP


title: tail-1386

description: Gene expression data from untreated P56 mouse skin


title: CEG 24h 67DAP

description:
P-CEG-67-24h
cDNA labelling from CEG strain after 24h growing in 67 g/L DAP

source_name: CEG strain after 24 h growing in 67 mg/L DAP


title: tail-1375


title: SiO2NPs_3.0µg/cm²_rep biol1_rep tech1 [US11183901_252665217056_S01_GE1_1100_Jul11_1_2]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665217056
Block: 2

source_name: A549 exposed to 3.0µg/cm² SiO2NPs, 24h


title: SiO2NPs_3.0µg/cm²_rep biol3_rep tech3 [US11183901_252665217058_S01_GE1_1100_Jul11_1_2]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665217058
Block: 2


title: SiO2NPs_3.0µg/cm²_rep biol2_rep tech2 [US11183901_252665217057_S01_GE1_1100_Jul11_1_2]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665217057
Block: 2


title: tail-1368


title: CEG 12h 67DAP

description:
P-CEG-67-12h
cDNA labelling from CEG strain after 12h growing in 67 g/L DAP

source_name: CEG strain after 12 h growing in 67 mg/L DAP


title: tail-1365


title: tail-1363


title: CEG PI

description:
P-CEG-PI
cDNA labelling from CEG strain preinoculum

source_name: CEG strain preinoculum rehidrated


title: tail-1361


title: A549_CTRL_rep biol3_rep tech3 [US11183901_252665217058_S01_GE1_1100_Jul11_1_4]

description:
Gene expression after 72h
Microarray #: 252665217058
Block: 4

source_name: A549 cells, 72h, no treatment


title: A549_CTRL_rep biol2_rep tech2 [US11183901_252665217057_S01_GE1_1100_Jul11_1_4]

description:
Gene expression after 72h
Microarray #: 252665217057
Block: 4


title: tail-1357

source_name: tail skin


title: A549_CTRL_rep biol3_rep tech3 [US11183901_252665217058_S01_GE1_1100_Jul11_1_1]

description:
Gene expression after 24h
Microarray #: 252665217058
Block: 1

source_name: A549 cells, 24h, no treatment


title: tail-1359


title: A549_CTRL_rep biol1_rep tech1 [US11183901_252665217056_S01_GE1_1100_Jul11_1_4]

description:
Gene expression after 72h
Microarray #: 252665217056
Block: 4


title: A549_CTRL_rep biol1_rep tech1 [US11183901_252665217056_S01_GE1_1100_Jul11_1_1]

description:
Gene expression after 24h
Microarray #: 252665217056
Block: 1


title: tail-1355


title: A549_CTRL_rep biol2_rep tech2 [US11183901_252665217057_S01_GE1_1100_Jul11_1_1]

description:
Gene expression after 24h
Microarray #: 252665217057
Block: 1


title: Li-7 treated xenograft-6

description: 2019 miRNAs were spotted on each array.

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid.

source_name: Hepatocellular carcinoma

growth_protocol: Tissues of Li-7 cells were transplanted into subcutane of nude mice. Then mice were assigned into control group or treated group.

treatment_protocol: Mice were injected subcutaneously 90μg of galectin-9 or PBS three times a week.

tag: growth condition

value: in vivo

value: 90ug of galectin-9


title: SiO2NPs_1.5µg/cm²_rep biol4_rep tech4 [US11183901_252665213711_S01_GE1_1100_Jul11_1_4]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665213711
Block: 4

source_name: A549 exposed to 1.5µg/cm² SiO2NPs, 24h


title: tail-1351

treatment_protocol: Mice were aged to 8 weeks, untreated

value: 8 weeks


title: Ctrl-LV GFP+ D4

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description:
5826629006_A
sampleID: S14

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing:
Analysis of the quantified output data was conducted using the limma version 3.22.4 from the R statistical language and other software packages from Bioconductor version 3.0.  Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.
data was  standardized to have mean zero and standard deviation one, and  log2 transformed

source_name: Ctrl-LV GFP+

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: Mononuclear Tonsil cells were maintained in D10 media (DMEM + 10% FCS supplemented with 2 mM GlutaMAX [Life Technologies], 100 U/ml penicillin/streptomycin [Life Technologies]). Culture supernatants were obtained 2 d after transfections and filtered through 0.45-mm syringe filterscells were then transduced with retroviral virons. Transduced T cells were FACS sorted based on GFP expression levels.

extract_protocol: Cells were washed twice with cold PBS and lysed with 100 µl of cold RLT buffer (QIAGEN, Germany) supplemented with 1% beta-mercaptoethanol (BM) (Sigma, St. Louis, MO USA), and transferred to 1.7 ml tubes with 250 µl of cold RLT/BM buffer and quickly stored at -80oC. The samples underwent nucleic acid isolation in a designated Pre-PCR room using Qiagen’s RNeasy Micro Kit and underwent DNase I treatment.  Total RNA concentrations were quantified using a NanoDrop 2000c spectrophotometer and quality was assessed using BioRad’s Experion automated electrophoresis system.  With each batch of samples a 500 ng HeLa RNA control and two water non-template negative controls were included.

treatment_protocol: 293T cells were transfected with lentivirus along with four expression vectors encoding the packaging proteins Rev, Tat, Gag/Pol, and the G-protein of vesicular stomatitis virus (VSV). Supernatant was collected at 24 and 48 hours and passed through a 0.22 µm filter. Virus was concentrated by spinning supernatant at 24,000 rpm for 90 minutes at 10 °C. Lentiviral preparations were titered on 293T cells, and CD4 T cells were transduced at an MOI of 2. Cells were transduced 36–48 hours after the start of culture by spinning at 1,500 rpm for 90 minutes at 37° C. Analysis was performed 5 days post-transduction for each experiment. Co-transduction of both control vectors (ZsGreen-LV + dNGFR-LV) was tested in pilot experiments and no difference in cell phenotype was observed when compared to single transduction with either control vector alone (ZsGreen-LV or dNGFR-LV) (data not shown). Sorted naïve tonsil cells were activated with anti-CD3+CD28 Ab coated beads and transduced with BCL6 or control lentiviral vectors as described above.

tag: donor id

value: sorted naïve tonsil cells

tag: activated with

value: anti-CD3+CD28 Ab coated beads

tag: transduced with

value: control lentiviral vectors

tag: timepoint

value: day 5 following LV infection

tag: cell population

value: Ctrl-LV GFP+


title: SiO2NPs_1.5µg/cm²_rep biol3_rep tech3 [US11183901_252665213710_S01_GE1_1100_Jul11_1_4]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665213710
Block: 4

tag: tissue

tag: cell line


title: Bcl6-LV GFP+ D6

description:
5826629023_A
sampleID: S62

source_name: Bcl6-LV GFP+

value: BCL6 lentiviral vectors

value: Bcl6-LV GFP+


title: SiO2NPs_1.5µg/cm²_rep biol2_rep tech2 [US11183901_252665213709_S01_GE1_1100_Jul11_1_4]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665213709
Block: 4


title: Ctrl-LV GFP+ D5

description:
5826629006_H
sampleID: S36


title: SiO2NPs_1.5µg/cm²_rep biol1_rep tech1 [US11183901_252665213708_S01_GE1_1100_Jul11_1_4]

description:
Gene expression after 24h
Microarray #: 252665213708
Block: 4


title: A549_CTRL_rep biol3_rep tech3 [US11183901_252665213710_S01_GE1_1100_Jul11_1_1]

description:
Gene expression after 24h
Microarray #: 252665213710
Block: 1


title: Li-7 treated xenograft-4

description: 2019 miRNAs were spotted on each array.

