title: single cell from posterior epiblast(Pre-streak), biological rep6

description: Gene expression data from single posterior epiblast cells (pre-streak)

source_name: Single cell from posterior epiblast at pre-streak stage(Oct4+, T+)


title: single cell from posterior epiblast(Pre-streak), biological rep5

status: Public on Aug 22 2008

type: RNA

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

country: Japan

institute: Nara Medical University

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software.  Data were normalized together with the default settings.  The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.  The absolute calls were calculated using MAS5.0 algorism with dCHIP default settings.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared from the PCR-amplified double-starnded cDNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

growth_protocol: Mice were sacrified and embryos were collected in Dulbecco’s modified Eagle Medium supplemented with 0.5% BSA (DMEM/BSA) at different days post coitum (dpc).  Noon of the day when the vaginal plugs of the mated females were identified was scored as 0.5 dpc.

extract_protocol: Single cell was lysed by adding to the tube containing cell lysis buffer, and the clude lysate was used for cDNA synthesis and amplification without purification.

treatment_protocol: Embryos were dissected in DMEM/BSA.  Embryonic fragments containing primordial germ cells (PGCs) or PGC precursors were cut out by glass needle and incubated with 0.05% trypsin/0.5 mM EDTA for 7 min, followed by dissociation into single cells by mouth pipette.  Dissociated single cells were randomly picked up for single cell cDNA amplification.

tag: Strain

tag: Genotype

value: Wild type

tag: cDNA amplified from single cellular RNA


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep4

description: Gene expression data from single lineage-restricted PGC precursors (Late-Streak/0-Bud stage)

source_name: single cell from lineage-restricted PGC precursors at Late-Streak/0-Bud stage(Blimp1+, Oct4+)


title: single cell from posterior epiblast(Pre-streak), biological rep3


title: single cell from posterior epiblast(Pre-streak), biological rep8


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep3


title: single cell from PGCs (Early-Head Fold stage), biological rep7

description: Gene expression data from single PGCs (Early head fold stage)

source_name: single cell from primordial germ cell (PGCs) at Early head fold stage(Blimp1+, stella+)


title: single cell from posterior epiblast(Pre-streak), biological rep7


title: Endometrium, postmenopausal, tibolone, 6

status: Public on Aug 21 2008

city: Rotterdam

first: Leen

middle: J

last: Blok

address: Dr Molewaterplein 40

department: Obstetrics & Gynecology

country: Netherlands

institute: Erasmus University Medical Center

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 6.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG 133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning procedures were carried out as described by Affymetrix, Santa Clara.

data_processing: The data were analyzed with RMAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T

organism: Homo sapiens

source_name: Endometrium from tibolone-treated postmenopausal woman

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

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

tag: Postmenopausal female. Tibolone treated. Patient 6.


title: single cell from posterior epiblast(Pre-streak), biological rep2


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep2


title: single cell from posterior epiblast(Pre-streak), biological rep4


title: Endometrium, postmenopausal, tibolone, 32

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 32.

tag: Postmenopausal female. Tibolone treated. Patient 32.


title: Endometrium, postmenopausal, tibolone, 30

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 30.

tag: Postmenopausal female. Tibolone treated. Patient 30.


title: Endometrium, postmenopausal, tibolone, 16

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 16.

tag: Postmenopausal female. Tibolone treated. Patient 16.


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep5


title: Endometrium, postmenopausal, tibolone, 26

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 26.

tag: Postmenopausal female. Tibolone treated. Patient 26.


title: single cell from PGCs (Early-Head Fold stage), biological rep2


title: Endometrium, postmenopausal, tibolone, 1

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 1.

tag: Postmenopausal female. Tibolone treated. Patient 1.


title: single cell from posterior epiblast(Pre-streak), biological rep1


title: Endometrium, postmenopausal, tibolone, 6-2

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 6, replicate (patient 6 has been arrayed twice).

tag: Replicate


title: Endometrium, postmenopausal, estradiol + MPA, 25

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol + medroxyprogesterone acetate treated. Patient 25.

source_name: Endometrium from estradiol- and MPA-treated postmenopausal woman

tag: Postmenopausal female. Estradiol + MPA treated. Patient 25.


title: Endometrium, postmenopausal, tibolone, 11

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 11.

tag: Postmenopausal female. Tibolone treated. Patient 11.


title: Endometrium, postmenopausal, estradiol + MPA, 29

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol + medroxyprogesterone acetate treated. Patient 29.

tag: Postmenopausal female. Estradiol + MPA treated. Patient 29.


title: Senescent cells, rep1

city: Cold Spring Harbor

first: Valery

last: Krizhanovsky

state: NY

address: 1 Bungtown Rd

country: USA

institute: Cold Spring harbor Laboratory

description: gene expression data from senescent cells

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000.

data_processing: data was analysed with ArrayAssist (Invitrogen), normalization was performed using GC-RMA algorithm

source_name: Senescent activated hepatic stellate cells

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

extract_protocol: RNAeasy Qiagen kit, according manufacturer instructions.

tag: fibrogenic cells of the liver


title: Growing cells, rep2

description: gene expression data from growing cells

source_name: Growing activated hepatic stellate cells


title: Senescent cells, rep2


title: Growing cells, rep1

description: gene expression data from growing cells


title: Endometrium, postmenopausal, tibolone, 11-2

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 11, replicate (patient 11 has been arrayed twice).


title: Endometrium, postmenopausal, estradiol + MPA, 19

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol + medroxyprogesterone acetate treated. Patient 19.

tag: Postmenopausal female. Estradiol + MPA treated. Patient 19.


title: Endometrium, postmenopausal, estradiol + MPA, 14

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol + medroxyprogesterone acetate treated. Patient 14.

tag: Postmenopausal female. Estradiol + MPA treated. Patient 14.


title: Endometrium, postmenopausal, estradiol, 36

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 36.

source_name: Endometrium from estradiol-treated postmenopausal woman

tag: Postmenopausal female. Estradiol treated. Patient 36.


title: Endometrium, postmenopausal, estradiol, 3

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 3.

tag: Postmenopausal female. Estradiol treated. Patient 3.


title: Endometrium, postmenopausal, estradiol, 8

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 8.

tag: Postmenopausal female. Estradiol treated. Patient 8.


title: Endometrium, postmenopausal, estradiol, 24

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 24.

tag: Postmenopausal female. Estradiol treated. Patient 24.


title: Endometrium, postmenopausal, estradiol + MPA, 9

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol + medroxyprogesterone acetate treated. Patient 9.

tag: Postmenopausal female. Estradiol + MPA treated. Patient 9.


title: Endometrium, postmenopausal, control, 37

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 37.

source_name: Endometrium from untreated postmenopausal woman

tag: Postmenopausal female. Untreated control. nr 37.


title: Endometrium, postmenopausal, control, 38

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 38.

tag: Postmenopausal female. Untreated control. nr 38.


title: Endometrium, postmenopausal, control, 22

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 22.

tag: Postmenopausal female. Untreated control. nr 22.


title: Endometrium, postmenopausal, estradiol, 13

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 13.

tag: Postmenopausal female. Estradiol treated. Patient 13.


title: Endometrium, postmenopausal, estradiol, 28

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 28.

tag: Postmenopausal female. Estradiol treated. Patient 28.


title: Endometrium, postmenopausal, control, 21

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 21.

tag: Postmenopausal female. Untreated control. nr 21.


title: Endometrium, postmenopausal, control, 12

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 12.

tag: Postmenopausal female. Untreated control. nr 12.


title: Endometrium, postmenopausal, control, 17

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 17.

tag: Postmenopausal female. Untreated control. nr 17.


title: Zip_Zn_rep1

city: Sydney

first: Liz

last: Musgrove

state: NSW

address: 384 Victoria Street, Darlinghurst

department: Cancer Research Program

country: Australia

institute: Garvan Institute of Medical Research

description: Clonal MCF-7 cells inducibly expressing c-Zip pretreated with ICI 182780 then treated with zinc

hyb_protocol: Probes were hybridised at 45 C for 16 h and then washed and doubly stained using the GeneChip 400 fluidics station according to the manufacturer's instructions

scan_protocol: Hewlett-Packard GeneArray Scanner (Affymetrix- Millennium Science, Surrey Hill, VIC, Australia)

data_processing: Signals obtained were analysed with Microarray Suite expression algorithm (version 5.0.1; Affymetrix)

source_name: Clonal MCF-7 ∆MT-Zip, ICI 182780 pretreatment then treated with Zn

label_protocol: Fluorescent cRNA probes for Affymetrix oligonucleotide microarray analysis were generated using the One-cycle Target labelling and Control Reagent package (Millennium Science, Box Hill, Vic Australia) according to the manufacturer's instructions

extract_protocol: Total RNA from three independent experiments was isolated from cells using the RNeasy mini kit (Qiagen Pty Ltd, Clifton Hill, Vic Australia) following the manufacturer's instructions.

treatment_protocol: Exponentially proliferating cells were growth arrested by pretreatment for 48 h with 10nM steroidal antiestrogen ICI 182780 and then treated with either 100nM E2 or 75 uM Zn (as ZnSO4). Vehicle controls for E2 or Zn were absolute ethanol and water respectively.

tag: Clonal derivative of MCF-7 transfected with inducible vector expressing c-Zip (p∆MT-Zip)


title: Zip_Zn_rep3

tag: Clonal derivative of MCF-7 transfected with inducible vector expressing c-ZIp (p∆MT-Zip)


title: Endometrium, postmenopausal, control, 12-2

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 12, replicate (control 12 has been arrayed twice).

tag: Replicate


title: Endometrium, postmenopausal, estradiol + MPA, 4

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol + medroxyprogesterone acetate treated. Patient 4.

tag: Postmenopausal female. Estradiol + MPA treated. Patient 4.


title: Endometrium, postmenopausal, estradiol, 23

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 23.

tag: Postmenopausal female. Estradiol treated. Patient 23.


title: Vector_Zn_rep3

description: Clonal MCF-7 cells (empty vector trasnsfected) pretreated with ICI 182780 then treated with zinc

source_name: Clonal MCF-7 ∆MT, ICI 182780 pretreatment then treated with Zn

tag: Clonal derivative of MCF-7 transfected with empty vector (p∆MT)


title: Myc_Zn_rep1

description: Clonal MCF-7 cells inducibly expressing c-Myc pretreated with ICI 182780 then treated with zinc

source_name: Clonal MCF-7 ∆MT-Myc, ICI 182780 pretreatment then treated with Zn

tag: Clonal derivative of MCF-7 transfected with inducible vector expressing c-Myc (p∆MT-Myc)


title: Endometrium, postmenopausal, control, 2

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 2.

