title: Q455C3 7021_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment

description: Q455C3 7021_TAM+_Carcinosarcoma


title: 124T (AB)_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment

status: Public on Jun 17 2010

type: genomic

city: Amsterdam

first: Petra

last: Nederlof

address: Plesmanlaan 121

department: Pathology

country: Netherlands

institute: The Netherlands Cancer Institute

description: 124T (AB)_TAM+_Carcinosarcoma

hyb_protocol: hybridization as describe in Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer 2007;7:43.

scan_protocol: ImaGene v6.0 software (BioDiscovery Inc) was used to translate the cy5/cy3 intensity ratios into average of the triplicates log2-ratio.

data_processing: average of triplicate Log2 ratios after Lowess pintip normalization

molecule: genomic DNA

organism: Homo sapiens

source_name: FFPE primary tumor material TAM+

label_protocol: Sample and reference DNA were labeled with the Cy5- or Cy3-conjugates from the Universal Linkages System (ULS; Kreatech biotechnology, Amsterdam, The Netherlands)

growth_protocol: FFPE tissue primary tumors used

extract_protocol: DNA isolation for arrayCGH was performed as described elsewhere. (20) In short, formalin-fixed paraffin-embedded FFPE tissue of uterine corpus cancer was used. Cases were discarded if the tumor cell percentage was below 70%.  Genomic DNA was isolated from 10*10µm thick paraffin slides. Slides were deparaffinized twice in xylene for 5 minutes, rehydrated in 100% (twice), 90%,70% ethanol and stained with hematoxylin. To remove formalin induced cross-links an overnight incubation in 1M NaSCN at 37°C was performed. Slides were subsequently washed in PBS twice for 10 minutes and air-dried. Tumor cells were collected by macro dissection by scraping from the slides and cells were transferred to a tube containing 200 µl ATL buffer (QIAamp® DNA Mini Kit cat 51304, Qiagen), 27 µl Proteinase-K was added and samples were incubated at 55°C while shaken at 450 rmp for at least 40 hours.  At intervals of 4, 16 and 24 hours additional 27 µl of Proteinase-K was added (Qiagen kit). Further isolation was done following the manufacturers instructions (Qiagen).

tag: gender

value: female

tag: tumor

value: endometrial

tag: histology

value: carcinosarcoma

source_name: genomic DNA from blood from 8 healthy females

tag: reference


title: Q442A5 1067_TAM-_Carcinosarcoma, carcinosarcoma without prior tamoxifen treatment

description: Q442A5 1067_TAM-_Carcinosarcoma

source_name: FFPE primary tumor material TAM-

value: genomic DNA from blood from 8 healthy females


title: Q442A8 1081_TAM-_Carcinosarcoma, carcinosarcoma without prior tamoxifen treatment

description: Q442A8 1081_TAM-_Carcinosarcoma


title: Q442C3 9034_TAM-_Carcinosarcoma, carcinosarcoma without prior tamoxifen treatment

description: Q442C3 9034_TAM-_Carcinosarcoma


title: Q442A2 4078_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment

description: Q442A2 4078_TAM+_Carcinosarcoma


title: Q442A4 1117_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment

description: Q442A4 1117_TAM+_Carcinosarcoma


title: 12002_TAM-_Serous adenocarc, Serous adenocarcinoma without prior tamoxifen treatment

description: 12002_TAM-_Serous adenocarc

value: Serous adenocarcinoma


title: 12003_TAM-_Serous adenocarc, Serous adenocarcinoma without prior tamoxifen treatment

description: 12003_TAM-_Serous adenocarc


title: 032T_TAM+_Serous adenocarc, Serous adenocarcinoma after >=2y tamoxifen treatment

description: 032T_TAM+_Serous adenocarc


title: 093T_TAM+_Serous adenocarc, Serous adenocarcinoma after >=2y tamoxifen treatment

description: 093T_TAM+_Serous adenocarc


title: 12006_TAM-_Serous adenocarc, Serous adenocarcinoma without prior tamoxifen treatment

description: 12006_TAM-_Serous adenocarc


title: HB376-07_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment


title: Q455C5 1006_TAM-_Serous adenocarc, Serous adenocarcinoma without prior tamoxifen treatment

description: Q455C5 1006_TAM-_Serous adenocarc


title: HB37213_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment


title: 12005_TAM-_Serous adenocarc, Serous adenocarcinoma without prior tamoxifen treatment

description: 12005_TAM-_Serous adenocarc


title: Q442A3 8040_TAM-_Carcinosarcoma, carcinosarcoma without prior tamoxifen treatment

description: Q442A3 8040_TAM-_Carcinosarcoma


title: Q449D4 6072_TAM+_Serous adenocarc, Serous adenocarcinoma after >=2y tamoxifen treatment

description: Q449D4 6072_TAM+_Serous adenocarc


title: Q455C4 6071_TAM+_Serous adenocarc, Serous adenocarcinoma after >=2y tamoxifen treatment

description: Q455C4 6071_TAM+_Serous adenocarc


title: 12004_TAM-_Serous adenocarc, Serous adenocarcinoma without prior tamoxifen treatment

description: 12004_TAM-_Serous adenocarc


title: HB376-09_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment


title: Q449C8 6091_TAM+_Serous adenocarc, Serous adenocarcinoma after >=2y tamoxifen treatment

description: Q449C8 6091_TAM+_Serous adenocarc


title: Q449D1 1111_TAM+_Serous adenocarc, Serous adenocarcinoma after >=2y tamoxifen treatment

description: Q449D1 1111_TAM+_Serous adenocarc


title: Q449D3 2049_TAM+_Serous adenocarc, Serous adenocarcinoma after >=2y tamoxifen treatment

description: Q449D3 2049_TAM+_Serous adenocarc


title: Q449D2 8047_TAM-_Serous adenocarc, Serous adenocarcinoma without prior tamoxifen treatment

description: Q449D2 8047_TAM-_Serous adenocarc


title: HB372-21_TAM+_Serous adenocarc, Serous adenocarcinoma after >=2y tamoxifen treatment

description: HB372-21_TAM+_Serous adenocarc


title: Q449C5 4048_TAM-_Serous adenocarc, Serous adenocarcinoma without prior tamoxifen treatment

description: Q449C5 4048_TAM-_Serous adenocarc


title: Q449C9 6120_TAM-_Serous adenocarc, Serous adenocarcinoma without prior tamoxifen treatment

description: Q449C9 6120_TAM-_Serous adenocarc


title: Q449C6 6076_TAM+_Serous adenocarc, Serous adenocarcinoma after >=2y tamoxifen treatment

description: Q449C6 6076_TAM+_Serous adenocarc


title: Q441C3 2054_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q441C3 2054_TAM-_Endometrioid

value: Endometrioid


title: Q442A9 6110_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q442A9 6110_TAM-_Endometrioid


title: Q441C2 1103_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q441C2 1103_TAM+_Endometrioid


title: Q441B9 6078_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q441B9 6078_TAM-_Endometrioid


title: Q441C1 7049_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q441C1 7049_TAM+_Endometrioid


title: Q442B0 9035_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q442B0 9035_TAM+_Endometrioid


title: retinal minus lens-treated tissue rep3

type: RNA

city: Tuebingen

first: Regan

last: Ashby

address: Calwerstrasse 7/1

department: Section of Neurobiology of the Eye

country: Germany

institute: University of Tuebingen

description: retinal minus lens-treated tissue rep3

hyb_protocol: see manufacturer's website (http://www.affymetrix.com/)

data_processing: GC-RMA

label: biotin

molecule: total RNA

organism: Gallus gallus

source_name: Amacrine cell layer from plus minus-treated bird

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10-100ng of total RNA (see manufacturer´s website: Expression Analysis Technical Manual, Two-Cycle Target Labeling Assay, Affymetrix).

extract_protocol: Total RNA from the amacrine cell layer was isolated from laser-capture microdissected (Zeiss, Bernried, Germany) 10µm thick sections using a RNeasy Micro Kit (Qiagen, Hilden, Germany), following the manufactures instructions. Labeled cRNA was prepared from three separate samples per condition and hybridized to Affymetrix GeneChip Chicken Genome arrays.

treatment_protocol: Chicks were monocularly treated with either -7D (n=3, growth stimulant) or +7D (n=3, growth suppressant) lenses for 24hrs (12pm to 12pm), with untreated age-matched chicks serving as a control (n=3). Chicks were kept under a 12:12hr light-dark cycle (lights on 7am, lights off 7pm, with an illumination of 500lux).

tag: tissue

value: Amacrine cell layer


title: retinal minus lens-treated tissue rep2

description: retinal minus lens-treated tissue rep2

scan_protocol: see manufacturer's website (http://www.affymetrix.com/)


title: Q441B8 2028_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q441B8 2028_TAM-_Endometrioid


title: Q437D0 2033_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q437D0 2033_TAM-_Endometrioid


title: retinal plus lens-treated tissue rep3

description: retinal plus lens-treated tissue rep3

source_name: Amacrine cell layer from plus lens-treated bird


title: Q441B5 8046_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q441B5 8046_TAM-_Endometrioid


title: Q437D1 3036_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q437D1 3036_TAM-_Endometrioid


title: retinal plus lens-treated tissue rep2

description: retinal plus lens-treated tissue rep2


title: Q441B7 2035_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q441B7 2035_TAM-_Endometrioid


title: retinal minus lens-treated tissue rep1

description: retinal minus lens-treated tissue rep1


title: retinal control tissue rep2

description: retinal control tissue rep2

source_name: Amacrine cell layer from untreated age-matched control bird


title: retinal control tissue rep3

description: retinal control tissue rep3


title: retinal control tissue rep1

description: retinal control tissue rep1


title: Q437C9 3024_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q437C9 3024_TAM-_Endometrioid


title: Q437C3 6104_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q437C3 6104_TAM-_Endometrioid


title: Q437C7 3023_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q437C7 3023_TAM-_Endometrioid


title: Q437C2 4081_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q437C2 4081_TAM+_Endometrioid


title: Q441B4 8075_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q441B4 8075_TAM-_Endometrioid


title: Q437C8 4038_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q437C8 4038_TAM-_Endometrioid


title: Q437C6 8066_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q437C6 8066_TAM-_Endometrioid


title: Q437C1 1071_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q437C1 1071_TAM+_Endometrioid


title: Q437B8 6108_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q437B8 6108_TAM+_Endometrioid


title: Q437B7 3032_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q437B7 3032_TAM+_Endometrioid


title: Q437C0 8042_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: Q437C0 8042_TAM-_Endometrioid


title: Q437B2 6107_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q437B2 6107_TAM+_Endometrioid


title: Q437B4 1132_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q437B4 1132_TAM+_Endometrioid


title: Q437B1 8050_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q437B1 8050_TAM+_Endometrioid


title: HB376-10_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment


title: Q437B6 1110_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q437B6 1110_TAM+_Endometrioid


title: Q437A9 8043_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q437A9 8043_TAM+_Endometrioid


title: HB372-24_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment


title: Q437A7  1131_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q437A7  1131_TAM+_Endometrioid


title: HB372-22_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment


title: HB376-11_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment


title: HB376-04_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment


title: HB384-07_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment


title: Q427D4 4074_TAM-_Carcinosarcoma, carcinosarcoma without prior tamoxifen treatment

description: Q427D4 4074_TAM-_Carcinosarcoma


title: HB372-05_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment


title: HB394-16_TAM+_Serous adenocarc, Serous adenocarcinoma after >=2y tamoxifen treatment

description: HB394-16_TAM+_Serous adenocarc


title: HB399-15 8048_TAM+_Serous adenocarc, Serous adenocarcinoma after >=2y tamoxifen treatment