tag: treatment


title: Li-7 treated xenograft-5

description: 2019 miRNAs were spotted on each array.


title: Ctrl-LV GFP+ D6

description:
5823049022_H
sampleID: S63


title: Bcl6-LV GFP+ D3

description:
5823049014_F
sampleID: S15


title: SiO2NPs_1.0µg/cm²_rep biol4_rep tech4 [US11183901_252665213950_S01_GE1_1010_Sep10_1_4]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665213950
Block: 4

source_name: A549 exposed to 1.0µg/cm² SiO2NPs, 24h


title: Bcl6-LV GFP+ D4

description:
5823049014_E
sampleID: S13


title: A549_CTRL_rep biol1_rep tech1 [US11183901_252665213708_S01_GE1_1100_Jul11_1_1]

description:
Gene expression after 24h
Microarray #: 252665213708
Block: 1


title: A549_CTRL_rep biol2_rep tech2 [US11183901_252665213709_S01_GE1_1100_Jul11_1_1]

description:
Gene expression after 24h
Microarray #: 252665213709
Block: 1


title: A549_CTRL_rep biol4_rep tech4 [US11183901_252665213711_S01_GE1_1100_Jul11_1_1]

description:
Gene expression after 24h
Microarray #: 252665213711
Block: 1


title: Li-7 treated xenograft-3

description: 2019 miRNAs were spotted on each array.


title: Ctrl-LV GFP+ D2

description:
5826629006_G
sampleID: S34


title: PC3 cells treated with SAM, biological replicate 3

type: genomic

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

country: Canada

institute: The University of British Columbia

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

source_name: PC3 cells treated with SAM

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from human prostate cancer cell lines using the Qiagen DNeasy Kit according to standard instructions.

value: human invasive prostate cancer cell line

value: S-adenosylmethionine (SAM)


title: Bcl6-LV GFP+ D5

description:
5823049022_B
sampleID: S35


title: Ctrl-LV GFP+ D3

description:
5826629006_B
sampleID: S16


title: Li-7 treated xenograft-1

description: 2019 miRNAs were spotted on each array.


title: PC3 cells treated with SAM, biological replicate 1


title: Li-7 treated xenograft-2

description: 2019 miRNAs were spotted on each array.


title: PC3 cells treated with SAM, biological replicate 2


title: Li-7 control xenograft-6

description: 2019 miRNAs were spotted on each array.

value: PBS


title: Li-7 control xenograft-5

description: 2019 miRNAs were spotted on each array.


title: LNCaP cells untreated, biological replicate 2

source_name: LNCaP cells untreated

value: LNCaP

value: human non-invasive prostate cancer cell line


title: Bcl6-LV GFP+ D2

description:
5823049022_A
sampleID: S33


title: LNCaP cells untreated, biological replicate 1


title: Li-7 control xenograft-4

description: 2019 miRNAs were spotted on each array.


title: Li-7 control xenograft-3

description: 2019 miRNAs were spotted on each array.


title: SiO2NPs_1.0µg/cm²_rep biol3_rep tech3 [US11183901_252665213950_S01_GE1_1010_Sep10_1_2]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665213950
Block: 2

value: Lung

value: Alveolar epithelium


title: SiO2NPs_1.0µg/cm²_rep biol2_rep tech2 [US11183901_252665213949_S01_GE1_1010_Sep10_1_2]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665213949
Block: 2


title: SiO2NPs_1.0µg/cm²_rep biol1_rep tech1 [US11183901_252665213948_S01_GE1_1010_Sep10_1_2]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665213948
Block: 2


title: SiO2NPs_0.1µg/cm²_rep biol2_rep tech2 [US11183901_252665213949_S01_GE1_1010_Sep10_1_3]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665213949
Block: 3

source_name: A549 exposed to 0.1µg/cm² SiO2NPs, 24h


title: Ctrl-LV GFP+ D1

description:
5823049022_I
sampleID: S65


title: SiO2NPs_0.1µg/cm²_rep biol3_rep tech3 [US11183901_252665213950_S01_GE1_1010_Sep10_1_3]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665213950
Block: 3


title: Gene expression miR-191 BioRep2_chip

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description:
Total RNA isolated 24 hours after transfection of miR-191 mature duplexes
SAMPLE 2

hyb_protocol: Standard Illumina TotalPrep RNA Amplification Kit protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalized using Illumina BeadStudio

source_name: HeLa cell_transfected with miR-191 duplex

growth_protocol: DMEM supplemented with 10% FBS

extract_protocol: Total RNA was isolated with TRIzol

treatment_protocol: mature miR-191 duplex or mock transfection (lipofectamine 2000 alone) was transfected with lipofectamine 2000 at a concentration of 100nM in the well

value: HeLa


title: Gene expression mock transfection BioRep2_chip

description:
Total RNA isolated 24 hours after mock transfection (lipofectamine 2000 alone)
SAMPLE 4

source_name: HeLa cell_mock transfection

label_protocol: Standard Illumina TotalPrep RNA Amplification Kit protocol


title: Bcl6-LV GFP+ D1

description:
5826629023_B
sampleID: S64


title: Li-7 control xenograft-2

description: 2019 miRNAs were spotted on each array.

value: in vivo


title: A549_CTRL_rep biol4_rep tech4 [US11183901_252665213948_S01_GE1_1010_Sep10_1_4]

description:
Gene expression after 24h
Microarray #: 252665213948
Block: 4


title: Li-7 control xenograft-1

description: 2019 miRNAs were spotted on each array.


title: SiO2NPs_0.1µg/cm²_rep biol1_rep tech1 [US11183901_252665213948_S01_GE1_1010_Sep10_1_3]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665213948
Block: 3


title: tail-1387

description: Gene expression data from untreated P56 mouse skin

value: tail skin

tag: age

value: 8 weeks

value: KO

value: no

tag: Sex

value: M


title: PC3 cells treated with vehicle control (SAH), biological replicate 3

value: S-adenosylhomocysteine (SAH) vehicle control


title: Li-7 treated cells-5

description: 2019 miRNAs were spotted on each array.

growth_protocol: Li- cells (5*10^4 cells a plate) were incubated for 24hour.

treatment_protocol: Galectin-9 (final concentration was 0.3μM) or PBS were added into each plate and incubated for additional 24 hour.