tag: Postmenopausal female. Untreated control. nr 2.


title: Zip_Zn_rep2


title: Myc_Zn_rep2


title: Myc_Zn_rep3


title: Vector_Zn_rep2


title: Vector_Zn_rep1


title: MCF7_E2_rep2

description: MCF-7 cells pretreated with ICI 182780 then treated with estrogen

source_name: MCF-7, ICI 182780 pretreatment then treated with E2

tag: MCF-7 human breast cancer cells


title: MCF7_E2_rep3


title: MCF7_EtOH_rep3

description: MCF-7 cells pretreated with ICI 182780 then treated with ethanol vehicle

source_name: MCF-7, ICI 182780 pretreatment then treated with ethanol vehicle


title: MCF7_EtOH_rep2


title: MCF7_EtOH_rep1


title: ePuro

city: Parkville

first: Jane

last: Visvader

state: Vic

address: 1G Royal Pde

department: Victorian Breast Cancer Research Consortium

institute: Walter and Eliza Hall Institute of Medical Research

description: Arrays were processed at the Australian Genome Research Facility (AGRF).

hyb_protocol: Affymetrix

scan_protocol: Affymetrix scanner 3000 7G

data_processing:
Statistical analysis was undertaken using R (www.r-project.org) and Bioconductor
(www.bioconductor.org) software. The expression values were checked for quality and consistency using statistical quality assessment and were normalized using the RMA algorithm. Control probes and a small number (147) of probe-sets showing no variability between arrays were filtered out before subsequent analysis. For the differential expression analysis, the Deaf-1 and control samples for each clone were treated as paired observations, to reflect the biological variation between clones. Statistical significance was assessed using empirical Bayes moderated paired t-tests as implemented in the limma package within the Bioconductor software.

source_name: ePuro

label_protocol: Affymetrix IVT Labelling Kit

extract_protocol:
Total RNA was harvested from two independent clones (C1 and E1) infected with either control or Deaf-1-expressing retrovirus.  RNA was purified using using the QIAGEN RNeasy Kit (Qiagen, Hilden, Germany)
and quality assessed by spectrophotometry and gel electrophoresis before
hybridisation to Affymetrix slides.

tag: E1 clone infected with control retrovirus.


title: imr-32,cdk4 siRNA,t=48,3

status: Public on Aug 20 2008

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

description: Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix

label: Biotin

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling 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.

growth_protocol: IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).

tag: Neuroblastoma cell line


title: imr-32,gfp siRNA, t=48, 4


title: imr-32,cdk4 siRNA,t=48, 2


title: cPuro

source_name: cPuro

tag: C1 clone infected with control retrovirus.


title: imr-32,gfp siRNA,t=48,3


title: imr-32,ccnd1 siRNA,t=48,3


title: NOD RIP-Aire27 islet rep2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Gender: male Age: 3 weeks Isolation: gradient and handpicking Strain: NOD

hyb_protocol: BioArray High Yield RNA transcript labeling T7 kit (Enzo Life Sciences)

scan_protocol: Standard Affymetrix protocol

data_processing: RMA

source_name: NOD islets, RIP-Aire27 transgenic

label_protocol: biotin

extract_protocol: RNA by LiCl method

tag: RIP-Aire transgenic


title: imr-32, cdk4 siRNA, t=48, 4


title: NHBE siLam_rep2

city: Bristol

first: Harry

last: Mellor

state: Avon

address: School of Medical Sciences, University Walk

department: Department of Biochemistry

country: United Kingdom

institute: University of Bristol

description: Data is part of NHBE siRhoBTB2 experiment.

hyb_protocol: Standard Affymetrix protocol

data_processing: GC-RMA algorithm

source_name: NHBE lung cells, siLam

label_protocol: cDNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen)

growth_protocol: Cells were maintained in NHBE media supplemented with the NHBE bulletkit (Lonza).

extract_protocol: Total RNA was extracted using the RNeasy kit from QIAGEN.

treatment_protocol: Cells were treated with siRNA oligonucleotide against RhoBTB2 for 72 hours. siRNA oligonucleotide was introduced into the cells using GeneFECTOR (Venn Nova).

tag: Primary cell culture. 27 year old male.


title: NHBE siRhoBTB2.1_rep3

source_name: NHBE lung cells, siRhoBTB2.1


title: NHBE siRhoBTB2.2_rep2

source_name: NHBE lung cells, siRhoBTB2.2


title: imr-32,gfp siRNA,T=48,2


title: imr-32,ccnd1siRNA, t=48, 4


title: NHBE siCYC_rep3

source_name: NHBE lung cells, siCyc.

tag: Primary cell culture 27 year old male.


title: imr-32,ccnd1 siRNA,T=48, 1


title: IMR-32 ,T=0, 1


title: MCF7_E2_rep1


title: imr-32,GFP,T=48, 1


title: eDeaf

source_name: eDeaf

tag: E1 clone infected with Deaf-1-expressing retrovirus.


title: imr-32,t=0,3


title: imr-32,t=0,2


title: NOD RIP-Aire27 islet rep1


title: NOD non-transgenic islet rep3

source_name: NOD islets, non-transgenic

tag: non-transgenic


title: NOD RIP-Aire27 islet rep3


title: NOD non-transgenic islet rep2


title: NOD non-transgenic islet rep1


title: NHBE siRhoBTB2.2


title: nasopharyngeal carcinoma, specimen T30

status: Public on Aug 16 2008

city: Madison

first: Paul

last: Ahlquist

state: WI

address: 1525 Linden Dr.

department: Oncology

institute: University of Wisconsin-Madison

description: Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.

hyb_protocol: Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.

scan_protocol: Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.

data_processing: Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.

source_name: nasopharynx

label_protocol: Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).

growth_protocol: Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.

extract_protocol: RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.

treatment_protocol: Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.

tag: nasopharyngeal carcinoma

tag: WHO histology

value: IIA

tag: Tumor Stage


title: Endometrium, postmenopausal, control, 33

description: Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 33.

tag: Postmenopausal female. Untreated control. nr 33.


title: nasopharyngeal carcinoma, specimen T28


title: nasopharyngeal carcinoma, specimen T26

value: IIB


title: nasopharyngeal carcinoma, specimen T27


title: nasopharyngeal carcinoma, specimen T29


title: nasopharyngeal carcinoma, specimen T21


title: nasopharyngeal carcinoma, specimen T25


title: nasopharyngeal carcinoma, specimen T16


title: NHBE siRhoBTB2.1_rep1

source_name: NHBE siRhoBTB2.1

tag: Primary lung cell line.

tag: 27 year old male.


title: nasopharyngeal carcinoma, specimen T31


title: nasopharyngeal carcinoma, specimen T14


title: nasopharyngeal carcinoma, specimen T20


title: nasopharyngeal carcinoma, specimen T19


title: nasopharyngeal carcinoma, specimen T22


title: nasopharyngeal carcinoma, specimen T18


title: NHBE siCyc 1

treatment_protocol: Cells were treated with siRNA oligonucleotide against Cyclophilin B for 72 hours. siRNA oligonucleotide was introduced into the cells using GeneFECTOR (Venn Nova).

tag: Primary cell culture.


title: nasopharyngeal carcinoma, specimen T24


title: NHBE siCyc_rep2

source_name: NHBE lung cells, siCyc


title: nasopharyngeal carcinoma, specimen T13


title: nasopharyngeal carcinoma, specimen T12


title: nasopharyngeal carcinoma, specimen T23


title: NHBE siLam.1


title: nasopharyngeal carcinoma, specimen T11


title: nasopharyngeal carcinoma, specimen T10


title: nasopharyngeal carcinoma, specimen T17


title: nasopharyngeal carcinoma, specimen T8


title: nasopharyngeal carcinoma, specimen T9


title: nasopharyngeal carcinoma, specimen T15


title: nasopharyngeal carcinoma, specimen T3


title: nasopharyngeal carcinoma, specimen T5


title: nasopharyngeal carcinoma, specimen T6


title: normal nasopharyngeal tissue, specimen N10

tag: normal


title: nasopharyngeal carcinoma, specimen T1


title: nasopharyngeal carcinoma, specimen T7


title: nasopharyngeal carcinoma, specimen T4


title: normal nasopharyngeal tissue, specimen N1

tag: Biopsy Negative Control


title: normal nasopharyngeal tissue, specimen N9


title: normal nasopharyngeal tissue, specimen N3


title: normal nasopharyngeal tissue, specimen N6

tag: Adjacent pair of T20


title: normal nasopharyngeal tissue, specimen N8

tag: Adjacent pair of T10


title: normal nasopharyngeal tissue, specimen N5

tag: Adjacent pair of T18


title: normal nasopharyngeal tissue, specimen N2


title: nasopharyngeal carcinoma, specimen T2


title: normal nasopharyngeal tissue, specimen N4


title: cDeaf

source_name: cDeaf

label_protocol: Affymetrix IVT Labeling Kit

tag: C1 clone infected with Deaf-1-expressing retrovirus.


title: normal nasopharyngeal tissue, specimen N7

tag: Adjacent pair of T7


title: CD8 memory T cell_Expansion_rep3

status: Public on Aug 15 2008

city: Denver

first: Eric

last: Clambey

state: CO

address: 1400 Jackson Street, Goodman Bldg, Rm K519

department: Immunology

institute: National Jewish Research & Medical Center

description: Expansion_rep4 belongs to the integrin a4 LOW subclass of clonal expansions.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix (GeneChip) Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000(type M10).

