title: Sh2b3 WT, biological rep3

first: Alberto

last: Ambesi-Impiombato

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

description: gene expression data from Sh2b3 wild type NOTCH1 induced leukemias

hyb_protocol: hybridized to the Mouse430_2 (Affymetrix) microarray chips according to manufacturer’s protocol

scan_protocol: Standard scan according to manufacturer's protocol

data_processing: Expression values were normalized with GC-RMA using the open-source Bioconductor software (www.bioconductor.org)

source_name: Sh2b3 wild type NOTCH1 induced tumors

label_protocol: 10 ng of RNA from each sample was amplified using the Ovation PicoSL WTA System (NuGen), labeled by the Encore BiotinIL Module (NuGen)

growth_protocol: Bone marrow from 8-week old C57BL6 or Sh2b3–/– mice was harvested and lineage depleted using the Mouse Lineage Cell Depletion Kit (Milteny). Lin- progenitor cells were subjected to two rounds of infection with MigR1-ΔE-Notch1 retroviral particles.

extract_protocol: RNA isolation from mice tumors was performed in triplicate using the RNeasy Micro kit (QIAGEN) according to manufacturer’s protocol.

treatment_protocol: Fifty thousand Lin-Sca1+ infected cells were transplanted into irradiated C57BL6 recipients via intravenous injection. Transplanted animals were monitored for leukemia development by flow cytometry analysis of GFP and CD4/CD8 expression in peripheral blood.

value: leukemia

value: Sh2b3 wild type ΔE-NOTCH1


title: Spindle-chromosome complex, biological rep3

status: Public on Nov 06 2013

type: RNA

city: Philadelphia

first: Edward

last: Romasko

state: PA

address: 3307 N Broad St

country: USA

institute: Temple University

description: Gene expression data from microsurgically isolated spindle-chromosome complexes from MII oocytes

hyb_protocol: 10 ug of labeled cDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to MOE430V2 GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: The data were preprocessed, summarized and normalized with Robust Multiarray Averaging (RMA), using a script written in R with Bioconductor libraries.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Spindle-chromosome complexes isolated from MII oocytes

label_protocol: Up to 50 ng of total RNA from each sample were subjected to two rounds of cDNA synthesis using the Arcturus RiboAmp HS Plus kit (Invitrogen).  Labeled cRNA was produced using the Affymetrix GeneChip Expression 3’ Amplification for IVT Labeling Kit (Affymetrix, Santa Clara, CA).  The biotin-labeled cRNA samples were fragmented and 10 µg were hybridized onto arrays.

growth_protocol: In vivo matured MII oocytes were collected from B6D2F1 mice injected with eCG, followed 48h later by 5 IU of human chorionic gonadotropin (hCG).  Sixteen hours later, cumulus cells were removed by incubation in M2 medium containing hyaluronidase (120 IU/ml, Sigma).

extract_protocol: Total RNA was extracted using the PicoPure RNA Isolation Kit (Arcturus/Life Technologies)

treatment_protocol: SCCs were isolated by microsurgery and MII oocytes, SCCs, and enucleated MII oocyte cytoplasts were collected in PicoPure Extraction Buffer for RNA extraction.

tag: sample type

tag: cell type

value: oocyte

tag: strain

tag: gender

value: female


title: Sh2b3 KO, biological rep3

city: New York

state: NY

description: gene expression data from Sh2b3-/- NOTCH1 induced leukemias

label: biotin

source_name: Sh2b-/-  NOTCH1 induced tumors

tag: tissue

tag: genotype

value: Sh2b3-/- ΔE-NOTCH1


title: Sh2b3 WT, biological rep2


title: MII oocyte, biological rep2

description: Gene expression data from MII oocytes

source_name: MII oocytes

value: MII oocytes


title: cytoplast, biological rep2

description: Gene expression data from enucleated MII oocyte cytoplasts

source_name: Enucleated MII oocyte cytoplasts

value: Enucleated MII oocyte cytoplasts


title: Spindle-chromosome complex, biological rep2

value: Spindle-chromosome complexes isolated from MII oocytes


title: Sh2b3 KO, biological rep1


title: cytoplast, biological rep3


title: Sh2b3 WT, biological rep1


title: Sh2b3 KO, biological rep2


title: cytoplast, biological rep4


title: Spindle-chromosome complex, biological rep1


title: MII oocyte, biological rep3

description: Gene expression data from MII oocytes


title: MII oocyte, biological rep4

description: Gene expression data from MII oocytes


title: cytoplast, biological rep1


title: Cell line VU-SCC-120_transfected_sample6

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
Raw data file:
US22502676_251485065101_S01_GE2-v5_95_Feb07_1_2.txt

hyb_protocol: Labeled samples were hybridized onto whole human genome GE 4×44K microarrays according to the manufacturers protocol (Agilent Technologies, Palo Alto, CA, USA)

scan_protocol: Scanning was performed using a microarray scanner G2505B (Agilent Technologies). Feature Extraction v9.5 using the manufacturers protocols (Agilent Technologies).

data_processing:
Normalization of the gene expression data was done within the R statistical software, using the Limma-package and comprised of RMA background correction, loess within-array normalization and A-quantile between-array normalization.
Then, missing values were imputed using the impute-package (impute.knn with default settings). Finally, the slide and dye effect have been removed by gene-wise linear regression using the log-intensity values.

organism: Homo sapiens

source_name: control

label_protocol: Labeling was performed using the Quick Amp Labeling kit (Agilent Technologies, Palo Alto, CA, USA), and according to the manufacturer's guidelines. Labeled RNA was purified using the RNeasy Mini Kit (QIAGEN Ltd., Venlo, the Netherlands)

growth_protocol: Retroviral vector containing either a scrambled control sequence (ctrl) or miRNA encoding sequence were transiently transfected in VU-SCC-120 Head and Neck cancer cell line and total RNA was isolated 72 hours after transfection.

extract_protocol: Total RNA extracted via the mirVana™ miRNA isolation kit (Ambion, Nieuwerkerk aan den IJssel, The Netherlands)

treatment_protocol: No treatment was applied

tag: cell line

tag: transfection

value: control


title: Cell line VU-SCC-120_transfected_sample4

description:
Raw data file:
US22502676_251485065100_S01_GE2-v5_95_Feb07_1_4.txt

value: VU-SCC-120 Head and Neck cancer cell line


title: Cell line VU-SCC-120_transfected_sample7

description:
Raw data file:
US22502676_251485065101_S01_GE2-v5_95_Feb07_1_3.txt


title: Cell line VU-SCC-120_transfected_sample8

description:
Raw data file:
US22502676_251485065101_S01_GE2-v5_95_Feb07_1_4.txt


title: Cell line VU-SCC-120_transfected_sample5

description:
Raw data file:
US22502676_251485065101_S01_GE2-v5_95_Feb07_1_1.txt


title: Cell line VU-SCC-120_transfected_sample3

description:
Raw data file:
US22502676_251485065100_S01_GE2-v5_95_Feb07_1_3.txt


title: Cell line VU-SCC-120_transfected_sample2

description:
Raw data file:
US22502676_251485065100_S01_GE2-v5_95_Feb07_1_2.txt


title: Cell line VU-SCC-120_transfected_sample1

description:
Raw data file:
US22502676_251485065100_S01_GE2-v5_95_Feb07_1_1.txt


title: Placenta_Folate deficient_rep4

city: Ste Anne-de-Bellevue

first: Romain

last: Lambrot

state: QC

address: 21111 Lakeshore road

department: Animal Science

country: Canada

institute: McGill University

description:
FD-45
Gene expression in the placenta of a fetus sired by a father exposed to a folate-deficient diet.

hyb_protocol: The labeled cRNA was then normalized, fragmented and hybridized on Agilent-028005 SurePrint G3 Mouse GE 8x60K arrays.

scan_protocol: The arrays were incubated in an Agilent Hybridization oven at 65ºC for 17 hours at 10 rpm. They were washed and scanned on an Agilent DNA Microarray Scanner C.

data_processing: Output from the Agilent Feature Extraction software were read into R, preprocessed and tested for differential expression using functions from the Bioconductor package Limma. The normexp method with an offset value of 16 was used for global background adjustment, followed by quantile normalization and a log2 transformation. The annotation for probes was retrieved from the Gene Expression Omnibus (GEO). Using the appropriate Limma functions, a linear model was fit to each gene separately. This linear model included the paternal diet as a categorical variable. Moderated t-tests were performed on the difference between the folate-deficient and -sufficient paternal diet groups.

source_name: Placenta, folate-deficient father, 18.5dpc

label_protocol: Cyanine 3-labeled CTP cRNA was produced using the Low Input Quick Amp Labeling Kit, according to manufacturer's instructions (Agilent Technologies, Mississauga, Canada).

