title: Ishikawa_Control_24h_rep3

description:
Cells known to possess both estrogen and progesterone receptors.
Ctrl_24h_3


title: Ishikawa_Control_8h_rep3

status: Public on Aug 13 2009

type: RNA

city: MASON

first: Jay

middle: Patrick

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

country: USA

institute: Procter & Gamble

description:
Cells known to possess both estrogen and progesterone receptors.
Ctrl_8h_3

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Human U133plus2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Ishikawa cell line, control, 8hr

label_protocol: Purified RNA was converted to cDNA target using SuperScript Choice system (Invitrogen Corp, Carlsbad, CA) and cDNA was converted to biotinylated cRNA probes using the ENZO BioArray transcript labeling kit (ENZO Life Sciences, Farmingdale, NY).

growth_protocol: Ishikawa cells were maintained and grown (to confluency or at a desired cell density between 500,000 - 1 million cells/mL) in DMEM/F-12 Medium (supplemented with 10% Fetal Bovine Serum + 1X penicillin/streptomycin) in xenoestrogen-free Corning plasticware.

extract_protocol: Total RNA was extracted using TRI-Reagent and protocol provided by supplier (Molecular Research Center, Cincinnati, OH).  Extracted RNA was further purified using Qiagen RNEasy columns and protocol provided by supplier (QIAgen, Valencia, CA).  Quadruplicate samples were advanced to target preparation and GeneChip processing.

treatment_protocol: Cells were gently washed in warm PBS and transferred to phenol red-free DMEM/F-12 Medium (supplemented with 10% Charcoal-Stripped Fetal Bovine Serum + 1X penicillin/streptomycin) in Corning Cell Culture Cluster wells overnight and then challenged with 1pM (very low, vL), 100pM (low, L), 10nM (high, H), and 1uM (very high, vH) levels of Bisphenol A.  Prior to collection, cells were washed in warm PBS, resuspended & briefly incubated in TRI-Reagent, & finally collected (in quintuplicate replicates) at each specific time point: 8 hours, 24 hours, and 48 hours.

tag: cell line

value: Ishikawa

tag: cell line derivation

value: 39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.

tag: treatment

value: vehicle control

tag: treatment time

value: 8 hours


title: Ishikawa_Control_8h_rep4

description:
Cells known to possess both estrogen and progesterone receptors.
Ctrl_8h_4


title: Ishikawa_Control_8h_rep2

description:
Cells known to possess both estrogen and progesterone receptors.
Ctrl_8h_2


title: Ishikawa_Control_24h_rep1

description:
Cells known to possess both estrogen and progesterone receptors.
Ctrl_24h_1

source_name: Ishikawa cell line, control, 24hr

value: 24 hours


title: Brain Cerebellum Pool_71

city: Woodbury

first: Chris

last: Zaleski

state: NY

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Labs

description: single chip, 1 replicate

hyb_protocol: 2 micrograms of  double-stranded cDNA were labeled and hybridized to Affymetrix tiling arrays containing probes against non-repepetitive portions of human chromosomes 21 and 22 essentially as described in Kapranov et al, Science. 2007 Jun 8;316(5830):1484-8.

scan_protocol: Arrays were scanned on Affymetrix GCS3000 scanner

data_processing:
See supplement materials of Djebali, S, et al (2009) Nature in press
Number Sequences: 10, Data: signal, Scale: Linear, AlgName: TAS, AlgVersion: 1.1.01, probe_coordinate_convention: 0_indexed_center

label: Biotin

molecule: polyA RNA

source_name: BD Clontech – Brain Cerebellum polyA RNA

label_protocol: 2 micrograms of polyA+ RNA were converted into double-stranded cDNA essentially as described in Kapranov et al, Science. 2007 Jun 8;316(5830):1484-8.

growth_protocol: 11 tissues poly A+ RNA was purchased and 5 cell lines were grown as suggested by ATCC

extract_protocol: see Kapranov, et al Science 2002

tag: tissue

value: cerebellum


title: baseline_cephgp_GM11995_rep2

city: Philadelphia

first: Renuka

last: Nayak

state: PA

address: 3516 Civic Center Blvd

institute: HHMI, University of Pennsylvania

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11995.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix GeneChip Human HG-Focus Target Array (U95v2). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix print default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Lymphoblastoid cell lines derived from GM11995

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells were grown at a density of 500,000 cells/ ml in RPMI 1640 with 15% FBS, 1% penicillin-streptomycin, 2mM L-glutamine at 37°C in a humidified 5% CO2 chamber.

extract_protocol: RNA was extracted using the Rneasy Mini-Kit (Qiagen) as per the manufacturer's instructions

tag: coriell cell line repository identifier


title: baseline_cephgp_GM11995_rep1


title: Brain Cerebellum Pool_72

description: single chip, 1 replicate


title: Brain Cerebellum Pool_70

description: single chip, 1 replicate


title: Brain Cerebellum Pool_69

description: single chip, 1 replicate


title: baseline_cephgp_GM11994_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11994.

source_name: Lymphoblastoid cell lines derived from GM11994


title: Brain Cerebellum Pool_68

description: single chip, 1 replicate


title: baseline_cephgp_GM11994_rep1


title: Brain Cerebellum Pool_67

description: single chip, 1 replicate


title: Ishikawa_Control_8h_rep1

description:
Cells known to possess both estrogen and progesterone receptors.
Ctrl_8h_1


title: baseline_cephgp_GM11993_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11993.

source_name: Lymphoblastoid cell lines derived from GM11993


title: Brain Cerebellum Pool_66

description: single chip, 1 replicate


title: Brain Cerebellum Pool_65

description: single chip, 1 replicate


title: baseline_cephgp_GM11993_rep1


title: S007_Scz_F_67

city: Stevenage

first: Amy

middle: MH

last: Molesworth

state: Hertfordshire

address: Gunnels Wood Road

department: R&D Computational Biology

country: United Kingdom

institute: GlaxoSmithKline

hyb_protocol: For each batch, 10ug total RNA was processed to Biotin-labeled cRNA and hybridized to HG-U133_Plus_2.0 GeneChips in accordance with the Affymetrix protocol (Affymetrix, Santa Clara, CA, USA,).

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and fluorescence intensity for each feature of the array was obtained by using GeneChip Operating Software (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: Brain BA10 post-mortem schizophrenic

extract_protocol: Total RNA was extracted from frozen BA10 using a Polytron type homogenizer (YellowLine DI 25 Basic) and TriZol reagent (Invitrogen, Paisley, UK) in a ratio of 1 ml of TriZol to 20 mg of tissue. RNA was further purified using RNeasy mini-columns (Qiagen, Valencia, CA, USA) including on-column DNAse-1 step and elution in water. Although pH was analysed in brain lysates using a pH meter, this was not considered to be rigorous enough to exclude or include samples and instead the RNA integrity number (RIN) was used to assess the quality of the RNA as the primary inclusion criterion. The quantity of extracted RNA was determined by spectrophotometry and quality was assessed using an Agilent 2100 Bioanalyzer (South Plainfield, NJ, USA) to determine the RIN. Based on the RIN, samples were classified into three quality groups—pass (RIN >7.0); borderline (RIN 6.0–7.0); fail (RIN<6.0). Following classification, there were 41 pass (RIN range of samples 7.0–9.0: average=7.7), 16 borderline (RIN range of samples 6.0–6.9; average=6.4) and 5 fail samples. Samples in the fail category were excluded from the study, and the remaining samples were randomized into four batches, containing an equal number of schizophrenic/control and male/female samples, for target generation and hybridization.

tag: gender

value: Female

tag: age

tag: post-mortem delay

tag: ph


title: baseline_cephgp_GM11992_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11992.

source_name: Lymphoblastoid cell lines derived from GM11992


title: S032_Scz_M_77

label_protocol: For each batch, 10ug total RNA was processed to Biotin-labeled cRNA and hybridized to HG-U133_Plus_2.0 GeneChips in accordance with the Affymetrix protocol (Affymetrix, Santa Clara, CA, USA,).

value: Male


title: Brain Cerebellum Pool_64

description: single chip, 1 replicate


title: baseline_cephgp_GM11933_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11933.

source_name: Lymphoblastoid cell lines derived from GM11933


title: Brain Cerebellum Pool_63

description: single chip, 1 replicate


title: Brain Cerebellum Pool_62

description: single chip, 1 replicate


title: Brain Cerebellum Pool_61

description: single chip, 1 replicate


title: C018_Control_F_67

source_name: Brain BA10 post-mortem control


title: Brain Cerebellum Pool_60

description: single chip, 1 replicate


title: baseline_cephgp_GM11992_rep1


title: S011_Scz_M_82


title: S022_Scz_M_44


title: baseline_cephgp_GM11932_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11932.

source_name: Lymphoblastoid cell lines derived from GM11932


title: Brain Cerebellum Pool_59

description: single chip, 1 replicate


title: C025_Control_F_88


title: baseline_cephgp_GM11931_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11931.

source_name: Lymphoblastoid cell lines derived from GM11931


title: S010_Scz_M_82


title: Brain Cerebellum Pool_57

description: single chip, 1 replicate


title: C020_Control_M_25


title: baseline_cephgp_GM11931_rep1


title: baseline_cephgp_GM11933_rep1


title: C006_Control_F_71


title: S006_Scz_M_79


title: Brain Cerebellum Pool_56

description: single chip, 1 replicate


title: C005_Control_M_91


title: S019_Scz_M_79


title: C023_Control_M_38


title: Brain Cerebellum Pool_58

description: single chip, 1 replicate


title: S023_Scz_F_97


title: baseline_cephgp_GM11930_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11930.

source_name: Lymphoblastoid cell lines derived from GM11930


title: C016_Control_M_60


title: Brain Cerebellum Pool_54

description: single chip, 1 replicate


title: Brain Cerebellum Pool_55

description: single chip, 1 replicate


title: baseline_cephgp_GM11920_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11920.

source_name: Lymphoblastoid cell lines derived from GM11920


title: Brain Cerebellum Pool_51

description: single chip, 1 replicate


title: Brain Cerebellum Pool_50

description: single chip, 1 replicate


title: Brain Cerebellum Pool_52

description: single chip, 1 replicate


title: baseline_cephgp_GM11930_rep1


title: Brain Cerebellum Pool_48

description: single chip, 1 replicate


title: baseline_cephgp_GM11920_rep1


title: baseline_cephgp_GM11919_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11919.

source_name: Lymphoblastoid cell lines derived from GM11919


title: baseline_cephgp_GM11918_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11918.