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software version 1 (MAS 5 statistical algorithm) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: CD8 clonal expansion

label_protocol: Amplified RNA samples were labeled with biotin using the Affymetrix GeneChip IVT labeling kit (Santa Clara, California).

growth_protocol: Cells were not subjected to any in vitro growth conditions.  Cells were directly frozen following their purification from mice.

extract_protocol: Total RNA was purified from all samples in parallel using the PicoPure RNA Isolation Kit (Arcturus, Mountain View, California).  To obtain enough RNA for microarray analysis, all samples were subjected to double RNA amplification using the RiboAmp OA RNA amplification kit (Arcturus).

treatment_protocol: CD8 memory T cells were purified by flow cytometric sorting directly from aged mice.  In order to purify these cells, samples were stained with a variety of fluorescently labelled antibodies that bound to cell surface molecules and sorted by use of a flow cytometer.  Once cells were purified, they were immediately frozen on crushed dry ice and stored at -80 C until time of RNA extraction.

tag: Mouse strain

value: C57BL/10SnJ; Gender:Female; Age:23 months; Tissue:Spleen and lymph nodes; Purified by protein expression:CD8+ CD122+ TCR Vb8.3+ MHC II-; Cell Purity:96%


title: CD8 memory T cell_Expansion_rep2

description: Expansion_rep2 belongs to the integrin a4 LOW subclass of clonal expansions.

value: C57BL/10SnJ; Gender:Female; Age:20 months; Tissue:Spleen and lymph nodes; Purified by protein expression:CD8+ CD122+ TCR Vb8.1/8.2+ MHC II-; Cell Purity:95%


title: CD8 memory T cell_Expansion_rep1

description: Expansion_rep1 belongs to the integrin a4 high subclass of clonal expansions.  This type of clonal expansion is very different than the integrin a4 low type of clonal expansion (represented by samples 2, 4, and 5).

value: C57BL/10SnJ; Gender:Female; Age:20 months; Tissue:Spleen and lymph nodes; Purified by protein expression:CD8+ CD122+ TCR Vb3+ MHC II-; Cell Purity:91%


title: CD8 memory T cell_PolyclonalAged_rep1

description: CD8 memory T cell_PolyclonalAged_rep1

source_name: Polyclonal, aged CD8 memory T cells

value: C57BL/10SnJ; Gender:Female; Age:20 months; Tissue:Spleen and lymph nodes; Purified by protein expression:CD8+ CD122+ TCR Vb3- MHC II-; Cell Purity:97%


title: CD8 memory T cell_PolyclonalAged_rep4

description: CD8 memory T cell_PolyclonalAged_rep4

value: B10.BR; Gender:Female; Age:23 months; Tissue:Spleen and lymph nodes; Purified by protein expression:CD8+ CD122+ TCR Vb14- MHC II-; Cell Purity:97%


title: CD8 memory T cell_PolyclonalAged_rep3

description: CD8 memory T cell_PolyclonalAged_rep3

value: C57BL/10SnJ; Gender:Female; Age:23 months; Tissue:Spleen and lymph nodes; Purified by protein expression:CD8+ CD122+ TCR Vb8.3- MHC II-; Cell Purity:66%


title: CD8 memory T cell_PolyclonalAged_rep2

description: CD8 memory T cell_PolyclonalAged_rep2

value: C57BL/10SnJ; Gender:Female; Age:20 months; Tissue:Spleen and lymph nodes; Purified by protein expression:CD8+ CD122+ TCR Vb8.1/8.2- MHC II-; Cell Purity:75%


title: NHBE siDBC2.1_rep2

source_name: NHBE lung cells, siDBC2.1

tag: Primary cell culture. 27 year old male.


title: CD8 memory T cell_Expansion_rep4

description: Expansion_rep5 belongs to the integrin a4 LOW subclass of clonal expansions.

value: B10.BR; Gender:Female; Age:23 months; Tissue:Spleen and lymph nodes; Purified by protein expression:CD8+ CD122+ TCR Vb14+ MHC II-; Cell Purity:98%


title: Uninfected D5_UT

status: Public on Aug 13 2008

city: Columbus

first: Jonathan

middle: P

last: Butchar

state: OH

address: 400 W. 12th Avenue

department: Internal Medicine

institute: The Ohio State University

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: R 2.7.1 and BioConductor 2.2.  gcrma package used to normalize and calculate expression values

source_name: peripheral blood monocytes

label_protocol: Affymetrix standard

growth_protocol: RPMI-1640 with 10% FBS

extract_protocol: Trizol

treatment_protocol: 100 MOI of F. novicida or Schu S4 for 24 hours

tag: healthy adult


title: Uninfected D6_UT


title: Schu S4 infected D6_S4


title: Schu S4 infected D7_S4


title: Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 1

status: Public on Aug 12 2008

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California, Davis

description: General seed coat collected from seeds containing linear-cotyledon embryos 175 (+/- 11) microns in length  as determined by median section using the LEICA LMD6000 system for microdissection.

hyb_protocol: Following fragmentation, five micrograms of cDNA was hybridized for 18 hr at 45°C with the GeneChip ATH1 Arabidopsis Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating system 1.4 (GCOS) using default analysis settings and global scaling as a normalization method. The mean target intensity of each array was set to 500.

organism: Arabidopsis thaliana

source_name: Arabidopsis linear-cotyledon stage general seed coat captured by LCM

label_protocol: 2 to 5 ng of total RNA was amplified using the WT-Ovation Pico RNA Amplification System (NuGEN, San Carlos, CA). cDNAs were fragmented and labeled with NuGEN FL-Ovation™ cDNA Biotin Module V2.

growth_protocol: Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20°C and 50% - 70% relative humidity.

extract_protocol: Total RNA was extracted using the RNaqueous Micro-Kit (Ambion, Austin, TX) using a modified protocol incorporating an on-column DNase treatment (Qiagen RNase-Free DNase Set) during column washes.

treatment_protocol: Siliques between 1.6 and 1.9 cm  long containing linear-cotyledon stage seeds were collected from 38-46 day old plants.  Siliques were sub-divided and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin.  Microdissection of compartments was carried out on sections using a Leica LMD6000 system.

tag: Genotype


title: Schu S4 infected D5_S4


title: Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 2

description: Chalazal seed coat collected from seeds containing linear-cotyledon embryos 175 (+/- 11) microns in length  as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis linear-cotyledon stage chalazal seed coat captured by LCM


title: Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2

description: Chalazal endosperm collected from seeds containing linear-cotyledon embryos 175 (+/- 11) microns in length  as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis linear-cotyledon stage chalazal endosperm captured by LCM


title: F. novicida infected D4_FN


title: Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 1

description: Embryo proper collected from seeds containing linear-cotyledon embryos 175 (+/- 11) microns in length  as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis linear-cotyledon stage embryo proper captured by LCM


title: F. novicida infected D3_FN


title: F. novicida infected D2_FN


title: Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 2


title: Uninfected D3_UT


title: F. novicida infected D1_FN


title: Laser capture microdissected (LCM) whole seed sections at the pre-globular stage, biological replicate 2

description: Serial sections of whole seeds collected from seeds containing pre-globular embryo propers of 2 to 8 cells as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis pre-globular stage whole seed sections captured by LCM

treatment_protocol: Siliques between 1.0 and 1.1 cm containing pre-globular stage seeds were collected from 38-46 day old plants.  Siliques were sub-divided and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin.  Microdissection of compartments was carried out on sections using a Leica LMD6000 system.


title: Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 2

description: Cellularized endosperm collected from seeds containing linear-cotyledon embryos 175 (+/- 11) microns in length  as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis linear-cotyledon stage cellularized endosperm captured by LCM


title: Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 2


title: Uninfected D4_UT


title: Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1


title: Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1


title: Uninfected D2_UT


title: Uninfected D1_UT


title: Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 1


title: Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 1

description: Chalazal seed coat collected from seeds containing pre-globular embryo propers of 2 to 8 cells as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis pre-globular stage chalazal seed coat captured by LCM


title: Laser capture microdissected (LCM) whole seed sections at the pre-globular stage, biological replicate 1


title: Laser capture microdissected (LCM) general seed coat at the pre-globular stage, biological replicate 1

description: General seed coat collected from seeds containing pre-globular embryo propers of 2 to 8 cells as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis pre-globular stage general seed coat captured by LCM


title: Laser capture microdissected (LCM) general seed coat at the pre-globular stage, biological replicate 2


title: Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2


title: Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 1

description: cellularized endosperm collected from seeds containing pre-globular embryo propers of 2 to 8 cells as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis pre-globular stage cellularized endosperm captured by LCM


title: Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 2

description: Chalazal endosperm collected from seeds containing pre-globular embryo propers of 2 to 8 cells as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis pre-globular stage chalazal endosperm captured by LCM


title: Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1


title: Laser capture microdissected (LCM) micropylar endospermr at the pre-globular stage, biological replicate 2

description: Micropylar endosperm collected from seeds containing pre-globular embryo propers of 2 to 8 cells as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis pre-globular stage micropylar endosperm captured by LCM


title: Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2

description: Embryo proper collected from seeds containing pre-globular embryo propers of 2 to 8 cells as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis pre-globular stage embryo proper captured by LCM


title: Laser capture microdissected (LCM) micropylar endosperm at the pre-globular stage, biological replicate 1


title: ged1 seedlings, biological rep2

city: Cambridge

first: Mun-Kit

last: Choy

state: Cambridgeshire

address: Box 110, Level 6, ACCI Building, Addenbrooke’s Hospital, Hills Road

department: Division of Cardiovascular Medicine

institute: University of Cambridge

description: Transcript abundance data from Arabidopis ged1 seedlings grown for 5 days in the dark followed by 2 days in the light

hyb_protocol: Following fragmentation, 12.7 ug of cRNA were hybridized for 16 hr on Arabidopsis ATH1 120405 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned by the Medical Research Council (MRC) GeneService at Hinxton Hall, Cambridge, UK.

data_processing: The data were analyzed by the Medical Research Council (MRC) GeneService at Hinxton Hall, Cambridge, UK using global scaling as normalisation method.

source_name: ged1 seedlings, biological rep2

label_protocol: cDNA was synthesised from 6.6 ug total RNA in accordance with the prescribed Affymetrix protocal. Biotinylated cRNA were prepared according to the standard Affymetrix protocol using Enzo BioArray High Yield RNA Transcript Labelling Kit.

growth_protocol: The seeds were spread on 0.7 % (w/v) micro agar containing half-strength Murashige and Skoog medium in a 9-cm petri dish stratified at 4 C in the dark for overnight.

extract_protocol: Concert Plant RNA Reagent (Invitrogen, Paisley, UK) using the manufacturer’s large-scale isolation protocol.

treatment_protocol: After the stratification, the dish was then removed to specified dark (22 C) and light (22 C under a mixture of cool white and GRO-LUX fluorescent lights in 3:2 ratio with average light intensity of 60 mole m-2 s-1 and 16-h diurnal photoperiod) periods.

