title: HBEC PMX-Purom-GFP-empty rep2

city: Dallas

first: Jerfiz

middle: D

last: Constanzo

state: Texas

address: 6001 Forest Park Road

department: Hematology Oncology

institute: University of Texas Southwestern Medical Center

description: Cells are immortalized, non- oncogenic by transduction with CDK4, hTERT  (telomerase) and short hairpin knockdown of P53 tumor suppressor

hyb_protocol: We hybridized the productin step #4 to human HT12 v4.0 Expression BeadChip from Ilumina according to the manufacturer’s instructions

scan_protocol: Standard Illumina scanning protocol

data_processing: We used R/Bioconductor package MBCB with default parameters to process raw data, background subtraction and quantile normalization. The linear value can be used for bar graph or further analysis according to study design base on normalized values higher than 120. After normalization value was transformed to Log (natural) value and median centered for Hierarchical Cluster analysis. For statistical analysis we utilized a false discovery rate (FDR) and benjamini hochberg test with a log ratio treshold of 0.6 and  p-value treshold of 0.3. Finaly values were analysed with Ingenuity Gene Set Enrichment sofrware (QIAGEN)

source_name: HBEC epithelial cell line

label_protocol: We processed 100 ng of total RNA with the Ambion TotalPrep Kit for Illumina arrays following manufacturers protocol

growth_protocol: Human bronchial epithelial cells  (HBECs) were transduced with retroviral particles containing PMX-Purom-GFP-emty or PMX-Purom-GFP-mFAK and positive clones selected with 2ug/mL Puromycing for 2 days.

extract_protocol: For total RNA extraction we used a RNA isolation kit (SIGMA) followed by DNase digestion and cleanup according to the manufacturer’s instructions

treatment_protocol: Gene expression profiles were obtained from exponentially growing HBEC cells in keratynocyte growth media supplemented with growth factors (Gibco)

value: HBEC


title: Quadruple (SB/Tg/K5Cre/Bcat) Q260 (1983)

status: Public on Jan 01 2016

type: RNA

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: Gene expression data from mouse tissue

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were normalized by Robust Multichip Average (RMA) using R with Bioconductor.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse Tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT Express protocol from 100 ng total RNA.

extract_protocol: Total RNA was extracted by Qiagen RNEasy kit according to the manufacturer's instructions.

tag: tissue

value: breast

tag: genotype

value: Quadruple (SB/Tg/K5Cre/Bcat)


title: NCI-HPN-F3K Colon p3 PreImmortal

city: Bethesda

first: Hesed

middle: Maria

last: Padilla-Nash

state: MD

address: 50 South Drive

department: Genetics Branch

country: USA

institute: NCI

description: female

hyb_protocol: The arrays were hybridized according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: The arrays were scanned using an Agilent Scanner System with the following settings:   5µm resolution scan, scan area (61 x21.6mm), single pass 5um scanning mode, eXtended Dynamic range, Dye channel Green, and Green PMT XDR Hi 100%, XDR Lo 10% . Images were quantified using Agilent Feature Extraction Software (version 8.1.1).

data_processing: Raw data were log2 transformed and normalized to 75 percentile according to Agilent protocol

label: Cy 3

source_name: mouse colon epithelial cells

label_protocol: The denatured probe was applied to the Agilent Mouse Gene Expression 4 X44K Microarray Kit along with 2xGE Hybridization Buffer according to the manufacturer's instructions.

extract_protocol: 700ng of total input RNA was used from each of the cell lines and uncultured  was labeled with Cy3 and fragmented before application to the microarray.

treatment_protocol: RNAwas extracted from the murine epithelial cells during the various stages of cellular transformation.   The uncultured colon epithelial cells served as a normal control. The Qiagen RNAeasy Mini Kit was used to extract the RNA according to manufacturer's protocols.

tag: Stage

tag: strain

tag: gender

value: female


title: HBEC PMX-Purom-GFP-empty rep1

description: Cells are immortalized, non- oncogenic by transduction with CDK4, hTERT  (human telomerase) and short hairpin knockdown of P53 tumor suppressor

organism: Homo sapiens

tag: cell type


title: Quadruple (SB/Tg/K5Cre/Bcat) Q190A

description: Gene expression data from mouse tissue


title: HBEC PMX-Purom-GFP-mFAK rep2


title: Quadruple (SB/Tg/K5Cre/Bcat) Q629

description: Gene expression data from mouse tissue


title: hlh-29 mutant, rep 2

city: Atlanta

first: Han Ting

last: Chou

state: GA

address: 1 University Park Drive

department: Biology

institute: Georgia State University

description:
Gene expression data from tm284 hlh-29 mutant young adults
TGT value =500; normalization factor (nf) = 1

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

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

data_processing: Data collection was carried out using GCOS 1.4 software (Affymetrix). analysis was performed using GeneSpring GX 11 Software (Aglient, Palo Alto,CA).  Probe intensity values were normalized to a target value of 500 with normalization factor equal to 1.

label: biotin

organism: Caenorhabditis elegans

source_name: hlh-29 mutant young adults, rep 2

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

growth_protocol: C. elegans animals were synchronized and grown to young adult stage at 20C

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

treatment_protocol: All animals were fed on NGM agar pads with OP50 bacteria lawn.

value: hermaphrodite

value: whole animal

tag: age

value: young adult


title: hlh-29 mutant, rep 1

source_name: hlh-29 mutant young adults, rep 1


title: HBEC PMX-Purom-GFP-mFAK rep1


title: PHH_HBV_12days_A

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.20.2). It was vst transformed and ssn normalized.

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: liver

value: primary human hepatocytes (PHH)


title: PHH_HBV_6days_B


title: PHH_HBV_6days_A


title: hlh-25 mutant, rep 3

description:
Gene expression data from VC1220 hlh-25 mutant young adults
TGT value =500; normalization factor (nf) = 1

source_name: hlh-25 mutant young adults, rep 3


title: hlh-25 mutant, rep 1

source_name: hlh-25 mutant young adults, rep 1


title: wild type, rep 3

description:
Gene expression data from N2 wild type young adults
TGT value =500; normalization factor (nf) = 1

source_name: wild type young adults, rep 3

value: wild type


title: wild type, rep 2

source_name: wild type young adults, rep 2


title: Triple (SB/Tg/k5Cre) T852

description: Gene expression data from mouse tissue

value: Triple (SB/Tg/k5Cre)


title: PHH_HBV_24hours_B


title: PHH_HBV_24hours_A


title: wild type, rep 1

source_name: wild type young adults, rep 1


title: hlh-25 mutant, rep 2

source_name: hlh-25 mutant young adults, rep 2


title: sto2-1

city: Melbourne

first: Staffan

last: Persson

address: Parkville, 3010,

department: School of Biosciences

country: Australia

institute: University of Melbourne

description: sto2 mutant was grown in the same growth condition as that with Col-0, and 3nd to 6th rosette leaves were harvested

hyb_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

data_processing: Raw data (CEL files) obtained from RNA hybridisation experiments were analyzed using software Robin ( Lohse et al., 2010),and online tool PageMan was used for over representation analysis

organism: Arabidopsis thaliana

source_name: three-week-old soil grown plants

growth_protocol: Seeds were sowed and grown in soil for three weeks under a 16-h-light (120-150 μE)/8-h-dark (22°C/18°C) regime before samples harvest.

extract_protocol: Total RNA was isolated using the RNeasy plant mini kit (Qiagen)

treatment_protocol: No additional treatment was applied

value: expanding rosette leaves

tag: genotype/variation

value: sto2 mutant


title: PHH_HBV_8hours_B


title: PHH_mock_12days_B


title: Col-0-1

description: Col-0 ecotype is used as wild type, and 3nd to 6th rosette leaves were harvested

scan_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual


title: sto2-3

label_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual


title: PHH_HBV_4hours_A


title: PHH_HBV_12days_B


title: PHH_HBV_8hours_A


title: Col-0-3


title: PHH_HBV_4hours_B


title: sto2-2


title: Col-0-2


title: PHH_mock_8hours_B


title: PHH_mock_6days_A


title: PHH_mock_24hours_A


title: PHH_mock_6days_B


title: PHH_mock_12days_A


title: PHH_mock_24hours_B


title: Osteosarcoma cell line - U2OS (aCGH)

type: genomic

first: Yuelin

middle: Jack

last: Zhu

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

description:
High molecular weight DNA
Tumor sampls were obtained from the tissues bank at the Laboratory of Oncology Research of the Rizzoli Orthopaedic Institute, Bologna, Italy

hyb_protocol: Reference and experimental samples DNA were co-hybridized on the high-resolution genome wide arrays containing 105,000 oligonucleotide probes. The average spatial resolution between the probes was 21.7 KB . The hybridization was carried out for 40h at 65°C.

scan_protocol: After washing, the slides were scanned on a laser-based microarray scanner (Agilent) using a resolution of 5 μm

data_processing: aCGH data were extracted (not normalized) using the default procedure in Agilent's Feature Extraction Software and visualized using Agilent CGH Analytics 3.4.27 software

molecule: genomic DNA

source_name: Osteosarcoma cell line (aCGH)

label_protocol: 3 μg of digested DNAs from samples and references were differentially labeled with dUTP-Cy5 and dUTP-Cy3 respectively in a random primer reaction

growth_protocol: Commercially available osteosarcoma cell lines were grown according to the supplier’s recommendations.

extract_protocol: Genomic DNA was isolated using a standard proteinase K digestion followed by phenol/chloroform/isoamyl alcohol extraction, precipitated with 3M sodium acetate (pH 5.2) and 100% ethanol. The pellet was washed with 70% ethanol and resuspended in TE.

tag: Sample type

value: cell line

source_name: genomic DNA from Promega

value: DNA reference


title: Osteoblast cell line - hFOB (aCGH)

source_name: Human Osteoblast cell line  (aCGH)


title: PHH_mock_8hours_A


title: Osteosarcoma cell line - G292 (aCGH)


title: PHH_mock_4hours_B


title: PHH_mock_4hours_A


title: Osteosarcoma cell line - CAL72 (aCGH)


title: Osteosarcoma cell line - 143B (aCGH)


title: S_2

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

country: United Kingdom

institute: Cerevance ltd

hyb_protocol: Standard Illumina hybridization protocol

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

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

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.