source_name: Lymphoblastoid cell lines derived from GM11918


title: Brain Cerebellum Pool_49

description: single chip, 1 replicate


title: baseline_cephgp_GM11917_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11917.

source_name: Lymphoblastoid cell lines derived from GM11917


title: baseline_cephgp_GM11919_rep1


title: baseline_cephgp_GM11917_rep1


title: S033_Scz_M_83


title: baseline_cephgp_GM11918_rep1


title: Brain Cerebellum Pool_47

description: single chip, 1 replicate


title: C022_Control_F_68


title: Brain Cerebellum Pool_46

description: single chip, 1 replicate


title: baseline_cephgp_GM11882_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11882.

source_name: Lymphoblastoid cell lines derived from GM11882


title: S001_Scz_F_75


title: baseline_cephgp_GM11881_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11881.

source_name: Lymphoblastoid cell lines derived from GM11881


title: C019_Control_F_46


title: S012_Scz_M_63


title: Brain Cerebellum Pool_45

description: single chip, 1 replicate

source_name: BD Clontech – Brain Cerebellum polyA RNA


title: baseline_cephgp_GM11881_rep1


title: S031_Scz_M_79


title: C008_Control_F_94


title: S004_Scz_F_88


title: S020_Scz_F_82


title: C021_Control_M_25


title: Brain Cerebellum Pool_44

description: single chip, 1 replicate


title: baseline_cephgp_GM11882_rep2


title: baseline_cephgp_GM11880_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11880.

source_name: Lymphoblastoid cell lines derived from GM11880


title: C002_Control_F_87


title: Brain Cerebellum Pool_43

description: single chip, 1 replicate


title: S026_Scz_M_72


title: baseline_cephgp_GM11932_rep1


title: S009_Scz_M_87


title: S028_Scz_F_28


title: baseline_cephgp_GM11880_rep1


title: Brain Cerebellum Pool_42

description: single chip, 1 replicate


title: Brain Cerebellum Pool_53

description: single chip, 1 replicate


title: baseline_cephgp_GM11879_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11879.

source_name: Lymphoblastoid cell lines derived from GM11879


title: Brain Cerebellum Pool_38

description: single chip, 1 replicate


title: Brain Cerebellum Pool_39

description: single chip, 1 replicate


title: baseline_cephgp_GM11879_rep1


title: C026_Control_M_58


title: Brain Cerebellum Pool_40

description: single chip, 1 replicate


title: baseline_cephgp_GM11840_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11840.

source_name: Lymphoblastoid cell lines derived from GM11840


title: baseline_cephgp_GM12005_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM12005.

source_name: Lymphoblastoid cell lines derived from GM12005


title: baseline_cephgp_GM11831_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11831.

source_name: Lymphoblastoid cell lines derived from GM11831


title: baseline_cephgp_GM11839_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11839.

source_name: Lymphoblastoid cell lines derived from GM11839


title: baseline_cephgp_GM11832_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11832.

source_name: Lymphoblastoid cell lines derived from GM11832


title: Brain Cerebellum Pool_35

description: single chip, 1 replicate


title: Brain Cerebellum Pool_37

description: single chip, 1 replicate


title: C015_Control_M_91

source_name: Brain BA10 post-mortem control


title: S008_Scz_F_81

source_name: Brain BA10 post-mortem schizophrenic


title: S002_Scz_M_82


title: Brain Cerebellum Pool_36

description: single chip, 1 replicate


title: baseline_cephgp_GM11830_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11830.

source_name: Lymphoblastoid cell lines derived from GM11830


title: S015_Scz_M_56


title: Brain Cerebellum Pool_34

description: single chip, 1 replicate


title: Brain Cerebellum Pool_31

description: single chip, 1 replicate


title: Brain Cerebellum Pool_32

description: single chip, 1 replicate


title: baseline_cephgp_GM11829_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM11829.

source_name: Lymphoblastoid cell lines derived from GM11829


title: Brain Cerebellum Pool_30

description: single chip, 1 replicate


title: baseline_cephgp_GM07357_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07357.

source_name: Lymphoblastoid cell lines derived from GM07357


title: baseline_cephgp_GM07357_rep2


title: C027_Control_M_90


title: C024_Control_F_78


title: S024_Scz_M_75


title: S013_Scz_F_65


title: Brain Cerebellum Pool_28

description: single chip, 1 replicate


title: baseline_cephgp_GM07346_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07346.

source_name: Lymphoblastoid cell lines derived from GM07346


title: Brain Cerebellum Pool_41

description: single chip, 1 replicate


title: baseline_cephgp_GM07347_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07347.

source_name: Lymphoblastoid cell lines derived from GM07347


title: baseline_cephgp_GM07346_rep1


title: baseline_cephgp_GM07345_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07345.

source_name: Lymphoblastoid cell lines derived from GM07345


title: C014_Control_M91


title: baseline_cephgp_GM07347_rep2


title: S027_Scz_M_77


title: baseline_cephgp_GM07345_rep2


title: Brain Cerebellum Pool_27

description: single chip, 1 replicate


title: Brain Cerebellum Pool_29

description: single chip, 1 replicate


title: C010_Control_F_90


title: S021_Scz_M_71


title: Brain Cerebellum Pool_26

description: single chip, 1 replicate


title: Brain Cerebellum Pool_25

description: single chip, 1 replicate


title: baseline_cephgp_GM07341_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07341.

source_name: Lymphoblastoid cell lines derived from GM07341


title: C007_Control_M_54


title: C028_Control_F_54


title: baseline_cephgp_GM07340_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07340.

source_name: Lymphoblastoid cell lines derived from GM07340


title: Brain Cerebellum Pool_24

description: single chip, 1 replicate

source_name: BD Clontech – Brain Cerebellum polyA RNA


title: Brain Cerebellum Pool_23

description: single chip, 1 replicate


title: C013_Control_M_61


title: Brain Cerebellum Pool_22

description: single chip, 1 replicate


title: Brain Cerebellum Pool_21

description: single chip, 1 replicate


title: S017_Scz_F_85


title: baseline_cephgp_GM07056_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07056.

source_name: Lymphoblastoid cell lines derived from GM07056


title: baseline_cephgp_GM07055_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07055.

source_name: Lymphoblastoid cell lines derived from GM07055


title: baseline_cephgp_GM07341_rep1


title: S005_Scz_M_82


title: baseline_cephgp_GM07056_rep2


title: baseline_cephgp_GM07055_rep1


title: S014_Scz_M_74


title: Brain Cerebellum Pool_19

description: single chip, 1 replicate


title: C017_Control_M_72


title: Brain Cerebellum Pool_18

description: single chip, 1 replicate


title: S025_Scz_M_41


title: Brain Cerebellum Pool_20

description: single chip, 1 replicate


title: Brain Cerebellum Pool_17

description: single chip, 1 replicate


title: Brain Cerebellum Pool_16

description: single chip, 1 replicate


title: baseline_cephgp_GM07050_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07050.

source_name: Lymphoblastoid cell lines derived from GM07050


title: baseline_cephgp_GM07051_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07051.

source_name: Lymphoblastoid cell lines derived from GM07051


title: baseline_cephgp_GM07051_rep2


title: baseline_cephgp_GM07049_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07049.

source_name: Lymphoblastoid cell lines derived from GM07049


title: baseline_cephgp_GM07049_rep1


title: healthy_donor_j_primary_T_lymphoblasts_8_hours_after_IL-2_deprivation_biol_rep3

city: Warszawa

first: Magdalena

last: Chechlinska

address: Roentgena 5

department: Department of Immunology

country: Poland

institute: Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology

hyb_protocol: 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx

data_processing: Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package

label: Biotin-Phycoerythrin

source_name: IL-2 dependent normal peripheral blood T lymphocytes after IL-2 withdrawal

label_protocol: Affymetrix protocol: 4,5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)

growth_protocol: As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])

extract_protocol: Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).

treatment_protocol: Primary, IL-2-dependent T lymphoblast cell lines were generated and propagated as previously described (Siwicki et al., Leuk Res 2008). Briefly, peripheral blood mononuclear cells (PBMC) derived from a healthy donor were suspended in a standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma]), activated for 24 h with 20 μg/ml of wheat germ agglutinin (WGA, Pharmacia) and subsequently cultured in the standard medium supplemented with 20 U/ml of rIL-2 (R&D). Cell samples were collected after 6-7 population doublings, 8-hrs incubation without IL-2, following triple thorough washing of the cells.

tag: Healthy, male donor, age 48, PBMC


title: immortalised_lineS9_8_hours_after_IL-2_deprivation_biol_rep3

source_name: spontaneously immortalised PBMC-derived T lymphocytes of NBS patient, after IL-2 withdrawal

label_protocol: Affymetrix protocol: 5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)

treatment_protocol: Spontaneously immortalized IL-2-dependent T cell line was derived  from PBMC of Nijmegen Breakage Syndrome patient and established and cultured as previously described (Siwicki et al., Exp Cell Res 2003). The cells followed 125 population doublings. Sample was collected  8 hours following IL-2 withdrawal.

tag: NBS patient, male, age 11, PBMC


title: healthy_donor_j_primary_T_lymphoblasts_before_IL-2_deprivation_biol_rep3

source_name: IL-2 dependent normal peripheral blood T lymphocytes from IL-2-containing cultures

treatment_protocol: Primary, IL-2-dependent T lymphoblast cell lines were generated and propagated as previously described (Siwicki et al., Leuk Res 2008). Briefly, peripheral blood mononuclear cells (PBMC) derived from a healthy donor were suspended in a standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma]), activated for 24 h with 20 μg/ml of wheat germ agglutinin (WGA, Pharmacia) and subsequently cultured in the standard medium supplemented with 20 U/ml of rIL-2 (R&D).  Cells were collected after 6-7 population doublings.


title: C011_Control_F_89

source_name: Brain BA10 post-mortem control


title: Brain Cerebellum Pool_13

description: single chip, 1 replicate


title: Brain Cerebellum Pool_14

description: single chip, 1 replicate


title: immortalised_lineS9_8_hours_after_IL-2_deprivation_biol_rep2


title: Brain Cerebellum Pool_15

description: single chip, 1 replicate


title: Brain Cerebellum Pool_12

description: single chip, 1 replicate


title: Brain Cerebellum Pool_11

description: single chip, 1 replicate


title: Brain Cerebellum Pool_33

description: single chip, 1 replicate


title: Brain Cerebellum Pool_10

description: single chip, 1 replicate


title: baseline_cephgp_GM07045_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07045.