value: ged1 mutant

tag: Phenotype

value: Pale


title: ged1 seedlings, biological rep3

source_name: ged1 seedlings, biological rep3


title: Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 1


title: Ws seedlings, biological rep2

description: Transcript abundace data from wild-type Arabidopis Ws seedlings grown for 5 days in the dark followed by 2 days in the light

source_name: Ws seedlings, biological rep2

value: Green


title: Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 2


title: Ws seedlings, biological rep3

source_name: Ws seedlings, biological rep3


title: Ws seedlings, biological rep1

source_name: Ws seedlings, biological rep1


title: ged1 seedlings, biological rep1

source_name: ged1 seedlings, biological rep1


title: CA2 Cre Sox17D

status: Public on Aug 11 2008

city: Toronto

first: Cheryle

last: Seguin

state: Ontario

address: 101 College St

country: Canada

institute: The Hospital for Sick Children

description: CA2 Cre Sox17D

hyb_protocol: 15 ug of fragmented cRNA was used to hyb for 17hrs on Affymetrix Human genome U133 Plus 2.0 arrays

scan_protocol: GeneChip Scanner 3000 7G

data_processing: MAS 5.0, All GeneChips were scaled to a median intensity setting of 500 and CEL files normalized across all probe sets

source_name: CA2, SOX17 expressing HESC - clone1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA

growth_protocol: Control, SOX7 O/E and SOX17 O/E HESC were cultured under standard tissue culture conditions on mitotically inactivated mouse embryo fibroblast feeder layers in Knockout DMEM (Gibco) supplemented with 15% Serum Replacement (Gibco), Glutamax (Invitrogen), penicillin/streptomycin (Gibco), 1 mM non-essential amino acids (Gibco), 0.5mM mercaptoethanol, and 10ug/mL recombinant FGF2 (Peprotech).

treatment_protocol: For the establishment of transgenic populations, media was supplemented with Puromycin (Sigma, 80µg/mL) or G418 (Gibco, 100µg/mL). Cultures of 80% confluent cultures were harvested between passages 2 and 4 for microarray analysis.

tag: Cell line established from CA2 HESC using pClip vector


title: CA2 Cre Sox17E

description: CA2 Cre Sox17E

source_name: CA2, SOX17 expressing HESC - clone2


title: CA2 NoCre Sox17E

description: CA2 NoCre Sox17E

source_name: CA2, parental control SOX17 HESC- clone2


title: CA2 NoCre Sox17D

description: CA2 NoCre Sox17D

source_name: CA2, parental control SOX17 HESC- clone1


title: CA1 NoCre Sox7I

description: CA1 NoCre Sox7I

source_name: CA1, parental control SOX7 HESC- clone2

tag: Cell line established from CA1 HESC using pClip vector


title: CA1 NoCre Sox7H

description: CA1 NoCre Sox7H

source_name: CA1, parental control SOX7 HESC- clone1


title: CA1 Cre Sox7I

description: CA1 Cre Sox7I

source_name: CA1, SOX7 expressing HESC - clone2


title: Mouse Wildtype Normal Lymph Node 9

status: Public on Aug 09 2008

city: Singapore

first: Seiichi

last: Mori

state: Singapore

address: Centre for Life Sciences #02-07, 28 Medical Drive

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

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

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

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

source_name: Mouse normal lymph node

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

extract_protocol: Snap-frozen samples in liquid nitrogen were used for extraction.  Total RNA was extracted by Qiagen RNEasy kit according to the manufacturer's instructions.

value: Wildtype

tag: Sampling age


title: Mouse Wildtype Normal Lymph Node 8


title: CA1 Cre Sox7H

description: CA1 Cre Sox7H

source_name: CA1, SOX7 expressing HESC - clone1


title: Mouse Myc-induced lymphoma 137

source_name: Lymphoma from Em-myc transgenic mouse

value: Em-myc transgenic

tag: Onset of age


title: Mouse Wildtype Normal Lymph Node 6


title: Mouse Wildtype Normal Lymph Node 5


title: Schu S4 infected D8_S4

source_name: peripheral blood monocytes


title: Mouse Myc-induced lymphoma 138


title: Mouse Myc-induced lymphoma 136


title: Mouse Wildtype Normal Lymph Node 2


title: Mouse Wildtype Normal Spleen 7

source_name: Mouse normal spleen


title: Mouse Myc-induced lymphoma 141


title: Mouse Myc-induced lymphoma 135


title: Mouse Wildtype Normal Lymph Node 4


title: Mouse Myc-induced lymphoma 133


title: Mouse Wildtype Normal Lymph Node 3


title: Mouse Myc-induced lymphoma 123


title: Mouse Myc-induced lymphoma 119


title: Mouse Wildtype Normal Lymph Node 1


title: Mouse Myc-induced lymphoma 126


title: Mouse Myc-induced lymphoma 128


title: Mouse Myc-induced lymphoma 131


title: Mouse Myc-induced lymphoma 129


title: Mouse Myc-induced lymphoma 130


title: Mouse Wildtype Normal Lymph Node 10


title: Mouse Myc-induced lymphoma 112


title: Mouse Myc-induced lymphoma 121


title: Mouse Myc-induced lymphoma 125


title: Mouse Myc-induced lymphoma 116


title: Mouse Myc-induced lymphoma 127


title: Mouse Myc-induced lymphoma 124


title: Mouse Myc-induced lymphoma 120


title: Mouse Myc-induced lymphoma 114


title: Mouse Myc-induced lymphoma 111


title: Mouse Myc-induced lymphoma 118


title: Mouse Myc-induced lymphoma 28


title: Mouse Myc-induced lymphoma 23


title: Mouse Myc-induced lymphoma 113


title: Mouse Myc-induced lymphoma 22


title: Mouse Myc-induced lymphoma 19


title: Mouse Myc-induced lymphoma 20


title: Mouse Myc-induced lymphoma 17


title: Mouse Myc-induced lymphoma 21


title: Mouse Myc-induced lymphoma 16


title: Mouse Myc-induced lymphoma 24


title: Mouse Myc-induced lymphoma 29


title: Mouse Myc-induced lymphoma 117


title: Mouse Myc-induced lymphoma 15


title: Mouse Myc-induced lymphoma 13


title: Mouse Myc-induced lymphoma 12


title: Mouse Myc-induced lymphoma 11


title: Mouse Myc-induced lymphoma 6


title: Mouse Myc-induced lymphoma 10


title: Mouse Myc-induced lymphoma 9


title: Mouse Myc-induced lymphoma 3


title: Mouse Myc-induced lymphoma 14


title: Mouse Myc-induced lymphoma 4


title: Mouse Myc-induced lymphoma 5


title: Mouse Myc-induced lymphoma 2


title: Mouse Myc-induced lymphoma 1


title: Mouse Myc-induced lymphoma 8


title: KINK-1 24 hrs., 2

city: Wuerzburg

first: Margarete

last: Schoen

country: Germany

institute: RVZ

description: Gene expression data from melanoma cells A375, treated with 5 u molar KINK-1 for 24 hrs

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on HG U 133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and vsn as normalization method using perfect match only.

source_name: melanoma cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (GeneChip® Expression Analysis Manual, Affymetrix).

extract_protocol: total RNA was isolated using the Rneasy Mini Kit from Quiagen (including Dnase digest)

treatment_protocol: A375 melanoma cells were grown in DMEM-medium to subconfluency, then treated for 12hrs / 24hrs with 5ul KINK-1

tag: A375 cell line


title: KINK-1 24 hrs., 1

growth_protocol: A375 melanoma cells were grown in DMEM-medium to subconfluency


title: Lymph node Aire-wild-type A

status: Public on Aug 08 2008

city: Stanford

first: David

last: Wong

address: 269 Campus Drive

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80538.gif

hyb_protocol: Affymetrix protocol

scan_protocol: AffyExp; Affymetrix experiment file (.EXP) info.; Protocol Type = AffyExp; Parameter Fluidics:Number of Wash B Cycles = 4; Parameter Fluidics:Number of Wash A1 Cycles = 10; Parameter Fluidics:Holding Temperature (C) = 25; Parameter Fluidics:Station = 1; Parameter Scanner:Scanner ID = 50208350; Parameter Fluidics:Number of Wash A2 Cycles = 10; Parameter Fluidics:Protocol = EukGE-WS2v4_450; Parameter Fluidics:Third Stain Time (seconds) = 600; Parameter Fluidics:Wash A2 Temperature (C) = 25; Parameter Fluidics:Number of Wash A3 Cycles = 15; Parameter Scanner:Scan Date = Jun 06 2007 10:55AM; Parameter Scanner:Scanner Type = M10; Parameter Sample Info:Chip Lot = 24JJA1; Parameter Scanner:Pixel Size = 1.56; Parameter Fluidics:Mixes per Wash A1 Cycle = 2; Parameter Sample Info:Comments = 25LJH2; Parameter Fluidics:Wash A3 Temperature (C) = 30; Parameter Header:Version = 1; Parameter Sample Info:Operator = gcsuser; Parameter Scanner:Number of Scans = 1; Parameter Fluidics:Module = 1; Parameter Header:Type = Affymetrix GeneChip Experiment Information; Parameter Fluidics:Mixes per Wash A3 Cycle = 4; Parameter Fluidics:Wash B Temperature (C) = 50; Parameter Fluidics:First Stain Time (seconds) = 600; Parameter Fluidics:Hybridize Date = Jun 06 2007 10:34AM; Parameter Fluidics:Second Stain Time (seconds) = 600; Parameter Sample Info:Sample Type = Mouse; Parameter Sample Info:Chip Type = Mouse430_2; Parameter Fluidics:Stain Temperature (C) = 25; Parameter Fluidics:Mixes per Wash B Cycle = 15; Parameter Fluidics:Wash A1 Temperature (C) = 25; Parameter Scanner:Filter = 570; Parameter Sample Info:Project = Anderson Peripheral AIRE; Parameter Fluidics:Mixes per Wash A2 Cycle = 4; Performer: David,,Wong

source_name: Lymph node Aire-wild-type A

label_protocol: Affymetrix protocol

extract_protocol: Affymetrix protocol

tag: Lymph node Aire-wild-type A


title: Spleen Aire-knockout B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80544.gif