value: in vitro

value: Galectin-9 (final concentration was 0.3?M)


title: Gene expression miR-191 BioRep1_chip

description:
Total RNA isolated 24 hours after transfection of miR-191 mature duplexes
SAMPLE 1


title: Li-7 treated cells-1

description: 2019 miRNAs were spotted on each array.


title: Li-7 treated cells-4

description: 2019 miRNAs were spotted on each array.


title: Li-7 treated cells-2

description: 2019 miRNAs were spotted on each array.


title: Li-7 treated cells-3

description: 2019 miRNAs were spotted on each array.


title: Placenta 5 Hypoxic 72h rep1

city: Pittsburgh

first: Jean-Francois

last: Mouillet

address: 204 Craft Ave

department: MWRI - OBGYN and Reproductive Sciences

institute: University of Pittsburgh

description:
miRNA expression in primary trophoblasts
mR.510.H72.5

hyb_protocol: The hybridization was performed using  miRNA Microarray System with miRNA Complete Labeling and Hyb Kit from Agilent following the manufacturer's instructions

scan_protocol: Slides were scanned on Agilent Technologies Scanner G2505C using the protocol miRNA_107_Sep09

data_processing: The miRNA microarray data were log2 transformed, normalized, and summarized using the Robust Multi-array Average algorithm implemented in the R package AgiMicroRNA

source_name: Primary human trophoblast third trimester

label_protocol: The labeling was performed using  miRNA Microarray System with miRNA Complete Labeling and Hyb Kit from Agilent following the manufacturer's instructions

growth_protocol: Primary trophoblasts were isolated from third trimester placentas after Trypsin/Dispase/DNaseI digestion followed by purification on a Percoll gradient. Primary trophoblasts were cultured for 48h  to 72h in DMEM supplemented with 10% FBS (Fetal Bovine Serum), 20 mM Hepes ph 7.4, and a mixture of penicilin-streptomycin-fungizone. Cells were maintained at 37ºC/5% CO2

extract_protocol: Total RNA were prepared using miRNeasy Mini Kit following the manufacturer's instructions

treatment_protocol: 3.3 million cells were seeded in 35 mm tissue culture plates. After 4 h, nonadherent cells were removed by three washes in PBS. The culture were replenished with 2 ml of culture medium, and were divided to standard or hypoxic growth conditions (20% O2, 8% O2, or 1% O2).

value: Primary trophoblast cells

value: Placenta

tag: culture conditions

value: hypoxic

tag: time


title: Placenta 5 Standard 72h rep1

description:
miRNA expression in primary trophoblasts
mR.509.N72.5

value: standard


title: SiO2NPs_0.1µg/cm²_rep biol4_rep tech4 [US11183901_252665213949_S01_GE1_1010_Sep10_1_4]

description:
Gene expression after 24h exposure to NPs
Microarray #: 252665213949
Block: 4


title: PC3 cells treated with vehicle control (SAH), biological replicate 1

value: human invasive prostate cancer cell line


title: Li-7 control cells-5

description: 2019 miRNAs were spotted on each array.

value: PBS


title: PC3 cells treated with vehicle control (SAH), biological replicate 2


title: A549_CTRL_rep biol2_rep tech2 [US11183901_252665213949_S01_GE1_1010_Sep10_1_1]

description:
Gene expression after 24h
Microarray #: 252665213949
Block: 1

value: Lung

value: Alveolar epithelium


title: A549_CTRL_rep biol3_rep tech3 [US11183901_252665213950_S01_GE1_1010_Sep10_1_1]

description:
Gene expression after 24h
Microarray #: 252665213950
Block: 1


title: Placenta 5 Hypoxic 48h rep1

description:
miRNA expression in primary trophoblasts
mR.508.H48.5


title: A549_CTRL_rep biol1_rep tech1 [US11183901_252665213948_S01_GE1_1010_Sep10_1_1]

description:
Gene expression after 24h
Microarray #: 252665213948
Block: 1


title: E18_Replicate1

city: New Delhi

first: Yogendra

last: Singh

state: New Delhi

address: Mall Road

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

hyb_protocol: Hybridization and washing steps were performed as per manufacturer’s instructions.

scan_protocol: The arrays were scanned by illumina iScan System.

data_processing: Background subtracted expression values for probes (Sample Probe Profile) were exported from illumina Gene expression version 1.9.0 and Supervised Normalization of Microarrays (snm) was used to generate normalized expression values for the samples.

source_name: Lymph Node

label_protocol: Biotinylated, purified antisense RNA was quantitated and 750ng of labeled cRNA was hybridized onto Illumina HumanHT-12 v4 Expression BeadChip arrays containing more than 47,000 probes representing more than 31,000 annotated genes.

extract_protocol: Total RNA was extracted from all the lymph node tissue samples using the manual TRIzol® (Invitrogen) method in BSL3 facility. The quantity and quality of the isolated RNA was determined using Nanodrop-1000 (Thermo Fischer Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA), respectively. RNA with RIN (RNA integrity number) value >7 was considered for further assessment as it reflects ideal value of integrated RNAs. These RNA samples had both 260/280 nm absorbance and 28S/18S rRNAs peak ratio greater than two. To obtain sufficient quantities of RNA for microarray, two-rounds of linear amplification of RNA were conducted using illumina TotalPrepTM RNA Amplification Kit (Applied Biosystems by Life Technologies, CA, USA)

value: Lymph Node

tag: diseasestatus

value: Lymph Node Tuberculosis


title: E19_Replicate2


title: E17_Replicate2


title: Li-7 control cells-3

description: 2019 miRNAs were spotted on each array.


title: Li-7 control cells-4

description: 2019 miRNAs were spotted on each array.


title: Placenta 5 Standard 48h rep1

description:
miRNA expression in primary trophoblasts
mR.507.N48.5


title: Li-7 control cells-2

description: 2019 miRNAs were spotted on each array.


title: Placenta 5 Standard 24h rep1

description:
miRNA expression in primary trophoblasts
mR.505.N24.5


title: E19_Replicate1


title: E18_Replicate2


title: E16_Replicate2


title: Placenta 5 Hypoxic 12h rep1

description:
miRNA expression in primary trophoblasts
mR.504.H12.5


title: Placenta 5 Hypoxic 24h rep1

description:
miRNA expression in primary trophoblasts
mR.506.H24.5


title: Placenta 4 Hypoxic 72h rep1

description:
miRNA expression in primary trophoblasts
mR.410.H72.4


title: Placenta 5 Standard 12h rep1

description:
miRNA expression in primary trophoblasts
mR.503.N12.5


title: E15_Replicate1


title: E16_Replicate1


title: E17_Replicate1


title: Control1_Replicate1

value: Healthy


title: E15_Replicate2


title: Placenta 4 Hypoxic 48h rep1

description:
miRNA expression in primary trophoblasts
mR.408.H48.4


title: Placenta 4 Standard 72h rep1

description:
miRNA expression in primary trophoblasts
mR.409.N72.4


title: Gene expression mock transfection BioRep1_chip

description:
Total RNA isolated 24 hours after mock transfection (lipofectamine 2000 alone)
SAMPLE 3