tag: cell line

value: Human Hodgkin Lymphoma

tag: treatment

value: 10 µM AEZS-136 - 2 hours


title: Osteosarcoma cell line - NY (aCGH)


title: Osteosarcoma cell line - MG63 (aCGH)


title: L5_2


title: CT_S_3

value: Control - 2 hours


title: CT_S_1


title: S_1


title: Osteosarcoma cell line - HUO9 (aCGH)


title: Osteosarcoma cell line - SAOS (aCGH)


title: S_3


title: Osteosarcoma cell line - HUO3N1 (aCGH)


title: L5_1


title: CT_S_2


title: Osteosarcoma cell line - OSACL (aCGH)


title: CT_L5_2


title: Osteosarcoma tumor - OS#16 (aCGH)

source_name: Osteosarcoma tumor (aCGH)

value: osteosarcoma tumor


title: Osteosarcoma cell line - HOS (aCGH)


title: Osteosarcoma cell line - HUO9N2 (aCGH)


title: Osteosarcoma tumor - OS#SN (aCGH)


title: L5_3


title: Osteosarcoma tumor - OS#46 (aCGH)


title: Osteosarcoma tumor - OS#15 (aCGH)


title: CT_L5_3


title: CT_L5_1


title: Osteosarcoma tumor - OS#12 (aCGH)


title: Osteosarcoma tumor - OS#13 (aCGH)


title: Osteosarcoma tumor - OS#mandibola (aCGH)


title: Osteosarcoma tumor - OS#2 (aCGH)


title: L4_2


title: L4_3


title: Osteosarcoma tumor - 23622 (aCGH)


title: CT_L4_1


title: CT_L4_3


title: K_2


title: Osteosarcoma tumor - 26713 (aCGH)


title: CT_L4_2


title: L4_1


title: Osteosarcoma tumor - 23579 (aCGH)


title: Osteosarcoma tumor - 25517 (aCGH)


title: CT_K_3


title: K_3


title: Osteosarcoma tumor - 26395 (aCGH)


title: Osteosarcoma tumor - 26442 (aCGH)


title: K_1


title: CT_K_2


title: BJAB mock r2

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

country: Germany

institute: University of Münster

hyb_protocol: hybridization was performed with HumanHT-12 v4 Expression Bead Chip kit (Illumina) according to manufacturer's protocol

scan_protocol: scanning was performed according to manufacturer's protocol

data_processing: The preprocessing pipeline was implemented in Mathworks MATLAB(R) and works similar to preprocessing Affymetrix CEL files: Measured gene expressions were imported on raw bead level (cf. supplementary TXT files). All 10 microarrays were preprocessed and normalized together. Their intensity distributions for all measured beads were equalized by quantile normalization. The background mode was fitted and removed and a spot filter was applied to exclude too dim beads (< mean background intensity). Intensities were log2-transformed and aggregated by measured sequence to form beadsets. Beadsets with more than 50% of their beads excluded by the spot filter were also excluded. Further analysis was performed on gene level using median aggregation and manufacturer’s annotations. For genes having multiple beadsets the one with the highest expression (in average over all arrays) was selected.

source_name: BJAB_empty vector (mock control)

label_protocol: RNA was transcribed and labeled by Illumina TotalPrep RNA Amplification kit according to manufacturer's protocol

growth_protocol: cell line BJAB was maintained in RPMI medium with 15% FBS at 37°C with 5% CO2

extract_protocol: total RNA was extracted using RNeasy kit (Qiagen) according to manufacturer's protocol

treatment_protocol: cell line BJAB was transduced with expression constructs for empty vector control (mock), CARMA1 WT, R35A, L225LI or R35A/L225LI using a lentiviral system

value: BJAB

value: NF-κB negative GCB DLBCL lymphoma cell line

value: expressing empty vector (mock control)


title: Osteosarcoma tumor - 25857 (aCGH)


title: Osteosarcoma tumor - 25491 (aCGH)


title: CT_K_1


title: Osteosarcoma tumor - 25712 (aCGH)


title: Osteosarcoma tumor - 25350 (aCGH)


title: Osteosarcoma tumor - 25268 (aCGH)


title: BJAB CARMA1 WT r1

source_name: BJAB_CARMA1 WT

value: expressing CARMA1 WT


title: Osteosarcoma tumor - 24954 (aCGH)


title: BJAB CARMA1 L225LI r2

source_name: BJAB_CARMA1 L225LI mutant

value: expressing CARMA1 L225LI mutant


title: Osteosarcoma tumor - 25696 (aCGH)


title: Osteosarcoma tumor - 25044 (aCGH)


title: Osteosarcoma tumor - 25384 (aCGH)


title: BJAB CARMA1 R35A+L225LI r1

source_name: BJAB_CARMA1 double mutant R35A/L225LI

value: expressing CARMA1 double mutant R35A/L225LI


title: Osteosarcoma tumor - 24875 (aCGH)


title: BJAB CARMA1 R35A r2

source_name: BJAB_CARMA1 point mutant R35A

value: expressing CARMA1 point mutant R35A


title: Osteosarcoma tumor - 24575 (aCGH)


title: BJAB mock r1


title: Osteosarcoma tumor - 24911 (aCGH)


title: Osteosarcoma tumor - 24949 (aCGH)


title: PP242_72_2

city: Lund

first: Kristoffer

last: von Stedingk

address: Scheelevägen 2

country: Sweden

institute: Lund University

description: Neuroblastoma SK-N_BE(2)c PP242 treated 72 hour hypoxia Sample #2

data_processing: Data was handled and normalized in BASE (https://casa4.bmc.lu.se/onk/). All data was mean background corrected followed by quantile normalization. Array control probes were removed.

source_name: SK-N_BE(2)c, PP242 treated 72h Hypoxia

extract_protocol: Total RNA was extracted with TRIZOL. Qualitywas extracted manually using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendation. The quality of the RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).  control was performed with Agilent 2100 Bioanalyser.

value: Neuroblastoma


title: BJAB CARMA1 L225LI r1


title: PP242_72_3

description: Neuroblastoma SK-N_BE(2)c PP242 treated 72 hour hypoxia Sample #3


title: BJAB CARMA1 R35A r1


title: Osteosarcoma tumor - 24779 (aCGH)


title: BJAB CARMA1 WT r2


title: Osteosarcoma tumor - 22981 (aCGH)


title: Osteosarcoma tumor - 24235 (aCGH)


title: Osteosarcoma tumor - 24805 (aCGH)


title: DMSO_72_4

description: Neuroblastoma SK-N_BE(2)c DMSO treated 72 hour hypoxia Sample #4

source_name: SK-N_BE(2)c, DMSO treated 72h Hypoxia


title: PP242_72_4

description: Neuroblastoma SK-N_BE(2)c PP242 treated 72 hour hypoxia Sample #4


title: Osteosarcoma tumor - 22900 (aCGH)


title: DMSO_72_3

description: Neuroblastoma SK-N_BE(2)c DMSO treated 72 hour hypoxia Sample #3


title: PP242_72_1

description: Neuroblastoma SK-N_BE(2)c PP242 treated 72 hour hypoxia Sample #1


title: PP242_48_4

description: Neuroblastoma SK-N_BE(2)c PP242 treated 48 hour hypoxia Sample #4

source_name: SK-N_BE(2)c, PP242 treated 48h Hypoxia


title: Osteosarcoma tumor - 22753 (aCGH)


title: BJAB CARMA1 R35A+L225LI r2


title: Osteosarcoma tumor - 22241 (aCGH)


title: DMSO_48_1

description: Neuroblastoma SK-N_BE(2)c DMSO treated 48 hour hypoxia Sample #1

source_name: SK-N_BE(2)c, DMSO treated 48h Hypoxia


title: DMSO_72_1

description: Neuroblastoma SK-N_BE(2)c DMSO treated 72 hour hypoxia Sample #1


title: PP242_48_2

description: Neuroblastoma SK-N_BE(2)c PP242 treated 48 hour hypoxia Sample #2


title: DMSO_48_2

description: Neuroblastoma SK-N_BE(2)c DMSO treated 48 hour hypoxia Sample #2


title: DMSO_48_4

description: Neuroblastoma SK-N_BE(2)c DMSO treated 48 hour hypoxia Sample #4


title: DMSO_48_3

description: Neuroblastoma SK-N_BE(2)c DMSO treated 48 hour hypoxia Sample #3


title: Osteosarcoma tumor - 18900 (aCGH)


title: Osteosarcoma tumor - 20772 (aCGH)


title: PP242_24_2

description: Neuroblastoma SK-N_BE(2)c PP242 treated 24 hour hypoxia Sample #2

source_name: SK-N_BE(2)c, PP242 treated 24h Hypoxia


title: CBW, 48h, rep2

city: beijing

first: xinzheng

last: huang

address: No. 2 Yuanmingyuan West Road, Haidian District

country: China

institute: Institute of Plant Protection, Chinese Academy of Agricultural Sciences

description:
Cotton plants were exposed to CBW larvae for 48h, biological replicate 2
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_I-48-2_(Cotton)

hyb_protocol: Cleaned total RNAs from each of the 24 samples were sent to CapitalBio Corporation in Beijing for microarray hybridization and preliminary data analysis.