description: HB399-15 8048_TAM+_Serous adenocarc


title: HB384-06_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment


title: retinal plus lens-treated tissue rep1

description: retinal plus lens-treated tissue rep1


title: HB37211_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment


title: Q427A1 8053_TAM-_Carcinosarcoma, carcinosarcoma without prior tamoxifen treatment

description: Q427A1 8053_TAM-_Carcinosarcoma


title: HB394-14_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment


title: Q427A6 2029_TAM+_Serous adenocarc, Serous adenocarcinoma after >=2y tamoxifen treatment

description: Q427A6 2029_TAM+_Serous adenocarc


title: HB37215_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment


title: Q427A7 5054_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q427A7 5054_TAM+_Endometrioid


title: Q437B0 9049_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q437B0 9049_TAM+_Endometrioid


title: Q427A2 3044_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: Q427A2 3044_TAM+_Endometrioid


title: HB399-9 2060_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: HB399-9 2060_TAM-_Endometrioid


title: HB399-8 2056_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: HB399-8 2056_TAM-_Endometrioid


title: HB399-7 1101_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: HB399-7 1101_TAM+_Endometrioid


title: HB399-5 4064_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: HB399-5 4064_TAM+_Endometrioid


title: HB399-4 4068inf_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: HB399-4 4068inf_TAM-_Endometrioid


title: HB394-13_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment


title: HB399-10 4051_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: HB399-10 4051_TAM-_Endometrioid


title: HB399-6 1064_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: HB399-6 1064_TAM+_Endometrioid


title: HB399-11 5052_TAM-_Endometrioid, Endometrioid carcinoma without prior tamoxifen treatment

description: HB399-11 5052_TAM-_Endometrioid


title: HB399-3 3038_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment

description: HB399-3 3038_TAM+_Endometrioid


title: HB394-15_TAM+_Endometrioid, Endometrioid carcinoma after >=2y tamoxifen treatment


title: CWR_Stat5a/b#2

status: Public on Apr 30 2010

city: Philadelphia

first: Marja

last: Nevalainen

state: PA

department: Cancer Biology

country: USA

institute: Thomas Jefferson University

description: Gene expression data from CWR22Rv1 cells transfected with Stat5a/b siRNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.

data_processing: The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR).  Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).

source_name: CWR22Rv1 cells, Stat5a/b down-regulated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.

extract_protocol: Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.

treatment_protocol: DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.

tag: cell line

tag: cell type

value: prostrate cancer


title: CWR_Stat3#2

description: Gene expression data from CWR22Rv1 cells transfected with Stat3 siRNA

source_name: CWR22Rv1 cells, Stat3 down-regulated


title: Autogamy_T20_rep3

status: Public on Mar 01 2010

city: Gif sur Yvette

first: nicolas

last: Agier

state: Ile de France

address: Avenue de la terrasse

department: transcriptomique

country: France

institute: CNRS

description: The resulting 16 bit images were analysed using the GenePix Pro 6.0® software.

hyb_protocol: Microarrays were hybridized using the GeneTAC Hybstation (Genomic Solutions)

scan_protocol: The slides were scanned using GenePix 4000B scanner equipped with laser to excite Cy3 and Cy5. All slides were scanned using 100% laser power and PMT voltage auto-adjustment.

data_processing: The data overview and preprocessing were processed using MANGO (MicroArray Normalization tool of GodMap) software (ref1), an R script that allows the user to make a complete differential analysis of several two colour microarrays from raw data file via an overview and a preprocessing of all the slides. The morphological background was substracted. single-color normalization adjusting across arrays the quantiles of the intensities distribution was computed using the normalizeQuantiles function of the R limma package (ref2: see rawdatatrieparID.txt file submitted to GEO as a Sup Table). For each slide, an arithmetic means was calculated from the normalized values obtained for all replicate spots corresponding to each probe

organism: Paramecium tetraurelia

label_protocol: RT stratagene FAIRPLAY microarray labeling kit

growth_protocol: Cells were grown in a wheat grass powder (Pines International Co., Lawrence, USA) infusion medium bacterized the day before use with Klebsiella pneumoniae, and supplemented with 0.8 mg/l of beta-sitosterol (Merck, Darmstadt, FRG). Unless otherwise stated, cells were maintained at 27°C. The progression of autogamy through the different stages of nuclear reorganization was monitored by DAPI staining of cells.

extract_protocol: Total RNA was extracted from unwashed cell pellets using the TRIzol (Invitrogen) procedure, modified by the addition of glass beads. After the Trizol/Chloroform treatment, the supernatant was precipitated with isopropanol, the pellet was washed with ethanol and finally resuspended in DEPC-treated water. The RNA concentration was estimated by optical density at 260 and 280 nm.

tag: Strain d4-2 is an entirely homozygous laboratory strain. d4-2 is a hybrid strain carrying a few genes from strain 29 in the genetic background of strain 51.

tag: T20 = 4000 cells per mL (3% vegetative, 0% skeins, 8% fragmented macronucleus, 89% with visible anlagen)


title: Autogamy_T11_rep2

tag: T11 = 4000 cells per mL (1% vegetative, 1% skeins, 57% fragmented macronucleus, 41% with visible anlagen)


title: Autogamy_T11_rep3


title: CWR_Stat3#3


title: DU145_Stat5a/b#3

description: Gene expression data from DU145 cells transfected with Stat5a/b siRNA

source_name: DU145 cells, Stat5a/b down-regulated


title: CWR_Stat3#1


title: CWR_Stat5a/b#1


title: DU145_Stat5a/b#1


title: Autogamy_T0_rep3

tag: T0 = 4000 cells per mL (44% vegetative, 23% skeins, 32% fragmented macronucleus)


title: Autogamy_T11_rep1


title: Autogamy_TV_rep3

tag: TV = vegetative culture at 803 cells per mL


title: DU145_ctrl#2

description: Gene expression data from DU145 cells transfected with scramble siRNA(control)

source_name: DU145 cells, control


title: CWR_Stat5a/b#3


title: DU145_Stat3#2

description: Gene expression data from DU145 cells transfected with Stat3 siRNA

source_name: DU145 cells, Stat3 down-regulated


title: DU145_ctrl#1


title: DU145_ctrl#3


title: CWR_ctrl#2

description: Gene expression data from CWR22Rv1 cells transfected with scramble siRNA(control)

source_name: CWR22Rv1 cells, control


title: CWR_ctrl#1


title: DU145_Stat5a/b#2


title: DU145_Stat3#3


title: Autogamy_TV_rep1


title: Autogamy_T0_rep2


title: Autogamy_T20_rep2


title: Autogamy_TV_rep2


title: CWR_ctrl#3


title: Autogamy_T20_rep1


title: small intestine, formula fed, 24 h, biological replicate 4

city: Frederiksberg

first: Jayda

last: Siggers

state: C

address: Roligehdsvej 30

department: Human Nutrition

country: Denmark

institute: University of Copenhagen

description: 24 h FORM biological replicate

hyb_protocol: Hybridization and washing were performed according to the manufacturer’s instructions (Genisphere) using Corning hybridization chambers (Biotech Line). cDNA (sample and reference), salmon sperm DNA (10 µg/µl) and hybridization buffer (3DNA Array 900, Genisphere) was mixed and applied under a 25 × 60 mm LifterSlip (Erie Scientific Company, Portsmouth, NH, USA) carefully avoiding air bubbles. Slides were incubated at 42 °C in a water bath over night, then rinsed with a preheated (42 °C) wash buffer 1 (3DNA Array 900, Genisphere). For 3DNA hybridization reaction mixes; capture reagent (3DNA Array 900, Genisphere), SDS-based hybridization buffer (3DNA Array 900, Genisphere), milliQ water and salmon sperm DNA (10 µg/µl) was mixed (final volume: 84 µl) then applied to each slide and incubated in a heated water bath (62 °C for 4 h, in darkness). Wash buffer 1 was preheated to 65 °C for the post 3DNA hybridization wash.

scan_protocol: Slides were scanned using a CCD-based imaging system (ArrayWoRx Biochip Reader auto, Applied Precision, Issaquah, WA, USA).

data_processing: Microarray image processing and spot finding were performed using GenePixPro 6.0 (Molecular Devices Corporation, Sunnyvale, CA, USA). Low intensity spots were flagged if they did not have at least 45% of their feature pixels more than two standard deviations above background, incorrectly placed spots were flagged manually. Data was saved to Acuity 4.0 (Molecular Devices Corporation) and normalized using the LOWESS method. Data points that were not represented in at least 70% of the microarrays were deleted. Differentially expressed genes were determined using ANOVA and student’s t-test, and P-values < 0.05 were considered statistically significant. Differentially expressed probe sets identified in Acuity were used for further pathway analysis. Data sets containing the official gene symbol identifiers (HUGO) and P-values were uploaded into Ingenuity’s [Ingenuity Pathway Analysis (IPA)] software (http://ingenuity.com, Ingenuity Systems, Redwood City, CA, USA). The IPA program searches the Ingenuity Pathway Knowledge Base (IPKB) for interactions (known from the literature) between the uploaded genes and all other contained in IPKB and generates a series of networks.

label: Oyster 550

organism: Sus scrofa

source_name: distal small intestine, formula fed, 24 h

label_protocol: 3DNA Array 900 expression array detection kits (Genisphere, Hatfield, PA, USA) were used for the labeling and cDNA synthesis of RNA in the present study. Labeling was done according to the manufacturer’s protocol for large-scale cDNA synthesis using 7 ug total RNA.

extract_protocol: Snap frozen intestinal tissue samples were thawed in RNAlater-ICE (Ambion, Nærum, Denmark). Total RNA was extracted using RNeasy Midi Kit with TRIZOL reagent (Qiagen, Ballerup, DK), as described in the manufacturer’s protocol. All RNA samples were treated with RNase-free DNase Set (Qiagen) according to the manufacturer's instructions. The quality and quantity of extracted total RNA was estimated by Agilent 2100 bioanalyzer, using the Nanochip 6000 (Agilent Technologies, Nærum, DK). Samples with a RNA integrity number (RIN) greater than or equal to 7.0 were used for further gene expression analysis.

treatment_protocol: Fifty-six preterm piglets were obtained from six litters delivered by caesarean section at 106 d of gestation (Danish Landrace × Yorkshire × Duroc, Askelygaard Farm, Roskilde, Denmark; term = 116 ± 2 d). Derivation, rearing, and catheterization of piglets was performed as previously described (1). The National Committee on Animal Experimentation in Denmark approved all procedures. The total parenteral nutrient solution (TPN) used was prepared as previously described (1) and was formulated to meet the nutrient requirements of the preterm pig . The enteral formula diet was made from three commercially available products used for feeding infants 0-2 years of age (per litre of water: 80 g Pepdite 2-0, 70 g Maxipro, and 75 mL Liquigen-MCT, all products kindly donated by SHS International, Liverpool, UK), as previously described (2). The energy and protein concentrations of the formula were designed to match the composition of porcine milk during lactation. Porcine colostrum was collected manually from sows (Danish Landrace × Yorkshire × Duroc, Askelygaard Farm, Roskilde, Denmark) within 6 hours of farrowing and stored at -20°C until used. For the first 48 h TPN was infused continuously and passive immunity was provided by administration of adult porcine serum via the arterial catheter using automatic infusion pumps (Infusomat Secura, Braun), as previously described (3). Immediately after birth, pigs were randomly assigned to seven treatment groups defined by the later enteral feeding regimen (15 mL/kg BW/3 h) for TPN, 8, 17 or 24 h with either colostrum (COLOS, n=6-7) or formula (FORM, n=8-13). Throughout the experiment, potential clinical signs of NEC (feeding intolerance, abdominal distension, haemorrhagic diarrhea and respiratory distress) were recorded every 3 h. The pigs were euthanized for tissue collection (sodium pentobarbital, 200 mg/kg BW, intra-arterially through the umbilical catheter), the GIT was macroscopically evaluated for NEC and tissue samples were collected and stored as previously described (3). For histological and in situ hybridization analyses, tissue samples were fixed in 4% formalin for 24 h then transferred to 70% ethanol and stored at 4˚C until later preparation. Additionally, 2 cm tissue samples were snap frozen in liquid nitrogen for gene expression analyses.       Reference List     1.  Bjornvad CR, Thymann T, Deutz NE, Burrin DG, Jensen SK, Jensen BB, Molbak L, Boye M, Larsson LI, Schmidt M, Michaelsen KF and Sangild PT. Enteral feeding induces diet-dependent mucosal dysfunction, bacterial proliferation and necrotizing enterocolitis in preterm pigs on parenteral nutrition. Am J Physiol Gastrointest Liver Physiol 00414, 2008.   2.  Sangild PT, Siggers RH, Schmidt M, Elnif J, Bjornvad CR, Thymann T, Grondahl ML, Hansen AK, Jensen SK, Boye M, Moelbak L, Buddington RK, Westrom BR, Holst JJ and Burrin DG. Diet- and colonization-dependent intestinal dysfunction predisposes to necrotizing enterocolitis in preterm pigs. Gastroenterology 130: 1776-1792, 2006.   3.  Siggers RH, Thymann T, Jensen BB, Molbak L, Heegaard PMH, Schmidt M, Buddington RK and Sangild PT. Elective cesarean delivery affects gut maturation and delays microbial colonization but does not increase necrotizing enterocolitis in preterm pigs. Am J Physiol Regul Integr Comp Physiol 294: R929-R938, 2008.