value: HeLa


title: Control1_Replicate2


title: E10


title: E7_Replicate2


title: E14


title: Placenta 4 Hypoxic 24h rep1

description:
miRNA expression in primary trophoblasts
mR.406.H24.4


title: Placenta 4 Standard 48h rep1

description:
miRNA expression in primary trophoblasts
mR.407.N48.4


title: Placenta 5 Standard 0h rep1

description:
miRNA expression in primary trophoblasts
mR.500.T0.5


title: Placenta 4 Hypoxic 12h rep1

description:
miRNA expression in primary trophoblasts
mR.404.H12.4


title: Placenta 4 Standard 12h rep1

description:
miRNA expression in primary trophoblasts
mR.403.N12.4


title: E13


title: E6


title: Placenta 4 Hypoxic 6h rep1

description:
miRNA expression in primary trophoblasts
mR.402.H6.4


title: Placenta 4 Standard 6h rep1

description:
miRNA expression in primary trophoblasts
mR.401.N6.4


title: E8_Replicate1


title: Placenta 4 Standard 24h rep1

description:
miRNA expression in primary trophoblasts
mR.405.N24.4


title: E4_Replicate2


title: Placenta 2 Standard 72h rep1

description:
miRNA expression in primary trophoblasts
mR.209.N72.2


title: E7_Replicate1


title: Placenta 2 Hypoxic 72h rep1

description:
miRNA expression in primary trophoblasts
mR.210.H72.2


title: E8_Replicate2


title: E11_Replicate2


title: E4_Replicate1


title: Placenta 2 Hypoxic 48h rep1

description:
miRNA expression in primary trophoblasts
mR.208.H48.2


title: Placenta 4 Standard 0h rep1

description:
miRNA expression in primary trophoblasts
mR.400.T0.4


title: Control2_Replicate1


title: Female C57BL/6 TCDD 1000 μg/kg rep2

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

institute: Ontario Institute for Cancer Research

description: HTMoGene11_022312W_PB106_S386_22LiverB.CEL

hyb_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

data_processing: Raw array data (CEL files) were loaded into the R statistical environment (v3.0.2) using the affy package (v1.28.0) of the BioConductor library. Data was investigated for distributional homogeneity, then pre-processed using the RMA algorithm. An updated Probe to Entrez Gene ID map, mogene11stv1mmentrezgcdf (v15.1.0), was used for annotation.

source_name: liver_female C57BL/6_TCDD treated_1000 μg/kg

growth_protocol: Animals were housed in Macrolon cages with pelleted Altromin 1314 feed  and tap water available ab libitum. The housing environment was maintained at 21°C with 50 ± 10% relative humidity and artificial illumination on a 12/12 hour light/dark cycle. Animals were housed individually to avoid aggressive behavior.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kits according to the manufacturer’s instructions (Qiagen, Mississauga, Canada). Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were treated by oral gavage with a single bolus of either one dosage of TCDD (125, 250, 500, or 1000 μg/kg) dissolved in corn oil vehicle or corn oil alone (10mL/kg).

tag: strain

value: Female

value: 12-15 weeks

tag: treated with

value: 1000 μg/kg TCDD

tag: exposure time

value: 96 hours

value: Liver


title: Placenta 2 Standard 48h rep1

description:
miRNA expression in primary trophoblasts
mR.207.N48.2

tag: cell type

value: Primary trophoblast cells


title: Control2_Replicate2


title: Female C57BL/6 TCDD 500 μg/kg rep4

description: HTMoGene11_022312W_PB104_S386_20LiverB.CEL

scan_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

source_name: liver_female C57BL/6_TCDD treated_500 μg/kg

value: 500 μg/kg TCDD


title: Female C57BL/6 TCDD 1000 μg/kg rep4

description: HTMoGene11_022312W_PB108_S386_24LiverB.CEL

label_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada


title: Female C57BL/6 TCDD 1000 μg/kg rep1

description: HTMoGene11_022312W_PB105_S386_21LiverB.CEL


title: Placenta 2 Standard 24h rep1

description:
miRNA expression in primary trophoblasts
mR.205.N24.2

value: Placenta


title: Female C57BL/6 TCDD 500 μg/kg rep2

description: HTMoGene11_022312W_PB102_S386_17LiverB.CEL


title: E11_Replicate1


title: Ago2 IP mock transfection BioRep1_chip

description: RNA isolated from Ago2 immunoprecipitation

extract_protocol: RNA was extracted with TRIzol reagent

treatment_protocol: mature miR-191 duplex at a concentration of 100nM was transfected with lipofectamine 2000

tag: antibody

value: Ago2 (Abcam ab57113)


title: Ago2 IP mock transfection BioRep2_chip


title: HSPC-MA9.31_treated_6h.rep2

city: Madrid

first: Sara

last: Alvarez

state: Madrid

address: C/Faraday 7

institute: NIMGenetics

hyb_protocol: The Agilent official protocol G4140-90040 for hybridization was used

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA, 3um resolution). We used the AgilentG3_GX_1color method (61x21.6 mm sscan area, Green dye channel, 3um).

data_processing: The scanned images were analyzed with Feature Extraction Software v10.7 using default parameters (protocol GE1-107_Sept09) to obtain background subtracted and spatially detrended Processed Signal intensities

source_name: CD34+ cord blood cells transduced with MLL-AF9 fusion gene

label_protocol: RNA was labeled using Cyanine-3 (Cy3) with low input quick amp labeling (v6.6, Sept 2012), following the manufacturer´s specificacions.

growth_protocol: Umbilical cord blood CD34+ cells were selected using immunomagnetic beads (Miltenyi Biotech) and stably transduced with retroviruses expressing empty vectors (HSPC control) or the MLL-AF9 (HSPC-MA9) fusion protein. Cells were cultured as described elsewhere ( Wei et al., cell 2008).

extract_protocol: RNA was extracted using Rneasy mini kit (Quiagen), quality was assessed using the Agilent 2100 Bioanalyzer.

treatment_protocol: HSPC-MA9 cells were cultured with 30 nm panobinostat or vehicle. After 6 and 24 hr cells were harvested, PBS washed and pelleted.

