title: Extrahepatic Bileduct and gallbladder en bloc at day 7 after rhusus rotvirus challenge miRNA rep3

description: Experimental group  at day 7

value: 7 days


title: Extrahepatic Bileduct and gallbladder en bloc at day 14 after normal saline injection miRNA rep2

status: Public on Oct 15 2013

type: RNA

city: Cincinnati

first: Jorge

middle: A

last: Bezerra

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology, Hepatology & Nutrition

country: USA

institute: Cincinnati Children's Hospital Medical Center

description: Control group at day 14

data_processing:
Expression was calculated using the comparative Ct method (Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3: 1101-8)
Normalization was done using average of 4 MammU6 probes on each plate.
The deltaCt values (Ct_Target − Ct_MammU6) were imported to GeneSpring GX 11.5 platform (Agilent Technologies, CA), converted to log2-based values and used for statistical analyses.
Fold Change worksheet reports each sample/average of 9 normal controls (i.e., D3_NS_1~3, D7_NS_1~3, D14_NS_1~3) ratios.

label: FAM

molecule: total RNA

organism: Mus musculus

label_protocol:
Reverse transcription into first strand cDNA was performed using reagents from TaqMan® MicroRNA RT Kit and Megaplex RT Primer Pools (Applied Biosystems, CA).
Quantitative real-time PCR was performed using the TaqMan® Array Rodent MicroRNA Card v2.0 (A and B) with the Universal PCR Master Mix, No AmpErase UNG using 7900 HT Fast Real-Time PCR System (Applied Biosystems).

growth_protocol: Balb/c mice were purchased from Charles River Laboratories (Wilmington, MA).

extract_protocol:
Extrahepatic bile ducts and gallbladder were microdissected en bloc at 3, 7 and 14 days after RRV or saline injection and stabilized with RNAlater (QIAGEN, CA).
3 sets of samples were generated for each time point (experimental and control groups), with each set containing 2-6 extrahepatic bileducts.
Total RNA was isolated from extrahepatic bileducts of RRV- or saline-injected mice using miRNeasy Mini Kit, according to the manufacturer’s protocol (QIAGEN, CA).
RNA integrity was verified using the Agilent 2100 Bioanalyser (Agilent Technologies, Inc., CA).

treatment_protocol: Newborn mice were injected with 20 μL of a solution containing 1.5x10^6 fluorescent-forming units of Rhesus rotavirus type-A or 0.9% NaCl (normal saline) intraperitoneally within 24 hours of birth.

tag: tissue

value: Extrahepatic Bileduct and gallbladder

tag: strain

value: Balb/c

tag: time

value: 14 days

tag: treatment

value: Normal saline


title: NFX1-123 overexpression replicate 6

city: Seattle

first: Rachel

last: Katzenellenbogen

state: WA

address: 1900 Ninth Ave

department: Adolescent Medicine

institute: Seattle Children's Research Institute

description:
condition 1
NHK6 FNFX1-123

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quality control was initially analyzed using GenomeStudio.  Box-whisker plots of raw signal intensity values for each sample showed that the distribution of intensities in each sample was similar.  Data were all log2 transformed followed by quantile normalization. Data were filtered based on the detection p-value, and only those probes with a detection p-value less than 0.01 across all samples were carried forward for analysis. Comparative analysis was performed to determine fold-change values between the normalized probe intensities, using the isogenic scramble shRNA control as the baseline.  We required a fold change of greater than or equal to 2 and the gene had to be detected in at least two of the three conditions.  Subsequent analyses were performed using GeneSpring GX11.5.1, and Excel.

label: biotin

organism: Homo sapiens

source_name: NFX1-123 overexpression

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

growth_protocol: NHKs were derived from neonatal foreskins and grown in EpiLife medium supplemented with calcium chloride (60 μM), human keratinocyte growth supplement (Life Technologies, Carlsbad, CA), and penicillin-streptomycin

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol

treatment_protocol: Cells were grown as above and harvested at 70-80% confluence.

value: neonatal foreskin

tag: cell type

value: keratinocytes


title: Extrahepatic Bileduct and gallbladder en bloc at day 7 after rhusus rotvirus challenge miRNA rep2

description: Experimental group  at day 7

value: Rhesus rotavirus


title: HF-18787-(1) Hind

type: genomic

city: South San Francisco

first: Peter

last: Haverty

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

hyb_protocol: Affymetrix 100K protocol

scan_protocol: Affymetrix 100K protocol

data_processing: Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization.  Ninety normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=100k) and analyzed at the same time.  One CEL file for each set (Xba and Hind) with the median signal intensity across the set was selected as the reference array.   The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows.  For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set.  The log2 ratios were centered to a median of zero and segmented using the DNAcopy package for the R statistical environment.

molecule: genomic DNA

label_protocol: Affymetrix 100K protocol

growth_protocol: Patient samples

extract_protocol: Qiagen DNA extraction kit was used according to the manufacturer's instructions

treatment_protocol: Untreated

tag: braf status

tag: sample id

value: melanoma tumor


title: Extrahepatic Bileduct and gallbladder en bloc at day 7 after normal saline injection miRNA rep3

description: Control group at day 7


title: Plastic_noFGF2_replicate1, S11_H031

city: Worcester

first: Tanja

last: Dominko

state: MA

address: 100 Institute Rd

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

hyb_protocol: aRNA was hybridized at 50C overnight using the HybBag mixing system with 1x OneArray Hybridization Buffer (Phalanx Biotech), 0.01mg/ml sheared salmon spearm DNA and 0.025mg/ml of labeled target. After hybridization, arrays were washed according to OneArray protocol.

scan_protocol: Raw intensity signals were captured using Molecular Dynamics Axon 4100A scanner, were measured using GenePixPro Software, and were stored in GPR format.

data_processing: R/Bioconductor was used to normalize and filter data. Background corrected data was normalized by adjusting columns to the same median value. Filtering was performed to leave probes with maximum intensity value across samples higher than 100. Intensity values lower than 5 were substituted with 5 to remove negative values. Data was log2 transformed and filtered to leave gene probes with standard deviation above median. Only gene probes belonging to groups 1 and 4 (group assignment by Phalanx Biotech) were selected for further analysis.

source_name: Adult human dermal fibroblasts, plastic, no FGF2

label_protocol: High-quality RNA (RIN>7.0) was converted to double-stranded cDNA and amplified using in vitro transcription that included amino-allyl UTP. The product ws conjugated with Cy5 NHS ester.

growth_protocol: Adult human dermal fibroblasts (CRL-2352, ATCC) were expanded at ambient oxygen on tissue culture plastic in DMEM/F12 + 10%FBS. At passage 7, they were cultured for seven days at 5% oxygen in DMEM/F12+10%FCIII at four experimental conditions.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen).

treatment_protocol: The four experimental conditions included growing adult human dermal fibroblasts in indicated conditions on glass; on tissue culture plastic; on glass with addition of 4ng/ml FGF2 (PeproTech); and on tissue culture plastic with addition of 4ng/ml FGF2 (PeproTech). Media was changed every three days.

tag: cell line

value: ATCC CRL-2352

value: adult human dermal fibroblasts

tag: surface

value: plastic


title: Extrahepatic Bileduct and gallbladder en bloc at day 7 after normal saline injection miRNA rep2

description: Control group at day 7


title: HF-18719-(1) Hind


title: Extrahepatic Bileduct and gallbladder en bloc at day 7 after rhusus rotvirus challenge miRNA rep1

description: Experimental group  at day 7


title: Extrahepatic Bileduct and gallbladder en bloc at day 7 after normal saline injection miRNA rep1

description: Control group at day 7


title: Plastic_noFGF2_replicate1, S11_H032


title: Plastic_plusFGF2_replicate2, S10_H030

source_name: Adult human dermal fibroblasts, plastic, FGF2


title: NFX1-123 shRNA1 replicate 5

description:
condition 3
NHK5 sh1NFX1-123

source_name: NFX1-123 shRNA1


title: NFX1-123 shRNA2 replicate 5

description:
condition 4
NHK5 sh3NFX1-123

source_name: NFX1-123 shRNA2


title: HF-18782-(1) Hind


title: Extrahepatic Bileduct and gallbladder en bloc at day 3 after rhusus rotvirus challenge miRNA rep3

description: Experimental group  at day 3

value: 3 days


title: Plastic_plusFGF2_replicate1, S9_H027


title: Extrahepatic Bileduct and gallbladder en bloc at day 3 after rhusus rotvirus challenge miRNA rep2