tag: preterm pig, 92% gestation

tag: 48 h TPN + 24 h enteral feeding

label: Oyster 650

source_name: distal small intestine, reference

tag: pooled from all pigs

tag: preterm pig (92% gestation)


title: small intestine, formula fed, 24 h, biological replicate 5

description: 24 h FORM biological replicate


title: small intestine, formula fed, 24 h, biological replicate 6

description: 24 h FORM biological replicate


title: small intestine, formula fed, 24 h, biological replicate 2

description: 24 h FORM biological replicate


title: small intestine, formula fed, 24 h, biological replicate 3

description: 24 h FORM biological replicate


title: small intestine, formula fed, 24 h, biological replicate 1

description: 24 h FORM biological replicate


title: Heart from mice treated with DMA 48 hours earlier -  Replicate 3

city: Campinas

first: Ana

middle: Carolina

last: Deckmann

state: Sao Paulo

address: Cidade Universitaria Zeferino Vaz

department: Medical Sciences

country: Brazil

institute: State University of Campinas

description: Biological replicate 3 of 3.

hyb_protocol: 10 micrograms of biotinilated cRNA sample was used per hybridization. The slides were hybridized using the Innova 4080 shaking incubator (Ge Healthcare) for 24 h at 37 C, 300 rpm. After washing, samples were detected by incubation with Cy5-streptavidin at room temperature for 30 minutes, no agitation.

scan_protocol: Following four cycles of 5 min-washes, slides were immediatelly dried by centrifugation at 1000 rpm for 2 min and scanned by Genepix 400B (Axon Instruments).

data_processing: The nonlinear intensity-dependent dye bias was normalized intra and inter slides using the Lowess method performed by Codelink package at Bioconductor repository (www.bioconductor.org). Fold changes were calculated by time-paired comparisons among treatment (DMA) samples with the control (DMSO) samples. P-values were generated by performing moderated t-statistic (Lonnstedt and Speed, 2002) on the comparison of normalized data points in the treatment versus the control samples. We selected genes showing significant p-value (< 0.05) and with fold changes > [2.0]. Differentially expressed genes were classified as induced (+) or repressed (-).

molecule: polyA RNA

organism: Mus musculus

source_name: cRNA from mice heart treated with DMA 48 hours earlier labeled with streptavidin-conjugated Cyanine-5 (red).

label_protocol: Briefly, after isolating the polyA-RNA molecules from total RNA by oligo-dT-T7 annealing, complementary double stranded DNA was synthesized and used as template for in vitro transcription by T7 RNA polymerase in presence of biotinilated rUTP. The resulting cRNA was hybridized to slides and finally conjugated with Cy5-streptavidin for detection in laser scanner.

extract_protocol: Total RNA samples were extracted from myocardium by Trizol Reagent and purified by RNAesy Columns purification kit (Qiagen) before spectrophotometric quantification and labeling protocols.

tag: mice heart

tag: DMA

tag: 48 hours


title: Heart from mice treated with DMA 24 hours earlier -  Replicate 3

description: Biological replicate 3 of 3.

source_name: cRNA from mice heart treated with DMA 24 hours earlier labeled with streptavidin-conjugated Cyanine-5 (red).

tag: 24 hours


title: small intestine, formula fed, 8 h, biological replicate 3

description: 8h FORM biological replicate

source_name: distal small intestine, formula fed, 8 h

tag: 48 h TPN + 8 h enteral feeding


title: Heart from mice treated with DMSO 48 hours earlier -  Replicate 1

description: Biological replicate 1 of 3.

source_name: cRNA from mice heart treated with DMSO 48 hours earlier labeled with streptavidin-conjugated Cyanine-5 (red).

tag: DMSO


title: small intestine, formula fed, 8 h, biological replicate 4

description: 8h FORM biological replicate


title: Heart from mice treated with DMSO 24 hours earlier -  Replicate 3

description: Biological replicate 3 of 3.

source_name: cRNA from mice heart treated with DMSO 24 hours earlier labeled with streptavidin-conjugated Cyanine-5 (red).


title: Heart from mice treated with DMSO 48 hours earlier -  Replicate 3

description: Biological replicate 3 of 3.


title: Heart from mice treated with DMSO 48 hours earlier -  Replicate 2

description: Biological replicate 2 of 3.


title: Heart from mice treated with DMA 48 hours earlier -  Replicate 1

description: Biological replicate 1 of 3.


title: Autogamy_T0_rep1


title: Heart from mice treated with DMSO 24 hours earlier -  Replicate 2

description: Biological replicate 2 of 3.


title: Heart from mice treated with DMA 24 hours earlier -  Replicate 1

description: Biological replicate 1 of 3.


title: Heart from mice treated with DMA 24 hours earlier -  Replicate 2

description: Biological replicate 2 of 3.


title: Heart from mice treated with DMA 48 hours earlier -  Replicate 2

description: Biological replicate 2 of 3.


title: small intestine, formula fed, 8 h, biological replicate 5

description: 8h FORM biological replicate


title: small intestine, formula fed, 8 h, biological replicate 1

description: 8h FORM biological replicate


title: Heart from mice treated with DMSO 24 hours earlier -  Replicate 1

description: Biological replicate 1 of 3.


title: small intestine, formula fed, 8 h, biological replicate 2

description: 8h FORM biological replicate


title: small intestine, colostrum fed, 24 h, biological replicate 5

description: 24 h COLOS biological replicate

source_name: distal small intestine, colostrum fed, 24 h


title: small intestine, colostrum fed, 24 h, biological replicate 4

description: 24 h COLOS biological replicate


title: small intestine, colostrum fed, 24 h, biological replicate 3

description: 24 h COLOS biological replicate


title: small intestine, colostrum fed, 24 h, biological replicate 2

description: 24 h COLOS biological replicate


title: small intestine, colostrum fed, 24 h, biological replicate 1

description: 24 h COLOS biological replicate


title: small intestine, colostrum fed, 8 h, biological replicate 5

description: 8 h COLOS biological replicate

source_name: distal small intestine, colostrum fed, 8 h


title: small intestine, colostrum fed, 8 h, biological replicate 4

description: 8 h COLOS biological replicate


title: small intestine, no feed, 0 h, biological replicate 1

description: TPN biological replicate

source_name: distal small intestine, no feed, 0 h

tag: 48 h TPN + 0 h enteral feeding


title: small intestine, colostrum fed, 8 h, biological replicate 3

description: 8 h COLOS biological replicate


title: small intestine, amniotic fluid fed, biological replicate 7

description: AF biological replicate

source_name: distal small intestine, amniotic fluid fed

extract_protocol: Snap frozen intestinal tissue samples were thawed in RNAlater-ICE (Ambion, Nærum, Denmark). Total RNA was extracted using RNeasy Midi Kit with TRIZOL reagent (Qiagen), as described in the manufacturer’s protocol. All RNA samples were treated with RNase-free DNase Set (Qiagen) according to the manufacturer's instructions. Snap frozen IPEC-J2 cells were thawed and total RNA was extracted using AllPrep DNA/RNA Mini Kit (Qiagen), according to the manufacturer’s protocol. The quality and quantity of extracted total RNA was estimated by Agilent 2100 bioanalyzer, using the Nanochip 6000 (Agilent Technologies, Nærum, DK). Extracted RNA was converted to first-strand cDNA by reverse transcription of 1 µg and 125 ng RNA from tissue and cell samples, respectively using QuantiTect Reverse Transcription Kit (Qiagen) according to the manufacture’s instructions (total volume: 20 µl). The cDNA was stored at -20°C until further use.

treatment_protocol: Thirty preterm piglets were obtained from three litters delivered by caesarean section at 106-107 d of gestation (Danish Landrace × Yorkshire × Duroc, Askelygaard Farm, Roskilde, Denmark; term = 116 ± 2 d). Surgery, rearing, and catheterization of piglets was performed as previously described (3). The National Committee on Animal Experimentation in Denmark approved all procedures.   Immediately after birth, pigs were randomly assigned to three treatment groups defined by the later enteral feeding regimen (15 mL/kg/3 h): porcine colostrum (COLOS, n = 7), control formula (FORM, n = 13), or formula plus porcine AF (AF, n = 10). A smaller fourth group of pigs were fed formula plus bovine amniotic fluid (bAF, n = 4).   For the first 48 h total parenteral nutrition (TPN) was infused continuously and passive immunity was provided by administration of adult porcine serum via the arterial catheter using automatic infusion pumps (Infusomat Secura, Braun), as previously described (5). The TPN solution used was prepared as previously described and was formulated to meet the nutrient requirements of the preterm pig (2). During the TPN period, boluses of pure AF (porcine or bovine) or sterile water (placebo) were administered (10 mL/kg) every 3 h.    During the enteral feeding period the water fraction (80%) of the formula was replaced with AF for the AF fed pigs. The enteral formula diet was made from three commercially available products used for feeding infants 0-2 years of age (per litre of water: 80 g Pepdite 2-0, 70 g Maxipro, and 75 mL Liquigen-MCT, all products kindly donated by SHS International, Liverpool, UK), as previously described (1). The energy and protein concentrations of the formula were designed to match the composition of porcine milk during lactation. Porcine colostrum was collected manually from a number of sows (Danish Landrace × Yorkshire × Duroc, Askelygaard Farm, Roskilde, Denmark) within 6 h of farrowing and stored at -20°C until used.  The piglets were evaluated for clinical symptoms of intestinal disease every 3 h (feeding intolerance, stool consistency and colour, abdominal distension and respiratory distress). If severe respiratory distress or abdominal distension was observed, euthanasia (sodium pentobarbital, 200 mg/kg , intra-arterially through the umbilical catheter) and tissue collection were done immediately. At tissue collection, the GIT was evaluated macroscopically for signs of NEC. The following scoring system was applied to characterize the extent of damage, as indicated by hemorrhage and/or necrosis that occurred in stomach, small intestine (proximal, mid and distal) and colon: 0, no damage; 1, occasional areas of violaceous mucosa (0-25% affected); 2, multiple areas of violaceous mucosa (25-50% affected); 3, severe hemorrhagic mucosa (50-75% affected); 4, extensive hemorrhage mucosa (>75% affected), with or without areas of necrosis.  The GIT samples were collected and stored as previously described (4). For gene expression analyses, tissue samples were snap frozen in liquid nitrogen.       Reference List     1.  Jensen AR, Elnif J, Burrin DG and Sangild PT. Development of Intestinal Immunoglobulin Absorption and Enzyme Activities in Neonatal Pigs Is Diet Dependent. J Nutr 131: 3259-3265, 2001.   2.  Sangild PT, Petersen YM, Schmidt M, Elnif J, Petersen TK, Buddington RK, Greisen G, Michaelsen KF and Burrin DG. Preterm birth affects the intestinal response to parenteral and enteral nutrition in newborn pigs.(vol 132, pg 2673, 2002). J Nutr 132: 3785-3794, 2002.   3.  Sangild PT, Siggers RH, Schmidt M, Elnif J, Bjornvad CR, Thymann T, Grondahl ML, Hansen AK, Jensen SK, Boye M, Moelbak L, Buddington RK, Westrom BR, Holst JJ and Burrin DG. Diet- and colonization-dependent intestinal dysfunction predisposes to necrotizing enterocolitis in preterm pigs. Gastroenterology 130: 1776-1792, 2006.   4.  Siggers RH, Thymann T, Jensen BB, Molbak L, Heegaard PMH, Schmidt M, Buddington RK and Sangild PT. Elective cesarean delivery affects gut maturation and delays microbial colonization but does not increase necrotizing enterocolitis in preterm pigs. American Journal of Physiology-Regulatory Integrative and Comparative Physiology 294: R929-R938, 2008.   5.  Siggers RH, Thymann T, Jensen BB, Molbak L, Heegaard PMH, Schmidt M, Buddington RK and Sangild PT. Elective cesarean delivery affects gut maturation and delays microbial colonization but does not increase necrotizing enterocolitis in preterm pigs. Am J Physiol Regul Integr Comp Physiol 294: R929-R938, 2008.

