title: MDA-MB-231 breast cell line subpopulation expressing CXCR4 treated with SDF-1alpha 1


title: MDA-MB-231 breast cell line subpopulation expressing CXCR4 treated with SDF-1alpha 3

status: Public on Apr 20 2010

type: RNA

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

country: USA

institute: Indiana University School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C onto Human HGU133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanned using Affymetrix GeneChip® Scanner 3000 7G

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 1000.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MDA-MB-231 cell line

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix standard single cycle 3' IVT protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were maintained in Minimum Essentail Media with 10% fetal calf serum, penecilin/streptomycin, and 1 nM Insulin. Cells were cultured for three days after sorting.

extract_protocol: Qiagen Rneasy

treatment_protocol: Cells were treated with SDF-1alpha (400ng/ml) for 1 hour or were left untreated.

tag: tissue

value: Breast cancer cell line

tag: cell line

tag: cell population

value: CXCR4 positive

tag: treatment


title: MDA-MB-231 breast cell line subpopulation expressing CXCR4 treated with SDF-1alpha 2


title: MDA-MB-231 breast cell line subpopulation expressing CXCR4 3


title: MDA-MB-231 breast cell line subpopulation not expressing CXCR4 2

value: CXCR4 negative


title: GCTFH_Rep1

city: San Diego

first: Shane

last: Crotty

state: CA

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

description: Gene expression data from CXCR5+ GL7+ CD4+ CD44high germinal center T follicular helper cells

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

organism: Mus musculus

source_name: mouse CXCR5+ GL7+ CD4 T cells

label_protocol: RNA quality of all samples was confirmed by BioAnalyzer Nano gel (Agilent), then probes were generated from 30ng total RNA by single round linear amplification using the Ovation Pico system (Nugen).

growth_protocol: All infections were done by intraperitoneal injection of 1-2 x 10^5 plaque-forming units (PFU) of LCMV Armstrong per mouse  Spleens were harvested 8 days after LCMV infection.

extract_protocol: RNA was isolated using Qiagen RNAeasy Mini spin columns (Qiagen), including QiaShredder and on-column digestion of genomic DNA. Some RNA samples were then concentrated using MinElute spin columns (Qiagen).

treatment_protocol: Splenocytes were isolated and CD4 T cells were enriched using CD4 negative selection magnetic bead purification (Miltenyi).  CD4+CD44+CD19-7AAD- cells were then sorted into TFH, GC Tfh and non-TFH populations on the basis of CXCR5 and GL7 expression using a FACSAria (BD Biosciences).

tag: strain

value: C57BL6/J Mice


title: GCTFH_Rep2


title: TFH_Rep2

description: Gene expression data from CXCR5+ GL7- CD4+ CD44high T follicular helper cells

source_name: mouse CXCR5+ GL7- CD4 T cells


title: Naïve CD4 T cells

description: Gene expression data from naïve CD4+ T Cells. (CD44low CD62Lhigh CD4 T cells from uninfected mice)

source_name: mouse naïve CD4 T cells


title: SAPKO_CXCR5_Positive_Rep1

description: Gene expression data from SAP-/- CXCR5+ CD4+ virus specific T follicular helper cells

source_name: mouse SAP-/- CXCR5+ CD4 T cells

growth_protocol: All infections were done by intraperitoneal injection of 1-2 x 10^5 plaque-forming units (PFU) of LCMV Armstrong per mouse. 6,000 naïve WT or Sh2d1a-/- SMtg (SMARTA LCMV-specific TCR transgenic) CD4 T cells were transferred per mouse, prior to LCMV infection.  Spleens were harvested 8 days after LCMV infection.

treatment_protocol: Splenocytes were isolated and antigen-specific CD4 T cells were enriched using anti-CD45.1-FITC and magnetic bead purification (Miltenyi). Virus-specific SMtg CD4+CD45.1+TCRβ+CD19-7AAD- cells were then sorted into TFH and non-TFH populations on the basis of CXCR5 expression using a FACSAria (BD Biosciences).