description: Experimental group  at day 3


title: NFX1-123 shRNA1 replicate 4

description:
condition 3
NHK4 sh1NFX1-123


title: NFX1-123 shRNA control replicate 5

description:
condition 2
NHK5 scramble

source_name: NFX1-123 shRNA control


title: NFX1-123 shRNA2 replicate 4

description:
condition 4
NHK4 sh3NFX1-123


title: Extrahepatic Bileduct and gallbladder en bloc at day 3 after rhusus rotvirus challenge miRNA rep1

description: Experimental group  at day 3


title: HF-18713-(1) Hind


title: NFX1-123 overexpression replicate 5

description:
condition 1
NHK5 FNFX1-123


title: Plastic_plusFGF2_replicate2, S10_H028


title: Plastic_plusFGF2_replicate1, S9_H025


title: HF-18689-(1) Hind


title: NFX1-123 overexpression replicate 4

description:
condition 1
NHK4 FNFX1-123


title: Plastic_plusFGF2_replicate1, S9_H026


title: HF-17688-(1) Hind


title: Glass_noFGF2_replicate2, S8_H023

source_name: Adult human dermal fibroblasts, glass, no FGF2

value: glass


title: Glass_noFGF2_replicate2, S8_H024


title: HF-17690-(1) Hind


title: HF-17686-(1) Hind


title: Extrahepatic Bileduct and gallbladder en bloc at day 3 after normal saline injection miRNA rep3

description: Control group at day 3


title: NFX1-123 shRNA1 replicate 3

description:
condition 3
NHK3 pB16E6 sh1NFX1-123

source_name: neonatal foreskin

tag: transduction


title: Glass_noFGF2_replicate2, S8_H022


title: HF-17687-(1) Hind


title: HF-18686-(1) Hind


title: NFX1-123 shRNA control replicate 4

description:
condition 2
NHK4 scramble


title: Plastic_plusFGF2_replicate2, S10_H029


title: Glass_noFGF2_replicate1, S7_H021


title: HF-17691-(1) Hind


title: NFX1-123 shRNA3 replicate 3

description:
condition 4
NHK3 pB16E6 sh3NFX1-123


title: Extrahepatic Bileduct and gallbladder en bloc at day 3 after normal saline injection miRNA rep2

description: Control group at day 3


title: HF-17684-(1) Hind


title: Extrahepatic Bileduct and gallbladder en bloc at day 3 after normal saline injection miRNA rep1

description: Control group at day 3


title: NFX1-123 shRNA control replicate 3

description:
condition 2
NHK3 pB16E6 scramble

value: scramble


title: Glass_noFGF2_replicate1, S7_H019


title: NFX1-123 overexpression replicate 3

description:
condition 1
NHK3 pB16E6 FNFX1-123


title: Glass_noFGF2_replicate1, S7_H020


title: Glass_plusFGF2_replicate2, S6_H017

source_name: Adult human dermal fibroblasts, glass, FGF2


title: Glass_plusFGF2_replicate2, S6_H018


title: HF-16922-(1) Hind


title: HF-17588-(1) Hind


title: HF-16894 Hind


title: NFX1-123 shRNA3 replicate 2

description:
condition 4
NHK2 pB16E6 sh3NFX1-123


title: NFX1-123 shRNA1 replicate 2

description:
condition 3
NHK2 pB16E6 sh1NFX1-123


title: NFX1-123 shRNA3 replicate 1

description:
condition 4
NHK1 pB16E6 sh3NFX1-123


title: NFX1-123 overexpression replicate 2

description:
condition 1
NHK2 pB16E6 FNFX1-123


title: NFX1-123 shRNA control replicate 2

description:
condition 2
NHK2 pB16E6 scramble


title: HF-16873 Hind


title: HF-16892 Hind


title: HF-16890 Hind


title: HF-16888 Hind


title: Glass_plusFGF2_replicate2, S6_H016


title: NFX1-123 shRNA1 replicate 1

description:
condition 3
NHK1 pB16E6 sh1NFX1-123


title: NFX1-123 shRNA control replicate 1

description:
condition 2
NHK1 pB16E6 scramble


title: Glass_plusFGF2_replicate1, S5_H014


title: Glass_plusFGF2_replicate1, S5_H013


title: ovarian cancer_hereditary H24

status: Public on Oct 14 2013

city: Lund

first: Katarina

last: Bartuma

address: Barn garan 2b

country: Sweden

institute: department of Oncology

description:
Nuclear RNA
ovarian cancer_hereditary

hyb_protocol: The cDNA mediated Annealing, Selection, extension and Ligation (DASL) assay (Illumina, San Diego, CA) containing 24 526 probes representative of  18 626 unique genes was used for whole genome expression analysis. The samples were randomly placed on the chips and were profiled following the manufacturer’s instructions.

scan_protocol: Standard Illumina BeadArrayReader S432 scanning protocol

data_processing: Samples with a raw average signal intensity <250 or <8000 detected genes were excluded (1 Lynch syndrome sample). The expression data for the 67 remaining samples were quartile normalized and a presence filter of 80% was applied to the genes across all samples with a detection p-value of <0.01. The data were imported into MeV 4.6.02 software and were log2 transformed and mean centered across assays. Significance analysis of microarray (SAM) was used to identify differentially expressed genes between the groups. The significant genes selected by SAM were used in complete linkage hierarchical clustering according to the Pearson distance metric. Discriminatory genes with a fold change >1.7 and FDR <0.1 were selected for pathway analysis in the Ingenuity Pathway Analysis software (IPA) (Ingenuity® systems, www.ingenuity.com).  Canonical pathways with more than three genes and p-values <0.05 were considered significant.

source_name: Ovarian cancer

extract_protocol: RNA was extracted from 3-5, 10-μm sections selected from non-necrotic tumor areas with >70% tumor cell content using the High Pure RNA Paraffin Kit (Roche, Castle Hill, Australia). RNA concentrations were determined using a NanoDrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE). Sufficient RNA (200 ng) with 260/280 ratios >1.8 was obtained from 68/72 (95%) samples, 26 out of 28 Lynch syndrome-associated tumors and 42 out of 44 sporadic tumors.

tag: histotype

value: S

tag: grade

tag: Stage

tag: age at diagnosis

tag: age of ffpe tissue


title: ovarian cancer_hereditary H29

description:
Nuclear RNA
ovarian cancer_hereditary

value: E


title: ovarian cancer_hereditary H27

description:
Nuclear RNA
ovarian cancer_hereditary

value: C

value: IC


title: ovarian cancer_hereditary H25

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H26

description:
Nuclear RNA
ovarian cancer_hereditary

value: IIIC


title: NFX1-123 overexpression replicate 1

description:
condition 1
NHK1 pB16E6 FNFX1-123


title: HF-16884 Hind


title: ovarian cancer_hereditary H17

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H28

description:
Nuclear RNA
ovarian cancer_hereditary

value: IA


title: ovarian cancer_hereditary H22

description:
Nuclear RNA
ovarian cancer_hereditary

value: IB


title: ovarian cancer_hereditary H20

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H18

description:
Nuclear RNA
ovarian cancer_hereditary

value: IIA


title: ovarian cancer_hereditary H12

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H13

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H14

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H9

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H10

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H19

description:
Nuclear RNA
ovarian cancer_hereditary


title: Glass_plusFGF2_replicate1, S5_H015


title: ovarian cancer_hereditary H6

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H4

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H16

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H8

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H11

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H5

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_sporadic E82

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_hereditary H3

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H2

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_hereditary H1

description:
Nuclear RNA
ovarian cancer_hereditary


title: ovarian cancer_sporadic E73

description:
Nuclear RNA
ovarian cancer_sporadic

value: IIIB


title: ovarian cancer_sporadic E29

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E79

description:
Nuclear RNA
ovarian cancer_sporadic

value: 3´

value: IV


title: ovarian cancer_sporadic E34

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E37

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E41

description:
Nuclear RNA
ovarian cancer_sporadic

value: IIC


title: ovarian cancer_sporadic E78

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E27

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E28

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E35

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E25

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E75

description:
Nuclear RNA
ovarian cancer_sporadic

value: M


title: ovarian cancer_sporadic E33

description:
Nuclear RNA
ovarian cancer_sporadic

value: IIB


title: ovarian cancer_sporadic E30

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E32

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E23

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E21

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E22

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E24

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E26

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E36

description:
Nuclear RNA
ovarian cancer_sporadic

value: IIIA


title: ovarian cancer_sporadic E17

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E18

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E20

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E16

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E19

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E15

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E9

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E14

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E6

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E13

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E7

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E5

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E3

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E12

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E4

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E2

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E11

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E1

description:
Nuclear RNA
ovarian cancer_sporadic


title: ovarian cancer_sporadic E8

description:
Nuclear RNA
ovarian cancer_sporadic


title: Jurkat Control 24h

status: Public on Oct 12 2013

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

description: Jurkat Ctrl 24h

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction. The normalization has been done using Illumina's BeadStudio.