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

organism: Gossypium hirsutum

source_name: whole cotton leaves_treated with cotton bollworm_48h

label_protocol: For each time point (6h, 12h, 24h, and 48h), the arrays were hybridized with Cy3 and Cy5 fluorescently labeled probe pairs of herbivore damaged plants plus the corresponding control. (Expression Analysis Technical Manual, 2001, Affymetrix). For each time point, three replicate treatments and controls were performed.

growth_protocol: Cotton seeds (Gossypium hirsutum cv. CCRI12) were grown in a growth chamber under 29/25°C temperature and a 16:8 h light:dark cycle, and water was added every two days. All plants were used in experiments at the 6-7 fully expanded true leaf stage, which occurred 5-6 weeks after sowing. Cotton bollworm (CBW; Helicoverpa armigera) larvae were reared on an artificial diet and maintained at 27 ± 2°C, 75 ± 10% relative humidity, and 14:10 h light:dark in the laboratory.

extract_protocol: A Modified hot borate method was used for RNA isolation.

treatment_protocol: For insect treatment, seven Helicoverpa armigera larvae (third instars) were placed on a group of three plants, which were kept within plastic bags (30 × 40 cm), until time of harvest, with samples for each time point maintained separately. Undamaged plants maintained under the same conditions were used as controls. Cotton leaves from control plants and plants exposed to H. armigera were harvested at 6 h, 12 h, 24 h, and 48 h after onset of herbivory. For each treatment group and time point, cotton leaves were harvested from the three plants per treatment group and flash frozen in liquid nitrogen.

tag: cultivar/variety

value: cv. CCRI12

value: whole cotton leaves

value: 6-7 fully expanded true leaf stage; 5-6 weeks after sowing

tag: treated with

value: Helicoverpa armigera

tag: harvest time point

value: 48h after onset of herbivory


title: Osteosarcoma tumor - 20490 (aCGH)

value: DNA reference


title: CBW, 48h, rep3

description:
Cotton plants were exposed to CBW larvae for 48h, biological replicate 3
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_I-48-3_(Cotton)


title: PP242_24_3

description: Neuroblastoma SK-N_BE(2)c PP242 treated 24 hour hypoxia Sample #3


title: PP242_48_1

description: Neuroblastoma SK-N_BE(2)c PP242 treated 48 hour hypoxia Sample #1


title: PP242_24_4

description: Neuroblastoma SK-N_BE(2)c PP242 treated 24 hour hypoxia Sample #4


title: Osteosarcoma tumor - 22231 (aCGH)

description:
High molecular weight DNA
Tumor sampls were obtained from the tissues bank at the Laboratory of Oncology Research of the Rizzoli Orthopaedic Institute, Bologna, Italy


title: PP242_48_3

description: Neuroblastoma SK-N_BE(2)c PP242 treated 48 hour hypoxia Sample #3


title: control, 48h, rep1

description:
Cotton plants under normal condition for 48h, biological replicate 1
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_C-48-1_(Cotton)

source_name: whole cotton leaves_untreated control_48h

value: none (untreated control)


title: CBW, 24h, rep3

description:
Cotton plants were exposed to CBW larvae for 24h, biological replicate 3
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_I-24-3_(Cotton)

source_name: whole cotton leaves_treated with cotton bollworm_24h

value: 24h after onset of herbivory


title: Osteosarcoma tumor - 22164 (aCGH)

value: osteosarcoma tumor


title: DMSO_72_2

description: Neuroblastoma SK-N_BE(2)c DMSO treated 72 hour hypoxia Sample #2


title: DMSO_24_3

description: Neuroblastoma SK-N_BE(2)c DMSO treated 24 hour hypoxia Sample #3

source_name: SK-N_BE(2)c, DMSO treated 24h Hypoxia


title: Osteosarcoma tumor - 20174 (aCGH)

source_name: genomic DNA from Promega


title: PP242_24_1

description: Neuroblastoma SK-N_BE(2)c PP242 treated 24 hour hypoxia Sample #1


title: control, 48h, rep3

description:
Cotton plants under normal condition for 48h, biological replicate 3
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_C-48-3_(Cotton)


title: CBW, 48h, rep1

description:
Cotton plants were exposed to CBW larvae for 48h, biological replicate 1
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_I-48-1_(Cotton)


title: DMSO_24_1

description: Neuroblastoma SK-N_BE(2)c DMSO treated 24 hour hypoxia Sample #1


title: CBW, 24h, rep1

description:
Cotton plants were exposed to CBW larvae for 24h, biological replicate 1
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_I-24-1_(Cotton)


title: DMSO_24_2

description: Neuroblastoma SK-N_BE(2)c DMSO treated 24 hour hypoxia Sample #2


title: control, 24h, rep3

description:
Cotton plants under normal condition for 24h, biological replicate 3
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_C-24-3_(Cotton)

source_name: whole cotton leaves_untreated control_24h


title: CBW, 12h, rep2

description:
Cotton plants were exposed to CBW larvae for 12h, biological replicate 2
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_I-12-2_(Cotton)

source_name: whole cotton leaves_treated with cotton bollworm_12h

value: 12h after onset of herbivory


title: C_2

description: Neuroblastoma SK-N_BE(2)c 0 hour Control Sample #2

source_name: SK-N_BE(2)c, 0h Control


title: CBW, 12h, rep3

description:
Cotton plants were exposed to CBW larvae for 12h, biological replicate 3
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_I-12-3_(Cotton)


title: CBW, 24h, rep2

description:
Cotton plants were exposed to CBW larvae for 24h, biological replicate 2
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_I-24-2_(Cotton)


title: CWR/ENZ+OLA rep3

city: Houston

first: Likun

last: Li

state: TX

address: 1515 Holcombe Blvd

department: GU Meducal Oncology

institute: MD Anderson Cancer Center

description: replicate 3

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

source_name: prostate cancer cell line

extract_protocol: Total RNA was isolated from VCaP, LNCaP, and CWR22Rv1 cells treated with ENZ, OLA, ENZ+OLA or vehicle control DMSO as described above using mirVana miRNA Isolation Kit (Invitrogen).

value: CWR

tag: disease state

value: metastatic

value: enzalutamide+olaparib


title: control, 48h, rep2

description:
Cotton plants under normal condition for 48h, biological replicate 2
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_C-48-2_(Cotton)


title: control, 12h, rep3

description:
Cotton plants under normal condition for 12h, biological replicate 3
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_C-12-3_(Cotton)

source_name: whole cotton leaves_untreated control_12h


title: C_4

description: Neuroblastoma SK-N_BE(2)c 0 hour Control Sample #4


title: CWR/ENZ+OLA rep1

description: replicate 1


title: CWR/ENZ+OLA rep2

description: replicate 2


title: control, 24h, rep2

description:
Cotton plants under normal condition for 24h, biological replicate 2
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_C-24-2_(Cotton)


title: C_1

description: Neuroblastoma SK-N_BE(2)c 0 hour Control Sample #1


title: CWR/OLA rep3

description: replicate 3

value: olaparib


title: CBW, 12h, rep1

description:
Cotton plants were exposed to CBW larvae for 12h, biological replicate 1
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_I-12-1_(Cotton)


title: C_3

description: Neuroblastoma SK-N_BE(2)c 0 hour Control Sample #3


title: control, 12h, rep2

description:
Cotton plants under normal condition for 12h, biological replicate 2
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_C-12-2_(Cotton)


title: CBW, 6h, rep3

description:
Cotton plants were exposed to CBW larvae for 6h, biological replicate 3
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_I-6-3_(Cotton)

source_name: whole cotton leaves_treated with cotton bollworm_6h

value: 6h after onset of herbivory


title: CBW, 6h, rep2

description:
Cotton plants were exposed to CBW larvae for 6h, biological replicate 2
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_I-6-2_(Cotton)


title: control, 24h, rep1

description:
Cotton plants under normal condition for 24h, biological replicate 1
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_C-24-1_(Cotton)


title: CWR/ENZ rep3

description: replicate 3

value: enzalutamide


title: control, 12h, rep1

description:
Cotton plants under normal condition for 12h, biological replicate 1
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_C-12-1_(Cotton)


title: CWR/OLA rep1

description: replicate 1


title: CWR/OLA rep2

description: replicate 2


title: control, 6h, rep3

description:
Cotton plants under normal condition for 6h, biological replicate 3
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_C-6-3_(Cotton)

source_name: whole cotton leaves_untreated control_6h


title: CBW, 6h, rep1

description:
Cotton plants were exposed to CBW larvae for 6h, biological replicate 1
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_I-6-1_(Cotton)


title: CWR/ENZ rep2

description: replicate 2


title: CWR/DMSO rep3

description: replicate 3

value: vehicle control DMSO


title: control, 6h, rep2

description:
Cotton plants under normal condition for 6h, biological replicate 2
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_C-6-2_(Cotton)

value: cv. CCRI12


title: CWR/DMSO rep2

description: replicate 2


title: CWR/ENZ rep1

description: replicate 1


title: 21-day-old rat Sertoli cell 3

city: Shanghai

first: Xiaoqin

last: Yin

state: Shanghai

address: No. 355 Luding Road, Shanghai 200062, P.R.China.

department: Shanghai Children’s Hospital

institute: School of medicine, Shanghai Jiao Tong University

description: Gene expression data from 21-day-old rat Sertoli cells, after Sertoli cells proliferation phase in rat puberty stage.

hyb_protocol: Biotin-labeled cDNA was hybridized to the rat gene 1.0 ST GenChip (Affymetrix) for 16 hours at 45°C using an Affymetrix-defined protocol.

scan_protocol: Genechips were scanned on the 3000 7G, an Affymetrix GeneChip scanner

data_processing: Processed by RMA

organism: Rattus norvegicus

source_name: testis

label_protocol: Fragmentation and labeling of the single-stranded cDNA were acquired using GeneChip® WT Terminal Labeling and Control Kit (Invitrogen).

growth_protocol: Sertoli cells were isolated and cultured in DMEM/F12 medium. Testes from rats were aseptically removed, decapsulated, and digested into cell suspension. Isolated cells were placed on a tissue cultured dish in DMEM/F12 supplemented with 10% fetal bovine serum.

treatment_protocol: After primary culture for another 24 hours, medium was changed again for re-purification and Sertoli cells formed a monolayer following rapid growth in the new medium.

value: Sertoli cells

value: 21 days-old


title: control, 6h, rep1

description:
Cotton plants under normal condition for 6h, biological replicate 1
Cotton plants (Gossypium hirsutum cv. CCRI12) were exposed to cotton bollworm (CBW; Helicoverpa armigera) larvae for 6h, 12h, 24h, and 48h (continuous feeding experiment). Control plants were harvested at the same time point. Whole cotton leaves were used for RNA isolation, labelling and array.
100807-10300F_C-6-1_(Cotton)

value: whole cotton leaves

value: 6-7 fully expanded true leaf stage; 5-6 weeks after sowing


title: CWR/DMSO rep1

description: replicate 1


title: VCaP/ENZ+OLA rep1

description: replicate 1

value: VCaP


title: VCaP/ENZ+OLA rep3

description: replicate 3


title: 21-day-old rat Sertoli cell 2


title: VCaP/ENZ+OLA rep2

description: replicate 2


title: 21-day-old rat Sertoli cell 1


title: VCaP/OLA rep3

description: replicate 3


title: 9-day-old rat Sertoli cell 3

description: Gene expression data from 9-day-old rat Sertoli cells, during Sertoli cells proliferation phase in rat neonatal stage.

value: 9 days-old


title: 9-day-old rat Sertoli cell 2


title: VCaP/OLA rep1

description: replicate 1


title: PC3_PML_Palbociclib_3

city: Montréal

first: Mathieu

last: Vernier

state: Quebec

address: 2900 Edouard Montpetit

department: Biochemistry

country: Canada

institute: Université de Montréal

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Gene 2.0 ST Chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G/4 Color Early Access.