source_name: Lymphoblastoid cell lines derived from GM07045


title: baseline_cephgp_GM07034_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07034.

source_name: Lymphoblastoid cell lines derived from GM07034


title: baseline_cephgp_GM07031_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07031.

source_name: Lymphoblastoid cell lines derived from GM07031


title: baseline_cephgp_GM07031_rep1


title: Brain Cerebellum Pool_9

description: single chip, 1 replicate


title: immortalised_lineS9_before_IL-2_deprivation_biol_rep2

source_name: spontaneously immortalised PBMC-derived T lymphocytes of NBS patient, from IL-2-containing cultures


title: immortalised_lineS9_before_IL-2_deprivation_biol_rep1

treatment_protocol: Spontaneously immortalized IL-2-dependent T cell line was derived  from PBMC of Nijmegen Breakage Syndrome patient and established and cultured as previously described (Siwicki et al., Exp Cell Res 2003). The cells followed 125 population doublings.


title: immortalised_lineS9_before_IL-2_deprivation_biol_rep3


title: Brain Cerebellum Pool_8

description: single chip, 1 replicate


title: immortalised_line5_8_hours_after_IL-2_deprivation_biol_rep3

source_name: spontaneously immortalised normal spleen-derived T lymphocytes after IL-2 withdrawal

treatment_protocol: Spontaneously immortalized IL-2-dependent T cell line was derived from normal spleen and established and cultured as previously described (Siwicki et al., Exp Gerontol 2000). The cells followed 222 population doublings. Sample was collected  8 hours following IL-2 withdrawal.

tag: Healthy male, age 56, spleen


title: immortalised_line5_8_hours_after_IL-2_deprivation_biol_rep2


title: baseline_cephgp_GM07017_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07017.

source_name: Lymphoblastoid cell lines derived from GM07017


title: immortalised_lineS9_8_hours_after_IL-2_deprivation_biol_rep1


title: baseline_cephgp_GM07022_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07022.

source_name: Lymphoblastoid cell lines derived from GM07022


title: Brain Cerebellum Pool_5

description: single chip, 1 replicate

source_name: BD Clontech – Brain Cerebellum polyA RNA


title: baseline_cephgp_GM07022_rep2


title: Brain Cerebellum Pool_7

description: single chip, 1 replicate


title: Brain Cerebellum Pool_4

description: single chip, 1 replicate


title: Brain Cerebellum Pool_3

description: single chip, 1 replicate


title: baseline_cephgp_GM07016_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07016.

source_name: Lymphoblastoid cell lines derived from GM07016


title: Brain Cerebellum Pool_6

description: single chip, 1 replicate


title: immortalised_line5_before_IL-2_deprivation_biol_rep2

source_name: spontaneously immortalised normal spleen-derived T lymphocytes from IL-2-containing cultures

treatment_protocol: Spontaneously immortalized IL-2-dependent T cell line was derived from normal spleen and established and cultured as previously described (Siwicki et al., Exp Gerontol 2000). The cells followed 222 population doublings.


title: Brain Cerebellum Pool_2

description: single chip, 1 replicate


title: baseline_cephgp_GM07002_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07002.

source_name: Lymphoblastoid cell lines derived from GM07002


title: baseline_cephgp_GM07002_rep1


title: immortalised_line5_before_IL-2_deprivation_biol_rep1


title: healthy_donor_6_primary_T_lymphoblasts_8_hours_after_IL-2_deprivation_biol_rep2

treatment_protocol: Primary, IL-2-dependent T lymphoblast cell lines were generated and propagated as previously described (Siwicki et al., Leuk Res 2008). Briefly, peripheral blood mononuclear cells (PBMC) derived from a healthy donor were suspended in a standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma]), activated for 24 h with 20 μg/ml of wheat germ agglutinin (WGA, Pharmacia) and subsequently cultured in the standard medium supplemented with 20 U/ml of rIL-2 (R&D). Cell samples were collected after 4-5 population doublings, after 8-hrs incubation without IL-2, following triple thorough washing of the cells.

tag: Healthy, male donor, age 42, PBMC


title: baseline_cephgp_GM07017_rep1


title: healthy_donor_43_primary_T_lymphoblasts_8_hours_after_IL-2_deprivation_biol_rep1

treatment_protocol: Primary, IL-2-dependent T lymphoblast cell lines were generated and propagated as previously described (Siwicki et al., Leuk Res 2008). Briefly, peripheral blood mononuclear cells (PBMC) derived from a healthy donor were suspended in a standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma]), activated for 24 h with 20 μg/ml of wheat germ agglutinin (WGA, Pharmacia) and subsequently cultured in the standard medium supplemented with 20 U/ml of rIL-2 (R&D). Cell samples were collected after 7-8 population doublings, after 8-hrs incubation without IL-2, following triple thorough washing of the cells.

tag: Healthy, male donor, age 36, PBMC


title: baseline_cephgp_GM07000_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM07000.

source_name: Lymphoblastoid cell lines derived from GM07000


title: immortalised_line5_8_hours_after_IL-2_deprivation_biol_rep1


title: healthy_donor_6_primary_T_lymphoblasts_before_IL-2_deprivation_biol_rep2

treatment_protocol: Primary, IL-2-dependent T lymphoblast cell lines were generated and propagated as previously described (Siwicki et al., Leuk Res 2008). Briefly, peripheral blood mononuclear cells (PBMC) derived from a healthy donor were suspended in a standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma]), activated for 24 h with 20 μg/ml of wheat germ agglutinin (WGA, Pharmacia) and subsequently cultured in the standard medium supplemented with 20 U/ml of rIL-2 (R&D).  Cells were collected after 4-5 population doublings.


title: immortalised_line5_before_IL-2_deprivation_biol_rep3


title: healthy_donor_43_primary_T_lymphoblasts_before_IL-2_deprivation_biol_rep1

treatment_protocol: Primary, IL-2-dependent T lymphoblast cell lines were generated and propagated as previously described (Siwicki et al., Leuk Res 2008). Briefly, peripheral blood mononuclear cells (PBMC) derived from a healthy donor were suspended in a standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma]), activated for 24 h with 20 μg/ml of wheat germ agglutinin (WGA, Pharmacia) and subsequently cultured in the standard medium supplemented with 20 U/ml of rIL-2 (R&D). Cells were collected after 7-8 population doublings.


title: Brain Cerebellum Pool_1

description: single chip, 1 replicate


title: baseline_cephgp_GM06994_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM06994.

source_name: Lymphoblastoid cell lines derived from GM06994


title: baseline_cephgp_GM06994_rep1


title: B biotype under 25 C (cy5) compared to Q biotype under 25 C (cy3)-slide8

city: Bet Dagan

first: Murad

last: Ghanim

address: Derech Hamakabim

department: Entomology

country: Israel

institute: Volcani Center

description: non

hyb_protocol: two probes to be compared were combined and purified (Qiagen PCR purification kit; Hilden, Germany), mixed in 3X SSC and supplemented with 20 µg poly(A) and 0.15% v/v SDS, and competitively hybridized to the B. tabaci microarray in a 65°C water bath for 16-18 h. Each microarray slide contained 5772 printed PCR products, each representing one EST. The slides were washed sequentially (2 min per wash) at ambient temperature in 1.14X SSC supplemented with 0.0285% SDS, then 1.14X SSC, 0.228X SSC and 0.057X SSC. Immediately after washing, arrays were spun dry at 1,000g for 5 min in a table-top centrifuge. The slides were scanned using an Agilent microarray scanner (Agilent Technologies, Santa Clara, CA, USA) to detect Cy3 and Cy5 fluorescence.

data_processing: Fluorescence intensity was quantified using Genepix Pro v6 (Axon Instruments, Union City, CA, USA). After excluding all bad hybridizing spots by visual assessment, the real intensity value of each spot was collected. Data were normalized and corrected to optimal microarray platform by taking into account local and global background intensities. The normalization method consisted of a calculation based on the ratio of medians from GenePix Pro microarray analysis software. This normalization method is based on removal of all gene-expression values higher than 15-fold and then calculating the average ratio of medians and multiplying of each value by the resulting correction factor (normalization factor medians), such that the average of the corrected ratios equals 1.0. The experiments were performed in triplicate and were reproducible, with Pearson correlation coefficients between repeat experiments for the genes that passed the significance test used (see below) of 0.86. All subsequent analyses were performed using the normalized ratio of medians as the value of gene expression, following log base 2 transformation. The ratio of medians of 25ºC-exposed and 40ºC-exposed whitefly transcripts were obtained for each gene.

organism: Bemisia tabaci

source_name: B biotype under 25 C

label_protocol: aminoallyl labeling

extract_protocol: trizol extraction

treatment_protocol: 25 C for 3 hours

tag: biotype

value: B

source_name: Q biotype under 25 C


title: baseline_cephgp_GM07000_rep2


title: B biotype under 25 C (cy5) compared to Q biotype under 25 C (cy3)-slide9

description: non

scan_protocol: The slides were scanned using an Agilent microarray scanner (Agilent Technologies, Santa Clara, CA, USA) to detect Cy3 and Cy5 fluorescence.

value: Q


title: B biotype under 40 C (cy5) compared to B biotype under 25 C (cy3)-slide6

description: non

source_name: B biotype under 40 C

treatment_protocol: 40 C for 3 hours


title: B biotype under 40 C (cy5) compared to B biotype under 25 C (cy3)-slide5

description: non


title: B biotype under 25 C (cy5) compared to Q biotype under 25 C (cy3)-slide7

description: non


title: B biotype under 40 C (cy5) compared to B biotype under 25 C (cy3)-slide4

description: non


title: baseline_cephgp_GM06993_rep2

description: Gene expression data at baseline from lymphoblastoid cells of individual GM06993.

source_name: Lymphoblastoid cell lines derived from GM06993


title: Q biotype under 40 C (cy5) compared to Q biotype under 25 C (cy3)-slide1

description: non

source_name: Q biotype under 40 C


title: baseline_cephgp_GM06985_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM06985.

source_name: Lymphoblastoid cell lines derived from GM06985


title: Q biotype under 40 C (cy5) compared to Q biotype under 25 C (cy3)-slide3

description: non


title: baseline_cephgp_GM06985_rep2


title: tumour_control_rep4

status: Public on Aug 12 2009

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized with the rank invariant normalization in the Illumina BeadStudio software (version 1.5.1.3).