source_name: Jurkat Control 24h

growth_protocol: Healthy human peripheral blood T cells were prepared as described previously (Zhu et al., Int J Cancer, 2007) and were more than 90% CD3 positive. For generating proliferating T cells, freshly isolated peripheral blood T cells were cultured at a density of 2x10P6P cells/ml and were activated with 1 μg/ml PHA overnight. Activated T cells were then washed three times and cultured for additional 5 days in the presence of 25 U/ml IL-2. Jurkat-16 and peripheral blood T cells were cultured in RPMI 1640 medium supplemented with 10% FCS, 50 µg/ml gentamicin (GIBCO laboratories, Grand Island, NY).

extract_protocol: RNA was extracted with the QIAGEN RNeasy Plus Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were plated in duplicates and treated for the indicated periods of time at 37 °C with solvent DMSO or 50 nM of Roc-A (>98% pure, assessed by HPLC) (BIOTREND Chemicals AG, Zurich, Swiss). Approximately 1 x 10P6P cells were collected and RNA was extracted as indicated.

value: DMSO

value: Blood

tag: array id


title: R5020, repl.1

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description:
T47D-MTVL is a breast cancer cell line carrying one stably integrated copy of the luciferase reporter gene driven by the MMTV promoter.

T47D-MTVL was stably infected with an inducible system for the expression of shRNAs. Cells stably express RedFP and KRAB repressor fused to the Tet regulator. Upon Dox treatment, cells express GFP and the cloned shRNA.

T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and empty shRNA expression vector (pLVTHM), uninduced (no doxycycline added).

R19
Treated with the progesterone analogue R5020 10nM for 6 hours, biological replicate 1 of 2.
Was also used as negative control for transfection.

hyb_protocol: After preheating at 65ºC for 5 min., for each sample, 750 ng of biotinylated cRNA were hybridized in a BeadChip Hyb Chamber with rocking 16 h at 58ºC. The day after, the bead arrays were washed with Illumina proprietary washing solutions in a Hybex waterbath: first with static incubation for 10 min at 55ºC in E1BC solution, followed by 10 rinses by dipping in the same solution and shaking 5 min at 90 rpm in an orbital shaker; the next wash was by dipping 10 times in 100% ethanol and shaking 10 min at 110 rpm in an orbital shaker; this was followed by another wash in E1BC solution with 10 dippings followed by 2 min shaking at 90 rpm. Washed bead arrays were blocked in E1 buffer 10 min in rocking incubator and 10 additional minutes with 2 ml of E1 buffer plus streptavidin-Cy3. The fluorescent reagent was washed away with E1BC solution with 10 dippings plus 5 min shaking at 140 rpm. Finally, Beadarrays were dried by centrifugation 4 min at 275 rcf, followed by scanning in an Illumina Beadstation.

scan_protocol: The Beadscan software was used to control the scanner, generate .tif images and extract the raw data as tabulated text files. Default settings for DirectHyb Gene Expression were used.

data_processing: The raw data was summarized per probe using the BeadStudio software Gene Expression module, and the summary data file was processed using the PILLA web interface tool (Lozano et al., unpublished), an implementation of the Lumi package (Du et al., 2008) developed within the Bioconductor project in the R statistical programming environment (Gentleman et al., 2004). Data were normalized using the rsn method and vst as the variance stabilization method. The log2 intensities were median centered and log ratios were computed as differences in log2 intensities for each probe. The SAM  (significance analysis of microarrays) two class unpaired comparison test was applied with 100 permutations to detect statistically significant differences in gene expression between treated and control conditions (Tusher et al., 2001).

source_name: T47D-MTVL, empty shRNA vector, progestin R5020

label_protocol: For each sample, 200 ng of total RNA were reverse transcribed, amplified by in vitro transcription and labelled with biotin-UTP using the Illumina Total Prep RNA amplification kit (IL1791, Ambion) following the manufacturer's instructions. Labelled sample quality was assessed by spectrophotometry and bioanalyzer.

growth_protocol: Cell lines were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100µg/ml streptomycin.

extract_protocol: Total RNA was extracted using the RNAsy Kit (Qiagen). RNA concentration was measured with a small volume spectrophotometer (Nanodrop). The quality of the RNA was analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay, with RIN ranging between 9.2 and 9.8.

treatment_protocol:
Plasmids for the lentivirus vector-mediated drug-inducible RNA interference system (pLVTHM, ptTR-KRAB-Red, pCMC-R8.91 and pMD.G) were provided by D. Trono (University of Geneva). For the production of viral particles containing the HIV-derived vectors, 2.5x10^6 HEK 293T cells (Clontech) were transfected with plasmids ptTR-KRAB-Red, pLVTHM (10µg), pCMV-R8.91 (6.5µg) and pMD.G (3.5µg) in 10 cm dishes using calcium phosphate. Medium was collected every 24 hours for 2 days and centrifuged 1h30min at 26.000 rpm at 4ºC in a sucrose gradient to concentrate viruses. Pellet containing viral particles was dissolved in medium and used for cell infection. Cells were infected using the spinoculation method, i.e., plates were centrifuged at 1,200 x g for 2 hr at 25 ºC.

Initially, a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with empty vector derived virus (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Dox treatment. Then cells were amplified in the absence of Dox until an experiment was performed. Doxycycline (Sigma) was added at 2.5 µg/ml when indicated. Along a 6-day treatment with Dox, cells were passaged at day 3. Serum-containing media was d with serum-free media at day 4 for growth arrest. At day 6, 10 nM progestin R5020 (or ethanol vehicle) was added for 6 h prior to RNA extraction.

value: breast cancer cells

value: progestin R5020

tag: shRNA

value: empty shRNA vector

tag: induction

value: uninduced (no doxycycline)


title: Control, CK1

city: Beijing

first: deqiang

last: zhang

address: No. 35, Qinghua East Road

department: College of Biological Sciences and Technology

country: China

institute: Beijing Forestry University

description: Expression data from one-year-old leaves of Populus simonii.

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

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

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

organism: Populus simonii

source_name: Populus simonii leaves from controls

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

growth_protocol: The cuttings were planted in basins (15 cm diameter × 10 cm depth) that contained a potting mix of a commercial medium and perlite at a ratio of 3:1. After sprouting and growth for about one year, healthy cuttings with approximately the same crown size and equal height were chosen and moved into growth chambers at the laboratory of Beijing Forestry University.

extract_protocol: Total RNA was extracted by the procedure of Chang et al. 1993. mRNA was isolated from total RNA (~0.5 mg for each treatment) using the PolyAtract mRNA Isolation System (Promega). Double-stranded cDNA was then synthesized from mRNA with the Universal RiboClone cDNA Synthesis System (Promega) following the manufacturer's protocol. The synthesized cDNA was dissolved in 50 μl TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by the RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The plants were transferred to a 42C and 25C chamber for high-temperature and control treatments, respectively. After six hours, all materials were collected, immediately frozen in liquid nitrogen, and stored at -80C until analyzed.

tag: age

value: 1 year

tag: tissue

value: leaves

value: control


title: R5020, repl.2

description:
T47D-MTVL is a breast cancer cell line carrying one stably integrated copy of the luciferase reporter gene driven by the MMTV promoter.

T47D-MTVL was stably infected with an inducible system for the expression of shRNAs. Cells stably express RedFP and KRAB repressor fused to the Tet regulator. Upon Dox treatment, cells express GFP and the cloned shRNA.

T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and empty shRNA expression vector (pLVTHM), uninduced (no doxycycline added).

R20
Treated with the progesterone analogue R5020 10nM for 6 hours, biological replicate 2 of 2.
Was also used as negative control for transfection.

tag: treatment


title: Control, CK2


title: Control, repl.1

description:
T47D-MTVL is a breast cancer cell line carrying one stably integrated copy of the luciferase reporter gene driven by the MMTV promoter.

T47D-MTVL was stably infected with an inducible system for the expression of shRNAs. Cells stably express RedFP and KRAB repressor fused to the Tet regulator. Upon Dox treatment, cells express GFP and the cloned shRNA.

T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and empty shRNA expression vector (pLVTHM), uninduced (no doxycycline added).