data_processing: The data were analyzed with the affymetrix Expression Console software using Affymetrix default analysis settings and RMA as normalization method. Transcripts with a fold change higher or equal to 1.5 and a p-value˂ 0.05 according to the two-sample student's t-test were selected for final determination.

source_name: PC3 prostate cancer cells infected with a vector expressing PML and treated with Palbociclib

label_protocol: Biotinylated cRNA were prepared according to the protocol from the Ambion® WT Expression kit for Affymettrix® GeneChip®Whole Transcrpit (WT) Expression Arrays

growth_protocol: Cells were cultured in RPMI 1640 (Wisent, Montréal, QC) supplemented with 10% fetal bovine serum (FBS; Wisent) and 1% penicillin G/streptomycin sulfate (Wisent).

extract_protocol: RNA isolation with RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: Cells were infected with an empty retrovirus or a retrovirus expressing PML and selected during three days with 5 µg/ml puromycin before subcutaneous injection in BALB/c 6-wk-old nude mice  Then, mice were treated for 5 consecutive days with palbociclib (100mg/kg/day diluted in sodium lactate 50mM pH4 given by gavage). Snap frozen tumor samples were transferred to RLT buffer (QIAGEN) for homogenisation first with micropestels and then by passing the samples through QIAshredder column (QIAGEN)

value: PC3 prostate cancer cells

tag: infection

value: PC3 cells infected with retrovirus expressing PML

tag: xenograft host

value: subcutaneous injection of infected PC3 cells in BALB/c 6-wk-old nude mice

tag: agent

value: mice were treated with palbociclib

value: Xenograft


title: PC3_PML_Palbociclib_1

tag: tissue


title: PC3_PML_vehicle_2

source_name: PC3 prostate cancer cells infected with a vector expressing PML and treated with vehicle

value: mice were treated with vehicle


title: PC3_PML_Palbociclib_2


title: PC3_PML_vehicle_1


title: VCaP/DMSO rep3

description: replicate 3

value: metastatic


title: PC3_PML_vehicle_3


title: VCaP/OLA rep2

description: replicate 2

value: olaparib


title: VCaP/DMSO rep1

description: replicate 1


title: VCaP/ENZ rep3

description: replicate 3

value: enzalutamide


title: 9-day-old rat Sertoli cell 1


title: VCaP/ENZ rep2

description: replicate 2


title: PC3_Vector_Palbociclib_3

source_name: PC3 prostate cancer cells infected with an empty vector and treated with palbociclib

value: PC3 cells infected with empty retrovirus


title: PC3_Vector_Palbociclib_2


title: PIP-chondrocytes-2

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Affymetrix Human Gene 1.0 ST Array (Cat No. 901085); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 3.2.)

data_processing:
Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization);

source_name: cartilage from proximal interphalangeal joint, cadaver A213

label_protocol: 350ng total RNA for NuGen Applause WT-Amp Plus ST System (M01199v2-1); Encore Biotin Module (M0111v5)

growth_protocol: Cartilage was minced and digested in 0.2% collagenase B (F. Hoffman La Roche) for 16 hours. The resulting cell suspension was filtered through a nylon mesh with pores of 70 μm (BD Pharma, Le Pont-De-Claix, France). Cells were counted and viability tested using trypan blue dye (Sigma-Aldrich, St. Louis, MO). Chondrocytes were expanded in monolayer at 37°C, 5% CO2 and 5%O2, in DMEM/Ham´s F-12, 1:1 supplemented with 10% fetal bovine serum (FBS, all PAA Laboratories) and 1%Penicilin/Streptomycin solution over three passages.

extract_protocol: extraction: TRIzol reagent (Life Technologies; Carlsbad, CA; Cat No 15596018); purification: RNeasy_MicroPLUS (Qiagen, Hilden, Germany; Cat No 74034) according to the modification of the RNeasy Plus Micro procedure for cells that allow the purification of total RNA containing small RNAs such as miRNA

value: cartilage from proximal interphalangeal joint (PIP)

value: female

value: chondrocytes


title: PC3_Vector_Palbociclib_1


title: PIP-chondrocytes-3

source_name: cartilage from proximal interphalangeal joint, cadaver Z188


title: PC3_Vector_vehicle_3

source_name: PC3 prostate cancer cells infected with an empty vector and treated with vehicle


title: VCaP/ENZ rep1

description: replicate 1


title: PC3_Vector_vehicle_2


title: VCaP/DMSO rep2

description: replicate 2

value: vehicle control DMSO


title: LNCaP/ENZ+OLA rep1

description: replicate 1

value: LNCaP

value: enzalutamide+olaparib


title: LNCaP/ENZ+OLA rep3

description: replicate 3


title: Control and treated sample Replication 3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description: Biological replicate 3. treated and control leaf tissues

hyb_protocol: 300 ng each of labeled Cyanine 3-CTP cRNA and Cyanine 5-CTP cRNA were mixed and fragmented to an average size of approximately 50 to 100 nucleotides with fragmentation buffer at 60°C for 30 minutes and the reaction was stopped by adding 2X GE HI-RPM hybridization buffer (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404).The samples were pipetted onto the gasket slide and hybridized onto a Custom Agilent  Eucalyptus 8x60k Microarray Gene expression  (AMADID: 59849 ) designed by Genotypic Technology Pvt.Ltd. The hybridization was carried out at 65°C for 16 hours in the Agilent Surehyb chambers.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

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

organism: Eucalyptus grandis

source_name: Eucalyptus grandis leaf, treated

label_protocol: The sample labeling was performed using Quick-Amp Labeling Kit, Two Color (Agilent Technologies, Part Number: 5190-0444). 500 ng of each of the Control and test samples were denatured along with WT primer at 65°C for 10 min followed by snapchilling on ice for 5 minutes. The cDNA master mix was added to the denatured RNA sample and incubated at 40°C for 2 hours for double stranded cDNA synthesis. Synthesized double stranded cDNA were used as template for cRNA generation by in vitro transcription(IVT) . Control samples were labeled with  Cy3 CTP and test samples with Cy5 CTP according to the experimental plan.  The samples were subjected to IVT reaction at 40°C for 2:30 hours. The Cyanine 3-CTP and Cyanine 5-CTP labeled cRNA sample was purified using Qiagen RNeasy column (Qiagen, Cat No: 74106). The quality assessed for yields and specific activity using the Nanodrop ND-1000

growth_protocol: Forty day old rooted cuttings of E. grandis was maintained in the vegetative multiplication garden of the Institute of Forest Genetics and Tree Breeding at Coimbatore, India

extract_protocol: Total RNA extracted using RNAqueous Total RNA Isolation Kit (Thermo Fisher) following manufacturer protocol.

treatment_protocol: The rooted cuttings were treated with -0.225 Mpa of polyethylene glycol in hoagland solution for three hours prior to RNA isolation from leaf tissues. Simultaneously, rooted cuttings were maintained in hoagland solution and was considered as control.

value: Leaf

value: 40 days old cuttings

source_name: Eucalyptus grandis leaf, control


title: LNCaP/ENZ+OLA rep2

description: replicate 2


title: knee-chondrocytes-2

source_name: cartilage from tibial plateau, cadaver A213

value: cartilage from knee (tibial plateau)


title: knee-chondrocytes-3

source_name: cartilage from tibial plateau, cadaver B58


title: LNCaP/OLA rep3

description: replicate 3


title: PIP-chondrocytes-1

source_name: cartilage from proximal interphalangeal joint, cadaver A199

value: male


title: PC3_Vector_vehicle_1

value: PC3 prostate cancer cells

value: subcutaneous injection of infected PC3 cells in BALB/c 6-wk-old nude mice


title: Control and treated sample Replication 1

description: Biological replicate 1. treated and control leaf tissues


title: Control and treated sample Replication 2

description: Biological replicate 2. treated and control leaf tissues


title: HSC-F CD4+ T cell Nef G63E SIVmac239 24h_rep3

city: Shinjuku-ku

first: Hiroyuki

last: Yamamoto

state: Tokyo

address: 1-23-1 Toyama

department: AIDS Research Center

country: Japan

institute: National Institute of Infectious Diseases

hyb_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

scan_protocol: We followed manufacturer's protocol, and used GeneChip® Scanner 3000 7G.

data_processing: Data acquisition and normalization (RMA) were used Affymetrix® Expression Console™ Software.

source_name: HSC-F CD4+ T cell line, cultured and infected with Nef G63E SIVmac239 for 24h

growth_protocol: 5 x 104 cells/total 200 μl/96-well U-bottomed plate, cultured for 24h at 37℃, 5% CO2

extract_protocol: RNeasy® Plus Mini Kit was used.

treatment_protocol: HSC-F CD4+ T cell: none. HSC-F CD4+ T cell SIVmac239: infected with SIVmac239, MOI 5. HSC-F CD4+ T cell Nef G63E SIVmac239: infected with Nef G63E SIVmac239, MOI 5.

tag: cell

value: HSC-F macaca fasicularis immortalized CD4+ T cell line

value: infected with Nef G63E SIVmac239


title: F4-luc_bm#2 (mRNA)

city: Taipei

first: Mong-Hsun

last: Tsai

address: 4F, No. 81, Chang-Xing St.