extract_protocol: Total RNA was extracted from placenta from different litters from 18.5 dpc fetuses sired by either a FS male (n=4) or an FD male (n=4), using the RNeasy Mini Kit (Qiagen, Mississauga, Canada) according to the manufacturer's instructions.

treatment_protocol: To generate experimental males, female C57BL/6 were fed either the folate-sufficient (FS, 2mg folic acid/kg, n=69) diet (TD.01369, Harlan Laboratories, Madison, WI) or the folate-deficient diet (FD, 0.3mg folic acid/kg, n=64) (TD.01546), two weeks prior to breeding with non-experimental C57BL/6 males that were fed regular mouse chow (8640 Rodent diet) (used only for breeding to generate experimental males). Females were maintained on the experimental diets through pregnancy and lactation. From weaning at PND21, male pups were given the same experimental diet as their in utero exposure until sacrifice as adults. To determine if the offspring health was sensitive to paternal diet, CD-1 mice were mated to males fed either the FS or FD diet throughout life (FS, n=32; FD, n=35; 2-3 month old). Total RNA was extracted from placenta from different litters from 18.5 dpc fetuses sired by either a FS male (n=4), or an FD male (n=4).

tag: strain/background

value: CD-1 x C57BL/6

value: placenta

tag: developmental stage

tag: diet of father

value: folate deficient


title: Placenta_Folate sufficient_rep4

description:
FS-41
Gene expression in the placenta of a fetus sired by a father exposed to a folate-sufficient diet.

source_name: Placenta, folate-sufficient father, 18.5dpc

value: folate sufficient


title: BM KSL WT2

city: Chiba

first: Satoru

last: Miyagi

state: Chiba

department: Graduate school of Medicine

country: Japan

institute: Chiba university

description: Gene expression in WT BM-derived KSL replicate2

hyb_protocol: A total of 600 ng of the labeled cRNA was used for each hybridization. The process of hybridization and washing was performed using a  Expression Hybridization Kit (Agilent) and a Gene Expression Wash Pack (Agilent), respectively.

scan_protocol: A DNA microarray scanner (Agilent ) was used for array scanning.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using following parameters (protocol GE1-107_sep09 and Grid:028005_D_F_20120201). Percentile shift algorithm is applied to data for normalization.

source_name: Bone marrow, KSL, WT, replicate 2

label_protocol: A total of 10 ng of total RNA was mixed with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent), amplified and labeled with Cyanine 3 using a Quick Amp Labeling Kit (Agilent)  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated using TRIZOL LS solution (Invitrogen) and then purified using RNeasy micro plus kit (QIAGEN).

treatment_protocol: HSCs (c-Kit+ Sca1+ Lineage- )  are sorted from  fetal liver or adult bone marrow and are subjected into RNA preparation.

tag: genetic background

tag: cell fraction

value: c-Kit+ Sca1+ Lineage-

value: HSCs

value: adult bone marrow

value: CreERT, Tif2bw/w


title: Placenta_Folate sufficient_rep3

description:
FS-37
Gene expression in the placenta of a fetus sired by a father exposed to a folate-sufficient diet.


title: Placenta_Folate sufficient_rep2

description:
FS-21
Gene expression in the placenta of a fetus sired by a father exposed to a folate-sufficient diet.


title: BM KSL KO2

description: Gene expression in KO BM-derived KSL replicate2

source_name: Bone Marrow, KSL, KO, replicate 2

value: CreERT, Tif2bf/f


title: Placenta_Folate sufficient_rep1

description:
FS-13
Gene expression in the placenta of a fetus sired by a father exposed to a folate-sufficient diet.


title: BM KSL KO

description:
Gene expression in Hp1gKD c-Kit+ Lineage- cells
BM KO
Bone Marrow, KSL, KO, replicate 1

source_name: Bone Marrow, KSL, KO

tag: genotype/variation

value: CreERT, Tif1bf/f (KO)


title: Placenta_Folate deficient_rep3

description:
FD-33
Gene expression in the placenta of a fetus sired by a father exposed to a folate-deficient diet.


title: Placenta_Folate deficient_rep1

description:
FD-25
Gene expression in the placenta of a fetus sired by a father exposed to a folate-deficient diet.


title: FL KSL KO

description:
Gene expression in KO fetal liver-derived KSL
FL KO
Fetal liver, KSL, KO, replicate 1

source_name: Fetal liver, KSL, KO

value: Fetal liver

value: Tie2-Cre, Tif1bf/f (KO)


title: Placenta_Folate deficient_rep2

description:
FD-28
Gene expression in the placenta of a fetus sired by a father exposed to a folate-deficient diet.


title: ckit+Lineage-

description:
Gene expression in progenitor cells
c-Kit+Lin-
ckit+Lineage- 8wks, replicate 1

source_name: ckit+Lineage- 8wks

extract_protocol: Total RNA was isolated using TRIZOL LS solution (Invitrogen) and  then purified using RNeasy micro plus kit (QIAGEN).

treatment_protocol: Long-term HSCs (CD34-ckit+Sca1+Lineage-), Short term-HSCs (CD34+ckit+Sca1+Lineage-), Progenitor cells (ckit+Sca1- Lineage-, and Lineage+), and differentiated cell (Lineage+) were sorted from mouse bone marraw.

value: ckit+Lineage-

value: progenitor cells

tag: gendar

value: Female

tag: age

value: 8 weeks


title: CD34+ckit+Sca1+Lineage-

description:
Gene expression in short-term HSCs
CD34+KSL
CD34+ckit+Sca1+Lineage- 8wks, replicate 1

source_name: CD34+ckit+Sca1+Lineage- 8wks

value: short-term HSCs


title: Lineage+

description:
Gene expression in differentiated cells
Lin+
Lineage+ 8wks, replicate 1

source_name: Lineage+ 8wks

value: Lineage+

value: differentiated cells


title: FL KSL WT

description:
Gene expression in WT fetal liver-derived KSL
FL WT
Fetal liver, KSL, WT, replicate 1

source_name: Fetal liver, KSL, WT

value: Tie2-Cre, Tif1bw/w (WT)


title: BM KSL WT

description:
Gene expression in Hp1aKD c-Kit+ Lineage- cells
BM WT
Bone marrow, KSL, WT, replicate 1

source_name: Bone marrow, KSL, WT

value: CreERT, Tif1bw/w (WT)


title: CD34-ckit+Sca1+Lineage-

description:
Gene expression in long-term HSCs
CD34-KSL
CD34-ckit+Sca1+Lineage-  8wks, replicate 1

source_name: CD34-ckit+Sca1+Lineage-  8wks

value: long-term HSCs


title: PFC_control_rep1

city: Boston

first: Huiping

last: Zhang

state: Massachusetts

address: 72 East Concord Street

department: Psychiatry

institute: Boston University School of Medicine

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was first normalized using the variance stabilizing transformation (VST), and then the robust spline normalization (RSN) in R; the batch effect was removed by sva package in R; and probes with intensities indistinguishable from background noise (detection P value > 0.05) exceeding half of the samples were removed.

source_name: Brain Prefrontal cortex

label_protocol: An in vitro transcription (IVT) reaction was carried out overnight in the presence of biotinylated UTP and CTP to produce biotin-labeled cRNA from the double stranded cDNA.

extract_protocol: Total RNA was extracted from postmortem PFC tissue using the miRNeasy Mini Kit (QIAGEN, Valencia, CA, USA).

value: Brain Prefrontal cortex

tag: aud status

value: Control

tag: Sex

value: female


title: PFC_case_20

description: AUD cases

value: Alcohol dependence

value: male


title: PFC_case_18

description: AUD cases

value: Alcohol Abuse


title: PFC_case_22

description: AUD cases


title: PFC_case_19

description: AUD cases


title: PFC_case_23

description: AUD cases


title: PFC_case_21

description: AUD cases


title: PFC_case_15

description: AUD cases


title: PFC_case_16

description: AUD cases


title: PFC_case_17

description: AUD cases


title: PFC_case_14

description: AUD cases


title: PFC_case_11

description: AUD cases


title: PFC_case_13

description: AUD cases


title: PFC_control_rep2

description: replicate 2


title: PFC_case_12

description: AUD cases


title: PFC_case_8

description: AUD cases


title: PFC_case_6

description: AUD cases


title: PFC_control_23

description: control


title: PFC_control_20

description: control


title: PFC_case_9

description: AUD cases


title: PFC_case_10

description: AUD cases


title: PFC_control_21

description: control


title: PFC_case_7

description: AUD cases


title: PFC_case_3

description: AUD cases


title: PFC_case_1

description: AUD cases


title: PFC_control_22

description: control


title: PFC_control_19

description: control


title: PFC_case_4

description: AUD cases


title: PFC_case_2

description: AUD cases


title: PFC_case_5

description: AUD cases


title: PFC_control_17

description: control


title: PFC_control_2

description: control


title: PFC_control_12

description: control


title: PFC_control_4

description: control


title: PFC_control_9

description: control


title: PFC_control_10

description: control


title: PFC_control_18

description: control


title: PFC_control_3

description: control


title: PFC_control_6

description: control


title: PFC_control_15

description: control


title: PFC_control_11

description: control


title: PFC_control_8

description: control


title: PFC_control_14

description: control


title: PFC_control_5

description: control


title: PFC_control_13

description: control


title: PFC_control_7

description: control


title: PFC_control_16

description: control


title: 11178 female head

city: Columbia

first: Elizabeth

middle: G

last: King

state: MO

address: 105 Tucker Hall

department: Biological Sciences

institute: University of Missouri

description: female head

hyb_protocol: Hybridization was performed by the Carver Center for Genomics Microarray Center at the University of Iowa, following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by the Carver Center for Genomics Microarray Center at the University of Iowa, following their standard operating protocol. See www.nimblegen.com.