R17
Untreated control, biological replicate 1 of 2.
Was also used as negative control for transfection in a larger experiment (GSE12299).

source_name: T47D-MTVL, empty shRNA vector, no progestin R5020

tag: cell type

value: vehicle (ethanol)


title: Jurkat Control 4h

description: Jurkat Ctrl 4h

source_name: Jurkat Control 4h


title: Jurkat Control 36h

description: Jurkat Ctrl 36h

source_name: Jurkat Control 36h


title: High-temperature treatment, H1

source_name: Populus simonii leaves from high-temperature treatments

value: high temperature


title: Jurkat Control 16h

description: Jurkat Ctrl 16h

source_name: Jurkat Control 16h


title: Jurkat Control 10h

description: Jurkat Ctrl 10h

source_name: Jurkat Control 10h


title: High-temperature treatment, H2


title: Control, repl.2

description:
T47D-MTVL is a breast cancer cell line carrying one stably integrated copy of the luciferase reporter gene driven by the MMTV promoter.

T47D-MTVL was stably infected with an inducible system for the expression of shRNAs. Cells stably express RedFP and KRAB repressor fused to the Tet regulator. Upon Dox treatment, cells express GFP and the cloned shRNA.

T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and empty shRNA expression vector (pLVTHM), uninduced (no doxycycline added).

R18
Untreated control, biological replicate 2 of 2.
Was also used as negative control for transfection in a larger experiment (GSE12299).


title: Jurkat Roc A 28h

description: Jurkat RocA 28h

source_name: Jurkat Roc A 28h

value: Roc-A 50nM


title: Jurkat Roc A 14h

description: Jurkat RocA 14h

source_name: Jurkat Roc A 14h


title: Jurkat Roc A 10h

description: Jurkat RocA 10h

source_name: Jurkat Roc A 10h


title: Jurkat Roc A 16h

description: Jurkat RocA 16h

source_name: Jurkat Roc A 16h


title: Jurkat Roc A 36h

description: Jurkat RocA 36h

source_name: Jurkat Roc A 36h


title: Jurkat Roc A 12h

description: Jurkat RocA 12h

source_name: Jurkat Roc A 12h


title: Jurkat Control 0h

description: Jurkat Ctrl 0h

source_name: Jurkat Control 0h


title: Jurkat Roc A 8h

description: Jurkat RocA 8h

source_name: Jurkat Roc A 8h


title: Jurkat Roc A 32h

description: Jurkat RocA 32h

source_name: Jurkat Roc A 32h


title: Jurkat Roc A 6h

description: Jurkat RocA 6h

source_name: Jurkat Roc A 6h


title: Jurkat Roc A 24h

description: Jurkat RocA 24h

source_name: Jurkat Roc A 24h


title: Jurkat Roc A 7h

description: Jurkat RocA 7h

source_name: Jurkat Roc A 7h


title: Jurkat Roc A 1h

description: Jurkat RocA 1h

source_name: Jurkat Roc A 1h


title: Tcell Control 36h

description: Tcell Ctrl 36h

source_name: Tcell Control 36h


title: Jurkat Roc A 5h

description: Jurkat RocA 5h

source_name: Jurkat Roc A 5h


title: ovarian cancer_sporadic E74

description:
Nuclear RNA
ovarian cancer_sporadic

source_name: Ovarian cancer

value: IA


title: Tcell Roc A 28h

description: Tcell RocA 28h

source_name: Tcell Roc A 28h


title: Tcell Control 24h

description: Tcell Ctrl 24h

source_name: Tcell Control 24h


title: Tcell Control 0h

description: Tcell Ctrl 0h

source_name: Tcell Control 0h


title: Tcell Roc A 20h

description: Tcell RocA 20h

source_name: Tcell Roc A 20h


title: Jurkat Roc A 4h

description: Jurkat RocA 4h

source_name: Jurkat Roc A 4h


title: Tcell Control 14h

description: Tcell Ctrl 14h

source_name: Tcell Control 14h


title: Tcell Roc A 14h

description: Tcell RocA 14h

source_name: Tcell Roc A 14h


title: Jurkat Roc A 2h

description: Jurkat RocA 2h

source_name: Jurkat Roc A 2h


title: Tcell Roc A 10h

description: Tcell RocA 10h

source_name: Tcell Roc A 10h


title: Tcell Control 6h

description: Tcell Ctrl 6h

source_name: Tcell Control 6h


title: Tcell Roc A 3h

description: Tcell RocA 3h

source_name: Tcell Roc A 3h


title: Tcell Roc A 6h

description: Tcell RocA 6h

source_name: Tcell Roc A 6h


title: Rhizobium etli with and without orotic acid, biological replicate 3

city: Cuernavaca

first: Sergio

middle: Manuel

last: Encarnación

state: Morelos

address: Av. Universidad S/N

department: Centro de Ciencias Genomicas

country: Mexico

institute: Universidad Nacional Autonoma de México

description: Biological replicate 3 of 3.

hyb_protocol: Both Cy3 and Cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 4 ul of water, then were incubated at 94 C  and added 45 ul of hybridization buffer Nexterion Hyb (SCOTT nexterion). The mixture was hybridized at 50 C for 14 to 16 h. Hybridized arrays were washed with 2X SSC, 0.1% SDS at 42 C for 2 min, and, subsequently, with 0.1X SSC at room temperature for 2 min, and twice with 0.1X SSC at room temperature for 2 min.

scan_protocol: The array was scanned using a pixel size of 10 um with a Scan Array Lite microarray scanner (Perkin-Elmer, Boston, MA). For each spot the Cy3 and Cy5 density mean value and the Cy3 and Cy5 background mean value were calculated with software ArrayPro® Analyzer from Media Cybernetics.

data_processing:
Background correction, lowest normalization, intensity filter, variance analysis of replicates and selection of differentially expressed genes were performed with GenArise software (http://www.ifc.unam.mx/genarise/). The software identifies differential expressed genes by calculating an intensity-dependent z-score that measures the number of standard deviations (SD) a data point is from the mean [zi=(Ri-mean(R))/sd(R)].
One biological replicate was washed the slide twice, because at the first time several grids was detected dirty, and in the second one this area was observed in perfect conditions. For that reasons I analyzed both  images and then we cut and pasted the grids 16 and 20 in data table obtained for best image (second washing).

organism: Rhizobium etli CFN 42

source_name: Total RNA from Rhizobium etli growth in Minimal Medium by 4 hrs.

label_protocol: 10 μg of total RNA were reversed transcribed into cDNA incorporating dUTP-Cy3 or dUTP-Cy5 and employing the CyScribe First-Strand cDNA labeling kit (Amersham Biosciences, New Jersey, USA). A dye-swap experiment was performed. Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Cy3 and 655 nm for Cy5.

growth_protocol: R. etli CE3 was grown overnight in PY medium. Cells were collected by centrifugation and washed twice with water. These cells were used to inoculate minimal medium ((1.6 mM KH2PO4, 0.83 mM MgSO4, 10 mM NH4Cl, 5 mM dextrose, 5 mM CaCl2, 18.49 µM FeCl3.6H2O, 2 µg/L biotin, 178  µM uracil) at an OD600 of  0.2.

extract_protocol: After 30 min incubation at 30 ºC with constant shaking (200 rpm), cells were collected by centrifugation at 5520 g for 5 min, flash-frozen, and stored in liquid nitrogen. Total RNA was extracted using RNeasy minikit (Qiagen, Hilden, Germany) following the manufacturer's instructions.

treatment_protocol: After 4 h incubation at 30 ºC with constant shaking (200 rpm), 100 ml culture was supplemented with 100 µg/ml orotic acid (treatment) and control cultures were supplemented with water.

tag: strain

value: Wild Type

source_name: Total RNA from Rhizobium etli growth in Minimal Medium with orotic acid by 4 hrs.


title: Jurkat Roc A 30min

description: Jurkat RocA 30min

source_name: Jurkat Roc A 30min


title: Tcell Roc A 1h

description: Tcell RocA 1h

source_name: Tcell Roc A 1h


title: Tcell Roc A 4h

description: Tcell RocA 4h

source_name: Tcell Roc A 4h


title: Tcell Roc A 2h

description: Tcell RocA 2h

source_name: Tcell Roc A 2h


title: 42hrs, U2OS, TN, 6-4-08

status: Public on Oct 11 2013

city: Hanover

first: Gavin

middle: D

last: Grant

state: NH

address: 7400 Remsen

department: Genetics

institute: Geisel School of Medicine

description: 42hrs, U2OS, TN, 6-4-08

hyb_protocol: Hyb using Agilent Hyb Kit

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro analysis software.