value: 6h exposure to 30nM panobinostat


title: Female C57BL/6 TCDD 500 μg/kg rep1

description: HTMoGene11_022312W_PB101_S386_16LiverB.CEL


title: Placenta 2 Hypoxic 24h rep1

description:
miRNA expression in primary trophoblasts
mR.206.H24.2

value: hypoxic


title: Placenta 2 Hypoxic 12h rep1

description:
miRNA expression in primary trophoblasts
mR.204.H12.2


title: Female C57BL/6 TCDD 250 μg/kg rep4

description: HTMoGene11_022312W_PB100_S386_15LiverB.CEL

source_name: liver_female C57BL/6_TCDD treated_250 μg/kg

value: 250 μg/kg TCDD


title: Placenta 2 Standard 12h rep1

description:
miRNA expression in primary trophoblasts
mR.203.N12.2

value: standard


title: HSPC-MA9.31_treated_6h.rep1

value: CD34+ cord blood cells transduced with MLL-AF9 fusion gene


title: Ago2 IP miR-191 BioRep2_chip


title: Placenta 2 Hypoxic 6h rep1

description:
miRNA expression in primary trophoblasts
mR.202.H6.2


title: Female C57BL/6 TCDD 250 μg/kg rep2

description: HTMoGene11_022312W_PB98_S386_12LiverB.CEL


title: Ago2 IP miR-191 BioRep1_chip


title: Female C57BL/6 TCDD 250 μg/kg rep3

description: HTMoGene11_022312W_PB99_S386_13LiverB.CEL


title: MDA-MB-231_mir-655-3p-inhibitor_rep2

city: Chicago

first: Ralph

middle: R

last: Weichselbaum

state: IL

address: 5841 S. Maryland Avenue, MC 9006

department: Radiation & Cellular Oncology

institute: University of Chicago

description:
inhibitor-655-3p
Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were log 2 transformed and normalized using quantile normalization with R

source_name: MDA-MB-231 transfected with 50nm of mir -655-3p-inhibitor

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

growth_protocol: DMEM with 10% Fetal Calf Serum

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

treatment_protocol: 290,000 cells were forward transfected with 50nM of Dharmacon micro-RNA mimic

tag: transfection

tag: incubation time


title: HSPC-MA9.6_treated_6h.rep1


title: MDA-MB-231_mir-655-3p-inhibitor_rep1

description:
inhibitor-655-3p
Replicate 1


title: Female C57BL/6 TCDD 250 μg/kg rep1

description: HTMoGene11_022312W_PB97_S386_11LiverB.CEL


title: HSPC-MA9.6_treated_6h.rep2


title: HSPC-MA9.1_treated_6h.rep2


title: Placenta 2 Standard 6h rep1

description:
miRNA expression in primary trophoblasts
mR.201.N6.2


title: Female C57BL/6 TCDD 125 μg/kg rep4

description: HTMoGene11_022312W_PB96_S386_10LiverB.CEL

source_name: liver_female C57BL/6_TCDD treated_125 μg/kg

value: 125 μg/kg TCDD


title: Placenta 2 Standard 0h rep1

description:
miRNA expression in primary trophoblasts
mR.200.T0.2


title: MDA-MB-231_mir-655-3p-mimic_rep2

description:
mir-655-3p
Replicate 2

source_name: MDA-MB-231 transfected with 50nm of mir -655-3p-mimic


title: HSPC-MA9.1_treated_6h.rep1


title: HSPC-MA9.31_treated_24h.rep2

value: 24h exposure to 30nM panobinostat


title: Placenta 1 Hypoxic 72h rep2

description:
miRNA expression in primary trophoblasts
mR.104.H72.1


title: Female C57BL/6 TCDD 500 μg/kg rep3

description: HTMoGene11_022312W_PB103_S386_18LiverB.CEL


title: Female C57BL/6 TCDD 125 μg/kg rep3

description: HTMoGene11_022312W_PB95_S386_09LiverB.CEL


title: Placenta 1 8% 72h rep1

description:
miRNA expression in primary trophoblasts
mR.103.T72x8.1


title: Female C57BL/6 TCDD 125 μg/kg rep2

description: HTMoGene11_022312W_PB94_S386_08LiverB.CEL


title: MDA-MB-231_mir-544a-inhibitor_rep2

description:
inhibitor-544a
Replicate 2

source_name: MDA-MB-231 transfected with 50nm of mir -544a-inhibitor


title: HSPC-MA9.31_treated_24h.rep1


title: Female C57BL/6 CornOil rep2

description: HTMoGene11_022312W_PB90_S386_03LiverB.CEL

source_name: liver_female C57BL/6_corn oil treated

value: Corn Oil vehicle


title: Female C57BL/6 CornOil rep4

description: HTMoGene11_022312W_PB92_S386_05LiverB.CEL

value: Female


title: MDA-MB-231_mir-544a-inhibitor_rep1

description:
inhibitor-544a
Replicate 1


title: Female C57BL/6 CornOil rep3

description: HTMoGene11_022312W_PB91_S386_04LiverB.CEL

value: 12-15 weeks


title: Placenta 1 Standard 0h rep2

description:
miRNA expression in primary trophoblasts
mR.100.T0.1


title: MDA-MB-231_mir-544a-mimic_rep1

description:
mir-544a
Replicate 1

source_name: MDA-MB-231 transfected with 50nm of mir -544a-mimic


title: MDA-MB-231_mir-544a-mimic_rep2

description:
mir-544a
Replicate 2


title: Female C57BL/6 TCDD 125 μg/kg rep1

description: HTMoGene11_022312W_PB93_S386_07LiverB.CEL


title: HSPC-MA9.6_treated_24h.rep2


title: HSPC-MA9.6_treated_24h.rep1


title: MDA-MB-231_mir-410-inhibitor_rep2

description:
inhibitor-410
Replicate 2

source_name: MDA-MB-231 transfected with 50nm of mir -410-inhibitor


title: MDA-MB-231_mir-410-inhibitor_rep1

description:
inhibitor-410
Replicate 1


title: HSPC-MA9.1_treated_24h.rep1


title: HSPC-MA9.1_treated_24h.rep2


title: HSPC-MA9.31_untreated_rep1

value: no exposure to 30nM panobinostat


title: Placenta 1 Hypoxic 72h rep1

description:
miRNA expression in primary trophoblasts
mR.10.H72.1


title: Placenta 1 Hypoxic 24h rep2

description:
miRNA expression in primary trophoblasts
mR.102.H24.1


title: HSPC-MA9.6_untreated_rep1


title: Female C57BL/6 CornOil rep1

description: HTMoGene11_022312W_PB89_S386_01LiverB.CEL

value: 96 hours


title: Placenta 1 8% 24h rep1

description:
miRNA expression in primary trophoblasts
mR.101.T24x8.1


title: Placenta 1 Standard 72h rep1

description:
miRNA expression in primary trophoblasts
mR.9.N72.1


title: Li-7 control cells-1

city: Kamakura

description: 2019 miRNAs were spotted on each array.