organism: Mus musculus

source_name: J558 tumour, control

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: Mice were inoculated subcutaneously with J558 myeloma cells at the dorsum of the neck and given standard rodent chow

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini Kit, followed by quantification using the NanoDrop spectrophotometer and qualitation using the Agilent Bioanalyzer

treatment_protocol: Control group was given distilled water while treatment group was given OPP (1500 ppm GAE) as drinks ad libitum

tag: strain

value: BALB/c

value: 10 weeks

value: male

tag: agent

value: control


title: tumour_treatment_rep2

description: replicate 2

source_name: J558 tumour, treatment

value: OPP


title: baseline_cephgp_GM06993_rep1


title: baseline_cephgp_GM06986_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM06986.

source_name: Lymphoblastoid cell lines derived from GM06986


title: tumour_treatment_rep1

description: replicate 1


title: tumour_control_rep3

description: replicate 3


title: Q biotype under 40 C (cy5) compared to Q biotype under 25 C (cy3)-slide2

description: non


title: tumour_treatment_rep3

description: replicate 3


title: tumour_control_rep2

description: replicate 2


title: tumour_control_rep1

description: replicate 1


title: Blood, human, rep1

first: Don

last: Baldwin

address: 277 John Morgan, 3620 Hamilton Walk

department: Pathology and Lab Medicine

institute: University of Pennsylvania

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GCS3000 7G scanner.

data_processing: The data were analyzed with the Microarray Suite version 5.0 (MAS 5.0) algorithm in Affymetrix Expression Console with default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: human blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: human cord blood stem cells transduced with control or BCR-ABL transgenes

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

treatment_protocol: in utero transfer to fetal goats

value: blood


title: Blood, human, rep2


title: baseline_cephgp_GM07034_rep1

source_name: Lymphoblastoid cell lines derived from GM07034


title: Blood, BCR-ABL goat, rep1

organism: Capra hircus

source_name: CML BCR-ABL goat blood


title: E14tg2a-shDAB2-285-4

city: Taoyuan

first: Chien-Ling

last: Huang

address: 259 Wen-Hwa 1st Road, Kwei-Shan

country: Taiwan

institute: Chang Gung University

description: Gene expression data from shDAB2-expressing E14tg2a

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix Mouse 430A array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using 2500 Scanner.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: E14tg2a cells were stably transfected with the plasmid encoding shDAB2-285; clone 4 of shDAB2-285 (285-4)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: The E14tg2a cells were cultured in GMEM supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1,000 U/ml LIF, 100 U/ml penicillin, and 100 mg/ml streptomycin.

extract_protocol: Total RNAs were isolated by Trizol (Invitrogen) and were further purified using the RNeasy mini kit (Qiagen).

treatment_protocol: In the normal growth condition as described above

tag: cell type

value: Mouse embryonic stem cells


title: Liver, BCR-ABL goat, rep3

source_name: CML BCR-ABL goat liver

value: liver


title: Blood, MIG goat, rep1

source_name: control MIG goat blood


title: Blood, normal goat, rep2

source_name: normal goat blood


title: Liver, human, rep3

source_name: human liver


title: Blood, normal goat, rep1


title: E14tg2a-vector-9

description: Gene expression data from vector control E14tg2a

source_name: E14tg2a cells were stably transfected with the vector control plasmid; clone 9 of the vector control (ES-V9)


title: Liver, human, rep4


title: Liver, BCR-ABL goat, rep2


title: Liver, BCR-ABL goat, rep1


title: Liver, human, rep5


title: Liver, human, rep2


title: Liver, human, rep1


title: Liver, MIG goat, rep7

source_name: control MIG goat liver


title: Liver, MIG goat, rep6


title: Liver, MIG goat, rep4


title: Liver, MIG goat, rep5


title: Liver, MIG goat, rep3


title: KD 3038 11d

city: Stanford

first: Stephen

last: Popper

state: CA

department: Division of Infectious Diseases, Dept. of Medicine

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40458.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: GenePix 4000A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

label_protocol: not provided

extract_protocol: Stratagene Universal Human Reference RNA, 1st rnd amp AW 11/01/01, 3ug

tag: source

extract_protocol: Paxgene Ambion amp 4ug

value: Whole blood

tag: disease state

value: KD


title: C 4012 Scarlet Fever

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40499.gif

value: Stratagene Universal Human Reference RNA, 1st rnd amp AW 11/01/01, 3ug

source_name: C 4012 Group A Beta Strep -?

tag: tissue

value: C-sf


title: KD 3039 10d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40565.gif

source_name: Stratagene Universal Human Reference RNA


title: KD 3037 5d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40533.gif


title: C 4024 Adenovirus

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40497.gif

source_name: C 4024 Adenovirus

value: C-ai


title: KD 3007 5d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40472.gif


title: KD 1502 11d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40511.gif


title: KD 3064 4d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40508.gif


title: Liver, MIG goat, rep2


title: Liver, MIG goat, rep1


title: C 4003 Adenovirus

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40517.gif

source_name: C 4003 Adenovirus


title: Liver, normal goat, rep4

source_name: normal goat liver


title: C 4030 Phenobarbital

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40522.gif

source_name: C 4030 Phenobarb rash/reaction

value: C-dr


title: KD 3004 3d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40467.gif


title: Liver, normal goat, rep2


title: KD 3046 6d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40461.gif


title: MCF-7 treated with DZNep+TSA+AZA rep 3

city: SINGAPORE

first: qiang

last: yu

address: BIOPOLIS STREET

country: Singapore

institute: GIS

description: MCF-7 treated with DZNep+AZA+TSA

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: The data was processed using BeadStudio GX 3.2 and were both normalized (rank invariant) and background-subtracted.

source_name: MCF-7 cells treated with DZNep, AZA and TSA and harvested after 72h

label_protocol: According to Illumina protocol

extract_protocol: Qiagen RNeasy Kit according to manufacturer's instructions

treatment_protocol: Cells were treated with 2.5 uM DZNep or 5uM AZA for 72 h, and TSA at 100 nM for 24 hours. For AZA treatment, the medium was replaced with freshly added AZA for every 24 h. For co-treatment of cells with DZNep and TSA, DZNep was added for 48 h followed by TSA for an additional 24 h.

value: breast cancer

tag: cell line

value: MCF-7 cells

tag: treatment group

value: DZNep+AZA+TSA


title: C 2001 Amoxicillin

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40568.gif

source_name: C 2001 Serum sickness/likely Amoxicillin


title: KD 3049 3d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40464.gif


title: C 4027 Adenovirus

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40567.gif

source_name: C 4027 Adenovirus


title: MCF-7 treated with DZNep+TSA rep 3

description: MCF-7 treated with DZNep+TSA

source_name: MCF-7 cells treated with DZNep and TSA and harvested after 72h

value: DZNep+TSA


title: MCF-7 treated with DZNep rep 3

description: MCF-7 treated with DZNep

source_name: MCF-7 cells treated with 2.5 ?M DZNep and harvested after 72h

value: DZNep


title: MCF-7 treated with AZA+TSA rep 3

description: MCF-7 treated with TSA+AZA

source_name: MCF-7 cells treated with TSA and AZA and harvested after 72h

value: TSA+AZA


title: C 4021 Adenovirus

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40518.gif

source_name: C 4021 Adenovirus


title: KD 3014  6d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40476.gif

source_name: KD 3014 preivig 6d


title: MCF-7 treated with AZA rep 3

description: MCF-7 treated with AZA

source_name: MCF-7 cells treated with 5 ?M AZA each day and harvested after 72h

value: AZA


title: Liver, normal goat, rep1


title: Adult_male_heart_ventricles_rep3

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Profile and compare the rhythm transcriptomes of atria and ventricles from adult male and female mice

hyb_protocol: The Fluor®_647-aha-dUTP labeled cDNA was co-hybridized with a distinct Alexa Fluor®_555-aha-dUTP labeled biological replica overnight at 50°C on a Duke Operon Mouse 36K oligonucleotide array V4.0 (GPL8928) following the "multiple yellow" hybridization design (Iacobas et al. Biochem Biophys Res Commun. 2006).

scan_protocol: After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned with A 4000B scanner (MDS, Toronto, Canada)) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in-house developed iterative algorithm, alternating within-array normalization with interarray normalization, until the average corrected ratio differed by <5% from the previous one.(Iacobas et al. Physiol Genomics 2005, PMID: 15585606)

label: Alexa Fluor®_647

label_protocol: 20ug total RNA extracted from atria was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

growth_protocol: Adult mice purchased from Charles River Laboratories International, Inc. (Wilmington, MA 01887)

extract_protocol: Total RNA was extracted using the TRIzol® protocol (Invitrogen, CA). RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Heart was removed and ventricles isolated and minced

tag: gender

value: male

tag: age

value: 2 month

value: ventricles


title: KD 3059 3d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40505.gif


title: KD 3026 8d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40563.gif


title: C 4020 Septra

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40551.gif

source_name: C 4020 Presumed Drug Reaction


title: MCF-7 treated with DZNep+AZA rep 3

description: MCF-7 treated with DZNep+AZA

source_name: MCF-7 cells treated with DZNep and AZA and harvested after 72h

value: DZNep+AZA


title: untreated MCF-7 rep 3

description: untreated MCF-7

source_name: untreated MCF-7 cells

value: untreated


title: Liver, normal goat, rep3

value: liver


title: Adult_male_heart_ventricles_rep4

hyb_protocol: The Fluor®_555-aha-dUTP labeled cDNA was co-hybridized with a distinct Alexa Fluor®_647-aha-dUTP labeled biological replica overnight at 50°C on a Duke Operon Mouse 36K oligonucleotide array V4.0 (GPL8928) following the "multiple yellow" hybridization design (Iacobas et al. Biochem Biophys Res Commun. 2006).

label: Alexa Fluor®_555

label_protocol: 20ug total RNA extracted from atria was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).