tag: healthy


title: small intestine, no feed, 0 h, biological replicate 2

description: TPN biological replicate


title: small intestine, colostrum fed, 8 h, biological replicate 2

description: 8 h COLOS biological replicate


title: small intestine, no feed, 0 h, biological replicate 3

description: TPN biological replicate


title: small intestine, colostrum fed, 8 h, biological replicate 1

description: 8 h COLOS biological replicate


title: small intestine, no feed, 0 h, biological replicate 4

description: TPN biological replicate


title: small intestine, no feed, 0 h, biological replicate 5

description: TPN biological replicate


title: small intestine, amniotic fluid fed, biological replicate 6

description: AF biological replicate


title: small intestine, amniotic fluid fed, biological replicate 5

description: AF biological replicate


title: small intestine, amniotic fluid fed, biological replicate 3

description: AF biological replicate


title: small intestine, amniotic fluid fed, biological replicate 4

description: AF biological replicate


title: small intestine, formula fed, biological replicate 6

description: FORM biological replicate

source_name: distal small intestine, formula fed


title: small intestine, amniotic fluid fed, biological replicate 1

description: AF biological replicate


title: small intestine, formula fed, biological replicate 2

description: FORM biological replicate

tag: NEC


title: small intestine, amniotic fluid fed, biological replicate 2

description: AF biological replicate

tag: minor lesions


title: small intestine, formula fed, biological replicate 3

description: FORM biological replicate


title: small intestine, formula fed, biological replicate 5

description: FORM biological replicate


title: small intestine, colostrum fed, biological replicate 5

description: COLOS biological replicate

source_name: distal small intestine, colostrum fed


title: small intestine, formula fed, biological replicate 1

description: FORM biological replicate


title: small intestine, formula fed, biological replicate 4

description: FORM biological replicate


title: DU145_Stat3#1

tag: cell line

tag: cell type


title: small intestine, colostrum fed, biological replicate 3

description: COLOS biological replicate


title: small intestine, colostrum fed, biological replicate 4

description: COLOS biological replicate


title: in vivo apc control plus apc blocking

status: Public on Feb 28 2010

city: Liverpool

first: Margarita

last: Perez-Casal

state: Merseyside

address: Daulby Street

department: Haematology

country: United Kingdom

institute: Royal Liverpool University Hospital

description: Comparing gene profile of cells on baseline gene expression and different treatments with in vivo derived MPs according to their apc content.

hyb_protocol: As per manufacturer's instructions.

scan_protocol: Digital imager Fuji.

data_processing: Data was normalised with the median value of each array and the background was removed on a local basis.

label: Biotin

source_name: huvec

label_protocol: Ampolabeling-kit from Superarray using 0.5ug RNA.

growth_protocol: Cells were cultured in Iscove's modified medium with 20% FCS, supplemented with Glutamine, Pen-Strep and EGF. Grown at 37C, 5% CO2 and media changed every 3 days.

extract_protocol: RNEasy Mini Kit from QIAGEN.

treatment_protocol: Cells were serum-straved overnight and then treated with serum-free medium containing 17nM apc plus apc blocking antibody in the media, for 4h prior to cell lysis and RNA extraction.

tag: confluent passage 3


title: in vivo apc control plus par1 blocking

treatment_protocol: Cells were serum-straved overnight and then treated with serum-free medium containing 17nM apc plus par1 antagonist in the media, for 4h prior to cell lysis and RNA extraction.


title: in vivo mp during rhAPC plus blocking apc

treatment_protocol: Cells were serum-straved overnight and then treated with serum-free medium containing mps derived from sepsis patient during rhAPC treatment and including apc blocking antibody in the media, for 4h prior to cell lysis and RNA extraction.

tag: passage 3 confluent


title: in vivo mp during rhAPC plus par1 blocking

treatment_protocol: Cells were serum-straved overnight and then treated with serum-free medium containing mps derived from sepsis patient during rhAPC treatment and including par1 antagonist in the media, for 4h prior to cell lysis and RNA extraction.


title: in vivo mp during rhAPC treatment

treatment_protocol: Cells were serum-straved overnight and then treated with serum-free medium containing mps derived from sepsis patient during rhAPC treatment, for 4h prior to cell lysis and RNA extraction.


title: small intestine, colostrum fed, biological replicate 1

description: COLOS biological replicate

tag: preterm pig, 92% gestation

tag: 48 h TPN + 24 h enteral feeding


title: in vivo apc control

treatment_protocol: Cells were serum-straved overnight and then treated with serum-free medium containing 17nM apc in the media, for 4h prior to cell lysis and RNA extraction.


title: in vivo untreated

description: Comparing gene profile of cells on baseline gene expression and different treatments with invo derived MPs according to their apc content.

treatment_protocol: Cells were serum-straved overnight and then treated with serum-free medium for 4h prior to cell lysis and RNA extraction.


title: pre-treatment in vivo mp

treatment_protocol: Cells were serum-straved overnight and then treated with serum-free medium containing mps derived from sepsis patient prior to rhAPC treatment, for 4h prior to cell lysis and RNA extraction.


title: EB, day 14, rep 6

status: Public on Feb 25 2010

city: Champaign

first: Feng

last: Hong

state: IL

address: 101 Illini Hall, MC-374, 725 South Wright Street

department: Statistics

institute: University of Illinois at Urbana Champaign

description: B6 mouse ESC

hyb_protocol: Affymetrix total RNA hybridization protocol

scan_protocol: Affymetrix scan protocol

data_processing: Data processed and normalized by dChip

source_name: embryoid bodies on 14th day

label_protocol: Biotin labeling protocol

growth_protocol: B6 mouse ESC were cultured on mouse embryonic feeders (MEFs) using standard methods in 15% FCS supplemented with LIF

extract_protocol: Total RNA was extracted from the different samples using the RNeasy kit (Quiagen) and amplified using a two-round linear amplification strategy

treatment_protocol: Undifferentiated ES cell samples were obtained by trypsinising near confluent plates of ES cells and depleting the MEFs  by plating the cells onto gelatin coated plates for 2 x 20 min. The ES on gelatin samples were MEF depleted ES cells seeded on gelatin coated dishes and cultured until they reached ~70% confluency. To ensure the undifferentiated ES cell samples are free from MEF contamination, MEF depleted ES cells that passaged once on gelatin were used as 0-day ES cell samples. To make EBs the ES cells on gelatin were seeded into nonadherent petri dishes and LIF was withdrawn to induce differentiation. Half of the EB media was changed every 3-4 days.

tag: EB


title: EB, day 14, rep 3

description: B6 mouse ESC


title: EB, day 14, rep 4

description: B6 mouse ESC


title: EB, day 14, rep 5

description: B6 mouse ESC


title: EB, day 4, rep 6

description: B6 mouse ESC

source_name: embryoid bodies on 4th day


title: EB, day 8, rep 6

description: B6 mouse ESC

source_name: embryoid bodies on 8th day


title: EB, day 14, rep 1

description: B6 mouse ESC


title: EB, day 14, rep 2

description: B6 mouse ESC


title: EB, day 8, rep 2

description: B6 mouse ESC


title: EB, day 4, rep 3

description: B6 mouse ESC


title: EB, day 8, rep 4

description: B6 mouse ESC


title: EB, day 4, rep 2

description: B6 mouse ESC


title: mES Oct4 FACS sorted, day 0, rep 6

description: B6 mouse ESC

source_name: mouse embroynic stem cells, sorted by FACS on Oct4 GFP reporter

tag: Undifferentiated mES


title: EB, day 8, rep 3

description: B6 mouse ESC


title: EB, day 4, rep 1

description: B6 mouse ESC


title: EB, day 4, rep 5

description: B6 mouse ESC


title: EB, day 8, rep 1

description: B6 mouse ESC


title: mES Oct4 FACS sorted, day 0, rep 5

description: B6 mouse ESC


title: mES Oct4 FACS sorted, day 0, rep 3

description: B6 mouse ESC


title: mES Oct4 FACS sorted, day 0, rep 2

description: B6 mouse ESC


title: mES Oct4 FACS sorted, day 0, rep 4

description: B6 mouse ESC


title: mES Oct4 FACS sorted, day 0, rep 1

description: B6 mouse ESC


title: EB, day 8, rep 5

description: B6 mouse ESC


title: mES on gelatin, day 0, rep 5

description: B6 mouse ESC

source_name: mouse embroynic stem cells on gelatin


title: mES on gelatin, day 0, rep 4

description: B6 mouse ESC


title: EB, day 4, rep 4

description: B6 mouse ESC


title: EB, day 4, rep 7

description: B6 mouse ESC


title: mES on gelatin, day 0, rep 6

description: B6 mouse ESC


title: mES on gelatin, day 0, rep 3

description: B6 mouse ESC


title: mES on gelatin, day 0, rep 2

description: B6 mouse ESC


title: transgenic_WB_rep6

status: Public on Feb 15 2010

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

hyb_protocol: The generated cDNAs (5 µg) were fragmented, biotinylated and hybridized using the NuGen FL-Ovation cDNA Biotin Module V2 following the manufacturer’s instructions. The resulting targets were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays.