source_name: Hepatocellular carcinoma

tag: growth condition

value: in vitro

value: PBS


title: Placenta 1 Hypoxic 48h rep1

description:
miRNA expression in primary trophoblasts
mR.8.H48.1

value: Primary trophoblast cells


title: Placenta 1 Standard 48h rep1

description:
miRNA expression in primary trophoblasts
mR.7.N48.1

value: Placenta


title: Placenta 1 Hypoxic 24h rep1

description:
miRNA expression in primary trophoblasts
mR.6.H24.1


title: Placenta 1 Standard 24h rep1

description:
miRNA expression in primary trophoblasts
mR.5.N24.1


title: Male C57BL/6 TCDD 1000 μg/kg rep4

description: HTMoGene11_022912W_PB128_S374_20_RNA.CEL

source_name: liver_male C57BL/6_TCDD treated_1000 μg/kg

value: Male

value: 1000 μg/kg TCDD

value: Liver


title: Male C57BL/6 TCDD 1000 μg/kg rep2

description: HTMoGene11_022912W_PB126_S374_18_RNA.CEL


title: Male C57BL/6 TCDD 1000 μg/kg rep3

description: HTMoGene11_022912W_PB127_S374_19_RNA.CEL


title: HSPC-MA9.1_untreated_rep2


title: Root grown under -Fe of WT plants Replicate 3

first: Tomoko

last: Nozoye

address: 1-1-1 yayoi bunkyo-ku

institute: The University of Tokyo

description: test

data_processing:
For the normalization it uses the average of five housekeeping genes: ZmUbiquitin; GRMZM2G118637.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_ZmUbiquitin)]

label: SYBR Green

organism: Zea mays

source_name: Fe deficient root

label_protocol: Total RNA (3 ug) was treated with RNase-free DNase I (Takara, Kyoto, Japan) to remove contaminating genomic DNA. First-strand cDNA was synthesized using ReverTra Ace reverse transcriptase (Toyobo, Tokyo, Japan) by priming with oligo-d(T)30. For quantitative RT-PCR, a fragment was amplified by PCR in a StepOnePlus Real-Time PCR system (Applied Biosystems, Foster City, CA, USA) with SYBR Green I and ExTaqTM Real-Time PCR Version (Takara) following the manufacturer’s instructions with 40 cycles at 95 oC for 15 seconds, 60C for 30 seconds and 72 oC for 30 seconds. The template concentration was adjusted to 30 ng per each reaction.

growth_protocol: Maize plants were germinated in a 5-L plastic container for 4 days, and then transferred to a 20-L plastic container with air bubbling. Fe deficiency was initiated 8 days after germination by transfer of the plants to Fe(III)-EDTA-free culture medium. Maize plants grown hydroponically under Fe-sufficient or Fe-deficient conditions for 5 days were harvested at the same time.

extract_protocol: RNA was prepared using RNeasy Plant Mini kit (Qiagen) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Fe deficiency treatment was initiated 8 days after germination by transfer of the plants to Fe(III)-EDTA-free culture medium.

tag: genotype/variation

value: WT(Alice)

value: Fe deficient

value: root


title: Root grown under -Fe of ys3 mutant plants Replicate 3

description: test

tag: tissue


title: Root grown under +Fe of ys3 mutant plants Replicate 3

description: test

source_name: Fe sufficient root

value: Fe sufficient


title: MDA-MB-231_mir-410-mimic_rep2

description:
mir-410
Replicate 2

source_name: MDA-MB-231 transfected with 50nm of mir -410-mimic

tag: cell line


title: MDA-MB-231_mir-410-mimic_rep1

description:
mir-410
Replicate 1


title: Male C57BL/6 TCDD 1000 μg/kg rep1

description: HTMoGene11_022912W_PB125_S374_17_RNA.CEL


title: HSPC-MA9.1_untreated_rep1

value: CD34+ cord blood cells transduced with MLL-AF9 fusion gene

tag: treatment


title: Root grown under -Fe of ys1mutant plants Replicate 3

description: test


title: Male C57BL/6 TCDD 500 μg/kg rep3

description: HTMoGene11_022912W_PB123_S374_15_RNA.CEL

source_name: liver_male C57BL/6_TCDD treated_500 μg/kg

tag: age

value: 500 μg/kg TCDD


title: Root grown under +Fe of ys1mutant plants Replicate 3

description: test


title: Male C57BL/6 TCDD 500 μg/kg rep4

description: HTMoGene11_022912W_PB124_S374_16_RNA.CEL

tag: Sex


title: Shoot grown under -Fe of ys3 mutant plants Replicate 3

description: test

source_name: Fe deficient shoot

value: shoot


title: Placenta 1 Standard 12h rep1

description:
miRNA expression in primary trophoblasts
mR.3.N12.1

source_name: Primary human trophoblast third trimester

tag: culture conditions

value: standard


title: Placenta 1 Hypoxic 12h rep1

description:
miRNA expression in primary trophoblasts
mR.4.H12.1

value: hypoxic

tag: time


title: Shoot grown under -Fe of ys1mutant plants Replicate 3

description: test


title: Placenta 1 Standard 0h rep1

description:
miRNA expression in primary trophoblasts
mR.0.T0.1


title: Placenta 1 Hypoxic 6h rep1

description:
miRNA expression in primary trophoblasts
mR.2.H6.1


title: Placenta 1 Standard 6h rep1

description:
miRNA expression in primary trophoblasts
mR.1.N6.1


title: Shoot grown under -Fe of WT plants Replicate 3

description: test


title: MDA-MB-231_mir-369-3p-inhibitor_rep1

description:
inhibitor-369-3p
Replicate 1

source_name: MDA-MB-231 transfected with 50nm of mir -369-3p-inhibitor


title: MDA-MB-231_mir-135a-inhibitor_rep2

description:
inhibitor-135a
Replicate 2

source_name: MDA-MB-231 transfected with 50nm of mir -135a-inhibitor


title: MDA-MB-231_mir-369-3p-mimic_rep2

description:
mir-369-3p
Replicate 2

source_name: MDA-MB-231 transfected with 50nm of mir -369-3p-mimic


title: MDA-MB-231_mir-369-3p-inhibitor_rep2

description:
inhibitor-369-3p
Replicate 2


title: Male C57BL/6 TCDD 500 μg/kg rep2

description: HTMoGene11_022912W_PB122_S374_14_RNA.CEL

value: 12-15 weeks

value: 96 hours


title: MDA-MB-231_mir-369-3p-mimic_rep1

description:
mir-369-3p
Replicate 1


title: Male C57BL/6 TCDD 250 μg/kg rep3

description: HTMoGene11_022312W_PB119_S374_11_RNA.CEL

source_name: liver_male C57BL/6_TCDD treated_250 μg/kg

value: 250 μg/kg TCDD


title: Male C57BL/6 TCDD 500 μg/kg rep1

description: HTMoGene11_022912W_PB121_S374_13_RNA.CEL


title: Root grown under +Fe of WT plants Replicate 3

description: test


title: Male C57BL/6 TCDD 250 μg/kg rep4

description: HTMoGene11_022312W_PB120_S374_12_RNA.CEL


title: MDA-MB-231_mir-135a-mimic_rep2

description:
mir-135a
Replicate 2

source_name: MDA-MB-231 transfected with 50nm of mir -135a-mimic


title: Shoot grown under +Fe of ys3 mutant plants Replicate 3

description: test

source_name: Fe sufficient shoot


title: Huh7 cell line metformin3

source_name: human hepatocellular carcinoma

growth_protocol: cell line: Cells were grown in RPM I 1640 supplemented with 10% fetal bovine serum in a humidified atmosphere of 5% CO2 at 37°C.

treatment_protocol: cell line: Huh7 cells were treated with 10 mM metformin or without metformin for 72 h.