title: MCF-7 treated with DZNep+TSA+AZA rep 2

description: MCF-7 treated with DZNep+AZA+TSA


title: MCF-7 treated with DZNep+AZA rep 2

description: MCF-7 treated with DZNep+AZA


title: Adult_male_heart_ventricles_rep2


title: MCF-7 treated with AZA+TSA rep 2

description: MCF-7 treated with TSA+AZA


title: MCF-7 treated with DZNep rep 2

description: MCF-7 treated with DZNep


title: C 2004 Adenovirus

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40548.gif

value: Stratagene Universal Human Reference RNA, 1st rnd amp AW 11/01/01, 3ug

source_name: C 2004 Adenovirus

value: Whole blood


title: MCF-7 treated with AZA rep 2

description: MCF-7 treated with AZA


title: MCF-7 treated with TSA rep 3

description: MCF-7 treated with TSA

source_name: MCF-7 cells treated with 100 nM TSA for the last 24h and harvested after 72h

value: TSA


title: MCF-7 treated with TSA rep 2

description: MCF-7 treated with TSA


title: MCF-7 treated with DZNep+TSA rep 2

description: MCF-7 treated with DZNep+TSA


title: untreated MCF-7 rep 2

description: untreated MCF-7


title: Adult_male_heart_atria_rep4

treatment_protocol: Heart was removed and atria isolated and minced

value: atria


title: Adult_male_heart_atria_rep3


title: C 4042 Adenovirus

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40498.gif

source_name: Stratagene Universal Human Reference RNA

source_name: C 4042 Adenovirus

value: C-ai


title: MCF-7 treated with DZNep+TSA rep 1

description: MCF-7 treated with DZNep+TSA

value: breast cancer

value: MCF-7 cells


title: MCF-7 treated with DZNep+AZA rep 1

description: MCF-7 treated with DZNep+AZA


title: MCF-7 treated with DZNep+TSA+AZA rep 1

description: MCF-7 treated with DZNep+AZA+TSA

value: DZNep+AZA+TSA


title: Adult_male_heart_ventricles_rep1


title: Adult_female_heart_ventricles_rep4

value: female


title: C 4016 Scarlet Fever

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40550.gif

source_name: C 4016 Positive Strep Group A

value: C-sf


title: Adult_male_heart_atria_rep2


title: MCF-7 treated with AZA+TSA rep 1

description: MCF-7 treated with TSA+AZA

value: TSA+AZA


title: KD 1505 5d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40545.gif

value: KD


title: MCF-7 treated with DZNep rep 1

description: MCF-7 treated with DZNep

value: DZNep


title: C 4005 Scarlet Fever

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40521.gif

source_name: C 4005 Group A Beta Strep


title: MCF-7 treated with TSA rep 1

description: MCF-7 treated with TSA


title: Adult_male_heart_atria_rep1

value: male

value: 2 month


title: C 4031 Steven Johnson

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40569.gif

source_name: C 4031 Steven Johnsons-etiology unknown

value: C-dr


title: MCF-7 treated with AZA rep 1

description: MCF-7 treated with AZA

value: AZA


title: KD 3033 4d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40530.gif

value: Stratagene Universal Human Reference RNA, 1st rnd amp AW 11/01/01, 3ug


title: KD 3027 5d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40523.gif

value: Whole blood


title: CRP* LB, Biological Rep1

city: University Park

first: Patrick

middle: C

last: Cirino

email: cirino@engr.psu.edu, rxk249@psu.edu

address: 226A Fenske lab

department: Chemical Engineering

institute: Penn State

description: CRP* LB, Biological Rep1

hyb_protocol: Fragmented, end-labeled cDNA was dissolved in hybridization cocktail and hybridized to Affymetrix GeneChip E. coli Genome 2.0 Arrays (approximately 10000 probe set) for 16 hours at 45oC. The details of GeneChip E. coli Genome 2.0 Arrays are described by Affymetrix.

scan_protocol: After hybridization, the hybridization cocktail was removed and the arrays were washed to remove unbound and non-specifically bound cDNA. Hybridization was detected by staining the arrays with streptavidin phycoerythrin. All washing and staining was performed using the Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’s instructions (Affymetrix Inc, Santa Clara, CA). Stained arrays were scanned using the Affymetrix GCS3000 7G scanner.

data_processing: A minimum of three data sets was generated for each of the four different conditions tested (based on the combination of the strains W3110 and PC05 in LB and LB+glucose media). Affymetrix Expression ConsoleTM software (Version 1.1) was used for background adjustment, normalization and summarization of chip level data in the form of feature intensity (CEL) files in order to generate probe set summarization (CHP) files, using the probe logarithmic intensity error (PLIER) method. Data from CHP files were then exported to a Microsoft Excel spreadsheet for further analysis. Signal values for 10208 probsets from GeneChip E. coli Genome 2.0 Arrays were filtered to extract probe set data for only the E. coli K-12 strain. All calculations and analyses were performed on the 4070 genes remaining after filtration.  Signal values were transformed to the log base for the pair-wise comparisons. A linear model was fitted to each gene using the Bioconductor software package LIMMA in the R environment. The linear model coefficients were used to calculate significant differences in expression levels for all pair-wise comparisons. The P-values were adjusted by the Benjamini-Hochberg method and genes with a P-value of <0.05 were considered as those with significantly different expression levels under different conditions tested. Data are reported as expression levels (signal values) or ratios of expression levels. Written code in R (file name: code.doc) can be found in supplementary material (http://www.che.psu.edu/Faculty/Cirino). Gene Annotations were transformed from AFFY probe set ID’s to Entrez gene IDs using NETAFFX on the Affymetrix website. The online database for annotation, visualization and integrated discovery (DAVID) and Kyoto Encyclopedia of Genes and Genome (KEGG) were used for pathway visualization and gene ontology (GO) classification.

organism: Escherichia coli

label_protocol: Total RNA concentration and purity were determined using a NanoDrop spectrophotometer and total RNA integrity was examined using an Agilent Bioanalyzer. Total RNA of sufficient concentration, purity, and integrity was labeled and subsequently hybridized to Affymetrix GeneChip microarrays by the Penn State DNA Microarray Facility according to the manufacturer's instructions (Affymetrix Inc, Santa Clara, CA). Briefly, 10 ug of total RNA was converted to cDNA using random primed reverse transcription. cDNA was purified by removing the RNA via hydrolysis with NaOH and then neutralizing the solution. Purified cDNA was fragmented and subsequently end-labeled with biotin.

growth_protocol: Cells grown for harvesting were prepared briefly as follows.  Overnight pre-seed cultures were prepared by inoculating 3 ml of LB medium (in 13 x 100 mm tube) with a few colonies from a fresh LB plate. The overnight cultures were used to inoculate, to an OD600 of 0.1, 50 ml LB media (with or without 0.4% glucose supplementation) seed cultures in a 250 ml shake-flask. The seed culture were grown at 37°C to an OD600 of ~2 and then were used to directly inoculate, to an OD600 of 0.02, 100 ml LB media (with or without 0.4% glucose supplementation) cultures in a 500 ml flask. These cultures were grown at 37°C and 250 rpm to an OD600 of 0.5.

extract_protocol: Cells from the 100 ml culture were harvested at an OD600 of 0.5 (early logarithmic growth phase) by immediately placing on ice, transferring to 50 ml falcon tubes and centrifuging at 4oC for 5 minutes before treating with lysozyme. Promega PureYieldTM RNA Midiprep System kit was used for RNA extraction. As a preliminary check, RNA yield and quality were determined by spectrophotometry according to the manufacturer’s protocol and the integrity of the purified RNA was determined by formaldehyde agarose gel electrophoresis.

treatment_protocol: Four different conditions were tested in this study: W3110 in LB medium (WT), W3110 in LB+glucose medium (WT G), PC05 in LB medium (CRP*), and PC05 in LB+glucose medium (CRP* G).

tag: growth condition

value: LB

tag: biological replicate

tag: genotype

value: crp*


title: CRP* LB, Biological Rep2

description: CRP* LB, Biological Rep2


title: CRP* LB+Glucose, Biological Rep5

description: CRP* LB+Glucose, Biological Rep5

value: LB+Glucose


title: CRP* LB, Biological Rep3

description: CRP* LB, Biological Rep3


title: Adult_female_heart_ventricles_rep2

value: ventricles


title: Adult_female_heart_ventricles_rep1

label_protocol: 20ug total RNA extracted from ventricles was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).


title: untreated MCF-7 rep 1

description: untreated MCF-7

value: breast cancer

value: MCF-7 cells

value: untreated


title: CRP* LB+Glucose, Biological Rep4

description: CRP* LB+Glucose, Biological Rep4


title: Adult_female_heart_ventricles_rep3

value: female


title: KD 3019 8d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40455.gif


title: CRP* LB+Glucose, Biological Rep3

description: CRP* LB+Glucose, Biological Rep3


title: C 4032 Adenovirus

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40566.gif

source_name: C 4032 Adenovirus

value: C-ai


title: C 4004 Scarlet Fever

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40519.gif

source_name: C 4004 Group A Beta Strep

value: C-sf


title: KD 3023 4d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40562.gif

value: KD


title: Adult_female_heart_atria_rep4

value: atria


title: CRP* LB+Glucose, Biological Rep1

description: CRP* LB+Glucose, Biological Rep1


title: CRP LB, Biological Rep3

description: CRP LB, Biological Rep3

value: wild-type


title: CRP LB, Biological Rep2

description: CRP LB, Biological Rep2


title: CRP* LB+Glucose, Biological Rep2

description: CRP* LB+Glucose, Biological Rep2


title: JAY270 x JAY309 biorep C

city: Durham

first: Juan Lucas

last: Argueso

state: SP

address: 371 CARL Building, Box 3054

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

description:
Total RNA was extracted from a mid-log phase JAY270 culture in rich media (YPD, 30C).
Total RNA was extracted from a mid-log phase JAY309 culture in rich media (YPD, 30C).

hyb_protocol: Equal amounts of Cy5 and Cy3-labeled cDNA (~2 ug each) were competitively hybridized to microarrays containing all S. cerevisiae ORFs and Intergenic regions.  The hybridization and array washing protocol was the same as described in DeRisi et al, 1997, Science 278:680.

scan_protocol: Array scanned in Genepix 4000b scanner.

data_processing: The log2 R/G ratio for all probes in the arrays were collapsed to a single value in the case of repeated probes and normalized according to the median value for the entire array.

organism: Saccharomyces cerevisiae

source_name: JAY270 cDNA labeled with Cy5, biological replicate C.

label_protocol: First strand cDNA was synthesized and labeled with dUTP-Cy5 using Invitrogen Superscript Direct Labeling kit according to manufacturer's instructions.

extract_protocol: Total yeast RNA was prepared according using hot acidic phenol protocol described in Ausubel et al (Current Protocols in Molecular Biology, Chapter 13, DOI: 10.1002/0471142727.mb1312s23).

source_name: JAY309 cDNA labeled with Cy3, biological replicate C. JAY309 is isogenic to S288c.