data_processing:
We performed standard quantile normalization and corrected for background effects using the normalize and backgroundCorrect functions in the oligo package in R
We created a custom probe-to-transcript map using the most recent version of the CDS file available at FlyBase (v. 5.48)
We identified probes containing SNPs in the DSPR RIL panel and eliminated any probes where the SNP had a significant effect
We eliminated genes with fewer than 4 probes associated with it.
We performed standard RMA using the basicRMA function in the oligo package to combine probe-specific data and generate a single expression measure per transcript
We performed a principal components analysis and corrected all expression measures for the first 10 principal components to minimize batch effects
We dropped any expression measures below background levels.

organism: Drosophila melanogaster

source_name: female head tissue, ~300 heads per sample

label_protocol: Labeling was performed by the Carver Center for Genomics Microarray Center at the University of Iowa, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Progeny from each cross were 3 -5 days old and raised on standard media in standard conditions.

extract_protocol: RNA was isolated using TRIzol Reagent (Life Technologies) and cleaned up using RNeasy Mini spin columns (Qiagen).

tag: maternal ril

tag: paternal ril


title: 11180 female head

description: female head


title: 11179 female head

description: female head


title: 11176 female head

description: female head


title: 11175 female head

description: female head


title: PFC_control_1

description: control


title: 11174 female head

description: female head


title: 11169 female head

description: female head


title: 11167 female head

description: female head


title: 11171 female head

description: female head


title: 11170 female head

description: female head


title: 11172 female head

description: female head


title: 11168 female head

description: female head


title: 11163 female head

description: female head


title: 11164 female head

description: female head


title: 11158 female head

description: female head


title: 11151 female head

description: female head


title: 11166 female head

description: female head


title: 11152 female head

description: female head


title: 11156 female head

description: female head


title: 11144 female head

description: female head


title: 11159 female head

description: female head


title: 11145 female head

description: female head


title: 11153 female head

description: female head


title: 11160 female head

description: female head


title: 11150 female head

description: female head


title: 11141 female head

description: female head


title: 11154 female head

description: female head


title: 11146 female head

description: female head


title: 11147 female head

description: female head


title: 11143 female head

description: female head


title: 11155 female head

description: female head


title: 11161 female head

description: female head


title: 11142 female head

description: female head


title: 11148 female head

description: female head


title: 11149 female head

description: female head


title: 11162 female head

description: female head


title: 11140 female head

description: female head


title: 11157 female head

description: female head


title: 11138 female head

description: female head


title: 11137 female head

description: female head


title: 11135 female head

description: female head


title: 11136 female head

description: female head


title: 11129 female head

description: female head


title: 11132 female head

description: female head


title: 11123 female head

description: female head


title: 11130 female head

description: female head


title: 11128 female head

description: female head


title: 11107 female head

description: female head


title: 11124 female head

description: female head


title: 11109 female head

description: female head


title: 11115 female head

description: female head


title: 11110 female head

description: female head


title: 11126 female head

description: female head


title: 11106 female head

description: female head


title: 11119 female head

description: female head


title: 11105 female head

description: female head


title: 11127 female head

description: female head


title: 11111 female head

description: female head


title: 11112 female head

description: female head


title: 11120 female head

description: female head


title: 11133 female head

description: female head


title: 11116 female head

description: female head


title: 11118 female head

description: female head


title: 11114 female head

description: female head


title: 11117 female head

description: female head


title: 11102 female head

description: female head


title: 11113 female head

description: female head


title: 11103 female head

description: female head


title: 11134 female head

description: female head


title: 11104 female head

description: female head


title: 11101 female head

description: female head


title: 11100 female head

description: female head


title: 11096 female head

description: female head


title: 11098 female head

description: female head


title: 11089 female head

description: female head


title: 11086 female head

description: female head


title: 11097 female head

description: female head


title: 11083 female head

description: female head


title: 11092 female head

description: female head


title: 11091 female head

description: female head


title: 11099 female head

description: female head


title: 11090 female head

description: female head


title: 11094 female head

description: female head


title: 11087 female head

description: female head


title: 11079 female head

description: female head


title: 11081 female head

description: female head


title: 11084 female head

description: female head


title: 11082 female head

description: female head


title: 11080 female head

description: female head


title: 11077 female head

description: female head


title: 11075 female head

description: female head


title: 11076 female head

description: female head


title: 11073 female head

description: female head


title: 11067 female head

description: female head


title: 11088 female head

description: female head


title: 11072 female head

description: female head


title: 11068 female head

description: female head


title: 11065 female head

description: female head


title: 11066 female head

description: female head


title: 11069 female head

description: female head


title: 11071 female head

description: female head


title: 11078 female head

description: female head


title: 11064 female head

description: female head


title: 11055 female head

description: female head


title: 11058 female head

description: female head


title: 11054 female head

description: female head


title: 11056 female head

description: female head


title: 11061 female head

description: female head


title: 11057 female head

description: female head


title: 11046 female head

description: female head


title: 11062 female head

description: female head


title: 11060 female head

description: female head


title: 11051 female head

description: female head


title: 11050 female head

description: female head


title: 11044 female head

description: female head


title: 11059 female head

description: female head


title: 11049 female head

description: female head


title: 11045 female head

description: female head


title: 11042 female head

description: female head


title: 11043 female head

description: female head


title: 11052 female head

description: female head


title: 11033 female head

description: female head


title: 11037 female head

description: female head


title: 11040 female head

description: female head


title: 11035 female head

description: female head


title: 11031 female head

description: female head


title: 11053 female head

description: female head


title: 11038 female head

description: female head


title: 11041 female head

description: female head


title: 11036 female head

description: female head


title: 11030 female head

description: female head


title: 11028 female head

description: female head


title: 11039 female head

description: female head


title: 11019 female head

description: female head


title: 11011 female head

description: female head


title: 11027 female head

description: female head


title: 11022 female head

description: female head


title: 11017 female head

description: female head


title: 11020 female head

description: female head


title: 11012 female head

description: female head


title: 11026 female head

description: female head


title: 11025 female head

description: female head


title: 11013 female head

description: female head


title: 11021 female head

description: female head


title: 11015 female head

description: female head


title: 11016 female head

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title: 11345 female head

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title: 11390 female head

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title: 11342 female head

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title: 11334 female head

description: female head


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description: female head


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description: female head


title: 11330 female head

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title: 11331 female head

description: female head


title: 11333 female head

description: female head


title: 11328 female head

description: female head


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description: female head


title: 11338 female head

description: female head


title: 11339 female head

description: female head


title: 11335 female head

description: female head


title: 11326 female head

description: female head


title: 11327 female head

description: female head


title: 11325 female head

description: female head


title: 11322 female head

description: female head


title: 11323 female head

description: female head


title: 11324 female head

description: female head


title: 11321 female head

description: female head


title: 11319 female head

description: female head


title: PFC_case_20

type: genomic

description: AUD cases

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
Data was normalized using controls normalization built-in GenomeStudio software V2011.1 (Methylation Module V1.9.0).
Series supplementary file signal_intensities.txt includes unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the QIAamp DNA Micro Kit (QIAGEN, Valencia, CA, USA)