scan_protocol: AffyExp; Affymetrix experiment file (.EXP) info.; Protocol Type = AffyExp; Parameter Fluidics:Number of Wash B Cycles = 4; Parameter Fluidics:Number of Wash A1 Cycles = 10; Parameter Fluidics:Holding Temperature (C) = 25; Parameter Fluidics:Station = 2; Parameter Scanner:Scanner ID = 50208350; Parameter Fluidics:Number of Wash A2 Cycles = 10; Parameter Fluidics:Protocol = EukGE-WS2v4_450; Parameter Fluidics:Third Stain Time (seconds) = 600; Parameter Fluidics:Wash A2 Temperature (C) = 25; Parameter Fluidics:Number of Wash A3 Cycles = 15; Parameter Scanner:Scan Date = Jun 06 2007 12:00PM; Parameter Scanner:Scanner Type = M10; Parameter Sample Info:Chip Lot = 24JJA1; Parameter Scanner:Pixel Size = 1.56; Parameter Fluidics:Mixes per Wash A1 Cycle = 2; Parameter Sample Info:Comments = 25LJH2; Parameter Fluidics:Wash A3 Temperature (C) = 30; Parameter Header:Version = 1; Parameter Sample Info:Operator = gcsuser; Parameter Scanner:Number of Scans = 1; Parameter Fluidics:Module = 4; Parameter Header:Type = Affymetrix GeneChip Experiment Information; Parameter Fluidics:Mixes per Wash A3 Cycle = 4; Parameter Fluidics:Wash B Temperature (C) = 50; Parameter Fluidics:First Stain Time (seconds) = 600; Parameter Fluidics:Hybridize Date = Jun 06 2007 10:34AM; Parameter Fluidics:Second Stain Time (seconds) = 600; Parameter Sample Info:Sample Type = Mouse; Parameter Sample Info:Chip Type = Mouse430_2; Parameter Fluidics:Stain Temperature (C) = 25; Parameter Fluidics:Mixes per Wash B Cycle = 15; Parameter Fluidics:Wash A1 Temperature (C) = 25; Parameter Scanner:Filter = 570; Parameter Sample Info:Project = Anderson Peripheral AIRE; Parameter Fluidics:Mixes per Wash A2 Cycle = 4; Performer: David,,Wong

source_name: Spleen Aire-knockout B

tag: Spleen Aire-knockout B


title: KINK-1 12 hrs., 2

description: Gene expression data from melanoma cells A375, treated with 5 u molar KINK-1 for 12 hrs


title: Spleen Aire-wild-type A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80540.gif

scan_protocol: AffyExp; Affymetrix experiment file (.EXP) info.; Protocol Type = AffyExp; Parameter Fluidics:Number of Wash B Cycles = 4; Parameter Fluidics:Number of Wash A1 Cycles = 10; Parameter Fluidics:Holding Temperature (C) = 25; Parameter Fluidics:Station = 1; Parameter Scanner:Scanner ID = 50208350; Parameter Fluidics:Number of Wash A2 Cycles = 10; Parameter Fluidics:Protocol = EukGE-WS2v4_450; Parameter Fluidics:Third Stain Time (seconds) = 600; Parameter Fluidics:Wash A2 Temperature (C) = 25; Parameter Fluidics:Number of Wash A3 Cycles = 15; Parameter Scanner:Scan Date = Jun 06 2007 11:14AM; Parameter Scanner:Scanner Type = M10; Parameter Sample Info:Chip Lot = 24JJA1; Parameter Scanner:Pixel Size = 1.56; Parameter Fluidics:Mixes per Wash A1 Cycle = 2; Parameter Sample Info:Comments = 25LJH2; Parameter Fluidics:Wash A3 Temperature (C) = 30; Parameter Header:Version = 1; Parameter Sample Info:Operator = gcsuser; Parameter Scanner:Number of Scans = 1; Parameter Fluidics:Module = 3; Parameter Header:Type = Affymetrix GeneChip Experiment Information; Parameter Fluidics:Mixes per Wash A3 Cycle = 4; Parameter Fluidics:Wash B Temperature (C) = 50; Parameter Fluidics:First Stain Time (seconds) = 600; Parameter Fluidics:Hybridize Date = Jun 06 2007 10:34AM; Parameter Fluidics:Second Stain Time (seconds) = 600; Parameter Sample Info:Sample Type = Mouse; Parameter Sample Info:Chip Type = Mouse430_2; Parameter Fluidics:Stain Temperature (C) = 25; Parameter Fluidics:Mixes per Wash B Cycle = 15; Parameter Fluidics:Wash A1 Temperature (C) = 25; Parameter Scanner:Filter = 570; Parameter Sample Info:Project = Anderson Peripheral AIRE; Parameter Fluidics:Mixes per Wash A2 Cycle = 4; Performer: David,,Wong

source_name: Spleen Aire-wild-type A

tag: Spleen Aire-wild-type A


title: Spleen Aire-knockout A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80541.gif

scan_protocol: AffyExp; Affymetrix experiment file (.EXP) info.; Protocol Type = AffyExp; Parameter Fluidics:Number of Wash B Cycles = 4; Parameter Fluidics:Number of Wash A1 Cycles = 10; Parameter Fluidics:Holding Temperature (C) = 25; Parameter Fluidics:Station = 1; Parameter Scanner:Scanner ID = 50208350; Parameter Fluidics:Number of Wash A2 Cycles = 10; Parameter Fluidics:Protocol = EukGE-WS2v4_450; Parameter Fluidics:Third Stain Time (seconds) = 600; Parameter Fluidics:Wash A2 Temperature (C) = 25; Parameter Fluidics:Number of Wash A3 Cycles = 15; Parameter Scanner:Scan Date = Jun 06 2007 11:23AM; Parameter Scanner:Scanner Type = M10; Parameter Sample Info:Chip Lot = 24JJA1; Parameter Scanner:Pixel Size = 1.56; Parameter Fluidics:Mixes per Wash A1 Cycle = 2; Parameter Sample Info:Comments = 25LJH2; Parameter Fluidics:Wash A3 Temperature (C) = 30; Parameter Header:Version = 1; Parameter Sample Info:Operator = gcsuser; Parameter Scanner:Number of Scans = 1; Parameter Fluidics:Module = 4; Parameter Header:Type = Affymetrix GeneChip Experiment Information; Parameter Fluidics:Mixes per Wash A3 Cycle = 4; Parameter Fluidics:Wash B Temperature (C) = 50; Parameter Fluidics:First Stain Time (seconds) = 600; Parameter Fluidics:Hybridize Date = Jun 06 2007 10:34AM; Parameter Fluidics:Second Stain Time (seconds) = 600; Parameter Sample Info:Sample Type = Mouse; Parameter Sample Info:Chip Type = Mouse430_2; Parameter Fluidics:Stain Temperature (C) = 25; Parameter Fluidics:Mixes per Wash B Cycle = 15; Parameter Fluidics:Wash A1 Temperature (C) = 25; Parameter Scanner:Filter = 570; Parameter Sample Info:Project = Anderson Peripheral AIRE; Parameter Fluidics:Mixes per Wash A2 Cycle = 4; Performer: David,,Wong

source_name: Spleen Aire-knockout A

tag: Spleen Aire-knockout A


title: Control 2

description: Gene expression data from melanoma cells A375, treated with 0.1% DMSO (vehicle)


title: Lymph node Aire-knockout B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80545.gif

scan_protocol: AffyExp; Affymetrix experiment file (.EXP) info.; Protocol Type = AffyExp; Parameter Fluidics:Number of Wash B Cycles = 4; Parameter Fluidics:Number of Wash A1 Cycles = 10; Parameter Fluidics:Holding Temperature (C) = 25; Parameter Fluidics:Station = 2; Parameter Scanner:Scanner ID = 50208350; Parameter Fluidics:Number of Wash A2 Cycles = 10; Parameter Fluidics:Protocol = EukGE-WS2v4_450; Parameter Fluidics:Third Stain Time (seconds) = 600; Parameter Fluidics:Wash A2 Temperature (C) = 25; Parameter Fluidics:Number of Wash A3 Cycles = 15; Parameter Scanner:Scan Date = Jun 06 2007 11:42AM; Parameter Scanner:Scanner Type = M10; Parameter Sample Info:Chip Lot = 24JJA1; Parameter Scanner:Pixel Size = 1.56; Parameter Fluidics:Mixes per Wash A1 Cycle = 2; Parameter Sample Info:Comments = 25LJH2; Parameter Fluidics:Wash A3 Temperature (C) = 30; Parameter Header:Version = 1; Parameter Sample Info:Operator = gcsuser; Parameter Scanner:Number of Scans = 1; Parameter Fluidics:Module = 2; Parameter Header:Type = Affymetrix GeneChip Experiment Information; Parameter Fluidics:Mixes per Wash A3 Cycle = 4; Parameter Fluidics:Wash B Temperature (C) = 50; Parameter Fluidics:First Stain Time (seconds) = 600; Parameter Fluidics:Hybridize Date = Jun 06 2007 10:34AM; Parameter Fluidics:Second Stain Time (seconds) = 600; Parameter Sample Info:Sample Type = Mouse; Parameter Sample Info:Chip Type = Mouse430_2; Parameter Fluidics:Stain Temperature (C) = 25; Parameter Fluidics:Mixes per Wash B Cycle = 15; Parameter Fluidics:Wash A1 Temperature (C) = 25; Parameter Scanner:Filter = 570; Parameter Sample Info:Project = Anderson Peripheral AIRE; Parameter Fluidics:Mixes per Wash A2 Cycle = 4; Performer: David,,Wong

source_name: Lymph node Aire-knockout B

tag: Lymph node Aire-knockout B


title: Control 1


title: Lymph node Aire-wild-type B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80542.gif