label_protocol: First strand cDNA was synthesized and labeled with dUTP-Cy3 using Invitrogen Superscript Direct Labeling kit according to manufacturer's instructions.


title: JAY270 x JAY309 biorep B

source_name: JAY270 cDNA labeled with Cy5, biological replicate B.

source_name: JAY309 cDNA labeled with Cy3, biological replicate B. JAY309 is isogenic to S288c.


title: Adult_female_heart_atria_rep2

description: Profile and compare the rhythm transcriptomes of atria and ventricles from adult male and female mice

value: 2 month


title: KD 3047 4d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40537.gif


title: CRP LB, Biological Rep1

description: CRP LB, Biological Rep1


title: Adult_female_heart_atria_rep1


title: CRP LB+Glucose, Biological Rep3

description: CRP LB+Glucose, Biological Rep3


title: Adult_female_heart_atria_rep3


title: Treatment: Temp 31 degrees, Time: 10 hours, replicate: 3

status: Public on Aug 11 2009

city: Lafayette

first: Mauricio

last: Rodriguez-Lanetty

state: LA

address: 300 E St Mary blvd

department: Biology

institute: University of Louisiana at Lafayette

description: cDNA probe synthesis was performed from 500ng total RNA using Superscript Reverse Transcripase (Invitrogen) and the Genisphere 3DNA-900 microarray kit according to the manufacturers’ instructions

hyb_protocol: Samples were hybridized using the Genisphere 900 3DNA kit components (vial 7 buffer) plus human Cot DNA (for blocking) Wash: 15 min (2X SSC/ 0.1% SDS at 65 degrees), 15 min 2X SSC RT, 15 min 0.2X SSC

scan_protocol: Slides were scanned using AXON GenePix4000B, and and image acquisition and quality control was performed using the software GenePix ® Pro 5.

data_processing: The value used were median foreground minus median background. Ratio-Intensity plots were constructed for each array data to explore whether or not intensity dependence of log ratios, which appears as curvature, was present.  rLowess curve fitting transformation was applied to the data. Quantile normalisation was also applied to mean log-intensities in order to make the distributions essentially the same across arrays. As the experimental design for this experiment was a reference microarray design the value represents the normalized log (Channel 1/channel 2)

organism: Acropora millepora

source_name: Coral larvae exposed to 31 degrees after 10 hours sample 3

label_protocol: Genisphere 900 3DNA Dendrimer

extract_protocol: The total RNA was extracted using Trizol/RNeasy kit. The integrity and quality of total RNA was assessed using a Bioanalyzer (Agilent Technology).

tag: stage

value: aposymbiotic

source_name: Reference Sample for coral larvae

tag: reference sample

value: Pooled samples at time t=0


title: CRP LB+Glucose, Biological Rep2

description: CRP LB+Glucose, Biological Rep2


title: Treatment: Temp 31 degrees, Time: 10 hours, replicate: 2

source_name: Coral larvae exposed to 31 degrees after 10 hours sample 2


title: CRP LB+Glucose, Biological Rep1

description: CRP LB+Glucose, Biological Rep1


title: Treatment: Temp 31 degrees, Time: 3 hours, replicate: 1

source_name: Coral larvae exposed to 31 degrees after 3 hours sample 1


title: Treatment: Temp 31 degrees, Time: 3 hours, replicate: 2

source_name: Coral larvae exposed to 31 degrees after 3 hours sample 2


title: C 4014 Scarlet Fever

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40500.gif

value: Stratagene Universal Human Reference RNA, 1st rnd amp AW 11/01/01, 3ug

source_name: C 4014 Positive Strep Group A

value: Whole blood


title: KD 1506 8d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40559.gif

source_name: Stratagene Universal Human Reference RNA


title: Treatment: Temp 31 degrees, Time: 3 hours, replicate: 3

source_name: Coral larvae exposed to 31 degrees after 3 hours sample 3


title: Treatment: Temp 28 degrees, Time: 10 hours, replicate: 3

source_name: Coral larvae exposed to 28 degrees after 10 hours sample 3


title: Treatment: Temp 28 degrees, Time: 10 hours, replicate: 1

source_name: Coral larvae exposed to 28 degrees after 10 hours sample 1


title: JAY270 x JAY309 biorep A

description:
Total RNA was extracted from a mid-log phase JAY270 cDNA labeled with Cy5, biological replicate A.
Total RNA was extracted from a mid-log phase JAY309 culture in rich media (YPD, 30C).

source_name: JAY309 cDNA labeled with Cy3, biological replicate A. JAY309 is isogenic to S288c.


title: Treatment: Temp 31 degrees, Time: 10 hours, replicate: 1

source_name: Coral larvae exposed to 31 degrees after 10 hours sample 1


title: Treatment: Temp 28 degrees, Time: 10 hours, replicate: 2

source_name: Coral larvae exposed to 28 degrees after 10 hours sample 2


title: KD 3054 3d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40494.gif


title: KD 3058 4d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40502.gif


title: C 2005 Adenovirus

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40549.gif

source_name: C 2005 Adenovirus


title: Treatment: Temp 28 degrees, Time: 3 hours, replicate: 1

source_name: Coral larvae exposed to 28 degrees after 3 hours sample 1


title: Treatment: Temp 24 degrees, Time: 10 hours, replicate: 3

source_name: Coral larvae exposed to 24 degrees after 10 hours sample 3


title: Treatment: Temp 28 degrees, Time: 3 hours, replicate: 3

source_name: Coral larvae exposed to 28 degrees after 3 hours sample 3


title: KD 3028 6d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40527.gif


title: KD 3016 7d

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40481.gif


title: C 4015 Phenobarbital

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40553.gif

source_name: C 4015 Probable Phenobarb Reaction

value: C-dr


title: Treatment: Temp 24 degrees, Time: 10 hours, replicate: 1

source_name: Coral larvae exposed to 24 degrees after 10 hours sample 1

source_name: Reference Sample for coral larvae


title: Treatment: Temp 28 degrees, Time: 3 hours, replicate: 2

source_name: Coral larvae exposed to 28 degrees after 3 hours sample 2


title: Treatment: Temp 24 degrees, Time: 10 hours, replicate: 2

source_name: Coral larvae exposed to 24 degrees after 10 hours sample 2


title: Treatment: Temp 24 degrees, Time: 3 hours, replicate: 3

source_name: Coral larvae exposed to 24 degrees after 3 hours sample 3


title: tissue type: 3-5 DAP caryopsis - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: 20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  3-5 days after pollination the central floret was removed from 10 spikes per collection and the caryopsis was frozen in liquid Nitrogen.  Development stage: [caryopsis, 3-5 DAP].  Sample type: [ developing seed].  Individual genetic trait genotype: [Chinese Spring].  Treatment application type: [No Treatment].

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Triticum aestivum

source_name: tissue type: 3-5 DAP caryopsis

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description:  20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  3-5 days after pollination the central floret was removed from 10 spikes per collection and the caryopsis was frozen in liquid Nitrogen.

extract_protocol: RNA Isolation Using Trizol And Qiagen RNAeasy Columns

tag: PO:0009010## (Organism Part); seed PO:0009010 (Cell type); seed development stages PO:0001170 (Development Stage); 1 after planting (Age); Cereal mix (Growth Media).


title: tissue type: 22 DAP embryo - rep1

description: 20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  22 days after pollination the central floret was removed from 10 spikes per collection and the embryo was frozen in liquid Nitrogen.  Development stage: [embryo 22 DAP].  Sample type: [embryo].  Individual genetic trait genotype: [Chinese Spring].  Treatment application type: [No Treatment].

source_name: tissue type: 22 DAP embryo

growth_protocol: Growth Description:  20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  22 days after pollination the central floret was removed from 10 spikes per collection and the embryo was frozen in liquid Nitrogen.


title: Treatment: Temp 24 degrees, Time: 3 hours, replicate: 1

source_name: Coral larvae exposed to 24 degrees after 3 hours sample 1


title: Treatment: Temp 24 degrees, Time: 3 hours, replicate: 2

data_processing: The value used were median foreground minus median background. Ratio-Intensity plots were constructed for each array data to explore whether or not intensity dependence of log ratios, which appears as curvature, was present.  rLowess curve fitting transformation was applied to the data. Quantile normalisation was also applied to mean log-intensities in order to make the distributions essentially the same across arrays. As the experimental design for this experiment was a reference microarray design the "value" represents the normalized log (Channel 1/channel 2)

source_name: Coral larvae exposed to 24 degrees after 3 hours sample 2

value: Coral larvae pooled at time T=0


title: tissue type: 3-5 DAP caryopsis - rep1


title: tissue type: 22 DAP embryo - rep3


title: tissue type: 22 DAP endosperm - rep1

description: 20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  22 days after pollination the central floret was removed from 10 spikes per collection and the endosperm was frozen in liquid Nitrogen.  Development stage: [endosperm 22 DAP].  Sample type: [other::endosperm].  Individual genetic trait genotype: [Chinese Spring].  Treatment application type: [No Treatment].

source_name: tissue type: 22 DAP endosperm

growth_protocol: Growth Description:  20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  22 days after pollination the central floret was removed from 10 spikes per collection and the endosperm was frozen in liquid Nitrogen.


title: tissue type: 3-5 DAP caryopsis - rep2


title: tissue type: anthers, before anthesis - rep3

description: 20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  2 days before anthesis the central floret was removed from 10 spikes per collection and the anthers were frozen in liquid Nitrogen.  Development stage: [anther, 2 days before anthesis].  Sample type: [other::anther].  Individual genetic trait genotype: [Chinese Spring].  Treatment application type: [No Treatment].

source_name: tissue type: anthers, before anthesis

growth_protocol: Growth Description:  20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  2 days before anthesis the central floret was removed from 10 spikes per collection and the anthers were frozen in liquid Nitrogen.

tag: PO:0009004## (Organism Part); gametophyte PO:0009004 (Cell type); inflorescence development stages PO:0001083 (Development Stage); 1 after planting (Age); Cereal mix (Growth Media).


title: tissue type: 22 DAP endosperm - rep3


title: tissue type: floral bracts, before anthesis - rep3

description: 20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  2 days before anthesis the central floret was removed from 10 spikes per collection and the bracts (lemma, palea, glumes) frozen in liquid Nitrogen.  Development stage: [bracts, 2 days before anthesis].  Sample type: [bracts].  Individual genetic trait genotype: [Chinese Spring].  Treatment application type: [No Treatment].