title: 11318 female head

description: female head


title: 11317 female head

description: female head


title: 11315 female head

description: female head


title: PFC_control_rep2

description: replicate 2


title: PFC_control_rep1

description: replicate 1


title: 11316 female head

description: female head


title: PFC_case_22

description: AUD cases


title: 11314 female head

description: female head


title: PFC_case_21

description: AUD cases


title: PFC_case_15

description: AUD cases


title: PFC_case_12

description: AUD cases


title: PFC_case_16

description: AUD cases


title: 11311 female head

description: female head


title: PFC_case_18

description: AUD cases


title: 11310 female head

description: female head


title: PFC_case_14

description: AUD cases


title: PFC_case_23

description: AUD cases


title: PFC_case_13

description: AUD cases


title: PFC_case_9

description: AUD cases


title: PFC_case_19

description: AUD cases


title: PFC_case_11

description: AUD cases


title: PFC_case_4

description: AUD cases


title: 11308 female head

description: female head


title: 11306 female head

description: female head


title: PFC_case_6

description: AUD cases


title: PFC_case_10

description: AUD cases


title: 11305 female head

description: female head


title: PFC_case_3

description: AUD cases


title: PFC_case_17

description: AUD cases


title: 11313 female head

description: female head


title: 11309 female head

description: female head


title: 11304 female head

description: female head


title: 11303 female head

description: female head


title: PFC_case_5

description: AUD cases


title: PFC_case_8

description: AUD cases


title: PFC_case_2

description: AUD cases


title: PFC_control_23

description: control


title: PFC_case_7

description: AUD cases


title: 11302 female head

description: female head


title: PFC_control_22

description: control


title: 11299 female head

description: female head


title: 11298 female head

description: female head


title: PFC_case_1

description: AUD cases


title: PFC_control_21

description: control


title: PFC_control_17

description: control


title: PFC_control_19

description: control


title: PFC_control_18

description: control


title: 11294 female head

description: female head


title: 11297 female head

description: female head


title: 11293 female head

description: female head


title: 11301 female head

description: female head


title: 11292 female head

description: female head


title: 11291 female head

description: female head


title: PFC_control_20

description: control


title: 11295 female head

description: female head


title: PFC_control_16

description: control


title: PFC_control_15

description: control


title: 11290 female head

description: female head


title: 11286 female head

description: female head


title: 11285 female head

description: female head


title: 11288 female head

description: female head


title: 11307 female head

description: female head


title: 11282 female head

description: female head


title: 11281 female head

description: female head


title: 11284 female head

description: female head


title: 11277 female head

description: female head


title: 11274 female head

description: female head


title: PFC_control_12

description: control


title: 11279 female head

description: female head


title: 11272 female head

description: female head


title: 11283 female head

description: female head


title: 11267 female head

description: female head


title: 11266 female head

description: female head


title: 11264 female head

description: female head


title: 11265 female head

description: female head


title: 11300 female head

description: female head


title: PFC_control_13

description: control


title: PFC_control_10

description: control


title: 11262 female head

description: female head


title: 11271 female head

description: female head


title: PFC_control_1

description: control


title: PFC_control_14

description: control


title: 11260 female head

description: female head


title: 3258_NRAS-BCL2_ABT_737

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), exon level expression were summarized from the corrected intensities and then quantile normalized.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.mps

source_name: Sca-1+ splenocytes in AML mice after ABT-737

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

growth_protocol: Spleen cells were labelled with anti-Sca-1+ antibodies coupled with microbeads from Miltenyi  and then sorted using an AutoMacs separator (Miltenyi Biotec, Bergisch Gladbach,  Germany).

extract_protocol: 5x106 to 107 Sca-1+ sorted cells were used to extract total RNA using TRIzol  10  (Invitrogen, CA, USA). Quantification and quality of the RNAs were assessed using a  Nanodrop (Thermoscientific, USA).

treatment_protocol: 75mg/kg 3 times per week for 33 days

tag: treatment

value: ABT-737 treated transgenic mice in FVB/N

value: FVB/N

value: NRASD12/BCL-2 double transgenic

tag: cell type

value: primitive Sca1+ cells from splenocytes


title: PFC_control_6

description: control

tag: tissue


title: 11257 female head

description: female head


title: 11254 female head

description: female head


title: PFC_control_7

description: control


title: 11255 female head

description: female head


title: PFC_control_5

description: control


title: PFC_control_8

description: control


title: 3518_NRAS-BCL2

source_name: Sca-1+ splenocytes in AML mice

value: ctrl transgenic mice in FVB/N

tag: genotype


title: PFC_control_11

description: control


title: 3626_NRAS-BCL2


title: 3248_NRAS-BCL2_ABT_737


title: PFC_control_2

description: control


title: PFC_control_4

description: control


title: 11253 female head

description: female head


title: 11280 female head

description: female head


title: 11248 female head

description: female head


title: 9152_NRAS-BCL2_ABT_737


title: 11251 female head

description: female head


title: 11261 female head

description: female head


title: 11269 female head

description: female head


title: 3622_NRAS-BCL2


title: 11247 female head

description: female head


title: 11268 female head

description: female head


title: 11246 female head

description: female head


title: PFC_control_3

description: control


title: 11276 female head

description: female head


title: 11245 female head

description: female head


title: dreb1a (CS872453) inflorescence, drought-treated, day 4, replicate 1

city: University Park

first: Zhao

last: SU

address: 354 N. Frear

department: Biology

institute: The Penn State University

description: Gene expression data from Arabidopsis dreb1a (CS872453) unopen flower buds sampled 4 days later from drought-treated plants

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed by using robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) with the R/Bioconductor package affy. and then converted to logarithm base 2.

organism: Arabidopsis thaliana

source_name: Arabidopsis dreb1a (CS872453) inflorescence sampled 4 days later from drought-treated plant

label_protocol: Standard Affymetrix protocol.

growth_protocol: Seeds were directly sown into pots containing 100g soil mixture of Metro-Mix 360 soil (Sun Gro Horticulture Canada Ltd) and Turface profile greens grade (Profile Products LLC) in 3:2 ratio by volume, with a maximum water-holding capacity of 100g (defined as 100% soil moisture). Seeds were stratified in a cold room for 2 d at 4 ℃ in the dark. After stratification, the pots with seeds were transferred into a Conviron growth chamber (Conviron Inc), which was set at our normal conditions (22 ℃, 16h day/8h night photoperied, ~300 μmol m-2 s-1 photon flux, 60% humidity) until just after flowering (bolting) when some of the plants were subjected to drought stress.

extract_protocol: Total RNA was isolated from unopened flower buds using RNeasy columns following instructions from the manufacturer (Qiagen, Valencia, CA, USA).

treatment_protocol: Arabidopsis were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest (about 50 days). For well-watered (control) plants, 90% of the soil water-holding capacity was maintained until tissue harvest or after seed maturation (pots were weighed and watered twice per day). Unopened flower samples were collected, from both treated and control plants, at day 0, 3, 4, 5, 10.

value: Unopen flower buds

tag: cultivar/ecotype

value: Arabidopsis at day 29 after seed germination


title: dreb1a (CS872453) inflorescence, drought-treated, day 4, replicate 2


title: dreb1a (CS872453) inflorescence, drought-treated, day 5, replicate 1

description: Gene expression data from Arabidopsis dreb1a (CS872453) unopen flower buds sampled 5 days later from drought-treated plants

source_name: Arabidopsis dreb1a (CS872453) inflorescence sampled 5 days later from drought-treated plant

value: Arabidopsis at day 30 after seed germination


title: 11244 female head

description: female head


title: dreb1a (CS872453) inflorescence, drought-treated, day 5, replicate 2


title: 11240 female head

description: female head


title: 11243 female head

description: female head


title: dreb1a (CS872453) inflorescence, drought-treated, day 3, replicate 1

description: Gene expression data from Arabidopsis dreb1a (CS872453) unopen flower buds sampled 3 days later from drought-treated plants

source_name: Arabidopsis dreb1a (CS872453) inflorescence sampled 3 days later from drought-treated plant

value: Arabidopsis at day 28 after seed germination


title: 11235 female head

description: female head


title: 11241 female head

description: female head


title: 11236 female head

description: female head


title: 11239 female head

description: female head


title: 11242 female head

description: female head


title: Wild type (Col-0) inflorescence, drought-treated, day 5, replicate 2

description: Gene expression data from Arabidopsis unopen flower buds sampled 5 days later from drought-treated plant

source_name: Arabidopsis inflorescence sampled 5 days later from drought-treated plant

tag: sample date

value: 5 days later

tag: stress

value: drought-treated


title: dreb1a (CS872453) inflorescence, drought-treated, day 3, replicate 2


title: Wild type (Col-0) inflorescence, drought-treated, day 5, replicate 1


title: Wild type (Col-0) inflorescence, drought-treated, day 4, replicate 2

description: Gene expression data from Arabidopsis unopen flower buds sampled 4 days later from drought-treated plant

source_name: Arabidopsis inflorescence sampled 4 days later from drought-treated plant

value: 4 days later


title: 11231 female head

description: female head


title: 11233 female head

description: female head


title: 11238 female head

description: female head


title: 11237 female head

description: female head


title: 11229 female head

description: female head


title: 11230 female head

description: female head


title: Wild type (Col-0) inflorescence, drought-treated, day 4, replicate 1


title: 11227 female head

description: female head


title: 11228 female head

description: female head


title: 11259 female head

description: female head


title: Wild type (Col-0) inflorescence, well-watered, day 5, replicate 2

description: Gene expression data from Arabidopsis unopen flower buds sampled 5 days later from well-watered plant

source_name: Arabidopsis inflorescence sampled 5 days later from well-watered plant

value: well-watered


title: 11234 female head

description: female head


title: 11226 female head

description: female head


title: 11232 female head

description: female head


title: PFC_control_9

description: control

value: Brain Prefrontal cortex

value: Control


title: 11224 female head

description: female head


title: 11223 female head

description: female head


title: 11225 female head

description: female head


title: 11222 female head

description: female head


title: 11220 female head

description: female head


title: 11219 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg050

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Institute

description: Gene expression data from Pdgfra-driven Glioblastoma mouse model

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Expression estimates were calculated using RMA in Bioconductor.