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

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using MAS 5.0

source_name: Whole brain

label_protocol: Targets were prepared from either 5 ng of immunoprecipitated (IP) mRNAs or 5 ng of whole brain (WB) total RNAs using the NuGen WT-Ovation Pico RNA amplification system.

growth_protocol: BAC-based flag-tagged PABP orx transgenic mice were generated following a procedure similar to that described for the generation of Homer1a-PABP transgenic mice (Maret et al., 2007). First, a flag-tagged poly (A) binding protein 1 rat cDNA (PABP) was cloned upstream of the internal ribosome entry site (IRES) of the plasmid pIRES2-eGFP (Clontech). Secondly, a 372 bp orx PCR fragment, corresponding to the 5’UTR sequence flanking the start codon, was cloned upstream the flag-tagged PABP. Third, another PCR fragment was cloned downstream of eGFP sequence and consisted of an FLP recombinase target (FRT)-flanked zeocine resistance cassette in 5’ of a 60 bp orx 3’UTR sequence just next to the stop codon.  A BAC (RP23-279L23, accession number AL591466) containing the orx gene and the PCR-amplified construct were electroporated in EL250 cells that have a recombination system activated under the control of a temperature-sensitive λ repressor (protocol adapted from Lee et al. 2001). Thus, shifting transiently these cells to 42°C for 15 minutes allowed a homologous recombination to occur and the replacement of the orx coding sequence in the BAC by the PCR-amplified bicistronic construct. The recombined BAC was selected by its zeocine resistance. This resistance cassette was then removed by arabinose promoter-driven flpe recombinase gene expression from EL250 cells, leaving a single FRT site behind. Finally the recombined BAC was purified (Qiagen Large-Construct kit, following manufacturer’s instructions) and the inserted-construct was fully sequenced before microinjection into BXD-F2 pronucleus (C57BL/6J X DBA/2J).

extract_protocol: Mice were anesthetized with pentobarbital (75mg/kg) and subsequently perfused with 20 ml PBS-heparin (2U/ml), 20 ml PBS-formaldehyde 1%, 15 ml Glycine 150 mM, 20 ml Tris-HCl 20 mM and 15 ml NaCl 150 mM spending 5 minutes per solution. Brains were removed and immediately placed on ice in 3 ml lysis buffer containing: Hepes KOH 50 mM (pH 7.3), EDTA 1mM, KCl 140 mM, glycerol 10%, Nonidet P40 0.5% (Applichem), dithiothreitol 1 mM, ribonucleoside-vanadyl complex 2 mM (NEB), heparin 1000 U/ml (Sigma-Aldrich), 1 complete mini protease inhibitor cocktail tablet (Roche) per 10 ml solution. They were then homogenized at maximum speed on ice in the lysis buffer. Large debris were removed by centrifugation at 18'000 g for 20 minutes at 4°C. The supernatant (~ 3ml) was incubated with 500 μl of anti-flag® M2 affinity gel beads (Sigma-Aldrich) and 5 μl rRNasin Ribonuclease Inhibitor (40 U/μl, Promega) overnight at 4°C on a wheel. After centrifugation the supernatant was removed and the beads were submitted to the following process. They were first washed three times with 7 ml of lysis buffer (Hepes KOH 50mM (pH 7.3), EDTA 1 mM, KCL 140 mM, glycerol 10%, NP-40 0.5%, DTT 1 mM), twice with 7 ml of wash buffer (Hepes KOH 50 mM pH 7.3, EDTA 1 mM, KCL 1 M, glycerol 10%, NP-40 0.5%, DTT 1 mM) and once with 7 ml TE solution (Tris-HCl 10 mM pH 7.5, EDTA 0.5 mM). The RNA-protein crosslink was then reversed by incubating the beads with 1.2 ml elution buffer (Tris-HCl 50 mM pH 7.5, EDTA 10 mM, SDS 1%, ribonucleoside-vanadyl complex 2 mM, 80 U rRNasin Ribonuclease inhibitor) for 6 hours at 65°C. After this step, 60 μl Tris-HCl 1 M pH 7,5, 12 μl NaCl 5 M and 100 μl proteinase K (20 mg/ml, Eurobio) were added to each sample for 45 minutes incubation at 50°C to digest proteins. Finally, mRNAs were isolated by a phenol-chloroform extraction followed by an isopropanol precipitation. The immunoprecipitated mRNA (IP-mRNA) pellet was washed twice in 70% ethanol and dissolved in 15 μl RNase free water.   Quantification and quality of the mRNAs were assessed by NanoDrop® ND-1000 spectrophotometer (Witec AG) and Agilent 2100 bioanalyzer chips. A concentration of 100 to 200 ng/µl mRNAs was routinely recovered from a single mouse brain. Total RNAs were isolated from a transgenic mice hypothalamus with RNAnow (Ozyme). 500 ng total RNAs were incubated 30 min at 37°C with 20 U DNAse I (Qiagen) and 20 U rRNasin Ribonuclease Inhibitor (Promega) followed by 10 min incubation at 75°C to inactivate the DNAse.

tag: strain

value: C57BL/6J X DBA/2J

tag: age

value: 11 and 14 weeks


title: transgenic_WB_rep2


title: transgenic_WB_rep8


title: transgenic_WB_rep9


title: transgenic_IP_rep6

source_name: mRNAs from orexin expressing cells cross-linked to a flag-tagged PABP protein and co-immunoprecipitated


title: transgenic_IP_rep5


title: transgenic_IP_rep7


title: transgenic_IP_rep2


title: transgenic_WB_rep4


title: transgenic_IP_rep4


title: transgenic_IP_rep8


title: transgenic_IP_rep3


title: mES on gelatin, day 0, rep 1

description: B6 mouse ESC


title: transgenic_IP_rep9


title: transgenic_WB_rep7


title: transgenic_WB_rep3


title: transgenic_WB_rep5


title: transgenic_WB_rep1


title: transgenic_IP_rep1


title: control vs. control. Replica 4

status: Public on Jan 06 2010

city: São Paulo

first: Paulo

middle: A.

last: Zaini

state: São Paulo

address: Av. Prof. Lineu Prestes, 748 - Butantã

department: Bioquímica

institute: Universidade de São Paulo

description: Control vs. Control (self-self) to assess hybridization noise. Biological replicate 2, technical replicate 2

hyb_protocol: Fluorescent cDNAs were combined and denatured by heating to 95°C for 2 min and quickly chilled on ice. The targets were then applied to the microarray slide and covered with a 24 x 60 mm coverslip (Corning). The hybridization proceeded for 16 h at 42°C. The slides were then washed in 1X SSC + 0.2% SDS for 10 min at 55°C, twice in 0.1X SSC + 0.2% SDS also for 10 min at 55°C, 0.1X SSC for 1 min at room temperature and finally in deionized water for 1 min at room temperature and dried with N2 gas.

scan_protocol: Scanning of microarray slides was carried out using a Generation III DNA scanner (GE Healthcare, Little Chalfont, England).

data_processing: Values of Alexa Fluor 555 and Alexa Fluor 647 fluorescence intensity of each microarray spot were extracted using the Array-Vision software, version 6.0 (Imaging Research, Inc., St Catherine's, Canada). Data normalization was performed using the LOWESS method, as detailed by (Koide et al. 2004). A gene was considered differentially expressed when more than 66.5% of the biological replicates were outside the intensity-dependent cutoff curves obtained by self-self hybridization experiments (Vencio and Koide 2005) and exhibited a fold-change higher then 2.0.

organism: Xylella fastidiosa

source_name: Xylella fastidiosa 9a5c control

label_protocol: Twenty ug of total RNA (from control or gomesin-treated sample) were reverse transcribed in cDNA, which was subsequently labeled with either Alexa Fluor 555 or 647 using the SuperScript indirect cDNA labeling system (Invitrogen, Carlsbad, CA).

growth_protocol: The virulent strain 9a5c and the avirulent strain J1a12 of Xylella fastidiosa used in this work were provided by Fundo de Defesa da Citricultura (Araraquara, São Paulo, Brazil). Both strains were isolated from Citrus sinensis (L.) Obesck trees exhibiting citrus variegated chlorosis (CVC) symptoms and established in laboratory (Li et al. 1999; Monteiro et al. 2001). Cells were reared on 2% agar periwinkle wilt (PW) broth medium (Davis et al. 1981) supplemented with 20% glucose and after seven days at 28ºC, the bacteria were transferred to liquid PW and incubated under agitation at 80 rpm for 7 additional days. The resulting pre-inoculum was diluted 1:1 in fresh PW medium and incubated at the same conditions until reaching the mid-log phase.

extract_protocol: A mid-log suspension of the strain 9a5c of X. fastidiosa was incubated with 50 uM of gomesin at 28ºC. As control, cells were incubated in the absence of the peptide. After 60 min, cells were harvested by centrifugation at 4.000 x g for 5 min at 25ºC and total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA). To remove residual genomic DNA, samples were treated with RQ1 RNase-free DNase (Promega, Madison, WI) and resulting RNA was quantified using a ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE). In order to evaluate RNA integrity, 200 ng of each sample were electrophoresed in agarose gel, stained with ethidium bromide, and visualized using an UV transilluminator (ImageMaster VDS, GE Healthcare, Little Chalfont, England).

treatment_protocol: Cells were treated with 50uM gomesin for 60 minutes.


title: control vs. control. Replica 3

description: Control vs. Control (self-self) to assess hybridization noise. Biological replicate 2, technical replicate 1


title: gomesin-treated for 60 minutes vs. control. Replica 8

description: Biological replicate 1, technical replicate 4

source_name: Xylella fastidiosa 9a5c gomesin-treated


title: gomesin-treated for 60 minutes vs. control. Replica 7

description: Biological replicate 1, technical replicate 3


title: control vs. control. Replica 1

description: Control vs. Control (self-self) to assess hybridization noise. Biological replicate 1, technical replicate 1


title: gomesin-treated for 60 minutes vs. control. Replica 6

description: Biological replicate 5, technical replicate 2


title: gomesin-treated for 60 minutes vs. control. Replica 3

description: Biological replicate 3, technical replicate 3


title: gomesin-treated for 60 minutes vs. control. Replica 5

description: Biological replicate 5, technical replicate 1


title: gomesin-treated for 60 minutes vs. control. Replica 1

description: Biological replicate 1, technical replicate 1


title: gomesin-treated for 60 minutes vs. control. Replica 2

description: Biological replicate 1, technical replicate 2


title: control vs. gomesin-treated for 60 minutes. Replica 2

description: Biological replicate 2, technical replicate 2


title: control vs. gomesin-treated for 60 minutes. Replica 3

description: Biological replicate 3, technical replicate 1


title: control vs. gomesin-treated for 60 minutes. Replica 4

description: Biological replicate 3, technical replicate 2


title: control vs. control. Replica 2

description: Control vs. Control (self-self) to assess hybridization noise. Biological replicate 1, technical replicate 2


title: control vs. gomesin-treated for 60 minutes. Replica 1

description: Biological replicate 2, technical replicate 1


title: control vs. gomesin-treated for 60 minutes. Replica 5

description: Biological replicate 4, technical replicate 1


title: control vs. gomesin-treated for 60 minutes. Replica 8

description: Biological replicate 6, technical replicate 2


title: control vs. gomesin-treated for 60 minutes. Replica 6

description: Biological replicate 4, technical replicate 2


title: ISC Control heart, technical replicate A RMA

status: Public on Jan 30 2010

city: Chicago

first: Stephanie

middle: K

last: Mewborn

address: 5841 S Maryland Ave

department: Medicine

institute: University of Chicago

description: Gene expression data from left ventricle of human heart with no LMNA mutation

hyb_protocol: cDNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 Array.  Microarrays were washed, stained, and scanned according to standard procedures.

scan_protocol: Standard Affymetrix protocols were used.

data_processing: Robust Microarray Analysis (RMA) and Affymetrix Microarray Suite 5.0 (Mas5) background correction and normalization were applied independently to the raw data sets using the Bioconductor open source software.  RankProducts (RP) was used to rank the probesets by fold change.

source_name: left ventricle patient with ischemic cardiomyopathy

label_protocol: cDNA was synthesized from 10 µg of total RNA using the Superscript Choice System (Invitrogen) and labeled using the BioArray High Yield RNA Transcript Labeling kit (Enzo Diagnostics).