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

scan_protocol: Standard Illumina scan protocol

data_processing: Standard Illumina data processing procedures

source_name: lung cancer brain metastatic cell line clone #2

label_protocol: Standard Illumina label protocol

growth_protocol: Cells were cultured in DME/F12+10% FBS+1%PS media under 1% O2 condition for 24h incubation.

extract_protocol: Total RNA of cells was isolated with Trizol solution and purified with QIAGEN columns.

treatment_protocol: No treatment

value: lung cancer brain metastatic


title: F4-luc_bm#7 (mRNA)

source_name: lung cancer brain metastatic cell line clone #7


title: LNCaP/OLA rep2

description: replicate 2

source_name: prostate cancer cell line

value: metastatic

value: olaparib


title: LNCaP/OLA rep1

description: replicate 1


title: F4-luc (mRNA)

source_name: parental cell line

value: lung cancer parental


title: Developing xylem_Eucalyptus tereticornis_Cardwell

description: Gene expression in developing xylem tissue of Cardwell

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Custom Agilent  Eucalyptus 8x60k Microarray Gene expression  (AMADID: 59849 ) designed by Genotypic Technology Pvt.Ltd.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). 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 (Agilent Technologies, Part Number 5188-5327)

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

organism: Eucalyptus tereticornis

source_name: Eucalyptus tereticornis, developing xylem, 8

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized 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 using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: The developing xylem tissues were collected from 19 year old standing trees maintained at Karunya Research Station, Coimbatore, India

extract_protocol: Total RNA was isolated using in-house protocol

value: Developing xylem_high holocellulose content

value: 19 year old standing tree

value: Cardwell


title: Developing xylem_Eucalyptus tereticornis_Kupiano

description: Gene expression in developing xylem tissue of Kupiano

source_name: Eucalyptus tereticornis, developing xylem, 14

value: Developing xylem_high lignin content

value: Kupiano


title: Developing xylem_Eucalyptus tereticornis_N Kennedy River

description: Gene expression in developing xylem tissue of N Kennedy River

source_name: Eucalyptus tereticornis, developing xylem, 49

value: N Kennedy River


title: LNCaP/ENZ rep3

description: replicate 3

value: LNCaP

value: enzalutamide


title: H.sapiens_CaCo-2 menthol treatment and control

city: Lucknow

first: Ajit

middle: K.

last: Shasany

state: Uttar Pradesh

address: P.O. CIMAP

department: Biotechnology Division

institute: CSIR-Central Institute of Medicinal and Aromatic Plants

description: Menthol  treated and untreated cells were harvested after 48 hrs and total RNA isolated from both samples.

hyb_protocol: Labelled cDNA Co-hybridised in HybStation (Genomics Solutions) using the Slide assembly. Slides placed in  for 16 h at 42 °C.  After hybridization Arrays were then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C at RT for 5 min prior to drying and scanning.

scan_protocol: Scanned on an Genomics Solution GeneTACTM UC4 Microarray Scanner. Images were quantified using GeneTac UC4 Feature Extraction Software.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. GeneMaths software from Genomics solution was used for analysis.

source_name: CaCo-2_menthol_48 hrs

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using InDirect Labelling  kit (ChipShot Indirect Labeling and Clean-Up System, Promega) according to the protocol provided by the manufacturers. Samples purified using  ChipShot Clean-Up System kit before hybridization.

growth_protocol: CaCo-2 (ATCC HTB37, human colon adenocarcinoma) cells were obtained from National Centre for Cell Science, Pune, India, and were grown in Dulbecco’s-modified eagle medium (DMEM) supplemented with 10% FBS. Undifferentiated cells were passaged upon reaching 80% confluence, at a split ratio of 1:4 using 0.25% trypsin in PBS.

extract_protocol: Menthol treated and control cells were harvested from the cultures directly into TriZol and total RNA isolated from both samples using protocol according to Manufacturer's protocol (Life Technologies)  with DNAse digestion.

treatment_protocol: The overnight grown cells were incubated with or without L-menthol dissolved in 100% DMSO at IC50 (12 µg/mL for L-menthol) in 5% CO2 incubator for 48 h. L-menthol was obtained from Sigma-Aldrich. Microarray profiling was done from total RNA (Trizol, Life Technologies) isolated from control as well as menthol treated cell lines.

value: CaCo-2;  ATCC HTB37

value: human colon adenocarcinoma

value: menthol for 48 hrs

source_name: CaCo-2_untreated cells

value: none (control) for 48 hrs


title: LNCaP/ENZ rep2

description: replicate 2


title: LNCaP/DMSO rep3

description: replicate 3

value: vehicle control DMSO


title: LNCaP/ENZ rep1

description: replicate 1


title: knee-chondrocytes-1

source_name: cartilage from tibial plateau, cadaver A199

value: cartilage from knee (tibial plateau)

value: male

value: chondrocytes


title: HSC-F CD4+ T cell SIVmac239 24h_rep3

source_name: HSC-F CD4+ T cell line, cultured and infected with SIVmac239 for 24h

label_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

value: HSC-F macaca fasicularis immortalized CD4+ T cell line

value: infected with SIVmac239


title: LNCaP/DMSO rep2

description: replicate 2

value: metastatic


title: HSC-F CD4+ T cell Nef G63E SIVmac239 24h_rep1

value: infected with Nef G63E SIVmac239


title: Control_MEP_2

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

hyb_protocol: Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

data_processing: Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method.  Resulting data were imported into GeneSpring GX v12.5 (Agilent Technologies, Santa Clara, CA, USA).  Expression values were normalized using quantile normalization with default settings.

source_name: megakaryocyte-erythroid progenitors (MEP; lineagelow c-Kit+ Sca-1- CD34low CD16/32low) from WT mice

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit as per manufacturer’s instructions, then DNase treated and purified.  RNA concentration was determined using the NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA).

tag: strain

value: Female


title: Wild-type Female 2

city: New York

first: Augustine

middle: MK

last: Choi

state: NY

address: 525 East 68th Street, Room M-522, Box 130

department: Department of Medicine

institute: Weill Cornell Medical College

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

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

data_processing: The data were analyzed using the Bioconductor package in R to perform RMA normalization.

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

growth_protocol: Mice were housed in the same animal facility with access to same food and water.

extract_protocol: RNA was isolated according to Qiagen RNAeasy Kit per manufacturers protocol

tag: strain background

value: Wild-type

tag: gender

value: female

value: lung


title: HSC-F CD4+ T cell SIVmac239 24h_rep1


title: HSC-F CD4+ T cell Nef G63E SIVmac239 24h_rep2


title: Developing xylem_Eucalyptus tereticornis_SW Mt. Garnet

description: Gene expression in developing xylem tissue of SW. Mt. Garnet

source_name: Eucalyptus tereticornis, developing xylem, 6

value: Developing xylem_high holocellulose content

tag: age

value: 19 year old standing tree

value: SW. Mt. Garnet


title: HSC-F CD4+ T cell SIVmac239 24h_rep2


title: HSC-F CD4+ T cell 24h_rep3

source_name: HSC-F CD4+ T cell line, cultured for 24h


title: Wild-type Female 1

tag: genotype/variation


title: Wild-type Male 3


title: LNCaP/DMSO rep1

description: replicate 1

value: LNCaP


title: Wild-type Female 3


title: Control_MEP_3

scan_protocol: Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.


title: HSC-F CD4+ T cell 24h_rep2


title: DKO_MEP_3

source_name: megakaryocyte-erythroid progenitors (MEP; lineagelow c-Kit+ Sca-1- CD34low CD16/32low) from SSB1 SSB2 KO mice


title: Control_MEP_4


title: Control_MEP_1


title: DKO_MEP_1


title: DKO_MEP_2


title: Wild-type Male 1


title: Wild-type Male 2


title: GR_siNS_2h_b4

city: Los Angeles

first: Dai-Ying

last: Wu

state: CA

address: 1441 Eastlake Ave, NOR 6314

institute: University of Southern California

description: rep 4

hyb_protocol: Labeling, hybridization and scanning was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.

data_processing: Bead summarized data was output from GenomeStudio. This data were normalized using neqc with limma (3.14.4) in R (2.15.3)

growth_protocol: A clonal line of U2OS cells that stably express wild-type rat GRγ were plated in 6-well dishes with medium supplemented with 5% fetal bovine serum.

extract_protocol: Total RNA was isolated using QIAshredder and RNeasy mini columns (Qiagen). The quality of RNA samples was evaluated by A260/A280 ratio which was at least 1.9 and the integrity was analyzed using electrophoresis on an Agilent Bioanalyzer using the Experion RNA Stdsens analysis kit (Biorad). For each experimental condition 5 ug of high quality total RNA was submitted to the Southern California Genotyping Consortium at the University of California, Los Angeles.

treatment_protocol: On the next day the cells were transfected with 60 pmol of siRNA per well using Lipofectamine RNAiMAX (Invitrogen) using manufacturer’s protocol. After 2 days (24hr time point), or 3 days (2 hr and 4 hr timepoints) cells were treated with Dex for the indicated times. All treatment groups were harvested at the same time.

tag: time point

tag: transfection

value: siNS


title: Control_GMP_4

source_name: granulocyte-macrophage progenitor (GMP; lineagelow c-Kit+ Sca-1- CD34high CD16/32high) from WT mice


title: GR_NI_4h_b2

description: rep 2

scan_protocol: Labeling, hybridization and scanning was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.

value: NI


title: GR_siHic5_2_4h_b1

description: rep 1

label_protocol: Labeling, hybridization and scanning was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.


title: IREB2 knock-out Female 2

source_name: IREB2 knock-out_female_lung

value: IREB2 Knockout (Irp2-/-)


title: IREB2 knock-out Female 3


title: GR_siNS_2h_b2

description: rep 2


title: GR_NI_2h_b4

description: rep 4


title: Control_GMP_3


title: HSC-F CD4+ T cell 24h_rep1

tag: treatment


title: Control_GMP_2


title: decidual cells, interleukin-1-beta, biological rep3

city: Columbus

first: Douglas

middle: A

last: Kniss

state: Ohio

address: 395 W. 12th Ave

department: Obstetrics and Gynecology

institute: Ohio State University

description: Gene expression data from decidual cells treated with interleukin-1-beta.

hyb_protocol: Affymetrix GeneChip expression arrays (GeneChip Human Gene 2.0 ST Array) were hybridized for 16 h in a 45°C incubator, rotated at 60 rpm.

scan_protocol: Hybridized arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Gene level differential expression analysis was performed using the Affymetrix Transcriptome Analysis Console (TAC) software version 1.0 using the default analytical pipeline, including the following algorithms: Tukey's Biweight averaging, unpaired single factor Analysis of Variance (ANOVA), and the Benjamini-Hochberg step-up false discovery rate (FDR)-controlling procedure.

label_protocol: 250 nanograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip Expression. Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).

growth_protocol: After written Institutional Review Board approval and informed consent, fibroblasts were prepared from the decidua parietalis of reflected fetal membranes obtained from uncomplicated pregnancies after elective repeat cesarean deliveries.  All specimens were obtained prior to the onset of labor.  The decidua was scraped from the maternal surface of the chorion, minced, and incubated with 25 mg/ml of collagenase (200 U/mg) (Worthington Biochemical) and 6.25 U/ml of DNase (Sigma-Aldrich).  Cell clusters in the final digestate were further disrupted by passage through a 23-gauge needle. The cells were enriched by centrifugation through discontinuous Percoll gradients, and then cultivated over three passages until >99% free of CD45+ leukocytes in basal medium, a phenol red-free 1:1 vol/vol mix of Dulbecco's Modified Eagle Medium (DMEM)/Ham’s F-12 (Life Technologies) with 100 U/ml penicillin, 100 µg/ml streptomycin, 0.25 µg/ml amphotericin B supplemented with 10% charcoal stripped calf serum (SCS).  Passaged, confluent, leukocyte-free decidual cells were primed for 13 days in basal medium supplemented with SCS containing 10-8 M 17β-estradiol (E2; Sigma-Aldrich) and 10-7 M medroxyprogesterone acetate (MPA; Sigma-Aldrich).  The cultures were then washed twice with PBS and switched to a defined medium consisting of basal medium (without the addition of SCS) plus ITS+ Premix (BD Biosciences), 5 μM FeSO4, 0.5 μM ZnSO4, 1 nM CuSO4 (Sigma-Aldrich), 50 μg/ml ascorbic acid (Sigma-Aldrich) and 50 ng/ml epidermal growth factor (BD Biosciences) with E2 and MPA overnight prior to experiments.  Cells from three different donors were used for the studies.