scan_protocol: AffyExp; Affymetrix experiment file (.EXP) info.; Protocol Type = AffyExp; Parameter Fluidics:Number of Wash B Cycles = 4; Parameter Fluidics:Number of Wash A1 Cycles = 10; Parameter Fluidics:Holding Temperature (C) = 25; Parameter Fluidics:Station = 2; Parameter Scanner:Scanner ID = 50208350; Parameter Fluidics:Number of Wash A2 Cycles = 10; Parameter Fluidics:Protocol = EukGE-WS2v4_450; Parameter Fluidics:Third Stain Time (seconds) = 600; Parameter Fluidics:Wash A2 Temperature (C) = 25; Parameter Fluidics:Number of Wash A3 Cycles = 15; Parameter Scanner:Scan Date = Jun 06 2007 11:32AM; Parameter Scanner:Scanner Type = M10; Parameter Sample Info:Chip Lot = 24JJA1; Parameter Scanner:Pixel Size = 1.56; Parameter Fluidics:Mixes per Wash A1 Cycle = 2; Parameter Sample Info:Comments = 25LJH2; Parameter Fluidics:Wash A3 Temperature (C) = 30; Parameter Header:Version = 1; Parameter Sample Info:Operator = gcsuser; Parameter Scanner:Number of Scans = 1; Parameter Fluidics:Module = 1; Parameter Header:Type = Affymetrix GeneChip Experiment Information; Parameter Fluidics:Mixes per Wash A3 Cycle = 4; Parameter Fluidics:Wash B Temperature (C) = 50; Parameter Fluidics:First Stain Time (seconds) = 600; Parameter Fluidics:Hybridize Date = Jun 06 2007 10:34AM; Parameter Fluidics:Second Stain Time (seconds) = 600; Parameter Sample Info:Sample Type = Mouse; Parameter Sample Info:Chip Type = Mouse430_2; Parameter Fluidics:Stain Temperature (C) = 25; Parameter Fluidics:Mixes per Wash B Cycle = 15; Parameter Fluidics:Wash A1 Temperature (C) = 25; Parameter Scanner:Filter = 570; Parameter Sample Info:Project = Anderson Peripheral AIRE; Parameter Fluidics:Mixes per Wash A2 Cycle = 4; Performer: David,,Wong

source_name: Lymph node Aire-wild-type B

tag: Lymph node Aire-wild-type B


title: Lymph node Aire-knockout A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80539.gif

scan_protocol: AffyExp; Affymetrix experiment file (.EXP) info.; Protocol Type = AffyExp; Parameter Fluidics:Number of Wash B Cycles = 4; Parameter Fluidics:Number of Wash A1 Cycles = 10; Parameter Fluidics:Holding Temperature (C) = 25; Parameter Fluidics:Station = 1; Parameter Scanner:Scanner ID = 50208350; Parameter Fluidics:Number of Wash A2 Cycles = 10; Parameter Fluidics:Protocol = EukGE-WS2v4_450; Parameter Fluidics:Third Stain Time (seconds) = 600; Parameter Fluidics:Wash A2 Temperature (C) = 25; Parameter Fluidics:Number of Wash A3 Cycles = 15; Parameter Scanner:Scan Date = Jun 06 2007 11:04AM; Parameter Scanner:Scanner Type = M10; Parameter Sample Info:Chip Lot = 24JJA1; Parameter Scanner:Pixel Size = 1.56; Parameter Fluidics:Mixes per Wash A1 Cycle = 2; Parameter Sample Info:Comments = 25LJH2; Parameter Fluidics:Wash A3 Temperature (C) = 30; Parameter Header:Version = 1; Parameter Sample Info:Operator = gcsuser; Parameter Scanner:Number of Scans = 1; Parameter Fluidics:Module = 2; Parameter Header:Type = Affymetrix GeneChip Experiment Information; Parameter Fluidics:Mixes per Wash A3 Cycle = 4; Parameter Fluidics:Wash B Temperature (C) = 50; Parameter Fluidics:First Stain Time (seconds) = 600; Parameter Fluidics:Hybridize Date = Jun 06 2007 10:34AM; Parameter Fluidics:Second Stain Time (seconds) = 600; Parameter Sample Info:Sample Type = Mouse; Parameter Sample Info:Chip Type = Mouse430_2; Parameter Fluidics:Stain Temperature (C) = 25; Parameter Fluidics:Mixes per Wash B Cycle = 15; Parameter Fluidics:Wash A1 Temperature (C) = 25; Parameter Scanner:Filter = 570; Parameter Sample Info:Project = Anderson Peripheral AIRE; Parameter Fluidics:Mixes per Wash A2 Cycle = 4; Performer: David,,Wong

source_name: Lymph node Aire-knockout A

tag: Lymph node Aire-knockout A


title: Spleen Aire-wild-type B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80543.gif

scan_protocol: AffyExp; Affymetrix experiment file (.EXP) info.; Protocol Type = AffyExp; Parameter Fluidics:Number of Wash B Cycles = 4; Parameter Fluidics:Number of Wash A1 Cycles = 10; Parameter Fluidics:Holding Temperature (C) = 25; Parameter Fluidics:Station = 2; Parameter Scanner:Scanner ID = 50208350; Parameter Fluidics:Number of Wash A2 Cycles = 10; Parameter Fluidics:Protocol = EukGE-WS2v4_450; Parameter Fluidics:Third Stain Time (seconds) = 600; Parameter Fluidics:Wash A2 Temperature (C) = 25; Parameter Fluidics:Number of Wash A3 Cycles = 15; Parameter Scanner:Scan Date = Jun 06 2007 11:51AM; Parameter Scanner:Scanner Type = M10; Parameter Sample Info:Chip Lot = 24JJA1; Parameter Scanner:Pixel Size = 1.56; Parameter Fluidics:Mixes per Wash A1 Cycle = 2; Parameter Sample Info:Comments = 25LJH2; Parameter Fluidics:Wash A3 Temperature (C) = 30; Parameter Header:Version = 1; Parameter Sample Info:Operator = gcsuser; Parameter Scanner:Number of Scans = 1; Parameter Fluidics:Module = 3; Parameter Header:Type = Affymetrix GeneChip Experiment Information; Parameter Fluidics:Mixes per Wash A3 Cycle = 4; Parameter Fluidics:Wash B Temperature (C) = 50; Parameter Fluidics:First Stain Time (seconds) = 600; Parameter Fluidics:Hybridize Date = Jun 06 2007 10:34AM; Parameter Fluidics:Second Stain Time (seconds) = 600; Parameter Sample Info:Sample Type = Mouse; Parameter Sample Info:Chip Type = Mouse430_2; Parameter Fluidics:Stain Temperature (C) = 25; Parameter Fluidics:Mixes per Wash B Cycle = 15; Parameter Fluidics:Wash A1 Temperature (C) = 25; Parameter Scanner:Filter = 570; Parameter Sample Info:Project = Anderson Peripheral AIRE; Parameter Fluidics:Mixes per Wash A2 Cycle = 4; Performer: David,,Wong

source_name: Spleen Aire-wild-type B

tag: Spleen Aire-wild-type B


title: KINK-1 12 hrs., 1


title: cell_X-24B

city: Yokohama, Kanagawa

first: Takeya

last: Kasukawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD63 mouse

hyb_protocol: RNA was subsequently fragmented and hybridized to the GeneChip according to manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: single cell from VZ/SVZ of cerebral wall, E14, CD1 mouse

label_protocol: cDNA samples were subjected to the one-cycle target labeling procedure for biotin labeling by in vitro transcription (Affymetrix)

extract_protocol: Small ventricular zone (VZ)/subventricular zone (SVZ) fragments or coritical plate (CP) fragments of dorso-lateral part of CD1 mouse cerebral wall at E14 were digested in 100ul of 0.25%Trypsin/0.5% Glucose /PBS for 5min at 37°C and triturated. After adding Hanks solution (Nakarai, Japan) with trypsin inhibitor (Ovomucoid, Sigma), singly-isolated cells were randomly picked up manually by glass-capillary under inverted microscope and transferred into PCR tubes containing 4.5ul of cell lysis buffer containing spike RNA: poly(A)-tailed Bacillus subtilis lys, dap, phe, and thr RNAs at 1000,100, 20, and 5 copies per cell, respectively.  Single cell was lysed by adding to the tube containing cell lysis buffer, and the clude lysate was used for cDNA synthesis and amplification without purification.

tag: Strain

tag: Tissue

value: dorsal forebrain


title: Mouse Myc-induced lymphoma 26

tag: Genotype


title: cell_X-3i

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD65 mouse


title: cell_X-22M

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD60 mouse


title: cell_X-23E

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD62 mouse


title: cell_X-24N

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD64 mouse


title: cell_X-8G

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD68 mouse


title: cell_X-4F

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD66 mouse


title: cell_X-21J

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD58 mouse


title: cell_X-23B

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD61 mouse


title: cell_X-5i

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD67 mouse


title: cell_X-22J

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD59 mouse


title: cell_X-8N

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD69 mouse


title: cell_X-9G

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD70 mouse


title: cell_X-20O

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD56 mouse


title: cell_X-21F

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD57 mouse


title: cell_X-20L

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD55 mouse


title: cell_X-17D

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD53 mouse


title: cell_X-20J

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD54 mouse


title: cell_X-16K

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD49 mouse


title: cell_X-15C

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD46 mouse


title: cell_X-15N

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD48 mouse


title: cell_X-11M

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD44 mouse


title: cell_X-16L

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD50 mouse


title: cell_X-10E

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD41 mouse


title: cell_X-10M

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD42 mouse


title: cell_D-18O

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD34 mouse


title: cell_D-8K

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD35 mouse


title: cell_D-18F

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD32 mouse


title: cell_X-17B

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD52 mouse


title: cell_D-18D

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD31 mouse


title: cell_X-15i

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD47 mouse


title: cell_E-19F

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD38 mouse

source_name: single cell from cortical plate of cerebral wall, E14, CD1 mouse


title: cell_X-11F

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD43 mouse


title: cell_X-10C

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD40 mouse


title: cell_D-18L

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD33 mouse


title: cell_D-18C

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD30 mouse


title: cell_C-16N

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD27 mouse


title: cell_C-20P

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD28 mouse


title: cell_E-12B

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD37 mouse


title: cell_X-16O

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD51 mouse


title: cell_D-9B

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD36 mouse


title: cell_X-11N

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD45 mouse


title: cell_C-14K

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD26 mouse


title: cell_C-11H

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD24 mouse


title: cell_C-13M

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD25 mouse


title: cell_C-10G

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD23 mouse


title: cell_C-23J

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD29 mouse


title: cell_B-7A

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD21 mouse


title: cell_B-5B

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD19 mouse


title: cell_B-22P

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD18 mouse


title: cell_B-14L

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD11 mouse


title: cell_B-17H

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD17 mouse


title: cell_B-6E

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD20 mouse


title: cell_B-16J

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD14 mouse


title: cell_B-17F

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD16 mouse


title: cell_B-9H

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD22 mouse


title: cell_B-16C

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD13 mouse


title: cell_B-9O

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD8 mouse


title: cell_B-16M

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD15 mouse


title: cell_A-23N

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD6 mouse


title: cell_B-15P

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD12 mouse


title: cell_A-5G

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD7 mouse


title: cell_A-11L

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD1 mouse


title: cell_A-17M

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD5 mouse


title: cell_A-15B

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD2 mouse


title: cell_A-15M

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD4 mouse


title: cell_B-10H

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD9 mouse


title: cell_B-14J

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD10 mouse


title: cell_A-15K

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD3 mouse


title: cerebrum_WT_18w_rep2

city: Cincinnati

first: nupur

last: dasgupta

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hopital Medical Center

description: Wildtype control mice

hyb_protocol: cRNAs were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChip Operating Software 1.1 (GCOS 1.1) using Affymetrix default analysis settings and global scaling to the same target intensity value

source_name: WILDTYPE cerebrum at 18 weeks

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

extract_protocol: Total RNA was extracted using TOTALLY RNA kit (Ambion Inc.) according to the manufacturer's instructions.