source_name: mouse brain

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

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

tag: strain

value: CD-1 nude

value: Pdgfra V544ins;p53null

tag: disease model

value: Glioblastoma


title: MCM3 at 6h

city: Calgary

first: Voon

middle: Wee

last: Yong

state: Alberta

address: 3330 Hospital drive NW

department: Clinical Neurosciences

institute: University of Calgary

description:
BTICs exposed to microglia conditioned medium
Gene expression data from 6h of MCM treatment

hyb_protocol: Following fragmentation, 15ug cRNA were hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Array at 45°C for 16h.

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

data_processing: Array data files were generated with GeneChip® Command Console® Software (AGCC) and statistical significant analysis was carried out on software of GeneSpringTM(Agilent Technologies). The Fold Change between treatment and control was based on the p<0.05 from unpaired T-test (Asymptotic and Benjamini Hochberg FDR).

source_name: 25EFhuman BTICs, MCM

label_protocol: 100 ng of RNA of each sample with RIN higher than 9 was labelled with 3' IVT Express Kit (Ambion)

extract_protocol: RNA was extracted using mirVana miRNA Isolation Kit (Ambion, Austin, USA) according to the manufacturer’s protocol. Total RNA was purified with RNeasy Plus Micro Kit (Qiagen, Valencia, USA) to remove genomic DNA.

tag: cell line

value: brain tumor initiating cells (BTICs)

tag: agent

value: microglia conditioned medium


title: 11221 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg059

tag: genotype/variation

value: Pdgfra E10 del.v2;p53null


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg051


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg058


title: MCM2 at 6h


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg052


title: MCM4 at 6h


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg060

value: Pdgfra WT;p53null


title: Control3 at 6h

description:
BTICs exposed to control medium
Gene expression data from 6h

source_name: 25EFhuman BTICs, control

value: control


title: MCM1 at 6h


title: 11218 female head

description: female head


title: EGFRvIII-driven Glioblastoma mouse model with p53 null background, pdg047

description: Gene expression data from EGFRVIII-driven Glioblastoma mouse model


title: EGFRvIII-driven Glioblastoma mouse model with p53 null background, pdg043


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg055

value: Pdgfra E7 del;p53null


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg056


title: Control1 at 6h


title: HepG2-Anoxia-3

city: Toronto

first: Nicholas

middle: J

last: Harding

state: ON

address: 101 College St

department: Informatics and Biocomputing Platform

institute: OICR

description: Anoxia

hyb_protocol: 750ng of cRNA generated from amplification and labeling were hybridized to 2 Human HT-12 v4.0 BeadChips.

scan_protocol: The BeadChips were scanned on the Illumina iScan platform after washing and staining.

data_processing: Data files were quantified in GenomeStudio Version 2011.1. All samples passed Illumina's sample dependent and independent quality control metrics with one sample having higher background and overall signal intensities resulting in lower detection calls relative to the other samples. This sample was included following normalization. Bead summary text files containing quality corrected median intensity values for each probe were loaded into the R statistical environment (v2.13.2). Data were normalized using the variance stabilizing method VSN as implemented by the beadarray package v2.2.0.

label_protocol: labeled using Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: Cells were grown adherent at 80% confluency on glass dishes that in contrast to plastic do not release oxygen. Growth medium: DMEM - Dulbecco's Modified Eagle Medium- Invitrogen.

extract_protocol: RNA was isolated using RNeasy Mini Kit (Qiagen) and quality assessed on an Agilent 2100 Bioanalyzer. 250 ng from each of 24 RNA samples (4 groups, 2 cell lines, triplicate)

value: hepatocellular carcinoma


title: HepG2-Normoxia-3

description: Normoxia


title: HepG2-Tunica-3

description: Tunicamycin


title: HepG2-Tg-3

description: Thapsigargin


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg054


title: Control2 at 6h


title: 11258 female head

description: female head


title: scrambled control-2

city: Irvine

first: Zhenyu

last: Jia

state: CA

address: 123 Schubert Ct.

department: Statistics

institute: The University of Akron

description:
human prostate cancer cells; scrambled control-2
human prostate cancer cells

hyb_protocol: Following Affymetrix protocol

scan_protocol: GeneChips were scanned using the Affymetrix Scanner.

data_processing: The raw Affymetrix expression values were normalized and analyzed for differential expression using the Limma package of the R program. T-tests were performed to establish p-values for differential expression.

source_name: 0810A-01_scrambled control-2

label_protocol: The University of California Genomics High Throughput Facility carried out the in vitro transcription and the hybridization according to their standard protocol (http://ghtf.biochem.uci.edu)

growth_protocol: Growth protocol: Human prostate cancer cells M12 were maintained in serum-free RMPI-1640 containing L-glutamine (10ng/ml), epidermal growth factor (0.1μM), dexamethazone, ITS (5μg/ml each of insulin, transferring and selenium), 0.05mg/ml gentamicin, and 2.5 ug/ml amphotericin B.

extract_protocol: RNA Purification: RNA was extracted from shSCR-M12 (scrambled control) or shEGR3-M12 cells using the RNeasy Plus kit (Qiagen) and resuspended in water. RNA integrity was assessed by electrophoresis on formaldehyde gels and the RNA was quantified using a Beckman Du800 spectrophotometer. The excellent quality of the RNA was confirmed using an Agilent Bioanalyzer 2100. One μg RNA was converted to cDNA using the Quanta qScript cDNA Super-mix (5 min at 25C; 30 min at 42oC; 5 min at 85oC) in a thermocycler.


title: 11217 female head

description: female head


title: 11214 female head

description: female head


title: 11215 female head

description: female head


title: 11216 female head

description: female head


title: 11213 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg049


title: clone 3-2

description:
human prostate cancer cells; clone 3-2
human prostate cancer cells

value: EGR3 knockdown


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg062


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg005

value: Pdgfra D842V;p53null


title: HCT116-Anoxia-3

description: Anoxia

growth_protocol: Cells were grown adherent at 80% confluency on glass dishes that in contrast to plastic do not release oxygen. Growth medium: RPMI Media 1640- Invitrogen

value: colon carcinoma


title: 11212 female head

description: female head


title: clone 2-1

description:
human prostate cancer cells; clone 2-1
human prostate cancer cells


title: 11211 female head

description: female head


title: HCT116-Tg-3

description: Thapsigargin


title: scrambled control-1

description:
human prostate cancer cells; scrambled control-1
human prostate cancer cells