tag: agent

value: metformin


title: Male C57BL/6 TCDD 250 μg/kg rep2

description: HTMoGene11_022312W_PB118_S374_10_RNA.CEL

tag: strain


title: MDA-MB-231_mir-127-5p-mimic_rep2

description:
mir-127-5p
Replicate 2

source_name: MDA-MB-231 transfected with 50nm of mir -127-5p-mimic


title: Huh7 cell line control3

value: control


title: Shoot grown under +Fe of ys1mutant plants Replicate 3

description: test


title: Female C57BL/6 TCDD 1000 μg/kg rep3

description: HTMoGene11_022312W_PB107_S386_23LiverB.CEL

source_name: liver_female C57BL/6_TCDD treated_1000 μg/kg

value: Female

tag: treated with


title: Shoot grown under +Fe of WT plants Replicate 3

description: control


title: Huh7 cell line metformin2


title: MDA-MB-231_mir-135a-mimic_rep1

description:
mir-135a
Replicate 1


title: MDA-MB-231_mir-135a-inhibitor_rep1

description:
inhibitor-135a
Replicate 1


title: Male C57BL/6 TCDD 250 μg/kg rep1

value: Male

tag: exposure time


title: MDA-MB-231_NT-microRNA-mimic-control_rep2

description:
NT-Control
Replicate 2

source_name: MDA-MB-231 transfected with 50nm of Non-targeting control

value: Non-targeting control


title: Root grown under -Fe of ys3 mutant plants Replicate 2

description: test


title: Root grown under -Fe of ys1mutant plants Replicate 2

description: test


title: MDA-MB-231_mir-127-5p-mimic_rep1

description:
mir-127-5p
Replicate 1


title: MDA-MB-231_NT-microRNA-mimic-control_rep1

description:
NT-Control
Replicate 1


title: Huh7 cell line control1


title: Male C57BL/6 TCDD 125 μg/kg rep3

source_name: liver_male C57BL/6_TCDD treated_125 μg/kg

value: 125 μg/kg TCDD

value: Liver


title: Huh7 cell line control2


title: Root grown under -Fe of WT plants Replicate 2

description: test

source_name: Fe deficient root

value: WT(Alice)

value: Fe deficient

value: root


title: Root grown under +Fe of ys3 mutant plants Replicate 2

description: test

source_name: Fe sufficient root

value: Fe sufficient


title: Huh7 cell line metformin1


title: Root grown under +Fe of ys1mutant plants Replicate 2

description: test


title: Male C57BL/6 TCDD 125 μg/kg rep2


title: Shoot grown under -Fe of ys3 mutant plants Replicate 2

description: test

value: shoot


title: Shoot grown under -Fe of ys1mutant plants Replicate 2

description: test


title: Root grown under +Fe of WT plants Replicate 2

description: test


title: Male C57BL/6 CornOil rep4

source_name: liver_male C57BL/6_corn oil treated

value: Corn Oil vehicle


title: BT-549_siControl_rep3

city: Lund

first: Christer

last: Larsson

address: Medicon Village, Bldg 404:C3

department: Laboratory Medicine

country: Sweden

institute: Lund university

description: Sample name: BTc3.a1.lbe1

scan_protocol: Standard Illumina iScan N240 scanning protocol Scan setting file: Direct Hyb

data_processing: The data were normalized using quantile normalization with BASE

source_name: BT-549 cells treated with siControl

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevC, (Modification of Amplification kit v 2.2)

extract_protocol: Qiagen Rneasy

value: BT-549 breast cancer cell line

value: siControl


title: BT-549_siPRKCD_rep3

description: Sample name: BTd3.a1.lbe1

source_name: BT-549 cells treated with siPRKCD

value: siPRKCD


title: Male C57BL/6 CornOil rep3

value: 12-15 weeks

value: 96 hours


title: MDA-MB-468_siControl_rep3

description: Sample name: 468c3.a1.lbe1

source_name: MDA-MB-468 cells treated with siControl

value: MDA-MB-468 breast cancer cell line


title: MDA-MB-468_siPRKCD_rep3

description: Sample name: 468d3.a1.lbe1

source_name: MDA-mB-468 cells treated with siPRKCD

value: MDA-mB-468 breast cancer cell line


title: Male C57BL/6 CornOil rep1

value: Male


title: Male C57BL/6 TCDD 125 μg/kg rep1


title: BT-549_siPRKCD_rep2

description: Sample name: BTd2.a1.lbe1


title: Male C57BL/6 CornOil rep2


title: MDA-MB-468_siPRKCD_rep2

description: Sample name: 468d2.a1.lbe1


title: BT-549_siPRKCD_rep1

description: Sample name: BTd1.a1.lbe1


title: Shoot grown under -Fe of WT plants Replicate 2

description: test

source_name: Fe deficient shoot


title: BT-549_siControl_rep2

description: Sample name: BTc2.a1.lbe1


title: MDA-MB-231_mir-655-3p-mimic_rep1

description:
mir-655-3p
Replicate 1

source_name: MDA-MB-231 transfected with 50nm of mir -655-3p-mimic


title: Shoot grown under +Fe of ys1mutant plants Replicate 2

description: test


title: Shoot grown under +Fe of WT plants Replicate 2

description: control


title: Root grown under -Fe of ys3mutant plants Replicate 1

description: test


title: Root grown under -Fe of WT plants Replicate 1

description: test


title: Root grown under +Fe of ys3 mutant plants Replicate 1

description: test


title: Root grown under +Fe of ys1mutant plants Replicate 1

description: test


title: Root grown under +Fe of WT plants Replicate 1

description: test


title: Shoot grown under +Fe of ys3 mutant plants Replicate 2

description: test


title: MDA-MB-468_siControl_rep2

description: Sample name: 468c2.a1.lbe1


title: Shoot grown under -Fe of ys3 mutant plants Replicate 1

description: test


title: Shoot grown under -Fe of WT plants Replicate 1

description: test


title: Shoot grown under -Fe of ys1mutant plants Replicate 1

description: test


title: Shoot grown under +Fe of ys1mutant plants Replicate 1

description: test


title: Shoot grown under +Fe of ys3 mutant plants Replicate 1

description: test


title: Shoot grown under +Fe of WT plants Replicate 1

description: control


title: BT-549_siControl_rep1

description: Sample name: BTc1.a1.lbe1


title: HTR8/Mhy1_1

city: La Jolla

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

description: HTR8/SVneo cells expressing Mycoplasma hyorhinis Mhy1 DNA methyltransferase

hyb_protocol: The labeled RNA samples (750 ng each) were hybridized overnight at 58°C to the HumanHT-12 v4 Expression BeadChip (Illumina). BeadChips were washed and developed using fluorolink streptavidin-Cy3 (GE Healthcare).

scan_protocol: BeadChips were scanned with a BeadArray Reader (Illumina).

data_processing: The raw data were processed using Feature Extraction software (Agilent). The statistical analysis and quantile normalization were performed using GeneSpring GX software (Agilent).

source_name: HTR8 cells expressing Mhy1_1 cells

label_protocol: The total RNA samples (500 ng each) were labeled using an Illumina RNA Amplification system (Ambion).