tag: 18 weeks normal mice, cerebrum


title: cerebrum_WT_10d_rep2

description: Wildtype control mice

source_name: WILDTYPE cerebrum at 10 days

tag: 10 days normal mice, cerebrum


title: cerebrum_WT_12w_rep1

description: Wildtype control mice

source_name: WILDTYPE cerebrum at 12 weeks

tag: 12 weeks normal mice, cerebrum


title: cerebrum_WT_20d_rep1

description: Wildtype control mice

source_name: WILDTYPE cerebrum at 20 days

tag: 20 days normal mice, cerebrum


title: cerebrum_WT_4w_rep2

description: Wildtype control mice

source_name: WILDTYPE cerebrum at 4 weeks

tag: 4 weeks normal mice, cerebrum


title: cerebrum_WT_20d_rep2

description: Wildtype control mice


title: cerebellum_WT_18w_rep2

description: Wildtype control mice

source_name: WILDTYPE cerebellum at 18 weeks

tag: 18 weeks old normal mice, cerebellum


title: cerebrum_WT_18w_rep1

description: Wildtype control mice


title: cerebrum_WT_0d_rep1

description: Wildtype control mice

source_name: WILDTYPE cerebrum at new born

tag: new born normal mice, cerebrum


title: cerebellum_WT_18w_rep1

description: Wildtype control mice


title: cerebrum_WT_12w_rep2

description: Wildtype control mice


title: cerebellum_WT_12w_rep2

description: Wildtype control mice

source_name: WILDTYPE cerebellum at 12 weeks

tag: 12 weeks old normal mice, cerebellum


title: cerebrum_WT_10d_rep1

description: Wildtype control mice


title: cerebellum_WT_10d_rep2

description: Wildtype control mice

source_name: WILDTYPE cerebellum at 10 days

tag: 10 days old normal mice, cerebellum


title: cerebellum_WT_0d_rep1

description: Wildtype control mice

source_name: WILDTYPE cerebellum at new born

tag: new born normal mice, cerebellum


title: cerebellum_WT_0d_rep2

description: Wildtype control mice


title: cerebrum_WT_4w_rep1

description: Wildtype control mice


title: cerebellum_WT_20d_rep2

description: Wildtype control mice

source_name: WILDTYPE cerebellum at 20 days

tag: 20 days old normal mice, cerebellum


title: cerebrum_WT_0d_rep2

description: Wildtype control mice


title: cerebellum_WT_4w_rep1

description: Wildtype control mice

source_name: WILDTYPE cerebellum at 4 weeks

tag: 4 weeks old normal mice, cerebellum


title: cerebellum_WT_4w_rep2

description: Wildtype control mice


title: cerebrum_4LPSNA_ 12w_rep2

description: V394L/V394L glucocerebrosidase mutation and PS-NA mice

source_name: 4L/PS-NA cerebrum at 12 weeks

tag: 12 weeks old 4L/PS-NA mice, cerebrum


title: cerebrum_4LPSNA_ 12w_rep1


title: cerebrum_4LPSNA_ 18w_rep1

source_name: 4L/PS-NA cerebrum at 18 weeks

tag: 18 weeks old 4L/PS-NA mice, cerebrum


title: cerebrum_4LPSNA_ 4w_rep2

source_name: 4L/PS-NA cerebrum at 4 weeks

tag: 4 weeks old 4L/PS-NA mice, cerebrum


title: cerebrum_4LPSNA_ 18w_rep2


title: cerebellum_WT_10d_rep1

description: Wildtype control mice


title: cerebellum_WT_20d_rep1

description: Wildtype control mice


title: cerebellum_WT_12w_rep1

description: Wildtype control mice


title: cerebrum_4LPSNA_ 4w_rep1


title: cerebellum_4LPSNA_ 18w_rep2

source_name: 4L/PS-NA cerebellum at 18 weeks

tag: 18 weeks old 4L/PS-NA mice, cerebellum


title: cerebellum_4LPSNA_ 18w_rep1


title: cerebrum_PSNA_ 18w_rep2

description: hypomorphic prosaposin deficient mice

source_name: PS-NA cerebrum at 18 weeks

tag: 18 weeks old PS-NA mice, cerebrum


title: cerebellum_4LPSNA_ 12w_rep1

source_name: 4L/PS-NA cerebellum at 12 weeks

tag: 12 weeks old 4L/PS-NA mice, cerebellum


title: cerebrum_PSNA_ 4w_rep1

description: hypomorphic prosaposin deficient mice

source_name: PS-NA cerebrum at 4 weeks

tag: 4 weeks old PS-NA mice, cerebrum


title: cerebrum_PSNA_ 0d_rep2

description: hypomorphic prosaposin deficient mice

source_name: PS-NA cerebrum at new born

tag: new born PS-NA mice, cerebrum


title: cerebrum_PSNA_ 0d_rep1

description: hypomorphic prosaposin deficient mice


title: cerebellum_4LPSNA_ 4w_rep1

source_name: 4L/PS-NA cerebellum at 4 weeks

tag: 4 weeks old 4L/PS-NA mice, cerebellum


title: cerebrum_PSNA_ 12w_rep2

description: hypomorphic prosaposin deficient mice

source_name: PS-NA cerebrum at 12 weeks

tag: 12 weeks old PS-NA mice, cerebrum


title: cerebellum_4LPSNA_ 4w_rep2


title: cerebellum_PSNA_ 12w_rep2

description: hypomorphic prosaposin deficient mice

source_name: PS-NA cerebellum at 12 weeks

tag: 12 weeks old PS-NA mice, cerebellum


title: cerebellum_PSNA_ 18w_rep1

description: hypomorphic prosaposin deficient mice

source_name: PS-NA cerebellum at 18 weeks

tag: 18 weeks old PS-NA mice, cerebellum


title: cerebellum_PSNA_ 0d_rep2

description: hypomorphic prosaposin deficient mice

source_name: PS-NA cerebellum at new born

tag: new born PS-NA mice, cerebellum


title: cerebrum_PSNA_ 4w_rep2

description: hypomorphic prosaposin deficient mice


title: cerebellum_4LPSNA_ 12w_rep2


title: cerebellum_PSNA_ 0d_rep1

description: hypomorphic prosaposin deficient mice


title: cerebellum_PSNA_ 4w_rep1

description: hypomorphic prosaposin deficient mice

source_name: PS-NA cerebellum at 4 weeks

tag: 4 weeks old PS-NA mice, cerebellum


title: cerebrum_PS-/-_ 20d_rep2

description: Prosaposin null mice

source_name: PS-/- cerebrum at 20 days

tag: 20 days old prosaposin knockout mice, cerebrum


title: cerebrum_PSNA_ 12w_rep1

description: hypomorphic prosaposin deficient mice


title: cerebrum_PS-/-_ 25d_rep2

description: Prosaposin null mice

source_name: PS-/- cerebrum at 25 days

tag: 25 days old prosaposin knockout mice, cerebrum


title: cerebellum_PSNA_ 18w_rep2

description: hypomorphic prosaposin deficient mice


title: cerebrum_PS-/-_ 20d_rep1

description: Prosaposin null mice


title: cerebrum_PSNA_ 18w_rep1

description: hypomorphic prosaposin deficient mice


title: cerebellum_PSNA_ 4w_rep2

description: hypomorphic prosaposin deficient mice


title: cell_E-19J

description: Gene expression data of single cell derived from VZ/SVZ of cerebral wall of E14 CD39 mouse

source_name: single cell from cortical plate of cerebral wall, E14, CD1 mouse

tag: Strain

tag: Tissue


title: cerebrum_PS-/-_ 10d_rep2

description: Prosaposin null mice

source_name: PS-/- cerebrum at 10 days

tag: 10 days old prosaposin knockout mice, cerebrum


title: cerebellum_PS-/-_ 25d_rep2

description: Prosaposin null mice

source_name: PS-/- cerebellum at 25 days

tag: 25 days old prosaposin knockout mice, cerebellum


title: cerebellum_PS-/-_ 10d_rep1

description: Prosaposin null mice

source_name: PS-/- cerebellum at 10 days

tag: 10 days old prosaposin knockout mice, cerebellum


title: cerebellum_PS-/-_ 0d_rep2

description: Prosaposin null mice

source_name: PS-/- cerebellum at new born

tag: new born prosaposin knockout mice, cerebellum


title: cerebellum_PSNA_ 12w_rep1

description: hypomorphic prosaposin deficient mice


title: cerebellum_PS-/-_ 25d_rep1

description: Prosaposin null mice


title: cerebellum_PS-/-_ 0d_rep1

description: Prosaposin null mice


title: cerebrum_PS-/-_ 0d_rep2

description: Prosaposin null mice

source_name: PS-/- cerebrum at new born

tag: new born prosaposin knockout mice, cerebrum


title: cerebrum_PS-/-_ 10d_rep1

description: Prosaposin null mice


title: cerebellum_PS-/-_ 10d_rep2

description: Prosaposin null mice


title: cerebrum_PS-/-_ 0d_rep1

description: Prosaposin null mice


title: cerebellum_PS-/-_ 20d_rep2

description: Prosaposin null mice

source_name: PS-/- cerebellum at 20 days

tag: 20 days old prosaposin knockout mice, cerebellum


title: cerebellum_PS-/-_ 20d_rep1

description: Prosaposin null mice


title: cerebrum_PS-/-_ 25d_rep1

description: Prosaposin null mice


title: KO TAC 2

status: Public on Aug 06 2008

city: Maastricht

first: Marc

last: van Bilsen

address: PO BOX 616

institute: Universiteit Maastricht

description: Gene expression data from TAC-induced PPARalpha-/- mice

hyb_protocol: Biotin labeled target complementary RNA (cRNA) was fractionated and hybridized to Affymetrix 430 2.0 Mouse Genome GeneChip according to manufacturer’s instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 / 7G

data_processing: Affymetrix GeneChip Operating Software (GCOS, version 1.4) was used to analyze image data. For each transcript represented on the array by a probe set, the expression algorithm computed the detection call (present, absent, or marginal), the detection p-value, and the signal which is an average intensity value for each probe set.