growth_protocol: Growth Description:  20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  2 days before anthesis the central floret was removed from 10 spikes per collection and the bracts (lemma, palea, glumes) frozen in liquid Nitrogen.


title: tissue type: 22 DAP embryo - rep2


title: tissue type: pistil, before anthesis - rep3

description: 20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  2 days before anthesis the central floret was removed from 10 spikes per collection and the pistils were frozen in liquid Nitrogen.  Development stage: [pistil, 2 days before anthesis].  Sample type: [other::pistil].  Individual genetic trait genotype: [Chinese Spring].  Treatment application type: [No Treatment].

source_name: tissue type: pistil, before anthesis

growth_protocol: Growth Description:  20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  2 days before anthesis the central floret was removed from 10 spikes per collection and the pistils were frozen in liquid Nitrogen.


title: tissue type: 22 DAP endosperm - rep2


title: tissue type: pistil, before anthesis - rep2


title: tissue type: floral bracts, before anthesis - rep2


title: tissue type: seedling, leaf - rep3

description: Three seeds were planted in a single 10 cm pot containing vermiculite.  20 pots were sown for each replicate.  When seedlings reached 10 cm (9-11 cm above surface of vermiculite) they were sampled randomly and vermiculite was removed by washing in RO water.  Leaves from 10 plants per collection were excised and frozen in liquid Nitrogen.  Development stage: [10 cm seedling].  Sample type: [leaf].  Individual genetic trait genotype: [Chinese Spring].  Treatment application type: [No Treatment].

source_name: tissue type: seedling, leaf

growth_protocol: Growth Description:  Three seeds were planted in a single 10 cm pot containing vermiculite.  20 pots were sown for each replicate.  When seedlings reached 10 cm (9-11 cm above surface of vermiculite) they were sampled randomly and vermiculite was removed by washing in RO water.  Leaves from 10 plants per collection were excised and frozen in liquid Nitrogen.

tag: PO:0009006## (Organism Part); shoot PO:0009006 (Cell type); vegetative growth PO:0007134 (Development Stage); 10 days after planting (Age); vermiculite (Growth Media).


title: tissue type: immature inflorescence - rep1

description: 20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  10 inflorescences about 2-3 cm in length were harvested per collection and frozen in liquid Nitrogen. .  .  Sample type: [inflorescence].  Individual genetic trait genotype: [Chinese Spring].  Treatment application type: [No Treatment].

source_name: tissue type: immature inflorescence

growth_protocol: Growth Description:  20 cm pots were sown with 2 seeds at a depth of 2 cm.  14 days after germination the weaker seedling was removed.  Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC.  10 inflorescences about 2-3 cm in length were harvested per collection and frozen in liquid Nitrogen.


title: tissue type: immature inflorescence - rep3


title: tissue type: floral bracts, before anthesis - rep1


title: tissue type: anthers, before anthesis - rep2


title: tissue type: seedling, leaf - rep2


title: tissue type: pistil, before anthesis - rep1


title: tissue type: immature inflorescence - rep2


title: tissue type: anthers, before anthesis - rep1


title: tissue type: seedling, leaf - rep1


title: tissue type: seedling, crown - rep1

description: Three seeds were planted in a single 10 cm pot containing vermiculite.  20 pots were sown for each replicate.  When seedlings reached 10 cm (9-11 cm above surface of vermiculite) they were sampled randomly and vermiculite was removed by washing in RO water.  The crown from 10 plants per collection was excised and frozen in liquid Nitrogen.  Development stage: [10 cm seedling].  Sample type: [crown].  Individual genetic trait genotype: [Chinese Spring].  Treatment application type: [No Treatment].

source_name: tissue type: seedling, crown

growth_protocol: Growth Description:  Three seeds were planted in a single 10 cm pot containing vermiculite.  20 pots were sown for each replicate.  When seedlings reached 10 cm (9-11 cm above surface of vermiculite) they were sampled randomly and vermiculite was removed by washing in RO water.  The crown from 10 plants per collection was excised and frozen in liquid Nitrogen.


title: tissue type: seedling, crown - rep2


title: tissue type: seedling, crown - rep3


title: tissue type: seedling, root - rep2

description: Three seeds were planted in a single 10 cm pot containing vermiculite.  20 pots were sown for each replicate.  When seedlings reached 10 cm (9-11 cm above surface of vermiculite) they were sampled randomly and vermiculite was removed by washing in RO water.  Roots from 10 plants per collection were excised at the base and frozen in liquid Nitrogen.  Development stage: [10 cm seedling].  Sample type: [root].  Individual genetic trait genotype: [Chinese Spring].  Treatment application type: [No Treatment].

source_name: tissue type: seedling, root

growth_protocol: Growth Description:  Three seeds were planted in a single 10 cm pot containing vermiculite.  20 pots were sown for each replicate.  When seedlings reached 10 cm (9-11 cm above surface of vermiculite) they were sampled randomly and vermiculite was removed by washing in RO water.  Roots from 10 plants per collection were excised at the base and frozen in liquid Nitrogen.

tag: PO:0009005## (Organism Part); root PO:0009005 (Cell type); vegetative growth PO:0007134 (Development Stage); 10 days after planting (Age); vermiculite (Growth Media).


title: tissue type: seedling, root - rep3


title: P19t2

city: Edmonton

first: Branko

last: Braam

department: Medicine / Nephrology

country: Canada

institute: Univ. of Alberta

hyb_protocol: According to BeadChip array manufacturer's protocol.

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e. mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray) after log2-transformation. P-value <0.05 was considered significant.

Non-normalized data are available in the 'GSE17582_non-normalized_data.txt' file, which is linked to the Series GSE17582 record as a supplementary file.

source_name: Monocyte from patient, 2wk EPO

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX).

growth_protocol: Monocytes were positively isolated from whole blood by CD14+ immunomagnetic beads (Dynabeads, Invitrogen, Carlsbad, CA). Cells were directly lysed and stored.

extract_protocol: mRNA was isolated from monocytes using Trizol reagent (Invitrogen/Gibco, USA) according to the manufacturer’s instruction. Subsequently, mRNA was purified with NucleoSpin® RNA II (Macherey-Nagel, Düren, Germany).

tag: patient number

tag: disease

value: cardiorenal syndrome (CRS)

tag: cell type

value: monocyte

tag: timepoint (weeks)

value: F

value: EPO, may rise in hemoglobin levels


title: tissue type: germinating seed, root - rep3

description: Seeds were germinated in 15 cm petri dishes on damp 3MM filter paper in a growth cabnet set at 22oC light for 16 hrs and 16oC dark for 8 hrs.  A single plate containing approximately 50 seeds was sown for each replicate.  For each collection for each replicate ten seeds with emerging roots and coleoptile were selected.  Roots were excised and frozen in liquid Nitrogen.  Sample type: [germinating seed].  Individual genetic trait genotype: [Chinese Spring].  Treatment application type: [No Treatment].

source_name: tissue type: germinating seed, root

growth_protocol: Growth Description:  Seeds were germinated in 15 cm petri dishes on damp 3MM filter paper in a growth cabnet set at 22oC light for 16 hrs and 16oC dark for 8 hrs.  A single plate containing approximately 50 seeds was sown for each replicate.  For each collection for each replicate ten seeds with emerging roots and coleoptile were selected.  Roots were excised and frozen in liquid Nitrogen.

tag: PO:0009005## (Organism Part); developing root (Cell type); germination PO:0007057 (Development Stage); 2 days after 2 days after germiniation (Age); 3MM filter paper (Growth Media).


title: tissue type: germinating seed, embryo - rep1

description: Seeds were germinated in 15 cm petri dishes on damp 3MM filter paper in a growth cabnet set at 22oC light for 16 hrs and 16oC dark for 8 hrs.  A single plate containing approximately 50 seeds was sown for each replicate.  For each collection for each replicate ten seeds with emerging roots and coleoptile were selected.  Embryos were excised and frozen in liquid Nitrogen.  Sample type: [germinating seed].  Individual genetic trait genotype: [Chinese Spring].  Treatment application type: [No Treatment].

source_name: tissue type: germinating seed, embryo

growth_protocol: Growth Description:  Seeds were germinated in 15 cm petri dishes on damp 3MM filter paper in a growth cabnet set at 22oC light for 16 hrs and 16oC dark for 8 hrs.  A single plate containing approximately 50 seeds was sown for each replicate.  For each collection for each replicate ten seeds with emerging roots and coleoptile were selected.  Embryos were excised and frozen in liquid Nitrogen.

tag: PO:0009009## (Organism Part); embryo (Cell type); germination PO:0007057 (Development Stage); 2 days after 2 days after germiniation (Age); 3MM filter paper (Growth Media).


title: P10t0

scan_protocol: According to BeadChip array manufacturer's protocol.

source_name: Monocyte from patient, baseline

tag: gender

tag: treatment group

value: EPO, kept on low hemoglobin levels


title: tissue type: germinating seed, embryo - rep2


title: P24t2

source_name: Monocyte from patient, 2wk no EPO

tag: age

value: M

value: No EPO


title: tissue type: germinating seed, embryo - rep3


title: P19t0


title: P10t2


title: tissue type: germinating seed, root - rep2


title: GZ15t0

source_name: Monocyte from healthy control

value: healthy

value: Healthy controls


title: P16t2


title: GZ4t0


title: tissue type: germinating seed, coleoptile - rep3

description: Seeds were germinated in 15 cm petri dishes on damp 3MM filter paper in a growth cabnet set at 22oC light for 16 hrs and 16oC dark for 8 hrs.  A single plate containing approximately 50 seeds was sown for each replicate.  For each collection for each replicate ten seeds with emerging roots and coleoptile were selected.  Coleoptiles were excised and frozen in liquid Nitrogen.  Sample type: [germinating seed].  Individual genetic trait genotype: [Chinese Spring].  Treatment application type: [No Treatment].

growth_protocol: Growth Description:  Seeds were germinated in 15 cm petri dishes on damp 3MM filter paper in a growth cabnet set at 22oC light for 16 hrs and 16oC dark for 8 hrs.  A single plate containing approximately 50 seeds was sown for each replicate.  For each collection for each replicate ten seeds with emerging roots and coleoptile were selected.  Coleoptiles were excised and frozen in liquid Nitrogen.

tag: PO:0020033## (Organism Part); coleoptile (Cell type); germination PO:0007057 (Development Stage); 2 days after 2 days after germiniation (Age); 3MM filter paper (Growth Media).