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

tag: gender

value: male

tag: developmental stage

value: adult

tag: organ

value: heart

tag: tissue

value: left ventricle

tag: genotype

value: LMNA wt

tag: data analysis algorithm

value: RMA


title: E161K heart, technical replicate A RMA

description: Gene expression data from left ventricle of human heart with E161K LMNA mutation

source_name: left ventricle patient with E161K LMNA mutation

value: LMNA E161K


title: E161K heart, technical replicate B RMA


title: 10 day MPTP treated VTA, biological rep 1

status: Public on Jan 01 2010

first: Sudarshan

last: Phani

address: 900 Walnut Street, JHN Suite 462

department: Farber Institute for Neurosciences

description: gene expression from 10 day MPTP treated adult VTA

hyb_protocol: Following fragmentation, samples were hybridized for 16-18 hours at on Affymetrix Mouse 430 2.0 gene chip.

scan_protocol: Gene Chips were scanned using Affymetrix Genechip Scanner 3000.

data_processing: The data were analyzed using Genespring 10.0 GX (Agilent Technologies), log2 transformed and RMA normalized.

source_name: 10 day MPTP treated VTA

label_protocol: Samples were fragmented and biotin labled using FL-Ovation cDNA Biotin Module V2 (Nugen) according to manufacturer's protocol.

growth_protocol: Transgenic hTH-GFP mice were singly housed for 9 weeks and treated with MPTP or saline for up to 10 days.

extract_protocol: Total RNA was extracted using an RNeasy Micro kit (Qiagen) according to manufacturer's protocol.  RNA was amplified and reverse transcribed into cDNA using WT-Ovation Pico RNA Amplification System (Nugen) according to protocol.

treatment_protocol: Mice were treated with 4mg/kg MPTP for 2 or 10 days or an equal volume of saline.  Mice were sacrificed 7 days after last injection.  Brains were removed and stored at -80C until laser capture microdissection.

tag: genome/variation

value: hTH-GFP transgenic

value: brain

value: ventral tegmental area (VTA)

value: dopamine (DA) neurons

tag: treatment group

value: MPTP 10 day


title: 10 day MPTP treated VTA, biological rep 3

tag: cell type


title: gomesin-treated for 60 minutes vs. control. Replica 4

description: Biological replicate 3, technical replicate 4


title: 2 day MPTP treated VTA, biological rep 3

description: gene expression from 2 day MPTP treated adult VTA

source_name: 2 day MPTP treated VTA

value: MPTP 2 day


title: Control VTA, biological rep 3

description: gene expression from untreated adult VTA

source_name: Untreated VTA

value: control


title: 2 day MPTP treated VTA, biological rep 2


title: 10 day MPTP treated VTA, biological rep 2


title: 2 day MPTP treated VTA, biological rep 1


title: control vs. gomesin-treated for 60 minutes. Replica 7

description: Biological replicate 6, technical replicate 1


title: Control VTA, biological rep 2


title: 10 day MPTP treated SN, biological rep 1

description: gene expression from 10 day MPTP treated adult SN

source_name: 10 day MPTP treated SN

value: substantia nigra (SN)


title: ISC Control heart, technical replicate B RMA


title: 2 day MPTP treated SN, biological rep 1

description: gene expression from 2 day MPTP treated adult SN

source_name: 2 day MPTP treated SN


title: 2 day MPTP treated SN, biological rep 2


title: Control SN, biological rep 1

description: gene expression from untreated adult SN

source_name: Untreated SN


title: Control SN, biological rep 3

description: gene expression from untreated adult SN


title: 10 day MPTP treated SN, biological rep 3


title: Control VTA, biological rep 1


title: 10 day MPTP treated SN, biological rep 2


title: GFP treated KK/H1J mouse liver number 22

city: Minneapolis

first: Salmaan

middle: A

last: Khan

state: MN

address: 420 Washington Ave, 7-162 MCB Building

department: BMBB

institute: University of Minnesota

description: 12-14 week old male obese KK/H1J mice, a polygenic model of type 2 diabetes and obesity, weighing approximately 35g.

hyb_protocol: Labeled cRNA was hybridized for 16 hours at 63oC using MAUI 12-bay hybridization system.

scan_protocol: Scanning was done using Affymetrix Genechip 3000 scanner.

data_processing: Raw intensity data was processed using Affymetrix Microarray Suite version 5.0 (MAS5) software for background correction, normalization and condensation. In addition, for each probe, a detection p-value associated with the signal to noise ratio was determined using MAS5.

source_name: liver

label_protocol: RNA samples were reverse transcribed to cRNA and biotin-labeled.

growth_protocol: Mice were fed ad libitum, individually housed and maintained on a 12:12 hour light-dark cycle, with lights turned on at 06:00. The mice were immediately sacrificed via cervical dislocation after anesthesia. The abdominal cavity was quickly opened. The liver was trimmed and rapidly frozen in liquid nitrogen and stored at -70oC for further analysis.

extract_protocol: TRIzol reagent (Invitrogen Corporation, Carlsbad, CA) was used to isolate total cellular RNA.

treatment_protocol: On day 0, adenovirus, Ad-GFP was administered via the tail vein at a dose of 2.5x1011 pfu.

value: 12-14 week old

tag: weight

value: approximately 35 g

value: liver


title: BPD treated KK/H1J mouse liver number 28

description: 2-14 week old male obese KK/H1J mice, a polygenic model of type 2 diabetes and obesity, weighing approximately 35g.

scan_protocol: Scanning was done using Affymetrix Genechip 3000 scanner

data_processing: Raw intensity data was processed using Affymetrix Microarray Suite version 5.0 (MAS5) software for background correction, normalization and condensation.  In addition, for each probe, a detection p-value associated with the signal to noise ratio was determined using MAS5.

treatment_protocol: On day 0, adenovirus, Ad-BPD (bisphosphatase deficient 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase) was administered via the tail vein at a dose of 2.5x1011 pfu.

value: male


title: GFP treated KK/H1J mouse liver number 31


title: BPD treated KK/H1J mouse liver number 36


title: 2 day MPTP treated SN, biological rep 3

value: adult


title: GFP treated KK/H1J mouse liver number 29


title: Control SN, biological rep 2

description: gene expression from untreated adult SN


title: GAL:NRD1 vs. wild-type (expression profile)

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description: GAL:NRD1 vs. wild-type expression profile

hyb_protocol: 6 μg  of biotinylated cDNA was hybridized at 45C for 16 hours, and then washed and stained according to Affymetrix protocol EukGE-WS2v4_450 in an Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned in an Affymetrix 7G scanner.

data_processing:
Raw data files were normalized with Affymetrix Tiling Analysis Software (TAS) v1.1. Treatment and control samples were quantile normalized in pairs using only perfect match probes with a bandwidth of 20.
The files ending in 'forward.bar' and 'reverse.bar' correspond to normalized signals from the forward and reverse strand, respectively.

organism: Saccharomyces cerevisiae

label_protocol: cDNA was fragmented by nuclease digestion in a solution containing 1X One-Phor-All buffer (GE Healthcare) and DNase I (GE Healthcare) at 37ｰC until the average fragment size was approximately 70 bp. The fragmentation reaction was stopped by incubating at 95C for 10 min. Fragmented samples were biotinylated with Biotin-N6-ddATP (Enzo Life Sciences) using terminal deoxynucleotidyl transferase at 37C for 2 hours.

growth_protocol: Cells were grown overnight in the indicated medium containing 10ug/ml doxycycline, diluted to OD600 0.003 in fresh medium and grown to an OD of 0.7.

extract_protocol: Total RNA was extracted from yeast cells by vortexing with glass beads in the presence of hot acid phenol and cleaned by phenol:chlorophorm extraction followed by ethanol precipitation. After DNaseI (GE Healthcare) treatment to remove residual genomic DNA, 25 ug of total RNA was incubated with random hexamers at 70C for 10 min, incubated at 15C for 30 min and reverse transcribed to single-stranded cDNA for 2 hours at 42C with Superscript II (Invitrogen) in the presence of 6 μg/ml Actinomycin D to prevent antisense artifacts. RNA was subsequently removed by hydrolysis and cDNA was cleaned up and concentrated on MinElute PCR purification columns (Qiagen).

tag: genotype/variation

value: Nrd1 mutant

tag: growth protocol

value: Cultures with strains containing NRD1 under the control of the GAL1 promoter  and either pRS415-Nrd1 or the vector alone were switched to media containing 2% glucose for 6hr after initial growth in SC-LEU + 2% galactose.

source_name: Wild-type

value: WT


title: SEN1tetO7 nucleosome profile

description: SEN1tetO7 nucleosome profile

hyb_protocol: Biotinylated samples were hybridized at 45°C for 16 hours, and then washed and stained according to Affymetrix protocol EukGE-WS2v4_450 in an Affymetrix Fluidics Station 450.

data_processing: Raw data files were normalized with Affymetrix Tiling Analysis Software (TAS) v1.1 and visualized with the Integrated Genome Browser. Treatment and control samples were quantile normalized in pairs using perfect match probes only with a bandwidth of 20.

source_name: Nucleosomal DNA from SEN1tetO7 yeast

label_protocol: DNA was fragmented by nuclease digestion in a solution containing 1X One-Phor-All buffer (GE Healthcare) and a DNase I mix at 37°C until the average fragment size was approximately 50 bp. The fragmentation reaction was stopped by incubating at 95°C for 10 min. Fragmented samples were biotinylated with Biotin-N6-ddATP using terminal deoxynucleotidyl transferase at 37°C for 2 hours.

growth_protocol: Cells were grown overnight in YPD containing 10ug/ml doxycycline, diluted to OD600 0.003 in fresh medium and grown to an OD of 0.7.

extract_protocol: Cells were pelleted, washed once with PBS and resuspended in zymolyase buffer with freshly added 10 mM β-mercaptoethanol. Zymolyase was added to a final concentration of 0.25 mg/mL and cells were spheroplasted at 30°C while gently rolling for 30 min. After zymolyase treatment, cells were pelleted at 6000rpm for 15 minutes and resuspended in micrococcal nuclease (MNase) buffer with freshly added 1 mM β-mercaptoethanol and 500 μM spermidine. The crosslinked genomic DNA was digested with different amounts of MNase (0, 25, 50, 75, 100, and 150 U) at 37°C for 30 min, after which reactions were stopped by adding 5% SDS, 50 mM EDTA. The digested samples were then treated with 2 mg/mL proteinase K and incubated at 65°C overnight. DNA was isolated by phenol/chloroform extraction and concentrated via ethanol precipitation. Following RNA digestion with RNase A, samples were run on agarose gel and the sample with the highest proportion of mononucleosomal DNA fragments was used for hybridizations.

treatment_protocol: Histone-DNA interactions were cross-linked by the addition of methanol-free formaldehyde (final concentration of 2%) into the culture for 30 minutes. Glycine was then added to a final concentration of 125mM for 5 minutes to neutralize the cross-linking reaction.