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken

source_name: Asynchronous U2OS RNA

label_protocol: Labeled using Agilent Quick Amp Labeling Kit

growth_protocol: DMEM (with 4.5 g/L glucose, L-glu, and sodium pyruvate) + 10% FBS, and 100U penn/strep. Humidified 37C incubator

extract_protocol: Total RNA isolated using Qiagen Rneasy kit

tag: reference

value: asynchronous U2OS total RNA

treatment_protocol: 42 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

tag: cells

value: 42 hr post release nocodazole blocked U2OS cells


title: 38hrs, U2OS, TN, 6-4-08

description: 38hrs, U2OS, TN, 6-4-08

treatment_protocol: Total RNA isolated using Qiagen Rneasy kit

treatment_protocol: 38 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 38 hr post release nocodazole blocked U2OS cells


title: 44hrs, U2OS, TN, 6-4-08

description: 44hrs, U2OS, TN, 6-4-08

treatment_protocol: 44 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cellsand added back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 44 hr post release nocodazole blocked U2OS cells


title: 40hrs, U2OS, TN, 6-4-08

description: 40hrs, U2OS, TN, 6-4-08

treatment_protocol: 40 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells and added back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 40 hr post release nocodazole blocked U2OS cells


title: 34hrs, U2OS, TN, 6-4-08

description: 34hrs, U2OS, TN, 6-4-08

treatment_protocol: 34 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 34 hr post release nocodazole blocked U2OS cells


title: 36hrs, U2OS, TN, 6-4-08

description: 36hrs, U2OS, TN, 6-4-08

treatment_protocol: 36 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 36 hr post release nocodazole blocked U2OS cells


title: 30hrs, U2OS, TN, 6-4-08

description: 30hrs, U2OS, TN, 6-4-08

treatment_protocol: 30 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 30 hr post release nocodazole blocked U2OS cells


title: 32hrs, U2OS, TN, 6-4-08

description: 32hrs, U2OS, TN, 6-4-08

treatment_protocol: 32 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 32 hr post release nocodazole blocked U2OS cells


title: 28hrs, U2OS, TN, 6-4-08

description: 28hrs, U2OS, TN, 6-4-08

treatment_protocol: 28 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 28 hr post release nocodazole blocked U2OS cells


title: 24hrs, U2OS, TN, 6-4-08

description: 24hrs, U2OS, TN, 6-4-08

treatment_protocol: 24 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 24 hr post release nocodazole blocked U2OS cells


title: 18hrs, U2OS, TN, 6-4-08

description: 18hrs, U2OS, TN, 6-4-08

treatment_protocol: 18 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cellsand added back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 18 hr post release nocodazole blocked U2OS cells


title: Tcell Roc A 36h

description: Tcell RocA 36h

source_name: Tcell Roc A 36h

value: Blood


title: 26hrs, U2OS, TN, 6-4-08

description: 26hrs, U2OS, TN, 6-4-08

treatment_protocol: 26 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 26 hr post release nocodazole blocked U2OS cells


title: 6hrs, U2OS, TN, 6-4-08

description: 6hrs, U2OS, TN, 6-4-08

treatment_protocol: 6 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 6 hr post release nocodazole blocked U2OS cells


title: 14hrs, U2OS, TN, 6-4-08

description: 14hrs, U2OS, TN, 6-4-08

treatment_protocol: 14 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 14 hr post release nocodazole blocked U2OS cells


title: 12hrs, U2OS, TN, 6-4-08

description: 12hrs, U2OS, TN, 6-4-08

treatment_protocol: 12 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 12 hr post release nocodazole blocked U2OS cells


title: 8hrs, U2OS, TN, 6-4-08

description: 8hrs, U2OS, TN, 6-4-08

value: asynchronous U2OS total RNA

treatment_protocol: 8 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells and added back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 8 hr post release nocodazole blocked U2OS cells


title: 22hrs, U2OS, TN, 6-4-08

description: 22hrs, U2OS, TN, 6-4-08

treatment_protocol: 22 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 22 hr post release nocodazole blocked U2OS cells


title: 4hrs, U2OS, TN, 6-4-08

description: 4hrs, U2OS, TN, 6-4-08

treatment_protocol: Total RNA isolated using Qiagen Rneasy kit

treatment_protocol: 4 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells and added back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 4 hr post release nocodazole blocked U2OS cells


title: 20hrs, U2OS, TN, 6-4-08

description: 20hrs, U2OS, TN, 6-4-08

treatment_protocol: 20 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 20 hr post release nocodazole blocked U2OS cells


title: 2hrs, U2OS, TN, 6-4-08

description: 2hrs, U2OS, TN, 6-4-08

treatment_protocol: 2 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells and added back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 2 hr post release nocodazole blocked U2OS cells


title: 0hrs, U2OS, TN, 6-4-08

description: 0hrs, U2OS, TN, 6-4-08

treatment_protocol: 0 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells and added back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 0 hr post release nocodazole blocked U2OS cells


title: 16hrs, U2OS, TN, 6-4-08

description: 16hrs, U2OS, TN, 6-4-08

treatment_protocol: 16 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 16 hr post release nocodazole blocked U2OS cells


title: 10hrs, U2OS, TN, 6-4-08

description: 10hrs, U2OS, TN, 6-4-08

treatment_protocol: 10 hr timepoint.  U2OS thymidine-nocodazole synch 6-4-08.  Plated 3*10^5 cells per p100. grew overnight. 5am added thy to 2.5mM arrested for 17hrs. at 10pm washed cells and added 100nm Noc to cells.  10AM released cells washed. saved floating cells andadded back to plates. Took RNA, protein, and FACS samples (1 plate each) every two hours saving floating cells for first 6 hours.

value: 10 hr post release nocodazole blocked U2OS cells


title: 42hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 42 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (42hr)


title: Jurkat Roc A 20h

description: Jurkat RocA 20h

source_name: Jurkat Roc A 20h

treatment_protocol: Cells were plated in duplicates and treated for the indicated periods of time at 37 °C with solvent DMSO or 50 nM of Roc-A (>98% pure, assessed by HPLC) (BIOTREND Chemicals AG, Zurich, Swiss). Approximately 1 x 10P6P cells were collected and RNA was extracted as indicated.

value: Roc-A 50nM


title: 44hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 44 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (44hr)


title: 40hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 40 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (40hr)


title: 32hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 32 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (32hr)


title: 38hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 38 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (38hr)


title: 36hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 36 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (36hr)


title: 30hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 30 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (30hr)


title: 34hrs, TT, U2OS, total RNA from 10-29-09

value: asynchronous U2OS total RNA

treatment_protocol: 34 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (34hr)


title: Tcell Roc A 8h

description: Tcell RocA 8h

source_name: Tcell Roc A 8h

value: Blood


title: 26hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 26 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (26hr)


title: Rhizobium etli with and without orotic acid, biological replicate 1

description: Biological replicate 1 of 3.

treatment_protocol: After 4 h incubation at 30 ºC with constant shaking (200 rpm), 100 ml culture was supplemented with 100 µg/ml orotic acid (treatment) and control cultures were supplemented with water.

value: Wild Type


title: ES5

city: Mumbai

first: Deepika

last: Suri

address: Homi Bhabha Road

department: DBS

country: India

institute: TIFR

description:
Gene expression in 15-month-old early stress animals, hippocampal brain tissue.
Biological replicate 5 of 5.

hyb_protocol: 600 ng Cy3-labeled samples for 8x15 arrays were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327). RNA from each biological replicate was hybridized onto one array, making the total number of arrays 8.

scan_protocol: Scanned on an Agilent Technologies G2505C scanner. Images were quantified using Agilent Feature Extraction Software 10.5.1.1.

data_processing: 75th-percentile shift normalization was done using GeneSpring GX 11 Software.

organism: Rattus norvegicus

source_name: Hippocampal tissue, early stress, 15 months

label_protocol: The samples for gene expression were labeled using the Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the  samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned-up double-stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP (Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol:
At fifteen months of age, control and ES animals (Control: n = 3 and ES: n = 5) were sacrificed, the hippocampi were dissected and stored at -70 prior to use. RNA was extracted from these tissue.