source_name: 0810A-01_scrambled control-1


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg027

value: Pdgfra C450 ins;p53null


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg061


title: 11210 female head

description: female head


title: clone 3-1

description:
human prostate cancer cells; clone 3-1
human prostate cancer cells


title: HepG2-Tunica-2

description: Tunicamycin


title: HepG2-Anoxia-2

description: Anoxia


title: clone 2-2

description:
human prostate cancer cells; clone 2-2
human prostate cancer cells


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg029


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg016

value: Pdgfra E10 del;p53null


title: HepG2-Tg-2

description: Thapsigargin


title: HCT116-Normoxia-3

description: Normoxia


title: 11208 female head

description: female head


title: 11205 female head

description: female head


title: 11204 female head

description: female head


title: 11206 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg053


title: EGFRvIII-driven Glioblastoma mouse model with p53 null background, pdg045


title: HepG2-Normoxia-2

description: Normoxia


title: HCT116-Tg-2

description: Thapsigargin


title: 11207 female head

description: female head


title: EGFRvIII-driven Glioblastoma mouse model with p53 null background, pdg048


title: 11203 female head

description: female head


title: EGFRvIII-driven Glioblastoma mouse model with p53 null background, pdg044


title: 11202 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg025


title: HCT116-Tunica-2

description: Tunicamycin


title: HCT116-Anoxia-2

description: Anoxia


title: HepG2-Anoxia-1

description: Anoxia


title: HCT116-Normoxia-2

description: Normoxia


title: HepG2-Tg-1

description: Thapsigargin


title: EGFRvIII-driven Glioblastoma mouse model with p53 null background, pdg041


title: 11199 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg020


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg004


title: 11201 female head

description: female head


title: EGFRvIII-driven Glioblastoma mouse model with p53 null background, pdg046


title: HCT116-Anoxia-1

description: Anoxia


title: 11196 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg064


title: 11197 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg003


title: 11195 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg030


title: 11198 female head

description: female head


title: HCT116-Tg-1

description: Thapsigargin


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg063


title: 11194 female head

description: female head


title: HepG2-Normoxia-1

description: Normoxia


title: HepG2-Tunica-1

description: Tunicamycin


title: HCT116-Normoxia-1

description: Normoxia


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg001


title: HCT116-Tunica-1

description: Tunicamycin


title: 11193 female head

description: female head


title: 11191 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg028


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg026


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg024


title: siEDAG_2

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

description: CD34+ cells infected with EDAG RNAi lentivirus, replicate 2

hyb_protocol: Fluorescence dye labeled cRNA was hybridized to Agilent Human Whole Genome 8*60K array according to the instructions of Agilent Gene Expression Hybridization Kit.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent GeneSpring GX 11.5 was used for background subtraction and Lowess normalization.

label_protocol: RNA was amplified and labeled using Agilent LowInput Quick Amp Labeling Kit.

growth_protocol: Human umbilical cord blood (UCB) was collected, using a clinically approved method, into heparin containing bags immediately after delivery, upon written approval by the mothers. CD34+ cells were isolated from UCB. Briefly, UCB mononuclear cells were obtained by Ficoll-Hypaque density gradient centrifugation and CD34+ cells were obtained using magnetic bead separation (Stem Cell Technologies, EasySep Human CD34 Positive Selection Kit, Cat#18056). More than 95% selected cells were CD34 positive assessed by FACS.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, Gaithersburg, MD) according to the manufacture’s instructions. The quantity of RNA in each sample was assessed spectrophotometerically (NanoDrop Technologies, Wilmington, DE) and RNA integrity was assessed by formaldehyde agarose gel electrophoresis.

treatment_protocol: For expansion, CD34+ cells were cultured in StemSpanTM SFEM serum-free medium (Stem Cell Technologies, Cat#09650) containing 100ng/ml rhSCF (Peprotech, Cat#300-07), 50ng/ml rhTPO (Peprotech, Cat#300-18), 50ng/ml rhIL-3 (Peprotech, Cat#200-03), and 50ng/ml rhFlt3-Ligand (Peprotech, Cat#300-19). In erythroid differentiation experiments, CD34+ cells were cultured in SFEM serum-free medium supplemented with 5U/ml rhEPO, 25ng/ml rhSCF and 20ng/ml rhIL-3. Erythroid differentiation was induced with EPO treatment for 4 days.

tag: gender

value: female

value: umbilical cord blood (UCB)

tag: transfection

value: EDAG RNAi lentivirus

source_name: CD34+ cells infected with control lentivirus

value: control lentivirus


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg006

value: CD-1 nude

value: Pdgfra V544ins;p53null

value: Glioblastoma


title: 11192 female head

description: female head


title: 11189 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg008


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg018


title: siEDAG_1

description: CD34+ cells infected with EDAG RNAi lentivirus, replicate 1


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg010


title: A549 cells 72 hours after infection

city: XI'AN

first: Li

last: Dengyun

address: Xinong Raod 22

institute: NWSUAF

description: 72h after A549 cells infected with a strain of the swine-origin influenza A(H1N1) virus isolated during the human swine flu outbreak of 2009

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software.For the normalization it uses the average of five housekeeping genes: RNU44, RNU24, RNU43, RNU6B, Mamm U6.ath-miR159a, RNU48
Series supplementary file fold-change.txt reports test/control (i.e.,infected A549/normal A549) ratios

label: FAM

source_name: lung

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: human alveolar adenocarcinoma cell line

tag: hours post-infection


title: A549 cells 24 hours after infection

description: 24h after A549 cells infected with a strain of the swine-origin influenza A(H1N1) virus isolated during the human swine flu outbreak of 2009


title: A549 cells 48 hours after infection

description: 48h after A549 cells infected with a strain of the swine-origin influenza A(H1N1) virus isolated during the human swine flu outbreak of 2009


title: 11186 female head

description: female head

tag: maternal ril


title: 11185 female head

description: female head

tag: paternal ril


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg017


title: normal A549 cells

description: normal A549 cells


title: 11182 female head

description: female head


title: 11184 female head

description: female head


title: 11190 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg002


title: 11181 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg057

value: Pdgfra E10 del.v2;p53null


title: EGFRvIII-driven Glioblastoma mouse model with p53 null background, pdg042


title: HCT116-Tunica-3

description: Tunicamycin


title: 11187 female head

description: female head


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg019


title: PDGFRA-driven Glioblastoma mouse model with p53 null background, pdg023


title: 231.ZKD4-TGF-β

status: Public on Nov 05 2013

city: Houston

first: Jia

last: Xu

state: TX

address: 1515 Holcombe Blvd.

department: Molecular & Cellular Oncology

institute: UT-M.D. Anderson Cancer Center

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

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

growth_protocol: cells were cultured and maintained in 231 culture medium

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

treatment_protocol: cells were treated with TGF-β (5ng/ml) for 2 hours

value: breast cancer

tag: cell subline


title: 231.ZKD5-R

description: Replicate of 231.ZKD5

tag: cell type


title: 231.Scr-TGF-β-R

description: Replicate of 231.Scr-TGF-β


title: Stable transfectant overexpressing TSC2 clone P technical replicate 2

city: Bangalore

first: Shalmali

last: Pradhan

state: Karnataka

address: Indian Institute of Science

department: MRDG

country: India

institute: Indian Institute of Science

description: Biological replicate 1 of 2. Technical replicate 2 of 2. Stable transfectant clone generated in KB cells overexpressing pcDNA3.1(+)/TSC2. Control Stable transfectant clone generated in KB cells overexpressing pcDNA3.1(+).

hyb_protocol: The Cy5 labeled cRNA (825 ng) from each of the two TSC2 overexpressing clones was mixed with the Cy3 labeled cRNA (825 ng) from the vector control clone. Each of these mixes was allowed to hybridize with a single array on the 4X44K slide. Altogether four such hybridizations were performed, two for each of the two TSC2 overexpressing clones. The hybridization was carried out in a hybridization oven on a rotisserie (four rotations per minute) at 65˚C for 17 hr.

scan_protocol: Scanned on an Agilent Scanner G2505C. Images were quantified using the Feature Extraction Software version 10.5.1.1 (Agilent Technologies, Santa Clara, CA).

data_processing: The background-corrected raw intensity values were used for analysis. Normalization was performed using the LOWESS algorithm. Differential expression of genes was calculated by averaging the normalized technical duplicates and comparing them with the biological duplicate. The MeV version 4.6 software (Dana-Farber Cancer Institute, Boston, MA) was used to sort statistically significant differentially expressed genes. Statistical filters were applied by using a cut off value of p<0.05 after performing a paired t-test on the technical replicates. Fold changes were calculated as follows: fold change = Cy5 mean processed value - Cy3 mean processed value, where Cy5 or Cy3 mean processed value represents the mean of the log-transformed (base-2) probe set values of the technical replicates.

source_name: Stable transfectant overexpressing pcDNA3.1(+)/TSC2 generated in Human oral squamous cell carcinoma cells

label_protocol: Two clones overexpressing TSC2 constituted the biological duplicates and each clone was in turn processed in duplicate, representing technical duplicates (P1, P2, G1 and G2). Total RNA (500 ng) samples from each of the samples (P1, P2, G1 and G2) and a vector control clone (V) were labeled separately using the Low RNA Input Linear Amplification Kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s protocol. Samples with specific activity of >8 pmol Cy3 or Cy5/mg cRNA were selected for competitive hybridization. The kit uses T7 RNA polymerase, which simultaneously amplifies the RNA and incorporates Cy3 (for samples P1, P2, G1 and G2) or Cy5 (for stable transfectant vector control clone V) labeled CTP in it.

growth_protocol: The stable transfectants (TSC2 overexpressing and vector control clones) were maintained in the complete DMEM supplemented with 0.5 mg/ml G418.