source_name: TAC-induced PPARalpha-/- mice

label_protocol: One-cycle target labeling according to Affymetrix manual

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

treatment_protocol: Wild-type and PPARalpha-/- mice were sham-operated or subjected to TAC for 28 days

tag: Three-month-old male PPARa-/- mice


title: KO TAC 1


title: WT TAC 4

description: Gene expression data from TAC-induced wild-type mice

source_name: TAC-induced wild-type mice


title: WT TAC 2


title: WT TAC 3


title: WT TAC 1


title: KO sham 2

description: Gene expression data from sham-operated PPARalpha-/- mice

source_name: sham-operated PPARalpha-/- mice


title: KO sham 3


title: KO TAC 4


title: KO sham 1


title: WT sham 3

description: Gene expression data from sham-operated wild-type mice

source_name: sham-operated wild-type mice


title: KO sham 4


title: WT sham 2


title: WT sham 4


title: WT sham 1


title: Erythroblast_SOD2+/+_repWT37

city: La Jolla

first: Florent

middle: M.

last: MARTIN

address: 10550 North Torrey Pines Road, MEM-151

department: Department of Molecular and Experimental Medicine

institute: The Scripps Research Institute

description: Gene expression data from Sod2+/+ sorted erythroblasts

hyb_protocol: The target cRNA generated from each sample was processed as per manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).  Briefly, spike controls were added to 10 µg fragmented cRNA before overnight hybridization on 430 2.0 arrays.  Our hybridization cocktail contained control oligo B2 and eukaryotic controls (Affymetrix), herring sperm DNA (Promega, Madison, WI), BSA (Invitrogen), hybridization buffer (Affymetrix recommended recipe) and water.  Cocktails were hybridized to GeneChip Mouse Genome 430 2.0 arrays (http://www.affymetrix.com/products/arrays/specific/mouse430_2.affx) at 45 °C for 16 hours.  After hybridization, arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned using a ScanArray 3000 running the GCOS v1.3.037 algorithm (Affymetrix), default settings and a target intensity of 250 for scaling according to the manufacturer’s protocol (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).  After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface.  3'/5' ratios for GAPDH and β-actin were confirmed to be within acceptable limits (all but one Sod2-/- sample GAPDH 3'/5' ratios were below 2.0; the off range sample was legitimately removed from analysis), and BioB spike controls were found to be present on all chips, with BioC, BioD and CreX also present in increasing intensity.  When scaled to a target intensity of 250, scaling factors for all arrays were within acceptable limits (4.089-7.955), as were background (48-67), Q values and mean intensities.

data_processing: Arrays were scanned using GCOS v1.3.037 (Affymetrix), default settings and a target intensity of 250 for scaling.  The data was RMA-normalized and log base 2-transformed through import of .CEL files on GeneSifter Version 2.3.7.2007.05.25 (VizX Labs, Seattle, WA).

source_name: Sorted erythroblasts, Sod2+/+

label_protocol: Total RNA from each sample was submitted to one-round cDNA synthesis to prepare biotinylated target RNA using standard Affymetrix protocol (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) as previously described (Lockhart et al. Nat Biotechnol, 1996. 14(13): p. 1675-80).  Briefly, 5 µg of total RNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer and a SuperScript II Reverse Transcriptase (Invitrogen).  Second-strand synthesis was performed using Escherichia coli DNA ligase and polymerase I (Invitrogen); Escherichia coli RNAse H (Invitrogen) removed the remaining total RNA.  The target was amplified and biotin-labeled through in vitro transcription (IVT) with biotinylated UTP and CTP ribonucleotides (Enzo Life Sciences, Farmingdale, NY), generating a biotinylated cRNA.  Quality and amount of cRNA were checked with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).

growth_protocol: Heterozygous B6-Sod2tm1Cje mice were bred in timed matings to obtain Sod2-/- (KO) and Sod2+/+ (WT) littermates at E13.5-16.5 of development to serve as donors for fetal liver cell transplantation.  Embryos were harvested; fetal livers were dissected and mechanically dissociated into single cell suspensions in culture medium (RPMI, 7% FCS, glutamine, penicillin-streptomycin, 10e-5 M betamercapto-ethanol).  C57BL/6 mice congenic at the Ly5 locus (B6.SJL_PtprcaPep3b/BoyJ [Ly5.1], National Cancer Institute) were used as recipients in order to allow for differentiation of host (Ly5.1) versus donor (Ly5.2) hematopoietic cells.  11–15 week old Ly5.1 host animals were subjected to 10.50 cGy (1,050 rad) of gamma irradiation divided into two equal doses 4 h apart on the day of transplant.  10e6 fetal liver cells, prepared as above, were injected intravenously into irradiated Ly5.1 congenic recipients. Animals were maintained on chlorinated water for 21 d after irradiation.  All experiments were approved by the Animal Use Committee (Friedman et al. J. Exp. Med. 2001).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit according to the manufacturer’s suggested ‘spin’ protocol for isolation of total RNA from animal cells (Qiagen, Valencia, CA).  Briefly, we disrupted and lysed 5-10 million sorted cells in RLT Buffer, homogenized and sheared genomic DNA through centrifugation on QIAshredder spin columns; we performed on-column DNA digestion with the RNase-Free DNase Set (Qiagen) and eluted total RNA in RNase-free water (Sigma-Aldrich).  Quality and amount of starting total RNA were checked with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA) and on formaldehyde-containing agarose gels.

treatment_protocol: Marrow was taken from femurs, tibias, pelvic girdles and humerus after Halothane (Halocarbon Laboratories, River Edge, NJ) vapor terminal inhalation in accordance with the American Veterinary Medical Association (AVMA) Panel on Euthanasia.  All animal procedures were approved by The Scripps Research Institute (TSRI) Institutional Animal Care and Use Committee (IACUC).  Bone marrow single cell suspensions were labeled with FITC-conjugated anti-CD71 and PE-conjugated anti-TER-119 monoclonal antibodies (mAbs; Pharmingen, BD Biosciences, San Jose, CA) in ice-cold 2 mM EDTA: 0.5% BSA: PBS.  Fc-R saturation was achieved by pre-incubation with a purified anti-CD16/32 mAb.  >=92% cell viability was ensured using the Trypan blue exclusion assay.  Prior to sorting, cells were centrifuged and resuspended in 1 mM EDTA: 25 mM HEPES: 1% FCS: PBS containing 10 μg/ml propidium iodide (PI; Sigma-Aldrich, St. Louis, MO).  Pairs of Sod2+/+ and Sod2-/- samples were sorted in parallel using two FACSDiva sorters (BD Biosciences) simultaneously; sorting was operated at medium pressure (35 psi) using 80 μm nozzles.  Purity and quality of preparations were ensured by microscope examination of Wright-Giemsa-stained sorted cells cytospun onto slides and by flow cytometry analysis using a FACSCalibur cytometer running CellQuest Pro (BD Biosciences).

value: C57BL/6 Ly5.1+, tissue:CD45.2+ transplanted bone marrow


title: Erythroblast_SOD2-/-_repKO31

description: Gene expression data from Sod2-/- sorted erythroblasts

source_name: Sorted erythroblasts, Sod2-/-


title: Erythroblast_SOD2-/-_repKO39


title: H1299 cells transduced with GFP expressing adenovirus 1

city: Nashville

first: Jennifer

last: Pietenpol

state: TN

address: 23rd Ave South at Pierce

department: Biochemistry

institute: Vanderbilt University Medical Center

description: To identify candidate p73 target genes from this series, log transformation and baseline transformation can be performed, duplicate samples can be averaged and samples can be filtered so that the maximum number of arrays with Absent calls = 2.

hyb_protocol: see Vanderbilt Microarray Shared Resource, Affymetrix

data_processing: Samples were processed using Stratagene ArrayAssist GC-RMA  algorithm.

source_name: H1299 lung carcinoma cells, transduced with pAd:GFP, 5 h

growth_protocol: Cells were cultured in DMEM (Invitrogen) containing 10% Fetal Bovine Serum.

extract_protocol: Total RNA was harvested using the Aurum Total RNA Mini Kit (Bio-Rad, Richmond, CA), using lysis buffer without beta-Mercaptoethanol.

treatment_protocol: H1299 cells were infected with control adenovirus, and the cells were harvested after 80% transduction efficiency was reached, as monitored by GFP fluorescence.

tag: Lung carcinoma cell line


title: Erythroblast_SOD2-/-_repKO35


title: Erythroblast_SOD2+/+_repWT33


title: jurkat_rep_2

status: Public on Aug 04 2008

city: Atlanta

first: Nathan

middle: J.

last: Bowen

state: GA

address: 223 James P Brawley Drive

department: Center for Cancer Research and Therapeutic Development

institute: Clark Atlanta University

description: Jurkat cells are an immortalized line of T lymphocyte cells that are used to study acute T cell leukemia. The cell line was established from peripheral blood of a human with T cell leukemia.

hyb_protocol: GeneChip Hybridization oven 640

scan_protocol: GeneChip Scanner

source_name: Jurkat cells rep 2

label_protocol: IVT Labeling Affymetrix

growth_protocol: RPMI-1640 (Mediatech), 10% FBS (Gibco), 2mmol/L L-glutamine (Mediatech), 100IU/ml penicillin, 100 microgram/ml streptomycin, 0.25 microgram/ml amphotericin B (all from Mediatech) at 37 degrees Celsius, 5% carbon dioxide, 95% air, and 80% relative humidity.

treatment_protocol: Allowed to reach 6 X 10 5 cells/ml.

tag: Jurkat, human T-acute lymphoblasic leukemia cell line


title: H1299 cells transduced with GFP expressing adenovirus 2

description: To identify candidate p73 target genes from this series, data can be log transformed and baseline transformed, and duplicate samples can be averaged and samples can be filtered so that the maximum number of arrays with Absent calls = 2.

scan_protocol: see Vanderbilt Microarray Shared Resource, Affymetrix

data_processing: Samples were processed using Stratagene ArrayAssist GC-RMA algorithm.

treatment_protocol: H1299 cells were infected with adenovirus expressing GFP, and the cells were harvested after 80% transduction efficiency was reached, as monitored by GFP fluorescence.