value: Sen1 mutant

source_name: DNAse treated total genomic DNA


title: Wild-type nucleosome profile

description: Wild type nucleosome profile

source_name: Nucleosomal DNA from wild type (R1158) yeast


title: SEN1tetO7 + sen1-2 DEAA vs. wild-type (expression profile)

description: SEN1tetO7 + sen1-2 DEAA vs. wild-type expression profile

source_name: SEN1tetO7 + sen1-2 DEAA

value: Strains were grown in SC-LEU with 10ug/ml doxycycline for 36 hours

value: Strains were grown in YPD with 10ug/ml doxycycline for 36 hours


title: SEN1tetO7 + sen1-2 vs. wild-type (expression profile)

description: SEN1tetO7 + sen1-2 vs. wild-type expression profile

source_name: SEN1tetO7 + sen1-2


title: BPD treated KK/H1J mouse liver number 23


title: negative control oligo-nucleotide treated E18 chicken spleen cells, replicate 4

city: Raleigh

first: Nares

last: Trakooljul

state: NC

address: 120 Broughton Dr

department: Animal Science

institute: North Carolina State University

description: Spleen cells treated with a negative control oligo-nucleotide, replicate 4

hyb_protocol: Each oligoarray slide was pre-hybridized for 45 min at 42 degrees Celsius in a solution consisting of 5x SSC, 0.1 % SDS and 1 % BSA. The slides were washed twice in 0.2x SSC and spin dried for 5 min at 1,000 x g. Five micrograms of the labeled aRNA samples were fragmented in 1x fragmentation buffer (Ambion, Austin, TX). Each of the fragmented aRNA samples was dried down in a speed vacuum and reconstituted in 30 microliters of DIG Easy Hyb solution (Roche Diagnostics Corporation, Indianapolis, IN) An equal amount of target and reference (pool) RNA samples was mixed with a hybridization cocktail (2.5 microliters of 10 mg/ml Yeast tRNA and 2.5 microliters of 10 mg/ml salmon testes DNA). The reference/target mixture was denatured for 2 min at 94 degrees Celsius and cooled at room temperature prior to loading onto a slide and overlaid with a 22 x 65 mm LifterSlip (Erie Scientific, Portsmouth, NH). The hybridization was carried out in a hybridization chamber (Corning #2551, Lowell, MA) overnight (14 hours) at 42 degrees Celsius in a water bath. After hybridization, slides were sequentially washed with solution A (1 x SSC, 0.2% SDS, and 0.5% DTT) at 42 degrees Celsius for 10 min, solution B (0.1 x SSC, 0.2% SDS, and 0.5% DTT) for 5 min at RT, and solution C (0.1 x SSC and 0.5% DTT) for 1 min at RT. The slides were finally rinsed with nuclease free water and spin dried.

scan_protocol: Scanned on a ScanArray 4000 scanner (Packard/ PerkinElmer) Images were quantified using ScanArray Express software version 3.0 (PerkinElmer)

data_processing: The data was processed using within- and across-array loess normalization method in JMP Genomics 3.0, SAS (Cary, NC). Data quality was evaluated using the MA plots process (log ratios versus sum log intensities of the two channels for each array) and the correlation and grouped scatter plots procedure (JMP Genomics 3.0).

source_name: Total RNA from negative control oligo-nucleotide treated E18 spleenocytes labeled with Cyanine-3 (green)

label_protocol: Twenty micrograms of amino allyl-modified aRNA were labeled with Cy3 reactive dye (GE Healthcare, UK) using the Amino Allyl MessageAmp™ II aRNA Amplification Kit. Dye incorporation and concentration of the purified labeled aRNA were determined with a NanoDrop ND-1000 spectrophotometer and analyzed using the web tool available at (www.ambion.com/tools/dye).

growth_protocol: Specific pathogen free (SPF) fertilized chicken eggs were obtained from Charles River Laboratories. Fertile eggs were incubated under standard conditions (incubator’s temperature was 37.5 degrees Celsius and relative humidity was 60%) with an automatic rotation on every hour. The incubation was terminated on embryonic day e18 where day e0 is defined as the day that fertile eggs were first placed in the incubator. Spleens were dissected from the chicken embryos and subjected to isolation of spleen cells.

extract_protocol: The cultured splenocytes were harvested, washed once with 1X PBS (pH 8.0) and immediately subjected to RNA extraction using the RNeasy Mini kit following the manufacturer’s protocols (Qiagen, CA). Total RNA was quantified using a NanoDrop ND-1000 spectrophotometer and assessed for quality using an RNA 6000 Nano Assay kit and Bioanalyzer 2100 (Agilent Technologies, CA). RNA amplification was performed using the Amino Allyl MessageAmp™ II aRNA Amplification kit (Ambion, TX).

treatment_protocol: Spleen cells were isolated using 0.025 % trypsin/PBS from embryonic day 18 chicken and seeded at a concentration of 9 x 106 cells in RPMI 1640 medium on 60 mm plates. Cell viability was assessed using trypan blue exclusion test (cell viability > 96%). Splenocyte cultures were immediately transfected with a negative control oligo-nucleotide (Dharmacon) at a final concentration of 90 nM using siPORT Amine buffer (Ambion) according to the manufacturer’s instructions. Cultures were maintained for 48 hrs, prior to microarray gene expression analysis, in RPMI 1640 with 20 % heat-inactivated FBS, L-glutamine, penicillin (100 U/ml), streptomycin (100 µg/ml), and fungizone (4 µg/ml) at 37 degrees Celsius with 5% CO2.

value: spleenocytes derived from E18 whole spleens

value: white Leghorn line 22

source_name: Reference RNA pool made from all 12 sample labeled with Cyanine-5 (red)

label_protocol: Twenty micrograms of amino allyl-modified aRNA were labeled with Cy5 reactive dye (GE Healthcare, UK) using the Amino Allyl MessageAmp™ II aRNA Amplification Kit. Dye incorporation and concentration of the purified labeled aRNA were determined with a NanoDrop ND-1000 spectrophotometer and analyzed using the web tool available at (www.ambion.com/tools/dye).


title: anti-miR-10a treated E18 chicken spleen cells, replicate 1

description: Spleen cells treated with miR-10a inhibitor, replicate 1

source_name: Total RNA from anti-miR-10a treated E18 spleenocytes labeled with Cyanine-3 (green)

treatment_protocol: Spleen cells were isolated using 0.025 % trypsin/PBS from embryonic day 18 chicken and seeded at a concentration of 9 x 106 cells in RPMI 1640 medium on 60 mm plates. Cell viability was assessed using trypan blue exclusion test (cell viability > 96%). Splenocyte cultures were immediately transfected with a synthetic miR-10a inhibitor (Dharmacon) at a final concentration of 90 nM using siPORT Amine buffer (Ambion) according to the manufacturer’s instructions. Cultures were maintained for 48 hrs, prior to microarray gene expression analysis, in RPMI 1640 with 20 % heat-inactivated FBS, L-glutamine, penicillin (100 U/ml), streptomycin (100 µg/ml), and fungizone (4 µg/ml) at 37 degrees Celsius with 5% CO2.


title: negative control oligo-nucleotide treated E18 chicken spleen cells, replicate 2

description: Spleen cells treated with a negative control oligo-nucleotide, replicate 2


title: anti-miR-143 treated E18 chicken spleen cells, replicate 3

description: Spleen cells treated with miR-143 inhibitor, replicate 3

source_name: Total RNA from anti-miR-143 treated E18 spleenocytes labeled with Cyanine-3 (green)

treatment_protocol: Spleen cells were isolated using 0.025 % trypsin/PBS from embryonic day 18 chicken and seeded at a concentration of 9 x 106 cells in RPMI 1640 medium on 60 mm plates. Cell viability was assessed using trypan blue exclusion test (cell viability > 96%). Splenocyte cultures were immediately transfected with a synthetic miR-143 inhibitor (Dharmacon) at a final concentration of 90 nM using siPORT Amine buffer (Ambion) according to the manufacturer’s instructions. Cultures were maintained for 48 hrs, prior to microarray gene expression analysis, in RPMI 1640 with 20 % heat-inactivated FBS, L-glutamine, penicillin (100 U/ml), streptomycin (100 µg/ml), and fungizone (4 µg/ml) at 37 degrees Celsius with 5% CO2.


title: negative control oligo-nucleotide treated E18 chicken spleen cells, replicate 3

description: Spleen cells treated with a negative control oligo-nucleotide, replicate 3


title: anti-miR-143 treated E18 chicken spleen cells, replicate 2

description: Spleen cells treated with miR-143 inhibitor, replicate 2


title: anti-miR-10a treated E18 chicken spleen cells, replicate 2

description: Spleen cells treated with miR-10a inhibitor, replicate 2


title: anti-miR-10a treated E18 chicken spleen cells, replicate 3

description: Spleen cells treated with miR-10a inhibitor, replicate 3


title: T+Tamoxifen_Replicate 2

city: Duarte

first: Selma

last: Masri

state: CA

address: 1500 E Duarte Rd

department: Tumor Cell Biology

institute: City of Hope

description: microRNA expression before and after resistance

hyb_protocol: Labeled RNA samples were dried using a speed vac and resuspended in Dnase/Rnase-free water.  Total amount of labeled RNA was mixed with blocking agent and hybridization buffer (provided with Agilent miRNA Labeling Reagent and Hybridization kit 5190-0408).  Hybridization was carried out at 55degreesC for 20hours in the Agilent hybridization chamber G2534A.  After hybridization chips were washed with the Gene expression wash buffer kit (Agilent 5188-5327) twice for 5 minutes.

scan_protocol: Slides were scanned using the Agilent scanner G2565BA for the one color setting.  Scan area for the 8x15K format was set at 61x21.6 mm, with a scan resolution of 5um, green dye channel and Green PMT set to 100%.

data_processing: Scanned data was analyzed with Feature Extraction (FE) software version 9.5.1.

source_name: T+Tamoxifen

label_protocol: 100ng total RNA was used for labeling reaction with pCp-Cy3 for 2 hours.  Following labeling protocol, labeled RNA was purified with micro Bio-Spin 6 columns (Bio-Rad 732-6221), according to manufacturers recommendations.

growth_protocol: Cells were grown long-term in the absence and presence of testosterone (T).  Where indicated, testosterone is labeled at T+inhibitor.  Cells were grown in charcoal-dextran stripped FBS containing MEM.

extract_protocol: Trizol Extraction for total RNA isolation, according to the maufacturer's recommendation.

treatment_protocol: Cells were grown constantly in the presence of testosterone (where indicated) and inhibitor.

tag: cell line

tag: tissue type

value: breast cancer


title: anti-miR-143 treated E18 chicken spleen cells, replicate 1

description: Spleen cells treated with miR-143 inhibitor, replicate 1


title: T+Letrozole_Replicate 3

source_name: T+Letrozole


title: anti-miR-143 treated E18 chicken spleen cells, replicate 4

description: Spleen cells treated with miR-143 inhibitor, replicate 4


title: SEN1tetO7 + empty vector vs. wild-type (expression profile)

description: SEN1tetO7 + empty vector vs. wild-type expression profile

source_name: SEN1tetO7 + empty vector


title: T+Letrozole_Replicate 1


title: negative control oligo-nucleotide treated E18 chicken spleen cells, replicate 1

description: Spleen cells treated with a negative control oligo-nucleotide, replicate 1


title: T+Letrozole_Replicate 2


title: T+Exemestane_Replicate 3

source_name: T+Exemestane


title: T+Tamoxifen_Replicate 3


title: SEN1tetO7 YPD vs. wild-type (expression profile)

description: SEN1tetO7 YPD vs. wild-type expression profile

source_name: SEN1tetO7 YPD


title: T+Anastrozole_Replicate 2

source_name: T+Anastrozole


title: T+Exemestane_Replicate 1


title: T+Exemestane_Replicate 2


title: anti-miR-10a treated E18 chicken spleen cells, replicate 4


title: T+Anastrozole_Replicate 5


title: T+Anastrozole_Replicate 4


title: Exemestane-Only_Replicate 3

source_name: Exemestane-Only


title: Testosterone-Only_Replicate 3

source_name: Testosterone-Only


title: Exemestane-Only_Replicate 1


title: LTED_Replicate 2

source_name: LTED


title: LTED_Replicate 1


title: Exemestane-Only_Replicate 2


title: LTED_Replicate 3


title: MCF-7aro Control_Replicate 3

source_name: MCF-7aro Control


title: MCF-7aro Control_Replicate 2


title: MCF-7aro Control_Replicate 1


title: T+Tamoxifen_Replicate 1


title: Efferent duct E2 treated 1

status: Public on Dec 31 2009

city: Pullman

first: Elizabeth

last: Snyder

state: WA

address: BioLife Science Building Rm 202

department: School of Molecular Biosciences

institute: Washington State University

hyb_protocol: Standard Affymetrix hybridization protocol (14 hrs, 45C, with continual rotation in a GeneChip Hybridization oven model 640) was used.  Array was washed using a GeneChip fluidics station 450 with protocol EukGE-WS2v4_450.

scan_protocol: Standard Affymetrix scanning protocol using an Affymetrix 3000-7G scanner was used.

data_processing:
Probe level analysis: RMA
Algorithm name: Percentile
Algorithm parameters: Percentile:75; CellMargin:2; OutlierHigh:1.500; OutlierLow:1.004; AlgVersion:6.0; FixedCellSize:TRUE; FullFeatureWidth:7; FullFeatureHeight:7; IgnoreOutliersInShiftRows:FALSE; FeatureExtraction:TRUE; PoolWidthExtenstion:2; PoolHeightExtension:2; UseSubgrids:FALSE; RandomizePixels:FALSE; ErrorBasis:StdvMean; StdMult:1.000000
Data transformation: Set measurements less than 0.01 to 0.01.
Per chip: Normalize to 50th percentile
Per gene: Normalize to median

source_name: Adult efferent duct, E2 treated

label_protocol: Fifty ng of sample RNA was labeled using the Ovation Biotin RNA Amplification and Labeling System Version 1.0 (NuGEN Technologies).