extract_protocol: Total RNA was isolated from the stably transfected KB cells using the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: The empty vector pcDNA3.1(+) and the pcDNA3.1(+)/TSC2 construct harboring a full-length human TSC2 gene were transfected separately in KB cells, using the Effectene® transfection reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Selection of transfected cells was started 48 hr post transfection with 1 mg/ml of G418 (Calbiochem®, Darmstadt, Germany) and continued until colonies were visible and well isolated from each other. Individual colonies were picked with cloning cylinders and cultured as independent stable clones. The stable clones overexpressing TSC2 or a vector control clone were selected using Western blotting and validated by semi-quantitative RT-PCR.

tag: treatment

value: Overexpressed TSC2

value: KB

source_name: Stable transfectant vector control clone V

value: Basal TSC2 expression


title: Stable transfectant overexpressing TSC2 clone G technical replicate 1

description: Biological replicate 2 of 2. Technical replicate 1 of 2. Stable transfectant clone generated in KB cells overexpressing pcDNA3.1(+)/TSC2. Control Stable transfectant clone generated in KB cells overexpressing pcDNA3.1(+).


title: 231.ZKD4-R

description: Replicate of 231.ZKD4


title: Stable transfectant overexpressing TSC2 clone G technical replicate 2

description: Biological replicate 2 of 2. Technical replicate 2 of 2. Stable transfectant clone generated in KB cells overexpressing pcDNA3.1(+)/TSC2. Control Stable transfectant clone generated in KB cells overexpressing pcDNA3.1(+).


title: mESCs treated with E2 and P4 in the presence of ATRA

city: Xi'an

first: Jingjing

last: Ma

address: No. 127 Changlexi Road

institute: Fourth Military Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Mouse Genome 430 2.0 GneChip micorarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the EukGE-WS2v5 protocol.

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

data_processing: The gene expression data were extracted using the Affymetrix Expression Console Software Version 1.0. Data analysis was conducted using the Partek GS 6.5 software (Partek, St Louis, MO).

label: boitin

source_name: mESCs were isolated at day 4 of pseudopregnancy

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

growth_protocol: mESCs were cultured in  medium (DMEM–F12, 1:1) containing 0.5% charcoal-stripped FBS, estradiol-17β (E2, 10 nM), and progesterone (P4, 1 μM) and incubated for 72h to induce decidulization.

treatment_protocol: mESCs were cultured with administration of E2 and P4 in the presence or absence of ATRA (10 μM) for 72h.

value: Kunming white (KM) strain

tag: age

value: 6-8 weeks after birth

tag: tissue

value: uterus

value: endometrial stroma cells

tag: passage


title: Adult male, head, rep 4

city: St Lucia

first: Stephen

last: Chenoweth

state: QLD

address: The School of Biological Sciences, The University of Queensland

country: Australia

institute: The University of Queensland, Australia

description: Sample 176

hyb_protocol: Hybridization was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following the standard NimbleGen operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following the standard NimbleGen operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was normalised via a log (base 2) transformation. Summarisation was performed by first taking the mean of replicated probes followed by the median of a probe set.

organism: Drosophila serrata

source_name: adult male, head

label_protocol: Labeling was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following the standard NimbleGen operating protocol. See www.nimblegen.com.

growth_protocol: A panel of 43 wild-derived inbred lines of D. serrata were used for the whole-body samples and a laboratory stock was used to obtain samples. All flies were reared in 10ml vials of a standard yeast medium and maintained at 25°C with a 12 hour day/night cycle. One generation before the collection of flies for RNA extraction, we used a density controlling procedure to minimise possible effects of developmental environment on gene expression. Each line was propagated with a uniform number of parents (5 virgin females with 3 virgin males) that were allowed to mate and lay eggs for 24 hours. Offspring were randomly collected as virgins from three replicate developmental vials per whole-body sample line and 50 replicate developmental vials for the tissue sample laboratory stock and aged for three days in same-sex groups of 5 flies. Two replicate pools of 30 flies per line per sex and four replicate pools of 100 flies were collected without the use of CO2 anaesthesia and snap frozen in liquid nitrogen for the whole-body and tissue samples, respectively.

extract_protocol: Each whole-body pool was homogenised in Trizol® and immediately stored at -80 degrees Celcius. During tissue disection, flies were suspended in RNALater® to inhibit RNA degradation, pools of 100 tissue disects were stored at -80 degrees Celsius. RNA extraction of the whole-body samples was performed by using the Trizol® procedure followed by RNA isolation using RNeasy minikits®. RNA extraction of the tissue samples was identical to that of the whole-body samples except that the Trizol® was added to 10µl of RNA Later®.

tag: line/stock

value: stock

tag: Sex

value: male

value: head


title: 231.ZKD4-TGF-β-R

description: Replicate of 231.ZKD4-TGF-β


title: 231.ZKD4


title: Stable transfectant overexpressing TSC2 clone P technical replicate 1

description: Biological replicate 1 of 2. Technical replicate 1 of 2. Stable transfectant clone generated in KB cells overexpressing pcDNA3.1(+)/TSC2. Control Stable transfectant clone generated in KB cells overexpressing pcDNA3.1(+).


title: 231.Scr


title: 231.Scr-TGF-β


title: 231.ZKD5


title: 231.ZKD5-TGF-β


title: 231.ZKD5-TGF-β-R

description: Replicate of 231.ZKD5-TGF-β


title: 231.Scr-R

description: Replicate of 231.Scr


title: mESCs treated with E2 and P4 in the absence of ATRA

value: female

tag: strain


title: Adult male, abdomen, rep 4

description: Sample 172

source_name: adult male, abdomen

value: abdomen


title: Adult female, abdomen, rep 4

description: Sample 174

source_name: adult female, abdomen


title: Adult male, testes, rep 3

description: Sample 160

source_name: adult male, testes

value: testes


title: Adult female, ovaries, rep 3

description: Sample 173

source_name: adult female, ovaries

value: ovaries


title: Caco2_HIF2A_3

city: Aurora

first: Louise

last: Glover

state: CO

institute: University Colorado Anschutz Medical Campus

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Standard NimbleGen protocol.

data_processing: The raw data from the arrays were analyzed as follows: the log2 ratio (enriched-Cy5/total input-Cy3) was calculated for each probe and data were then smoothed by averaging across a sliding window of 3 neighboring probes shifting 1 probe at a time, minimizing noise from single probes. The median and standard deviation were calculated from the smoothed ratios for each sample. The median was subtracted from each ratio and divided by the standard deviation to center and normalize the data from each array. To summarize the enrichment for an entire promoter, the top 4 probe values were averaged for a given promoter region to approximate the 75th percentile value.

source_name: Caco-2 cell extract immunoprecipitated with anti-HIF-2a antibody

label_protocol: Standard NimbleGen protocol.

growth_protocol: Caco-2 cells (5 x 10^6) were plated in several 150mm plates and grown to confluency.

extract_protocol: ChIP assays were performed essentially as described in http://www.millipore.com/techpublications/tech1/mcproto407.

treatment_protocol: Cells were cultured under hypoxic (1% O2) conditions for 6 hours, then crosslinked with 1% formaldehyde for 10min at 4C.

tag: cell line

tag: chip antibody

value: anti-HIF-2a (Novus Biologicals, cat# NB100-122, lot # AN)

source_name: Caco-2 cell extract not immunoprecipitated (input)

tag: antibody


title: Caco2_HIF1A_3

source_name: Caco-2 cell extract immunoprecipitated with anti-HIF-1a antibody

value: anti-HIF-1a (Novus Biologicals, cat # NB100-134, lot # D2)


title: Caco2_HIF1A_2


title: Adult male, abdomen, rep 3

description: Sample 168


title: Caco2_HIF1A_1


title: Adult male, thorax, rep 3

description: Sample 161

source_name: adult male, thorax

value: thorax


title: Caco2_HIF2A_2


title: Adult male, accessory glands, rep 3

description: Sample 164

source_name: adult male, accessory glands

value: accessory glands


title: Adult male, head, rep 3

description: Sample 165


title: Adult female, head, rep 4

description: Sample 169

source_name: adult female, head


title: Adult male, testes, rep 4

description: Sample 175


title: Adult female, thorax, rep 2

description: Sample 166

source_name: adult female, thorax


title: Caco2_HIF2A_1


title: Adult female, head, rep 3

description: Sample 159


title: Adult female, thorax, rep 4

description: Sample 171


title: Adult male, accessory glands, rep 4

description: Sample 167


title: Adult male, thorax, rep 4

description: Sample 170


title: Adult female, abdomen, rep 3

description: Sample 158


title: Adult female, ovaries, rep 2

description: Sample 162


title: Adult female, abdomen, rep 2

description: Sample 157


title: Adult male, accessory glands, rep 2

description: Sample 163


title: Adult male, accessory glands, rep 1

description: Sample 152


title: Adult male, abdomen, rep 1

description: Sample 149


title: M. tuberculosis-Acid-NO treated

city: Amherst

first: Andrea

last: Cossu

state: MA

address: 102 Holdsworth way

department: Department of Food Science

institute: University of Massachusetts, Amherst

description: Technical (spot) replicates 1 to 5. Mycobacterium tuberculosis, Acid-NO treated.