RNA was prepared using the Qiagen RNeasy mini kit following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were subjected to the early stress (ES) of maternal separation. The litters were randomly assigned to the control or ES groups. Pups in the ES group were separated from the dams from postnatal day 2 (P2) to postnatal day 14 (P14) for a period of three hours at the same time each day, while pups of the control group were left undisturbed except for routine animal facility handling. Post P14 the ES animals were left undisturbed and all litters were weaned at P30. To determine the effect of ES on the hippocampal transcriptome in middle-aged animals, microarray analysis was performed.

value: Sprague Dawley

value: hippocampus

value: 15 months

value: early stress of maternal separation


title: Rhizobium etli with and without orotic acid, biological replicate 2 (swap)

description: Biological replicate 2 of 3.


title: C3

description:
Gene expression in 15-month-old control animals, hippocampal brain tissue.
Biological replicate 3 of 3.

source_name: Hippocampal tissue, control, 15 months

value: control


title: C2

description:
Gene expression in 15-month-old control animals, hippocampal brain tissue.
Biological replicate 2 of 3.


title: ES4

description:
Gene expression in 15-month-old early stress animals, hippocampal brain tissue.
Biological replicate 4 of 5.


title: 24hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: Total RNA isolated using Qiagen Rneasy kit

treatment_protocol: 24 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (24hr)


title: 20hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 20 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (20hr)


title: ES2

description:
Gene expression in 15-month-old early stress animals, hippocampal brain tissue.
Biological replicate 2 of 5.


title: 22hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 22 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (22hr)


title: 16hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 16 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (16hr)


title: 14hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 14 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (14hr)


title: 12hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 12 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (12hr)


title: 10hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 10 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (10hr)


title: 18hrs, TT, U2OS, total RNA from 10-29-09

value: asynchronous U2OS total RNA

treatment_protocol: 18 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (18hr)


title: 46hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 46 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (46hr)


title: 6hrs, TT, U2OS, total RNA from 10-29-09

description: 6hrs, TT, U2OS, total RNA from 10-29-09

source_name: 6hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 6 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (6hr)


title: 28hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 28 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (28hr)


title: 8hrs, TT, U2OS, total RNA from 10-29-09

description: 8hrs, TT, U2OS, total RNA from 10-29-09

source_name: 8hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 8 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (8hr)


title: C1

description:
Gene expression in 15-month-old control animals, hippocampal brain tissue.
Biological replicate 1 of 3.

value: Sprague Dawley

value: hippocampus


title: ESd

description:
Gene expression in 2-month-old early stress animals, hippocampal brain tissue.
Biological replicate 4 of 4.

source_name: Hippocampal tissue, early stress, 2 months

label_protocol: The samples for gene expression were labeled using the Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the  samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned-up double-stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol:
At two months of age, control and ES animals (n = 4 per group) were sacrificed, the hippocampi were dissected and stored at -70 prior to use. RNA was extracted from these tissues.

RNA was prepared using the Qiagen RNeasy mini kit following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The animals were subjected to the early stress (ES) of maternal separation. The litters were randomly assigned to the control or ES groups. Pups in the ES group were separated from the dams from postnatal day 2 (P2) to postnatal day 14 (P14) for a period of three hours at the same time each day, while pups of the control group were left undisturbed except for routine animal facility handling. Post P14 the ES animals were left undisturbed and all litters were weaned at P30. To determine the effects of early life adverse events on the hippocampal transcriptome in young adulthood, microarray analysis was performed.

value: 2 months

value: early stress of maternal separation


title: ESa

description:
Gene expression in 2-month-old early stress animals, hippocampal brain tissue.
Biological replicate 1 of 4.


title: ESb

description:
Gene expression in 2-month-old early stress animals, hippocampal brain tissue.
Biological replicate 2 of 4.


title: ES1

description:
Gene expression in 15-month-old early stress animals, hippocampal brain tissue.
Biological replicate 1 of 5.

value: 15 months


title: 4hrs, TT, U2OS, total RNA from 10-29-09

description: 4hrs, TT, U2OS, total RNA from 10-29-09

source_name: 4hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 4 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (4hr)


title: ESc

description:
Gene expression in 2-month-old early stress animals, hippocampal brain tissue.
Biological replicate 3 of 4.


title: Ca

description:
Gene expression in 2-month-old control animals, hippocampal brain tissue.
Biological replicate 1 of 4.

source_name: Hippocampal tissue, control, 2 months

value: control


title: Cd

description:
Gene expression in 2-month-old control animals, hippocampal brain tissue.
Biological replicate 4 of 4.


title: Cc

description:
Gene expression in 2-month-old control animals, hippocampal brain tissue.
Biological replicate 3 of 4.


title: Cb

description:
Gene expression in 2-month-old control animals, hippocampal brain tissue.
Biological replicate 2 of 4.


title: 2hrs, TT, U2OS, total RNA from 10-29-09

description: 2hrs, TT, U2OS, total RNA from 10-29-09

source_name: 2hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 2 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (2hr)


title: 0hrs, TT, U2OS, total RNA from 10-29-09

description: 0hrs, TT, U2OS, total RNA from 10-29-09

source_name: 0hrs, TT, U2OS, total RNA from 10-29-09

treatment_protocol: 0 hr timepoint.  U2OS double thymidine synch. 2.5mM thy.  Plated 2.7e5 cells per p100 on 10-26-09. 18hr block, 8hr release, 18hr block. RNA samples taken every 2 hrs.

value: Thymidine blocked U2OS cells (0hr)


title: 38hrs, TT, U2OS, 6/27/07

description: 38hrs, TT, U2OS, 6/27/07

treatment_protocol: Total RNA isolated using Qiagen Rneasy kit

treatment_protocol: 38 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (38hr)


title: 32hrs, TT, U2OS, 6/27/07

description: 32hrs, TT, U2OS, 6/27/07

treatment_protocol: 32 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (32hr)


title: 34hrs, TT, U2OS, 6/27/07

description: 34hrs, TT, U2OS, 6/27/07

value: asynchronous U2OS total RNA

treatment_protocol: 34 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (34hr)


title: 36hrs, TT, U2OS, 6/27/07

description: 36hrs, TT, U2OS, 6/27/07

treatment_protocol: 36 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (36hr)


title: MyoD-derived sarcoma_Tumor 78 (MDKP)

city: Durham

first: Jordan

last: Blum

state: NC

address: 450 Research Dr LSRC RmB232

institute: Duke University Medical Center

description: Gene expression from sarcomas derived from MyoD+ cells

hyb_protocol: fluidic station: Affymetrix GeneChip®  Fluidics Station 450 [software: Affymetrix GeneChip® Command Console Fluidics Control 3.0.0.1214], hybridization oven new: Affymetrix GeneChip®  hybridization Oven 645

scan_protocol: Affymetrix GeneChip® Scanner 7G. Affymetrix GeneChip® Command Console Scan Control 3.0.0.1214, sample register: Affymetrix GeneChip® Command Console Portal 3.0.1.1229, image viewer: Affymetrix GeneChip® Command Console Viewer 3.0.0.1214

data_processing: Affymetrix Expression Console version 1.1

source_name: MDKP mice injected with IP tamoxifen

label_protocol: MessageAmp™ Premier RNA Amplification Kit (Part Number 4385821, AM1792, 4383452)

extract_protocol: Tumor sections stabilized in RNAlater and RNA extracted by grinding in liquid nitrogen and use of the Qiagen RNEasy Micro kit.  Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A [software: 2100 Expert B.02.08.SI648] (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer [software: NanoDrop 8000 2.1.0] (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip®  Mouse Genome 430A 2.0 arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

value: mixed 129 S4/SvJae  x C57/Bl6

tag: sarcoma derived from

value: MyoD+ cells

tag: genotype

value: mutant Kras and loss of both alleles of p53 in MyoD+ cells

tag: sarcoma/tumor

value: MyoD-derived sarcoma (MDKP)

value: > 6 weeks old


title: MyoD-derived sarcoma_Tumor 75 (MDKP)


title: MyoD-derived sarcoma_Tumor 73 (MDKP)


title: MyoD-derived sarcoma_Tumor 77 (MDKP)


title: 30hrs, TT, U2OS, 6/27/07

description: 30hrs, TT, U2OS, 6/27/07

treatment_protocol: 30 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (30hr)


title: MyoD-derived sarcoma_Tumor 74 (MDKP)


title: MyoD-derived sarcoma_Tumor 76 (MDKP)


title: Jurkat Roc A 3h

description: Jurkat RocA 3h

source_name: Jurkat Roc A 3h

treatment_protocol: Cells were plated in duplicates and treated for the indicated periods of time at 37 °C with solvent DMSO or 50 nM of Roc-A (>98% pure, assessed by HPLC) (BIOTREND Chemicals AG, Zurich, Swiss). Approximately 1 x 10P6P cells were collected and RNA was extracted as indicated.