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) and after the addition of chloroform and centrifugation, the aqueous phase was applied to a miRNeasy spin column (Qiagen) and processed according to the manufacturer’s protocol. This included on-column DNase digestion using the RNase-Free DNase kit (Qiagen) to remove contaminating genomic DNA.

treatment_protocol: The cultures were treated with PBS containing 0.1% bovine serum albumin (vehicle control) or with 1 ng/ml of IL-1β (R&D Systems) for 6 h.

value: decidua

tag: cell type

value: fibroblast

tag: time

value: 6 h


title: Control_GMP_1


title: decidual cells, interleukin-1-beta, biological rep2

source_name: decidual cells treated with interleukin-1-beta


title: decidual cells, vehicle, biological rep3

description: Gene expression data from decidual cells treated with vehicle.

source_name: decidual cells treated with vehicle

value: vehicle


title: IREB2 knock-out Female 1


title: decidual cells, vehicle, biological rep2


title: decidual cells, interleukin-1-beta, biological rep1


title: DKO_GMP_4

source_name: granulocyte-macrophage progenitor (GMP; lineagelow c-Kit+ Sca-1- CD34high CD16/32high) from SSB1 SSB2 KO mice


title: IREB2 knock-out Male 2

source_name: IREB2 knock-out_male_lung

value: male


title: IREB2 knock-out Male 1


title: GR_siHic5_2_0h_b3

description: rep 3


title: GR_siHic5_5_0h_b4

description: rep 4


title: DKO_GMP_3


title: DKO_GMP_2


title: decidual cells, vehicle, biological rep1


title: GR_siNS_4h_b3

description: rep 3


title: liver progenitor cells from YFP – 2

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: YFP negative cells  untreated (replicate 2)

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.12) ' R.3.0.0

source_name: liver progenitor cells from YFP – 2

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA from sorted cells was obtained using the RNeasy Micro Kit (Qiagen GmbH, Hilden, Germany). RNA from whole liver samples was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. Total RNA was retrotranscribed using a high-capacity complementary DNA reverse-transcription kit (Applied Biosystems, Foster City, CA) and amplified using Platinum® SYBR® Green qPCR SuperMix-UDG (Life Technologies) in a 7900 HT instrument (Applied Biosystems).

treatment_protocol: YFP positive cells were obtained by liver perfusion method from mice treated with DDC diet (n=4) for 5 weeks. Livers were perfused with EGTA solution (NaCl 137 mM, KCl 5.4 mM, NaH2PO4H2O 0.64 mM, Na2HPO4 0.85 mM, HEPES 1mM, NaHCO3 4.17 mM, EGTA 0.5 mM and glucose 5mM, pH= 7.4) at a flow rate of 5ml/min until liver gets pale. After that, the liver was perfused with collagenase solution (NaCl 137 mM, KCl 5.4 mM, NaH2PO4H2O 0.64mM, Na2HPO4 0.85 mM , HEPES 1 mM, NaHCO3 4.17 mM and CaCl2·2H2O 3.8 mM, pH=7.4) containing Collagenase A 0.5 g/L (Roche Diagnostics GmbH, Manheim, Germany) at a flow rate of 5 mL/min for 11 minutes. The digested liver was minced in Petri dish with ice cold 1x Hank’s Balanced Salt Solution (HBSS) (Biological Industries) and filtered through 70-μm cell strainer (BD Biosciences, Erembodegen, Belgium). The undigested liver was re-digested with collagenase solution containing 0.5 g/L Collagenase A, 0.5 g/L Pronase and 50 mg/L DNAse I (Roche Diagnostics GmbH) and stirred for 30 minutes at 37°C before liver homogenates were filtered using a 70-μm cell strainer. After slow centrifugations at 100g for 2 minutes the supernatant was centrifuged at 300g for 5 minutes and the pellet containing non-parenchymal cells were sorted on a FACSAria (BD Biosciences). YFP+ gate was established based on wild type mice. Dead cells were excluded by Live/Dead cell stain kit (Life Technologies, Eugene, Oregon) and YFP+ cells were collected in RLT buffer.

tag: type of yfp

value: YFP -


title: DKO_GMP_1

value: Female


title: GR_siHic5_2_2h_b4

description: rep 4


title: shRNA Shp2 sample 2

city: Rochester

first: Glynis

middle: Aileen

last: Scott

state: New York

address: 601 Elmwood Ave

department: Dermatology

institute: University of Rochester School of Medicine

description:
tumor with Shp2 knockdown (Sample 2)
tumor, melanoma

hyb_protocol: Following fragmentation, 25 ng/uL of fragmented sscDNA were hybridized for 16 hr at 45oC on GeneChip Human Gene ST2.0arrays.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the FS450_0007 fluidics script.

data_processing: GeneChip Command Console Software (Affymetrix, Santa Clara CA). All samples were normalized by the GC-RMA method (Gene Chips Robust Multichip Analysis). Differentially expressed genes were defined by differences in expression levels with a signficance of p<0.05 (ANOVA).

source_name: xenograft tumors

growth_protocol: cells were grown subcutaneously in NSG mice until tumors were formed (approximately 6 weeks).Total RNA was extracted and differentially expressed genes were identified.

extract_protocol: Trizol was used for extration of total RNA from tumors after tumors were harvested. Shp2 knockdown was confirmed by RT-PCR and ICH.

treatment_protocol: Shp2 knockdown compared with non-target controls

tag: cell line

value: 1205Lu Metastatic Human melanoma cell line

value: Shp2 knockdown

tag: growth protocol

value: grown as xenograft tumors in NSG mice


title: liver progenitor cells from YFP – 3

description: YFP negative cells  untreated (replicate 3)

source_name: liver progenitor cells from YFP – 3


title: liver progenitor cells from YFP – 1

description: YFP negative cells  untreated (replicate 1)

source_name: liver progenitor cells from YFP – 1


title: GR_siHic5_5_2h_b2

description: rep 2


title: [14P0010317-M16 -/- postDP]

city: Ichikawa-shi

first: SHOICHI

last: TAKIKITA

state: Chiba

address: 1-7-1 Kounodai

department: Department of Immunology and Pathology

institute: The Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine

description: Sample 16

hyb_protocol: Illumina Gene Expression system Hyb E1 and Block Buffer kit,

scan_protocol: Standard Illumina scanning protocol

data_processing: Data processing was performed using GeneSpring GX version GX11.5.

source_name: postselected DP cells

label_protocol: TargetAmp™- Nano Labeling Kit for Illumina® Expression BeadChip®

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Quiagen).

value: thymocytes


title: NT-sample 3

description:
tumor expression non-target shRNA (sample 3)
tumor, melanoma

value: control


title: GR_siHic5_5_24h_b2

description: rep 2


title: shRNA Shp2 sample 1

description:
tumor with Shp2 knockdown (Sample 1)
tumor, melanoma


title: GR_NI_2h_b3

description: rep 3


title: GR_siHic5_5_4h_b1

description: rep 1


title: NT-sample 2

description:
tumor expression non-target shRNA (sample 2)
tumor, melanoma


title: liver progenitor cells from YFP+ UTR 2

description: YFP positive cells  untreated (replicate 2)

source_name: liver progenitor cells from YFP+ UTR 2

value: YFP+ UTR


title: liver progenitor cells from YFP+ DDC 3

description: YFP positive cells  obtained from mice treated with DDC (replicate 3)

source_name: liver progenitor cells from YFP+ DDC 3

value: YFP+ DDC


title: [14P0010317-M15 +/+ postDP]

description: Sample 15


title: liver progenitor cells from YFP+ UTR 1

description: YFP positive cells  untreated (replicate 1)

source_name: liver progenitor cells from YFP+ UTR 1


title: shRNA Shp2 sample 3

description:
tumor with Shp2 knockdown (Sample 3)
tumor, melanoma


title: GR_siHic5_2_24h_b2

description: rep 2


title: NT-sample 1

description:
tumor expression non-target shRNA (sample 1)
tumor, melanoma


title: [14P0010317-M14 -/- CD4SP 03]

description: Sample 14

source_name: CD4SP cells


title: [14P0010317-M12 -/- CD4SP 02]

description: Sample 12


title: liver progenitor cells from YFP+ DDC 1

description: YFP positive cells  obtained from mice treated with DDC (replicate 1)

source_name: liver progenitor cells from YFP+ DDC 1


title: liver progenitor cells from YFP+ DDC 2

description: YFP positive cells  obtained from mice treated with DDC (replicate 2)

source_name: liver progenitor cells from YFP+ DDC 2


title: WT_A

first: Lianbo

last: Yu

state: OH

address: 1800 Cannon Drive

department: Center for Biostatistics

institute: The Ohio State University

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Affymetrix Eukaryotic Hybridization Controls (Affymetrix) and Oligo B2, 3nM (Affymetrix) •Heat 65oC for 5 minutes, 99oC for 5 minutes, 45oC for 5 minutes centrifuge top speed for 5 minutes  •Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0002

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using AGCC.

data_processing: The data were normalized by RMA method with Affymetrix Expression Console software. Linear model and moderated t-test was used for testing differentially expressed genes by using SAS and R packages.

source_name: preadipocyte cell line

label_protocol: Sample were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Dulbecco's Modified Eagle Medium containing 10% calf serum and 0.1% 50mg/mL gentamicin.