growth_protocol: Human fibrosarcoma HT1080 cells were grown in DMEM medium supplemented with 10% fetal bovine serum (FBS; Atlanta Biologicals). Human transformed first trimester extravillous HTR8/SVNeo trophoblast cells were grown in RPMI-1640 medium supplemented with 5% FBS. Cells were normally plated at a 20% density and harvested for the analysis at an 80-90% density. Cell cultures were maintained under standard culturing conditions at 37°C and 5% CO2.

extract_protocol: Cultured cells were lyzed using TRIreagent and purified using a Direct-zol RNA column (Zymo Research). The purified RNA was quantified using a Nanodrop ND-1000 spectrophotometer (Thermo Scientific). The RNA purity was estimated by measuring the OD260/280 and the OD260/230 ratios. The RNA integrity was determined using an Experion automated electrophoresis system (Bio-Rad).

treatment_protocol: For transfection plasmid DNA was purified using a HiSpeed Plasmid Midi Column (Qiagen). HT1080 and HTR8 cells were grown in 24-well plates to reach a 50% density. Cells were transfected using the purified plasmid DNA (500 ng), Lipofectamine LTX (1 µl) and PLUS reagent (0.5 µl, Invitrogen) in 200 µl Opti-Mem I medium. In 48 h post-transfection cells were plated at a 20% density in the respective medium supplemented with blasticidin S (5 µg/ml, Invitrogen). Stable cell lines were generated by picking and expanding blasticidin-resistant foci.

tag: expressed protein


title: HTR8/Mhy1_2

source_name: HTR8 cells expressing Mhy1, replicate of 9372850042_A


title: MDA-MB-468_siPRKCD_rep1

description: Sample name: 468d1.a1.lbe1


title: MDA-MB-468_siControl_rep1

description: Sample name: 468c1.a1.lbe1


title: Male C57BL/6 TCDD 125 μg/kg rep4


title: HT1080/Mhy2

description: HT1080 cells expressing Mycoplasma hyorhinis Mhy2 DNA methyltransferase

source_name: HT1080 cells expressing Mhy2 cells


title: FL_ProB.3_miRNA

city: Philadelphia

first: Kyoko

last: Hayakawa

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

description: miRNA expression of fetal liver Pro-B cells, replidate 3

hyb_protocol: Labeled RNA was hybridized to the Agilent mouse miRNA microarray at 55 °C for 20 hours

scan_protocol: Hybridized slides were scanned on an Agilent scanner and fluorescent intensities of hybridization signals were extracted using Agilent Feature Extraction software.

data_processing: data were quantile normalized

source_name: Fetal liver, Pro-B cells, replicate 3

label_protocol: 100 ng total RNA was dephosphorylated with Calf Intestinal Phosphatase and then end-labeled with Cyanine-3-pCp using T4 RNA ligase

extract_protocol: Total RNA was isolated using TRIzol reagent

treatment_protocol:
For each bone marrow sort, 3 female BALB/c mice were sacrificed and a single cell suspension was prepared from bone marrow after flushing femur and tibia using a 1ml syringe and a 25 gauge needle. This generated 1 Fr. B/C sorted sample. Total of 3 individual sorts.
For each fetal liver sort, a BALB/c mouse with embryos at day 16 of gestation was sacrificed, embryos (average of 8) were sacrificed, and a single cell suspension was prepared from liver by gentle dissociation between 2 frosted glass slides. This generated 1 Fr. B/C sorted sample. Total of 3 individual sorts.

value: BALB/c mice

tag: developmental stage

value: Fetus

value: Fetal Liver


title: HT1080/Mhy1_2 replicate

description: HT1080 cells expressing Mycoplasma hyorhinis Mhy1 DNA methyltransferase

source_name: HT1080 cells expressing Mhy1, replicate of 9249907030_A


title: HT1080/LacZ control

description: HT1080 cells expressing LacZ control plasmid

source_name: HT1080 cells expressing LacZ, reference cells

value: LacZ


title: HT1080/Mhy1_1

source_name: HT1080 cells expressing Mhy1


title: HT1080 control

description: Parental HT1080 cells

source_name: HT1080 control cells

value: parental


title: HTR8/Mhy2_2

description: HTR8/SVneo cells expressing Mycoplasma hyorhinis Mhy2 DNA methyltransferase

source_name: HTR8 cells expressing Mhy2, replicate of 9372850042_C


title: Mature fruiting body biological sample 1

city: Shatin

first: Xuanjin

last: Cheng

address: Rm 386, Science Center South Block

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

hyb_protocol: The labeled cDNAs were hybridized using the NimbleGen mixer and hybridization system (http://www.nimblegen.com/support/dna-microarray-support.htmll).

scan_protocol: The slides were scanned with NimbleGen MS 200 Microarray Scanner using manufacturer's protocol (http://www.nimblegen.com/support/dna-microarray-support.htmll).

data_processing: The data were extracted and normalized using the NimbleScan software.

organism: Coprinopsis cinerea

source_name: Coprinopsis cinerea mature fruiting body

label_protocol: The cDNA samples were labeled with Cy3 with the NimbleGen One-color DNA labeling kit according to the manufacturer's protocol (http://www.nimblegen.com/support/dna-microarray-support.htmll).

growth_protocol: The C. cinerea strain used is a dikaryotic strain (with 50% Okayama-7 origin) backcrossed with Okayama-7, the monokaryotic strain used for the genome sequencing project, for 5 generations. This strain is about 98.44% homologous to Okayama-7 while retaining the ability to fruit. The strain was cultivated on YMD medium containing 0.4% yeast extract, 1% malt extract and 0.4% potato dextrose solidified with Bacto® agar. Mycelium was cultivated on agar plates at 37oC for about 1 week until the mycelium grew over the whole agar surface. Fruiting body development was induced by incubating the mycelia culture at 25oC under a light/dark regime of 12/12 hr. The incubator was kept at a relative humidity higher than 60% for the production of fruiting bodies.

extract_protocol: The RNAs were extracted by the RNeasy Plant Mini Kit (Qiagen). Samples were freshly scraped or cut into the mortar soaked with liquid nitrogen and were immediately grinded to fine powder by pestle. About 100mg of samples were transferred to each RNase-free microcentrifuge tube containing 450μl Buffer RLC and the tubes were  vortexed to homogenize the samples. The lysate were then transferred to QIAshredder spin column and centrifuged for 2 min at 10000rpm. The supernatant of the flowthrough were transferred to new microcentrifuge tubes. For each tube, 200μl 100% ethanol was added to the cleared lysate and mixed by pipeting. The mixtures together with any precipitates, were transferred to an RNeasy spin column and centrifuged for 15s at 10000rpm. The flow through was discarded. After that, the spin column was washed by 700μl Buffer RW1 followed by 500μl Buffer RPE wash for two times. After drying the spin column by centrifuge for 1 min at full speed, 40μl RNase-free water was  added to the column to elute the RNA and kept at -80oC until use  .

treatment_protocol: All sample handling instruments including mortars, pestles, forceps and scissors were prebaked at 300oC overnight to remove RNase and cooled to -20oC before use. Latex gloves and barrier tips were used to ensure minimum RNase contamination.

value: mature fruiting body