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen) and associated extraction protocol.

treatment_protocol: Castrated adult male 129BL/6 mice were allowed to recover 14 days after surgery, treated with 0.015 mg estradiol (in 100 microL 10% EtOH in sesame oil), and efferent duct collected 12 hours later.

value: Efferent duct

value: 14d post castrated, 12 hr post 0.015 mg estradiol (in 100 microL 10% EtOH in sesame oil) treatment


title: Testosterone-Only_Replicate 2


title: Efferent duct E2 treated 2


title: Efferent duct TP treated 1

source_name: Adult efferent duct, TP treated

treatment_protocol: Castrated adult male 129BL/6 mice were allowed to recover 14 days after surgery, treated with 0.015 mg testosterone propionate (in 100 microL 10% EtOH in sesame oil), and efferent duct collected 12 hours later.

value: 14d post castrated, 12 hr post 0.015 mg testosterone propionate (in 100 microL 10% EtOH in sesame oil) treatment


title: Caput epididymis TP treated 2

source_name: Adult caput epididymis, TP treated

label_protocol: Ten micrograms of sample RNA was labeled using GeneChip One-Cycle Target Labeling (Affymetrix).

treatment_protocol: Castrated adult male 129BL/6 mice were allowed to recover 14 days after surgery, treated with 0.015 mg testosterone proprionate (in 100 microL 10% EtOH in sesame oil), and caput epididymis collected 12 hours later.

value: Caput epididymis

value: 14d post castrated, 12 hr post 0.015 mg testosterone proprionate (in 100 microL 10% EtOH in sesame oil) treatment


title: Caput epididymis sham-castrated 1

source_name: Adult caput epididymis, 14d post sham-castratation

treatment_protocol: Sham-castrated adult male 129BL/6 mice were allowed to recover 14 days after surgery, treated with vehicle (100 microL 10% EtOH in sesame oil), and caput epididymis collected 12 hours later.

value: 14d post sham-castrated, 12 hr post vehicle (100 microL 10% EtOH in sesame oil) treatment


title: Caput epididymis castrated 2

source_name: Adult caput epididymis, 14d post castratation

treatment_protocol: Castrated adult male 129BL/6 mice were allowed to recover 14 days after surgery, treated with vehicle (100 microL 10% EtOH in sesame oil), and caput epididymis collected 12 hours later.

value: male

value: 14d post castrated, 12 hr post vehicle (100 microL 10% EtOH in sesame oil) treatment


title: Efferent duct sham-castrated 2

source_name: Adult efferent duct, 14d post sham-castratation

treatment_protocol: Sham-castrated adult male 129BL/6 mice were allowed to recover 14 days after surgery, treated with vehicle (100 microL 10% EtOH in sesame oil), and efferent duct collected 12 hours later.

value: adult


title: Efferent duct TP treated 2


title: Efferent duct castrated 2

source_name: Adult efferent duct, 14d post castratation

treatment_protocol: Castrated adult male 129BL/6 mice were allowed to recover 14 days after surgery, treated with vehicle (100 microL 10% EtOH in sesame oil), and efferent duct collected 12 hours later.


title: Caput epididymis sham-castrated 2


title: Efferent duct sham-castrated 1


title: T2DM preadipocyte 5128 Cy3 slide 786

city: Maastricht

first: Florence

last: van Tienen

address: Universiteitssingel 50

department: Genetics and Cell biology

institute: Maastricht University

description: Array-Pro analyzer software (MediaCybernetics, Bethesda, USA).

hyb_protocol: Hybridization was performed using the Operon Human oligo collection V2 (21521 features) spotted on CodeLink slides (Amersham Biosciences) printed by the Microarray Facility (University Medical Center Utrecht, The Netherlands). T2DM patients and controls were paired on each slide based on respectively gender, age and BMI. Two-color microarray hybridizations were performed including dye-swap for technical replication. Hybridizations, washings, and slide drying were performed on a Tecan HS4800 hybridization station. Slides were blocked in 5xSSC, 25% Formamide, 0.1% SDS, 1% BSA (Sigma, St Louis, USA) for 1 hour. 120 pmol of each dye-labeled aRNA sample (2% - 4.5% dye incorporation) was fragmented using RNA fragmentation buffer (Ambion), mixed with 100 ug tRNA (Roche, Mannheim, Germany) and 50 ug Herring sperm DNA (Invitrogen) in 120 ul hybridization solution [5xSSC, 25% Formamide, 0.1% SDS], denaturated for 5 minutes at 95 degrees C, hybridized for 16 hours at 42 degrees C and washed 3 times with decreasing concentrations of SSC and SDS (1xSSC, 0.2%SDS; 0.1xSSC, 0.2%SDS; 0.1xSSC).

scan_protocol: Array scanning was performed on an Axon 4000B scanner with laser power 100% for both channels and three photo multiplier settings for respectively the red and the green channel (1000 and 888 to detect low expressed probes, 756 and 671 to detect highly expressed probes (around 0.05% of all spots saturated) and an intermediate setting of 878 and 779).

data_processing: First, bad and missing spots were excluded from further analysis. Secondly, the number of missing data and spots with intensities below background was computed for each gene for all three scanning powers. For each gene, the intensities obtained from the scanning power with the least missing and most values above background were kept. If more than one scan setting was suitable for a spot, then the scanning at medium power was preferred over high power, which was itself preferred over the low setting. The foreground intensities of the remaining genes were analyzed using a Gaussian linear regression model including labeling efficiency, dye swap, hybridization days, background level, sex, age, BMI and a random effect to take into account multiple observations on the same subject. The inference criterion used for comparing the models is their ability to predict the observed data, i.e., models are compared directly through their minimized minus log-likelihood. When the numbers of parameters in models differ, they are penalized by adding the number of estimated parameters, a form of the Akaike information criterion (AIC). For each gene, the group was then added to the model. A gene was found to be differentially expressed if the AIC decreased compared to the model not containing the group.

source_name: preadipocytes

label_protocol: 1 ug RNA from each sample with a RIN>7, was amplified using the Amino-Allyl MessageAmp II aRNA kit (Ambion, Austin, USA) to generate amino-allyl aRNA (AA-aRNA). AA-aRNA was generated according to manufacturer’s protocol with a modification in the ratio UTP: AA-UTP, which was changed from 1:1 to 7:3. RNA integrity was assessed by determining the aRNA size. Each amino AA-aRNA sample was coupled to Cy3 or Cy5 (Amersham Biosciences, GE healthcare, Little Chalfont, UK) and purified with the RNeasy Minelute clean-up kit (Qiagen).

growth_protocol: At fasted state, subcutaneous adipose tissue biopsy samples were taken caudal from the umbilicus via liposuction under local anesthesia and subsequently treated with collagenase. The cell suspension was filtered through 500µm nylon mesh and spun at 220 × g for 1 min to separate preadipocytes from mature adipocytes. Preadipocytes were suspended in 5 ml DMEM medium containing 10% fetal calf serum (Gibco-Invitrogen, Carlsbad, USA) and 1% glutamax/ penecillin/streptomycin (Gibco-Invitrogen), grown for 2 passages and frozen. Control and T2DM preadipocytes were taken into culture in parallel and cultured for 3 passages till a 90% confluent 162cm2 culture flask was obtained per sample (passage 5 - 9) for RNA isolation.

extract_protocol: Total RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, USA) and purified with the RNeasy clean-up kit (Qiagen, Valencia, USA), according to manufacturer’s protocol.

value: preadipocyte

tag: age (yr)

value: 56 T2DM

tag: bmi


title: Caput epididymis E2 treated 1

source_name: Adult caput epididymis, E2 treated

treatment_protocol: Castrated adult male 129BL/6 mice were allowed to recover 14 days after surgery, treated with 0.015 mg estradiol (in 100 microL 10% EtOH in sesame oil), and caput epididymis collected 12 hours later.

tag: strain

tag: age


title: Control preadipocyte 5394 Cy3 slide 781

tag: gender

tag: sample type

value: control


title: Caput epididymis TP treated 1

tag: tissue


title: T2DM preadipocyte 5128 Cy3 slide 778


title: Efferent duct castrated 1

value: 14d post castration, 12 post vehicle (100 microL 10% EtOH in sesame oil) treatment


title: Caput epididymis castrated 1


title: Control preadipocyte 5616 Cy5 slide 777

value: female


title: T2DM preadipocyte 5469 Cy3 slide 776

value: 73 T2DM


title: Control preadipocyte C4 Cy5 slide 778


title: Control preadipocyte 5616 Cy5 slide 776


title: T2DM preadipocyte 5064 Cy5 slide 781

value: 52 T2DM


title: Control preadipocyte 5410 Cy5 slide 775


title: T2DM preadipocyte 5263 Cy5 slide 774

value: 40 T2DM


title: Caput epididymis E2 treated 2


title: T2DM preadipocyte 5395 Cy3 slide 775

value: 45 T2DM


title: Control preadipocyte 5870 Cy3 slide 773


title: Control preadipocyte 5280 Cy3 slide 774


title: T2DM preadipocyte 5064 Cy3 slide 770


title: Control preadipocyte 5394 Cy5 slide 769


title: T2DM preadipocyte 5469 Cy5 slide 765


title: T2DM preadipocyte 5263 Cy3 slide 767


title: T2DM preadipocyte 5060 Cy3 slide 771

value: 41 T2DM


title: T2DM preadipocyte 5395 Cy5 slide 773


title: Control preadipocyte 5280 Cy5 slide 767


title: T2DM preadipocyte 5064 Cy3 slide 769


title: Control preadipocyte 5317 Cy5 slide 770


title: Control preadipocyte 5085 Cy5 slide 771


title: Control preadipocyte 5616 Cy3 slide 764

source_name: preadipoyctes


title: Control preadipocyte 5870 Cy5 slide 768


title: T2DM preadipocyte 5395 Cy3 slide 768


title: T2DM preadipocyte 5395 Cy5 slide 766


title: T2DM preadipocyte 5471 Cy3 slide 777

value: 62 T2DM


title: Control preadipocyte 5616 Cy3 slide 765


title: T2DM preadipocyte 5128 Cy5 slide 763

tag: disease state


title: Control preadipocyte 5410 Cy3 slide 766


title: T2DM preadipocyte 5471 Cy5 slide 764


title: T2DM preadipocyte 5128 Cy5 slide 762

source_name: preadipocyte


title: Control preadipocyte C4 Cy3 slide 763


title: Control preadipocyte 5085 Cy3 slide 761


title: Control preadipocyte 5317 Cy3 slide 760


title: Control preadipocyte C2 Cy3 slide 762


title: T2DM preadipocyte 5064 Cy5 slide 760


title: T2DM preadipocyte 5060 Cy5 slide 761