title: tissue type: germinating seed, coleoptile - rep2


title: tissue type: germinating seed, coleoptile - rep1


title: GZ5t0


title: tissue type: seedling, root - rep1


title: tissue type: germinating seed, root - rep1


title: P8t2


title: P12t2


title: P12t0


title: P24t0


title: P2t2


title: P16t0


title: GZ22t0


title: P9t0


title: P2t0


title: P8t0


title: P23t2


title: P9t2


title: GZ7t26


title: P23t0


title: P7t2


title: GZ16t0


title: P3t2


title: md319-1

type: genomic

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

description: Array experiments were performed according to the standard protocols for Affymetrix GeneChip Mapping 250K arrays (Gene Chip Mapping 500K Assay Manual (P/N 701930 Rev2.), Affymetrix Inc., Santa Clara, CA).

hyb_protocol: Hybridized probes were captured by streptavidin-phycoerythrin conjugates using Fluidics Station 450

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA)

data_processing: QC, genotype calling and log2 ratios were produced in the Affymetrix GeneChip Genotyping Analysis Software (GTYPE) 4.1. The Dynamic Model (DM) algorithm was used to perform single sample QC. The QC specification for 250K is a Call Rate > 93% using the algorithm defaults. Genotype calls were made using the BRLMM algorithm. Parameter settings(CNAT 4.0.1): Transition decay 5 Mb, Median normalization and 0Mb smoothing factor. The reference set used consisted of 96 CEU samples from the HapMap project (www.hapmap.org/downloads/raw_data/affy500k/).

label: Total genomic DNA was digested with a restriction enzyme (Nsp1), ligated to an appropriate adapter for the enzyme, and subjected to PCR amplification using a single primer

molecule: genomic DNA

source_name: Microdissected lung cancer sample

label_protocol: After digestion with DNase I, the PCR products were labeled with a biotinylated nucleotide analogue using terminal deoxynucleotidyl transferase and hybridized to the microarray

extract_protocol: Extraction of genomic DNA was performed using QIAamp DNA Mini kit (Qiagen) according to the manufacturer's instructions.

value: Microdissected lung cancer sample


title: md234A


title: P3t0


title: md296-1


title: 6A

source_name: Lung cancer sample

value: Lung cancer sample


title: 37A


title: P7t0


title: 48A


title: md13-1


title: GZ21t0


title: 81A


title: TSP3

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description: 1 of 3 replicates in this condition

hyb_protocol: Standard Affymetrix protocol for Gene ST Array

data_processing: Default (RMA) for Gene ST Array

source_name: Cells cultured in 20µg/mL Thrombospondin-1

extract_protocol: Qiagen RNeasy

value: Aortic vascular smooth muscle cells


title: 88A


title: 39A


title: 365A


title: 373B


title: 347A


title: 367A


title: md367A


title: 342A


title: P15t2


title: P11t0


title: GZ9t0


title: 359A


title: P11t2


title: TSP2

description: 1 of 3 replicates in this condition

scan_protocol: Standard Affymetrix protocol for Gene ST Array


title: P15t0


title: 361A


title: TSP1

description: 1 of 3 replicates in this condition

label_protocol: Standard Affymetrix protocol for Gene ST Array


title: Man+TSP2

description: 1 of 3 replicates in this condition

source_name: Cells cultured in 25 mM mannose + 20µg/mL Thrombospondin-1


title: GZ1t0


title: Man+TSP3

description: 1 of 3 replicates in this condition


title: GZ18t0


title: 33A


title: 338A


title: Man3

description: 1 of 3 replicates in this condition

source_name: Cells cultured in 25 mM mannose


title: P18t2


title: 299B


title: P18t0


title: 296A


title: 297A


title: 331A


title: Man+TSP1

description: 1 of 3 replicates in this condition


title: 310A


title: Man2

description: 1 of 3 replicates in this condition


title: Man1

description: 1 of 3 replicates in this condition


title: LG3

description: 1 of 3 replicates in this condition

source_name: Cells cultured in low (5 mM) glucose


title: P17t2


title: P17t0


title: 284A


title: 271A


title: 295B


title: 27A


title: 258A


title: 265A


title: LG1

description: 1 of 3 replicates in this condition


title: GZ26t0


title: 319A


title: 32A


title: GZ25t0


title: HG+TSP2

description: 1 of 3 replicates in this condition

source_name: Cells cultured in high (25 mM) glucose  and 20µg/mL Thrombospondin-1 (TSP)


title: 229A


title: 234A


title: 207A


title: HG+TSP3

description: 1 of 3 replicates in this condition


title: P6t2


title: HG+TSP1

description: 1 of 3 replicates in this condition


title: 189A


title: 195B


title: P6t0


title: P22t2


title: 197B


title: HG3

description: 1 of 3 replicates in this condition

source_name: Cells cultured in high (25 mM) glucose


title: 256A


title: 172C


title: 165C


title: P22t0


title: 305A


title: 175B


title: P4t2


title: HG2

description: 1 of 3 replicates in this condition


title: P4t0


title: HG1

description: 1 of 3 replicates in this condition


title: f2#358 versus pool Mouse Brain tissue set 2

status: Public on Aug 10 2009

city: Los Angeles

first: Leslie

last: Ingram-drake

department: Medicine/MIMG/Human Genetics

institute: UCLA

description: Brain tissue from 292 F2 female and male mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast, Brain tissue were dissected and flash frozen in LN2 and stored at -80°C.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: Strain:C57BL/6J and C3H/HeJ Age:20 weeks Gender:Male

source_name: pool

tag: Strain:C57BL/6J and C3H/HeJ  Age:24 weeks (150 randomly selected F2)


title: 162A


title: f2#357 versus pool Mouse Brain tissue set 2


title: 13A


title: 131A


title: f2#353 versus pool Mouse Brain tissue set 2


title: f2#351 versus pool Mouse Brain tissue set 2


title: f2#347 versus pool Mouse Brain tissue set 2


title: 12B


title: f2#339 versus pool Mouse Brain tissue set 2


title: f2#345 versus pool Mouse Brain tissue set 2


title: f2#338 versus pool Mouse Brain tissue set 2


title: f2#346 versus pool Mouse Brain tissue set 2


title: 11C


title: LG2

description: 1 of 3 replicates in this condition


title: f2#337 versus pool Mouse Brain tissue set 2


title: f2#317 versus pool Mouse Brain tissue set 2


title: f2#329 versus pool Mouse Brain tissue set 2


title: f2#321 versus pool Mouse Brain tissue set 2


title: f2#344 versus pool Mouse Brain tissue set 2


title: 112B


title: f2#322 versus pool Mouse Brain tissue set 2


title: f2#328 versus pool Mouse Brain tissue set 2


title: f2#327 versus pool Mouse Brain tissue set 2


title: f2#318 versus pool Mouse Brain tissue set 2


title: f2#319 versus pool Mouse Brain tissue set 2


title: f2#320 versus pool Mouse Brain tissue set 2


title: f2#336 versus pool Mouse Brain tissue set 2


title: f2#309 versus pool Mouse Brain tissue set 2


title: f2#307 versus pool Mouse Brain tissue set 2


title: f2#308 versus pool Mouse Brain tissue set 2


title: f2#306 versus pool Mouse Brain tissue set 2


title: f2#303 versus pool Mouse Brain tissue set 2


title: f2#301 versus pool Mouse Brain tissue set 2


title: f2#297 versus pool Mouse Brain tissue set 2


title: f2#316 versus pool Mouse Brain tissue set 2


title: f2#295 versus pool Mouse Brain tissue set 2


title: f2#299 versus pool Mouse Brain tissue set 2


title: f2#302 versus pool Mouse Brain tissue set 2


title: f2#290 versus pool Mouse Brain tissue set 2


title: f2#283 versus pool Mouse Brain tissue set 2


title: f2#288 versus pool Mouse Brain tissue set 2


title: f2#300 versus pool Mouse Brain tissue set 2


title: f2#282 versus pool Mouse Brain tissue set 2


title: f2#267 versus pool Mouse Brain tissue set 2


title: f2#276 versus pool Mouse Brain tissue set 2


title: f2#277 versus pool Mouse Brain tissue set 2


title: f2#279 versus pool Mouse Brain tissue set 2


title: f2#280 versus pool Mouse Brain tissue set 2


title: f2#269 versus pool Mouse Brain tissue set 2


title: f2#278 versus pool Mouse Brain tissue set 2


title: f2#281 versus pool Mouse Brain tissue set 2


title: f2#268 versus pool Mouse Brain tissue set 2


title: f2#266 versus pool Mouse Brain tissue set 2


title: f2#265 versus pool Mouse Brain tissue set 2


title: f2#258 versus pool Mouse Brain tissue set 2


title: f2#263 versus pool Mouse Brain tissue set 2


title: f2#257 versus pool Mouse Brain tissue set 2


title: f2#255 versus pool Mouse Brain tissue set 2


title: f2#260 versus pool Mouse Brain tissue set 2


title: f2#254 versus pool Mouse Brain tissue set 2


title: f2#259 versus pool Mouse Brain tissue set 2


title: f2#248 versus pool Mouse Brain tissue set 2


title: f2#232 versus pool Mouse Brain tissue set 2


title: f2#240 versus pool Mouse Brain tissue set 2


title: f2#246 versus pool Mouse Brain tissue set 2


title: f2#253 versus pool Mouse Brain tissue set 2


title: f2#234 versus pool Mouse Brain tissue set 2


title: f2#230 versus pool Mouse Brain tissue set 2


title: f2#223 versus pool Mouse Brain tissue set 2


title: f2#241 versus pool Mouse Brain tissue set 2


title: f2#231 versus pool Mouse Brain tissue set 2


title: f2#247 versus pool Mouse Brain tissue set 2


title: f2#233 versus pool Mouse Brain tissue set 2


title: f2#298 versus pool Mouse Brain tissue set 2


title: f2#242 versus pool Mouse Brain tissue set 2


title: f2#229 versus pool Mouse Brain tissue set 2


title: f2#235 versus pool Mouse Brain tissue set 2


title: f2#224 versus pool Mouse Brain tissue set 2


title: f2#243 versus pool Mouse Brain tissue set 2


title: f2#219 versus pool Mouse Brain tissue set 2


title: f2#355 versus pool Mouse Brain tissue set 2

tag: Strain:C57BL/6J and C3H/HeJ Age:20 weeks Gender:Female


title: f2#361 versus pool Mouse Brain tissue set 2


title: f2#349 versus pool Mouse Brain tissue set 2


title: f2#218 versus pool Mouse Brain tissue set 2