value: Roc-A 50nM

value: Blood


title: MyoD-derived sarcoma_Tumor 79 (MDKP)


title: undifferentiated pleomorphic sarcoma_Tumor 26 (UPS)

description: Gene expression from sarcomas derived from Pax7+ cells

source_name: P7KP mice injected with IP tamoxifen

value: Pax7+ cells

value: mutant Kras and loss of both alleles of p53 in Pax7+ cells

value: undifferentiated pleomorphic sarcoma (UPS)


title: 16hrs, TT, U2OS, 6/27/07

description: 16hrs, TT, U2OS, 6/27/07

treatment_protocol: 16 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (16hr)


title: undifferentiated pleomorphic sarcoma_Tumor 9 (UPS)


title: undifferentiated pleomorphic sarcoma_Tumor 72 (UPS)


title: 24hrs, TT, U2OS, 6/27/07

description: 24hrs, TT, U2OS, 6/27/07

treatment_protocol: 24 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (24hr)


title: 28hrs, TT, U2OS, 6/27/07

description: 28hrs, TT, U2OS, 6/27/07

treatment_protocol: 28 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (28hr)


title: 14hrs, TT, U2OS, 6/27/07

description: 14hrs, TT, U2OS, 6/27/07

value: asynchronous U2OS total RNA

treatment_protocol: 14 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (14hr)


title: 22hrs, TT, U2OS, 6/27/07

description: 22hrs, TT, U2OS, 6/27/07

treatment_protocol: 22 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (22hr)


title: 18hrs, TT, U2OS, 6/27/07

description: 18hrs, TT, U2OS, 6/27/07

treatment_protocol: 18 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (18hr)


title: 26hrs, TT, U2OS, 6/27/07

description: 26hrs, TT, U2OS, 6/27/07

treatment_protocol: 26 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (26hr)


title: 8hrs, TT, U2OS, 6/27/07

description: 8hrs, TT, U2OS, 6/27/07

treatment_protocol: 8 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (8hr)


title: 10hrs, TT, U2OS, 6/27/07

description: 10hrs, TT, U2OS, 6/27/07

treatment_protocol: 10 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (10hr)


title: 6hrs, TT, U2OS, 6/27/07

description: 6hrs, TT, U2OS, 6/27/07

treatment_protocol: 6 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (6hr)


title: 12hrs, TT, U2OS, 6/27/07

description: 12hrs, TT, U2OS, 6/27/07

treatment_protocol: Total RNA isolated using Qiagen Rneasy kit

treatment_protocol: 12 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (12hr)


title: 20hrs, TT, U2OS, 6/27/07

description: 20hrs, TT, U2OS, 6/27/07

treatment_protocol: 20 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (20hr)


title: 0hrs, TT, U2OS, 6/27/07

description: 0hrs, TT, U2OS, 6/27/07

treatment_protocol: 0 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (0hr)


title: 4hrs, TT, U2OS, 6/27/07

description: 4hrs, TT, U2OS, 6/27/07

treatment_protocol: 4 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (4hr)


title: 2hrs, TT, U2OS, 6/27/07

description: 2hrs, TT, U2OS, 6/27/07

treatment_protocol: 2 hr timepoint.  U2OS, double thymidine synch, 2.5mM thymidine. plated 2.5*10^5 cells per plate, 18hr block then 8hr release, then 18hr block, RNA sample taken every 2 hrs.

value: Thymidine blocked U2OS cells (2hr)


title: undifferentiated pleomorphic sarcoma_Tumor 27 (UPS)

value: mixed 129 S4/SvJae  x C57/Bl6

value: Pax7+ cells

value: mutant Kras and loss of both alleles of p53 in Pax7+ cells

value: undifferentiated pleomorphic sarcoma (UPS)

value: > 6 weeks old


title: embryonal RMS_Tumor 13 (eRMS)

value: embryonal RMS (eRMS)


title: embryonal RMS_Tumor 70 (eRMS)


title: embryonal RMS_Tumor 15 (eRMS)


title: 46hrs, TT, U2OS, 10-3-07

description: 46hrs, TT, U2OS, 10-3-07

value: asynchronous U2OS total RNA

treatment_protocol: 46 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (46hr)


title: 36hrs, TT, U2OS, 10-3-07

description: 36hrs, TT, U2OS, 10-3-07

treatment_protocol: 36 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (36hr)


title: embryonal RMS_Tumor 10 (eRMS)


title: undifferentiated pleomorphic sarcoma_Tumor 14 (UPS)


title: 38hrs, TT, U2OS, 10-3-07 array 2

description: 38hrs, TT, U2OS, 10-3-07 array 2

treatment_protocol: 38 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (38hr)


title: Aggregate (premalignant) 3

city: la jolla

first: Michael

last: Karin

address: 9500 gilman dr

institute: UCSD

description:
5038690042_F
replicate 3

data_processing: The data were normalized using quantile normalization (Fortran 90).

source_name: liver

label_protocol: Biotin labeling using Standard Illumina protocol

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.

value: Aggregate (premalignant) Hepatocyte


title: 42hrs, TT, U2OS, 10-3-07

description: 42hrs, TT, U2OS, 10-3-07

source_name: Asynchronous U2OS RNA

treatment_protocol: 42 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (42hr)


title: 40hrs, TT, U2OS, 10-3-07

description: 40hrs, TT, U2OS, 10-3-07

treatment_protocol: 40 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (40hr)


title: 34hrs, TT, U2OS, 10-3-07

description: 34hrs, TT, U2OS, 10-3-07

treatment_protocol: 34 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (34hr)


title: 32hrs, TT, U2OS, 10-3-07 array 2

description: 32hrs, TT, U2OS, 10-3-07 array 2

treatment_protocol: 32 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (32hr)


title: 44hrs, TT, U2OS, 10-3-07 array 2

description: 44hrs, TT, U2OS, 10-3-07 array 2

treatment_protocol: 44 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (44hr)


title: 28hrs, TT, U2OS, 10-3-07

description: 28hrs, TT, U2OS, 10-3-07

treatment_protocol: 28 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (28hr)


title: Non aggregate 3

description:
5038690042_E
replicate 3

value: Non aggregate (premalignant) Hepatocytes


title: embryonal RMS_Tumor 18 (eRMS)

value: mixed 129 S4/SvJae  x C57/Bl6

value: Pax7+ cells


title: ES3

description:
Gene expression in 15-month-old early stress animals, hippocampal brain tissue.
Biological replicate 3 of 5.

treatment_protocol: Animals were subjected to the early stress (ES) of maternal separation. The litters were randomly assigned to the control or ES groups. Pups in the ES group were separated from the dams from postnatal day 2 (P2) to postnatal day 14 (P14) for a period of three hours at the same time each day, while pups of the control group were left undisturbed except for routine animal facility handling. Post P14 the ES animals were left undisturbed and all litters were weaned at P30. To determine the effect of ES on the hippocampal transcriptome in middle-aged animals, microarray analysis was performed.

value: Sprague Dawley

value: hippocampus

value: 15 months

value: early stress of maternal separation


title: embryonal RMS_Tumor 52 (eRMS)

value: mutant Kras and loss of both alleles of p53 in Pax7+ cells

value: embryonal RMS (eRMS)

value: > 6 weeks old


title: 20hrs, TT, U2OS, 10-3-07 array 2

description: 20hrs, TT, U2OS, 10-3-07 array 2

value: asynchronous U2OS total RNA

treatment_protocol: 20 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (20hr)


title: 30hrs, TT, U2OS, 10-3-07

description: 30hrs, TT, U2OS, 10-3-07

treatment_protocol: Total RNA isolated using Qiagen Rneasy kit

treatment_protocol: 30 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (30hr)


title: 16hrs, TT, U2OS, 10-3-07

description: 16hrs, TT, U2OS, 10-3-07

treatment_protocol: 16 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (16hr)


title: 22hrs, TT, U2OS, 10-3-07

description: 22hrs, TT, U2OS, 10-3-07

treatment_protocol: 22 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (22hr)


title: 26hrs, TT, U2OS, 10-3-07 array 2

description: 26hrs, TT, U2OS, 10-3-07 array 2

treatment_protocol: 26 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (26hr)


title: 14hrs, TT, U2OS, 10-3-07 array 2

description: 14hrs, TT, U2OS, 10-3-07 array 2

treatment_protocol: 14 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (14hr)


title: 24hrs, TT, U2OS, 10-3-07

description: 24hrs, TT, U2OS, 10-3-07

treatment_protocol: 24 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (24hr)


title: 18hrs, TT, U2OS, 10-3-07

description: 18hrs, TT, U2OS, 10-3-07

treatment_protocol: 18 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (18hr)


title: undifferentiated pleomorphic sarcoma_Tumor 19 (UPS)

value: mixed 129 S4/SvJae  x C57/Bl6

value: Pax7+ cells

value: undifferentiated pleomorphic sarcoma (UPS)