extract_protocol: mRNA was isolated by Rneasy (Qiagen, Valencia, CA)

treatment_protocol: no treatment

value: female-derived

value: wild type (C57Bl/6J)


title: GR_siHic5_5_4h_b2

description: rep 2


title: WT_3


title: GR_siNS_2h_b1

description: rep 1

value: siNS


title: [14P0010317-M09 +/+ CD4SP 01]

description: Sample 9


title: [14P0010317-M10 -/- CD4SP 01]

description: Sample 10


title: [14P0010317-M13 +/+ CD4SP 03]

description: Sample 13


title: KO_B

value: aldh1a1 knock out


title: GR_NI_0h_b2

description: rep 2

value: NI


title: KO_C


title: [14P0010317-M11 +/+ CD4SP 02]

description: Sample 11


title: [14P0010317-M08 -/- preDP 04]

description: Sample 8

source_name: preselected DP cells


title: liver progenitor cells from YFP+ CDE 3

description: YFP positive cells  obtained from mice treated with CDE (replicate 3)

source_name: liver progenitor cells from YFP+ CDE 3

value: YFP+ CDE


title: GR_siHic5_5_2h_b4

description: rep 4


title: liver progenitor cells from YFP+ CDE 2

description: YFP positive cells  obtained from mice treated with CDE (replicate 2)

source_name: liver progenitor cells from YFP+ CDE 2


title: liver progenitor cells from YFP+ CDE 1

description: YFP positive cells  obtained from mice treated with CDE (replicate 1)

source_name: liver progenitor cells from YFP+ CDE 1


title: KO_A


title: [14P0010317-M07 +/+ preDP 04]

description: Sample 7


title: WT_2


title: GR_siHic5_5_24h_b3

description: rep 3


title: GR_siHic5_2_0h_b4

description: rep 4


title: GR_siHic5_2_2h_b1

description: rep 1


title: [14P0010317-M06 -/- preDP 03]

description: Sample 6


title: GR_NI_24h_b1

description: rep 1


title: male breast cancer 296

city: Lund

first: Ida

last: Johansson

address: Department of Oncology Clinical Sciences Lund University BMC C13

department: Oncology

institute: Lund University

hyb_protocol: BAC aCGH microarrays were hybridized as described (PMID: 17334996)

scan_protocol: Arrays were washed as described (PMID: 17334996) and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for tumor sample were stored as channel 1 (ch1) whereas quantified intensities for reference sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots were removed and regarded as missing values if flagged during image-analysis. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Normalization was performed by applying popLowess (PMID: 17953745). Spots from dye-swap hybridization were merged using geometric mean of ratios after normalization.

source_name: male breast cancer

label_protocol: Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions using the Invitrogen Bioprime aCGH Genomic Labeling Module as described (PMID:17334996).

extract_protocol: DNA was extracted from fresh frozen tissue using a modification of a back-extraction protocol from the organic phase of the Qiagen Lipid mini RNA kit (Qiagen, Valencia, CA) as follows: 1 M Tris-buffer containing 4 M Guanidine Thiocyanate and 50 mM Sodium Citrate, followed by glycogen precipitation.

tag: size

tag: nhg

tag: er

tag: pr

source_name: normal genomic DNA from Promega

tag: sample type

value: reference


title: male breast cancer 305


title: LF treated with purmo x24hrs, rep2

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

hyb_protocol: cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to GeneChips (Affymetrix Inc., Santa Clara, CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Probesets were considered expressed if at least one sample had an RMA expression value greater than the mean of the negative control probesets; 18,494 probesets were considered expressed. Differential gene expression between the control and mutant mice was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates. Heatmap displays were created using the freely available MeV package ( http://www.tm4.org/mev/).

source_name: Lung fibroblast isolated from whole lung, purmorphamine

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

growth_protocol: Mouse lung was digested into single cell suspension and lung fibroblast was enriched and grown on tissue culture plate in DMEMF12/10%FCS. Primary fibroblasts were passaged no more than 3 times before discarded.

extract_protocol: RNA was extracted using RNeasy Mini Kit (Qiagen).

treatment_protocol: Freshly isolated fibroblasts were split into triplicate wells and treated with vehicle or purmorphamine 5um for 24 hours before RNA was isolated.

tag: strain/background

value: wild-type

value: male

value: 8 weeks

value: lung fibroblasts

value: purmorphamine


title: [14P0010317-M05 +/+ preDP 03]

description: Sample 5

tag: strain


title: male breast cancer 304


title: LF treated with purmo x24hrs, rep3

tag: gender

tag: age


title: GR_siNS_0h_b4

description: rep 4

tag: time point


title: GR_siHic5_5_2h_b1

description: rep 1

tag: transfection


title: [14P0010317-M04 -/- preDP 02]

description: Sample 4


title: male breast cancer 281

value: II

value: positive


title: LF treated with purmo x24hrs, rep1

tag: genotype/variation

tag: treatment


title: male breast cancer 292

value: I

value: negative


title: GR_siHic5_5_4h_b4

description: rep 4


title: [14P0010317-M02 -/- preDP 01]

description: Sample 2

tag: cell type

value: thymocytes


title: LF control, rep3

source_name: Lung fibroblast isolated from whole lung, control

value: vehicle


title: GR_siHic5_5_0h_b3

description: rep 3


title: male breast cancer 303


title: [14P0010317-M03 +/+ preDP 02]

description: Sample 3


title: sgp130Fc rep 3

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

institute: Monash University

description: SAMPLE 8

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Total RNA was labelled and hybridised to Illumina MouseRef-8 v2.0 Expression BeadChips (Illumina) according to Illumina standard protocols. Each sample had two or three biological replicates. Raw intensity output from Illumina GenomeStudio was background corrected and normalized by using the neqc method. Probes were only kept in analysis if they achieved a GenomeStudio detection p value of less than 0.1 in at least two arrays. Proportion of expressed probes in each array was estimated using the propexpr method. Manufacturer probe annotation was used. Linear models were fitted to each gene. Differential expression was assessed with empirical Bayes moderated t-statistics. Genes were considered to be differentially expressed if they achieved a false discovery rate of less than 0.1. All analyses were carried out in R using the Bioconductor R package limma.

source_name: sgp130Fc _adipose

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

extract_protocol: total RNA was extracted from tissue using Bioline mini-kit column according to the manufacturer instructions. Invitrogen DNAse I was used as a last step.

tag: strain background

value: sgp130Fc transgenic

value: 26 weeks

tag: status

value: high-fat fed obese mouse

tag: tissue

value: adipose tissue


title: [14P0010317-M01 +/+ preDP 01]

description: Sample 1


title: male breast cancer 267

tag: size


title: LF control, rep2


title: male breast cancer 279

tag: nhg


title: male breast cancer 270

tag: er


title: LF control, rep1


title: sgp130Fc rep 2

description: SAMPLE 7


title: GR_siHic5_2_0h_b1

description: rep 1


title: GR_siNS_24h_b2

description: rep 2

value: siNS


title: male breast cancer 263

tag: pr

value: reference


title: male breast cancer 251

tag: sample type


title: male breast cancer 243


title: GR_NI_4h_b3

description: rep 3

value: NI


title: GR_NI_2h_b1

description: rep 1


title: male breast cancer 242


title: GR_siNS_24h_b4

description: rep 4


title: GR_siNS_0h_b1

description: rep 1


title: male breast cancer 254


title: GR_siHic5_2_4h_b2

description: rep 2


title: IL6 KO rep 3

description: SAMPLE 5

source_name: IL6 KO_adipose

value: IL6 knock-out

value: 25 weeks


title: IL6 KO rep 2

description: SAMPLE 4


title: IL6 KO rep 1

description: SAMPLE 3


title: sgp130Fc rep 1

description: SAMPLE 6


title: mature ovary-Orb_IP-rep3

city: MONTPELLIER

first: Simonelig

last: Martine

address: 141, rue de la Cardonille

department: Genetics and Development

institute: Institut de Genetique Humaine - CNRS

description: Orb RIP-chip

hyb_protocol: Cy3 and Cy5 labelled aRNA samples were mixed in equal proportions and hybridized at 37°C for 12 hours with the Automated Slide Processor (ASP) on INDAC oligonucleotide microarrays.

scan_protocol: Microarrays were immediately scanned at 10 µm resolution in both Cy3 and Cy5 channels with a GenePix 4200AL scanner (Molecular Devices) with a variable PMT voltage to obtain maximal signal intensities. ArrayVision software was used for feature extraction.

data_processing: We performed Significant Analysis of Microarrays (SAM) with False Discovery Rate (FDR) 0.01 to identify mRNAs that were enriched at least 1.5 fold in Orb RIP compared to mock RIP.

organism: Drosophila melanogaster

source_name: Orb IP , mature ovaries

label_protocol: RNA were labelled with Cy3 or Cy5 using the Ambion kit Amino Allyl Message Amp II

extract_protocol: not provided

tag: antibody

value: Orb (6H4 (DSHB) )

value: ovary

tag: developmental stage

value: 3-5 day-old

value: female

source_name: mock IP, mature ovaries

value: commercial mouse IgGs


title: male breast cancer 228

value: III


title: Wild Type rep 1

description: SAMPLE 1

value: wild type

value: 24 weeks


title: male breast cancer 215

value: positive

value: negative


title: mature ovary-Orb_IP-rep5

description: Orb RIP-chip

tag: gender


title: mature ovary-Orb_IP-rep6

description: Orb RIP-chip


title: male breast cancer 210


title: GR_siNS_4h_b1

description: rep 1


title: GR_NI_4h_b1

description: rep 1


title: GR_siHic5_2_2h_b2

description: rep 2


title: male breast cancer 236


title: mature ovary-Orb_IP-rep4

description: Orb RIP-chip


title: GR_siHic5_2_4h_b4

description: rep 4


title: male breast cancer 200

value: II


title: GR_siNS_4h_b4

description: rep 4


title: Wild Type rep 2

description: SAMPLE 2

tag: age

value: high-fat fed obese mouse

value: adipose tissue


title: mature ovary-Orb_IP-rep2

description: Orb RIP-chip


title: mature ovary-Orb_IP-rep1

description: Orb RIP-chip


title: GR_NI_0h_b3

description: rep 3

tag: time point


title: male breast cancer 195

value: reference


title: early ovary-Orb_IP-rep6

description: Orb RIP-chip

source_name: Orb IP , ovaries from newly eclosed females

label_protocol: RNA were labelled with Cy3 or Cy5 using the Ambion kit Amino Allyl Message Amp II.