hyb_protocol: Hybridization was performed following the Recommended Sample Preparation and Hybridization Protocol drawn-up by the MYcroarrays® Company (Biodiscovery LLC) with some modifications. 220µl of hybridization solution (66µl of 20X SSPE (3M NaCl, 20mM EDTA, 118.2mM NaH2PO4, 81.8mM Na2HPO4), 10% formamide, 0.01mg/ml BSA, 0.01% Tween-20, 1mM DTT, 1% manufacturer control oligos, 10µg of each target coupled-aRNA, RNAse-free water to final volume) was prepared and pre-warmed at 56°C. Hybridizations were carried out in a water bath at 55°C for 18h with OneArray Sealed Hybridization Chambers (PhalanxBio Inc., Palo Alto, CA, USA). After incubation, slides were washed twice with SSPE 1X- 0.1mM DTT for 2 min followed by a 30 sec final wash with 0.25 X SSPE – 0.1mM DTT, dried with air-spray and immediately scanned.

scan_protocol: Scans were carried out with the GenePix AXON 4200A instrument (Axon Instruments) at 5-um resolution with full dynamic range of signal intensities at 1 – 65.000 in two-colour red/green mode (635nm and 532 nm filters).

data_processing:
The intensities of the two dyes for each spot were quantified using the GenePix 6.0 Software and calculated as the mean of median intensity of each replicate spot for each gene. Total array intensity was used to normalize spot signal intensities with the ratio-mean based algorithm option. Subtraction of local feature background median was achieved as default. Negative corrected intensities were set to 10.
A change of 2-fold in the intensities with a p-value < 0.05 was considered significant for a differential gene expression. Data were transformed in normalized log2 ratio (Alexa Fluor dye 555/647) representing MTB-exp/MTBk-.

label: Alexa Fluor 555

organism: Mycobacterium tuberculosis H37Rv

source_name: M. tuberculosis acid-NO treated

label_protocol: Forty µg samples of amplified RNA (aRNA) were labelled with either Alexa Fluor dye 647 or 555  purchased from Invitrogen, USA, following the manufacturer's protocol. Purification of coupled aRNA was performed by the RNeasy purification system (Qiagen) and incorporation of dye was evaluated using the Nanodrop spectrophotometer. Before hybridization, coupled aRNA was fragmented using the RNA fragmentation reagents (Ambion, Inc) following the manufacturer's protocol.

growth_protocol: MTB H37Rv (ATCC 25618) was cultured in Middlebrook 7H9 medium (Sigma-Aldrich, MO, USA) supplemented with  0.2% glycerol (Sigma-Aldrich, MO, USA), 0.05% Tween 80 (Sigma-Aldrich, MO, USA) and 10% v/v albumin dextrose catalase (ADC, Sigma-Aldrich, MO, USA) in 25 cm2 vented tissue culture flasks (T25) positioned up-right at 37°C before stress treatment.

extract_protocol: Total RNA extracted with the RiboPure-Bacteria Kit (Ambion, Inc). Mycobacterial cells were re-suspended in 350µl of RNAwiz solution and transferred to a 0.5ml RNAse-free skirted screw-cap microcentrifuge tube containing 250µl of 0.1mm ice-cold Zirconia Beads. Tubes were immediately processed in the RiboLyser RNA Lysing Machine (RiboLyser FP120-HY-230, Hybaid) for 2 cycles (30s at speed 6.5 with 1 min of cooling interval between each bead beating step). Remaining steps were performed according to the manufacturer’s instructions. All RNA samples were treated with Dnase I (Ambion, Inc)  and  purified by RNeasy column (Qiagen). RNA yield and purity was evaluated with the Nanodrop spectrophotometer (NanoDrop1000, Thermo Scientific) and RNA quality was examined by Denaturing Gel Electrophoresis. We carried out three independent experiments on three different flasks. Good quality RNA samples obtained from each pellet were then pooled together and used for microarray experiments to get an average of three separate experiments. mRNA was obtained by using the MICROBExpress Bacterial mRNA Purification Kit (Ambion) and was lineary amplified bu using the MessageAmp II Bacterial Kit (Ambion, Inc).

treatment_protocol: Mid-log-phase cells were treated with a 7H9/ADC/Tw80 buffered pH 5.3 medium with a final concentration of 5 mM of sodium nitrite (NaNO2) (Sigma) and exposed to the stress for 3 hours at 37°C. Cells were harvested by centrifugation at 5800 x g for 15min at 4°C and re-suspended in RNAlater solution (Sigma). Pellets were then incubated overnight at 4°C and stored at -80°C until RNA extraction.

value: acid-nitrosative multi-stress

label: Alexa Fluor 647

source_name: M. tuberculosis control untreated

growth_protocol: MTB H37Rv (ATCC 25618) was cultured in Middlebrook 7H9 medium (Sigma-Aldrich, MO, USA) supplemented with  0.2% glycerol (Sigma-Aldrich, MO, USA), 0.05% Tween 80 (Sigma-Aldrich, MO, USA) and 10% v/v albumin dextrose catalase (ADC, Sigma-Aldrich, MO, USA) in 25 cm2 vented tissue culture flasks (T25) positioned up-right at 37°C until mid-log phase.

treatment_protocol: Mid-log-phase cells were grown in 7H9/ADC/Tw80 medium for 3h at 37°C. Cells were harvested by centrifugation at 5800 x g for 15min at 4°C and re-suspended in RNAlater solution (Sigma). Pellets were then incubated overnight at 4°C and stored at -80°C until RNA extraction.


title: Adult male, abdomen, rep 2

description: Sample 155


title: Adult male, testes, rep 2

description: Sample 156


title: Adult male, head, rep 2

description: Sample 148


title: Adult male, testes, rep 1

description: Sample 147


title: Adult female, abdomen, rep 1

description: Sample 153


title: Osteosarcoma stem cells, biological rep4

city: Edinburgh

first: Lisa

last: Pang

address: Easter Bush Estate

country: United Kingdom

institute: Roslin Institute

description:
CSC_04
Gene expression data from osteosarcoma stem cells.

hyb_protocol: 5 μg of cRNA was hybridised for 16 hr at 45oC to the Affymetrix GeneChip® Canine Genome 2.0 Array by ARK-Genomics (Edinburgh).

scan_protocol: GeneChips were scanned using the Affymetrix™ GeneTitan (ARK-Genomics (Edinburgh)).

data_processing: GC-RMA data was generated by Partek® Genomics Suite™. The data was analysed with Partek® Genomics Suite™ (ARK-Genomics (Edinburgh)).

organism: Canis lupus familiaris

source_name: Canine osteosarcoma stem cells isolated from the primary tumour cell line KTOSA5

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetix IVT express protocol (revision 1 of the manual, 2008) by ARK-Genomics (Edinburgh).

growth_protocol: The KTOSA5 cell line was derived from an osteosarcoma affecting the right hind leg of an 8-year-old, chemotherapy naive, female, entire Rottweiler. The cells were grown in DMEM at 5% CO2 at 37 oC. Canine mesenchymal stem cells (MSC) were derived from the bone marrow of 21 recently euthanised dogs of mixed breeds. All samples were taken with the owners consent and approval of the Local Institutional Animal Care and Ethics Committee. MSCs were grown in DMEM containing Glutamax-I at 5% CO2 at 37 oC.

treatment_protocol: Osteosarcoma stem cells were derived from the KTOSA5 cell line by plating as single cells in serum-free conditional medium which contained William's E Medium with GlutaMAX supplemented with putrescine (100 μM), sodium selenite (30 nM), transferring (25 μg/ml), insulin (20 μg/ml), human recombinant bFGF (10 ng/ml) and EGF (10 ng/ml).

tag: breed

value: Rottweiler

value: osteosarcoma stem cells

tag: disease state

value: cancerous


title: Adherent osteosarcoma cells, biological rep3

description:
ADH_03
Gene expression data from osteosarcoma adherent cells.

source_name: Canine adherent osteosarcoma cells, a primary cell line KTOSA5

value: adherent osteosarcoma cells


title: Adult female, thorax, rep 1

description: Sample 154


title: Adult male, head, rep 1

description: Sample 144