title: Aggregate (premalignant) 1

description:
5038690042_B
replicate 1

value: Aggregate (premalignant) Hepatocyte


title: pleomorphic RMS_Tumor 65 (pRMS)

value: pleomorphic RMS (pRMS)


title: pleomorphic RMS_Tumor 49 (pRMS)

value: mutant Kras and loss of both alleles of p53 in Pax7+ cells


title: 2hrs, TT, U2OS, 10-3-07 array 2

description: 2hrs, TT, U2OS, 10-3-07 array 2

source_name: 2hrs, TT, U2OS, 10-3-07 array 2

treatment_protocol: 2 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (2hr)


title: Aggregate (premalignant) 2

description:
5038690042_D
replicate 2


title: Non aggregate 1

description:
5038690042_A
replicate 1

value: Non aggregate (premalignant) Hepatocytes


title: pleomorphic RMS_Tumor 63 (pRMS)

value: > 6 weeks old


title: 4hrs, TT, U2OS, 10-3-07

description: 4hrs, TT, U2OS, 10-3-07

value: asynchronous U2OS total RNA

treatment_protocol: 4 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (4hr)


title: HCC 3

description:
5038690027_F
replicate 3

value: fully malignant HCC


title: Normal Hepatocyte 3

description:
5038690027_C
replicate 3

value: Normal Hepatocyte


title: Non aggregate 2

description:
5038690042_C
replicate 2


title: 12hrs, TT, U2OS, 10-3-07

description: 12hrs, TT, U2OS, 10-3-07

treatment_protocol: 12 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (12hr)


title: HCC 2

description:
5038690027_E
replicate 2


title: pleomorphic RMS_Tumor 38 (pRMS)


title: 10hrs, TT, U2OS, 10-3-07

description: 10hrs, TT, U2OS, 10-3-07

treatment_protocol: 10 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (10hr)


title: HCC 1

description:
5038690027_D
replicate 1


title: pleomorphic RMS_Tumor 37 (pRMS)


title: 8hrs, TT, U2OS, 10-3-07 array 2

description: 8hrs, TT, U2OS, 10-3-07 array 2

source_name: 8hrs, TT, U2OS, 10-3-07 array 2

treatment_protocol: 8 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (8hr)


title: pleomorphic RMS_Tumor 39 (pRMS)


title: 0hrs, TT, U2OS, 10-3-07

description: 0hrs, TT, U2OS, 10-3-07

treatment_protocol: 0 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (0hr)


title: Normal Hepatocyte 2

description:
5038690027_B
replicate 2


title: TSG101-deficient vs. -proficient Cell Replicate 1

city: Taipei City

first: Tzu-Hao

last: Cheng

address: No. 155, Sec. 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang-Ming University

description: Biological replicate 1 of 2. TSG101-deficient vs. -proficient Cell.

hyb_protocol: Samples were applied to microarrays enclosed in hybridization chambers and washed sequentially.

scan_protocol: Scanned on a GenePix 4000B scanner. Images were quantified using AxImageIO Software (version 2.0.2.4).

data_processing: GenePix Pro version 4.0.0.54 was used as the Feature Extraction Software and the default computed normolization was performed.

source_name: TSG101-proficient cell

label_protocol: 2 µg of total RNA were converted to DNA and labeled with Cys-3 or Cys-5.

growth_protocol: Saos-2 and Saos-2-2 were cultured in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA extraction using Trizol following manufacturer's instructions.

treatment_protocol: not applicable.

tag: cell line

value: parental cell of Saos-2-2, without TSG101 shRNA

source_name: TSG101-deficient cell

value: expressing TSG101 shRNA


title: 6hrs, TT, U2OS, 10-3-07

description: 6hrs, TT, U2OS, 10-3-07

treatment_protocol: 6 hr timepoint. U2OS, double thymidine synch 10-3-07, 2.5mM thymidine. Plated 3*10^5 cells per plate, 18 hr block then 8 hr release, the 18hr block. RNA samples taken every 2hrs.

value: Thymidine blocked U2OS cells (6hr)


title: TSG101-deficient vs. -proficient Cell Replicate 2

description: Biological replicate 2 of 2. TSG101-deficient vs. -proficient Cell.


title: Normal Hepatocyte 1

description:
5038690027_A
replicate 1


title: Control vs. Treated FGF8 3

status: Public on Oct 10 2013

city: St-Hyacinthe

first: Christopher

last: Price

state: QC

address: 3200 rue Sicotte

country: Canada

institute: University of Montreal

hyb_protocol: hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: This is a place holder for the Tecan scanning protocol.

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

organism: Bos taurus

label_protocol: labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: Bovine granulosa cells collected from follicules from 2-6mm in diameter. Cells were cultured in MEM/F12 without serum but with FSH (10ng/ml) and insulin (10ng/ml) during 5 days.

extract_protocol:
PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

treatment_protocol: On the morning of day 5, cells were treated with FGF8 (10ng/ml for two hours.

tag: breed

value: Holstein

tag: time

value: 0 hours

value: granulosa

value: 2 hours


title: Control vs. Treated FGF8 2


title: Treated vs. Control FGF8 2


title: Treated vs. Control FGF8 3


title: Treated vs. Control 3

scan_protocol: Tecan scanning protocol.

extract_protocol:
total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices
amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

treatment_protocol: On the morning of day 5, cells were treated with FGF18 (10ng/ml) for two hours.

value: Holstein crossbreds from abattoir

value: granulosa cells

value: FGF18 2hrs

value: untreated control


title: Treated vs. Control 2


title: Control vs. Treated 3


title: Control vs. Treated FGF8 1


title: Treated vs. Control 1


title: Control vs. Treated 2


title: Treated vs. Control FGF8 1


title: embryonal RMS_Tumor 5 (eRMS)

value: mixed 129 S4/SvJae  x C57/Bl6

value: Pax7+ cells

value: mutant Kras and loss of both alleles of p53 in Pax7+ cells

value: embryonal RMS (eRMS)

value: > 6 weeks old


title: undifferentiated pleomorphic sarcoma_Tumor 1 (UPS)

value: undifferentiated pleomorphic sarcoma (UPS)


title: Control vs. Treated 1


title: Top2α replicate 1

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

hyb_protocol: Hybridization was performed according to standard Nimblegen procedure

scan_protocol: Scanning was performed with NimbleScan.

data_processing: Nimblegen array intensity files were read and log2 enrichments (log2 bound/input ratios) for each individual probe were calculated using the R package Ringo (version 1.14.0, R version 2.12.1). To remove dye artifacts , both arrays were loess-normalized and scale normalized using the normalizeWithinArrays and normalizeBetweenArrays function from the limma package (version 3.6.9)

source_name: Top2α ChIP DNA from ES cells

label_protocol: According to Nimblegen guidelines

growth_protocol: ES cells were grown as dercribed previously (Bibel 2007)

extract_protocol: ChIP experiments were performed as described before (F. Mohn et al., Mol Cell 30, 755 (Jun 20, 2008)), starting with 70 µg of chromatin and 5 µg of the Top2α antibody and the material was amplified using whole genome amplification kit (Sigma) before labeling for hybridization.

value: wild type

value: ES cells

tag: chip antibody

value: anti-Top2α (Santa Cruz, sc5346)

source_name: Input DNA from ES cells

value: none (input)


title: Lung26953_NMapping250K_Nsp

city: Tokyo

first: Hironori

last: Ninomiya

address: 3-8-31 Ariake, Koutou ward

department: pathology

country: Japan

institute: The Japanese Foundation for Cancer Research

description: Hybridized to 250K_Nsp

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing:
After appropriate normalization of mean array intensities, signal ratios between tumours and anonymous normal references were calculated in an allele-specific manner, and allele-specific copy numbers were inferred from the observed signal ratios based on the hidden Markov model using CNAG/AsCNAR 3.0 software (http://www.genome.umin.jp).
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: lung adenocarcinoma specimen

label_protocol: Affymetrix standard protocol

extract_protocol: standard DNA extraction using QIAGEN

tag: gender

value: male

tag: group

value: ALK fusion positive


title: GTB12727_NMapping250K_Nsp

description: Hybridized to 250K_Nsp

value: female


title: Lung29582_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB27265_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung28615_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung12872_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB26020_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Top2α replicate 2


title: Lung10027_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB19854_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB22231_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB12552_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB21449_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung26813_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB24704_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB9616_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB27998_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung10172_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung18012_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB26422_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB9968_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung20653_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB24461_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung6445_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB8993_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB8398_NMapping250K_Nsp

description: Hybridized to 250K_Nsp