value: newly eclosed

source_name: mock IP, ovaries from newly eclosed females


title: early ovary-Orb_IP-rep4

description: Orb RIP-chip


title: male breast cancer 198


title: GR_siNS_4h_b2

description: rep 2

tag: transfection

value: siNS


title: male breast cancer 178


title: early ovary-Orb_IP-rep2

description: Orb RIP-chip


title: early ovary-Orb_IP-rep5

description: Orb RIP-chip


title: male breast cancer 182a

value: I


title: GR_siHic5_5_0h_b1

description: rep 1


title: male breast cancer 179


title: male breast cancer 182b


title: GR_siHic5_5_0h_b2

description: rep 2


title: male breast cancer 192


title: early ovary-Orb_IP-rep3

description: Orb RIP-chip

value: Orb (6H4 (DSHB) )


title: male breast cancer 180


title: GR_NI_24h_b3

description: rep 3

value: NI


title: GR_NI_2h_b2

description: rep 2


title: Pak1 knockout treated with ionizing radiation , biological rep3

city: Washington

first: Mona

last: Motwani

state: DC

address: 2300 I St NW

institute: George Washington University

description: Pak1 knock-out mouse embryonic fibroblasts treated with IR

hyb_protocol: Samples were processed using the Affymetrix hybridization, wash and stain kits. 200µl of the hybridization mixture was hybridized onto each Mouse Exon 1.0 st array. Hybridized at 45°C with 60rpm rotation for 17 hours in Affymetrix hybridization oven 640

scan_protocol: Affymetrix Genechip scanner 3000 7G

data_processing: Data were processed using Genespring GX 10.0.2 (Affymetrix Technologies,Inc) . The raw data was summerized using RMA16 algorithm which is inbuilt in Genespring GX,followed by the log transformation, baseline transformation and finally quantile normalization.

source_name: knock-out

label_protocol: rRNA reduced samples were amplified and labelled using Genechip WT cDNA Synthesis/Amplification Kit and GeneChip WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA)

growth_protocol: The PAK1 KO mouse is a classic whole-body gene-ablation model on the C57Bl6J strain background 1.  MEFs were isolated from day 13.5 WT or Pak1−/− embryos.

extract_protocol: TRIzol was used for the RNA extraction, manufacturer's instructions were followed

treatment_protocol: WT and Pak1−/− MEFs were immortalized with SV40 T antigen and were maintained in DME supplemented with 10% FBS

value: mouse embryonic fibroblasts

value: ionizing radiation

tag: genotype

value: Pak1 knock-out

tag: genetic background


title: Pak1 knockout treated with ionizing radiation , biological rep2

tag: cell type

tag: treatment


title: GR_siHic5_2_2h_b3

description: rep 3


title: GR_siNS_24h_b3

description: rep 3


title: male breast cancer 170


title: GR_siHic5_2_24h_b3

description: rep 3


title: GR_NI_24h_b4

description: rep 4


title: male breast cancer 167

value: III


title: Pak1 knockout treated with ionizing radiation , biological rep1


title: GR_siNS_0h_b2

description: rep 2


title: early ovary-Orb_IP-rep1

description: Orb RIP-chip

value: ovary

value: female

value: commercial mouse IgGs


title: GR_siHic5_5_2h_b3

description: rep 3


title: male breast cancer 161

value: positive


title: Pak1 knockout , biological rep1

description: Pak1 knock-out mouse embryonic fibroblasts


title: Wildtype MEFs treated with ionizing radiation,biological rep1

description: wildtype mouse embryonic fibroblasts treated with IR

source_name: Wildtype

value: Wildtype


title: Wildtype MEFs treated with ionizing radiation,biological rep2


title: Pak1 knockout , biological rep3


title: Wildtype MEFs treated with ionizing radiation,biological rep3


title: male breast cancer 159

value: negative


title: GR_siNS_2h_b3

description: rep 3


title: Wildtype MEFs ,biological rep2

description: wildtype mouse embryonic fibroblasts


title: GR_siHic5_2_0h_b2

description: rep 2


title: Wildtype MEFs ,biological rep3

description: wildtype mouse embryonic fibroblasts


title: male breast cancer 165

value: II


title: male breast cancer 151

value: reference


title: GR_siNS_0h_b3

description: rep 3


title: Pak1 knockout , biological rep2


title: male breast cancer 166


title: male breast cancer 157


title: male breast cancer 137


title: male breast cancer 138


title: male breast cancer 131


title: GR_NI_0h_b4

description: rep 4


title: GR_NI_4h_b4

description: rep 4


title: GR_siHic5_2_4h_b3

description: rep 3


title: GR_siHic5_5_4h_b3

description: rep 3


title: GR_NI_24h_b2

description: rep 2


title: PlasmaExs_grazing_4mo

city: Tsukuba

first: Susumu

last: Muroya

state: Ibaraki

address: Ikenodai 2

department: Animal Products Research Division

institute: NARO Institute of Livestock and Grassland Science

description: Gene expression in plasma exosome of grazing cattle at 4 mo

hyb_protocol: Whole amount of Cy3-labelled cRNA sample was dried and rehydrated following the manufacturers instructions. Then the sample was applied to hybridization to Agilent custom microarray SurePrint G3 8x60K designed for bovine miRNA trascriptomics corresponding to miRBase ver. 19, for 20 hours at 55 ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37 ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The signals of hybridized probes were detected using an Agilent Microarray Scanner (Agilent) at scan resolution 3um with one color scan setting for custom microarray SurePrint G3 8x60K slide corresponding to miRBase ver. 19 (Agilent).

data_processing: The scanned images were analyzed with Agilent Feature Extraction 10.7.3.1 (Agilent) using default parameters. The data were imported to GeneSpring GX (Agilent) and were normalized to 90 percentile.

organism: Bos taurus

source_name: plasma exosome, grazing, 4 mo, mixture (n=3)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the miRNA Complete Labeling Reagent and Hyb kit (Agilent) according to the manufacturer's instructions.

growth_protocol: In the first 4 months from early June to late October, the grazing cattle were fed on the pasture, whereas the housed cattle were fed in a free-stall barn. In the last 3 months, from late October to the following mid-January, both groups were fed with grass silage in the free-stall barn.

extract_protocol: Total RNA including miRNA was extracted from plasma exosome samples using the mirVana microRNA isolation kit (Ambion, Austin, TX) for microarray analysis of plasma samples according to the manufacturer’s protocols. The quantity and quality of the RNA were determined by Agilent Bioanalyzer 2100 with an RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA). Three exosomal RNA samples for each feeding treatment (grazing or housed) and time point (0, 1, 2, or 4 mo) were mixed together.

treatment_protocol: Blood samples were drawn from the jugular vein of each animal and the plasma was prepared as 0.1% EDTA, followed by storage at -80ºC until use. The blood samples were collected at 0, 1, 2, 4, and 7 months (mo) in a 7-month experimental period. Ten ml of the plasma sample was mixed with 20 ml of PBS and centrifuged at 1,200 g, 4ºC for 20 min. The supernatant was centrifuged at 12k g, 4ºC for 45 min, and further centrifuged at 110k g, 4ºC for 120 min. The precipitation was suspended in PBS and centrifuged at 110k g, 4ºC for 70 min to obtain exosome sample pellet.

value: Plasma exosome

value: Grazing

value: 4 months


title: PlasmaExs_grazing_0mo

description: Gene expression in plasma exosome of grazing cattle at 0 mo

source_name: plasma exosome, grazing, 0 mo, mixture (n=3)

value: 0 month


title: PlasmaExs_housed_4mo

description: Gene expression in plasma exosome of housed cattle at 4 mo

source_name: plasma exosome, housed, 4 mo, mixture (n=3)

value: Housed


title: PlasmaExs_grazing_1mo

description: Gene expression in plasma exosome of grazing cattle at 1 mo

source_name: plasma exosome, grazing, 1 mo, mixture (n=3)

value: 1 month


title: Wildtype MEFs ,biological rep1

description: wildtype mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: PlasmaExs_housed_0mo

description: Gene expression in plasma exosome of housed cattle at 0 mo

source_name: plasma exosome, housed, 0 mo, mixture (n=3)


title: PlasmaExs_housed_2mo

description: Gene expression in plasma exosome of housed cattle at 2 mo

source_name: plasma exosome, housed, 2 mo, mixture (n=3)

value: 2 months


title: PlasmaExs_housed_1mo

description: Gene expressionin plasma exosome of housed cattle at 1 mo

source_name: plasma exosome, housed, 1 mo, mixture (n=3)


title: PlasmaExs_grazing_2mo

description: Gene expression in plasma exosome of grazing cattle at 2 mo

source_name: plasma exosome, grazing, 2 mo, mixture (n=3)


title: male breast cancer 91

source_name: male breast cancer

value: III

source_name: normal genomic DNA from Promega


title: male breast cancer 78


title: male breast cancer 77


title: male breast cancer 103


title: GR_NI_0h_b1

description: rep 1

value: NI


title: GR_siHic5_5_24h_b1

description: rep 1


title: male breast cancer 76


title: GR_siNS_24h_b1

description: rep 1

value: siNS


title: GR_siHic5_2_24h_b4

description: rep 4


title: male breast cancer 67


title: GR_siHic5_2_24h_b1

description: rep 1


title: male breast cancer 69


title: ER_siNS_4h_b1

description: rep 1

growth_protocol: A clonal line of U2OS cells that stably express wild-type rat ER were plated in 6-well dishes with medium supplemented with 5% fetal bovine serum.


title: GR_siHic5_5_24h_b4

description: rep 4


title: male breast cancer 60


title: male breast cancer 52


title: ER_siNS_24h_b2

description: rep 2


title: male breast cancer 75


title: male breast cancer 46


title: ER_siHic5_2_24h_b2

description: rep 2


title: male breast cancer 42


title: ER_siHic5_2_0h_b3

description: rep 3


title: male breast cancer 43


title: ER_siHic5_2_0h_b4

description: rep 4


title: ER_siHic5_2_24h_b3

description: rep 3


title: male breast cancer 37


title: male breast cancer 28


title: male breast cancer 36


title: ER_siHic5_2_0h_b1

description: rep 1


title: ER_siNS_0h_b4

description: rep 4


title: ER_siNS_0h_b2

description: rep 2


title: ER_siNS_0h_b1

description: rep 1


title: ER_siHic5_2_24h_b4

description: rep 4


title: ER_siHic5_2_4h_b4

description: rep 4


title: male breast cancer 1