value: SAP-/- C57BL6/J Mice


title: TFH_Rep1


title: SAPKO Naïve

description: Gene expression data from SAP-/- naïve CD4+ T Cells. (CD44low CD62Lhigh CD4 T cells from uninfected mice)

source_name: mouse SAP-/- naive CD4 T cells


title: SAPKO_CXCR5_Negative_Rep1

description: Gene expression data from SAP-/- CXCR5- CD4+ virus specific T  cells

source_name: mouse SAP-/- CXCR5- CD4 T cells


title: NonTFH_Rep1

description: Gene expression data from CXCR5- CD4+ CD44high T cells

source_name: mouse CXCR5- CD4 T cells


title: SAPKO_CXCR5_Negative_Rep2

description: Gene expression data from SAP-/- CXCR5- CD4+ virus specific T cells


title: 1-5_E12h_Rep2_ATH1

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: Sterilised seeds were put on agar plates and kept in +4C and darkness for 3 days.  Seeds were treated with 70 % ethanol + 0.1 % Tween-20 for two minutes. They were then washed briefly with 95 % ethanol and dried.  Sterilised seeds were put in rows (20-25 seeds/row) on square (12 x 12 cm) agar plates. After stratification, the plates were put in vertical position under light (LD growth chamber) and kept for 7 days. The seedlings were then treated with liquid medium for 12 or 24 h directly on the plates, and root tips from the treated seedlings were harvested for RNA extraction.  1 Agar, nutrients and sucrose were mixed with water, and pH was adjusted to 5.7. The medium was then autoclaved and poured into square petri dishes.  50/plate 23 C average, 23C day, 23C night 100 % average, 100 % day, 100 % night Murashige & Skoog basal salt mixture. Modifications: 1 % sucrose was added and pH was adjusted to 5.7.

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

organism: Arabidopsis thaliana

source_name: AtIPT8/pga22, estradiol, 12h

label_protocol: Labelled using protocol described in manual "Affymetrix GeneChip Expression Analysis Technical Manual", One-Cycle target labelling

extract_protocol: Qiagen RNAeasy kit protocol

treatment_protocol: The seedlings were treated directly on the agar plates with liquid medium (control) or liquid medium containing 5uM 17-beta-estradiol or 5uM trans-zeatin for 12 and 24 h.

tag: developmental stage

value: primary root tip (5 mm)

tag: genetic background

value: Wassilewskija

tag: genetic variation

value: T-DNA knock out mutation in IPT8

tag: treatment time

value: 12 hours


title: Control Clone M-2

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

description: Gene expression analysis of control EML cells

hyb_protocol: Hybridization to Affymetrix® GeneChip® Mouse Genome 430 2.0 arrays was carried out following standard Affymetrix® protocols.

scan_protocol: GeneChips® were scanned using a GeneChip Scanner 3000

data_processing: Affymetrix® microarray image data were collected with Affymetrix® GeneChip® Operating Software using default parameters. We used the Bioconductor 'affy' software package for further data analysis. Signal intensities were calculated with the 'rma' function using default parameters, including quantile normalization and log2 transformation. Detection p-values were calculated with the 'mas5calls' function using default parameters.

label: Biotin

source_name: Control EML cells

label_protocol: Biotinylated cRNA were prepared from 5 microg. total RNA following standard Affymetrix® protocols

growth_protocol: EML cells were maintained in Iscove’s modified Dulbecco’s medium (IMDM) containing 20% heat-inactivated horse serum (Invitrogen, Carlsbad, CA, USA) and supplemented with 15% conditioned medium from the BHK/MKL cell line containing rat stem cell factor.

extract_protocol: RNA was extracted from three biological replicates of control and HOXB4 overexpressing KLS-EML cells using the RNeasy MinElute Cleanup Kit (Qiagen).

treatment_protocol: The BD IMag Mouse Hematopoietic Progenitor Cell Enrichment Set (anti-Ter119, anti-B220, anti-Mac-1, anti-Gr1, anti-CD3e) (BD Biosciences, San Jose, CA, USA) was used for lineage depletion experiments.  Experiments were done according to manufacturer’s guidelines.

tag: hoxb4 overexpression

value: Control


title: 1-6_E12h_Rep3_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)


title: 1-13_Z24h_Rep1_ATH1

source_name: AtIPT8/pga22, zeatin, 24h

value: trans-zeatin

value: 24 hours


title: 1-12_E24h_Rep2_ATH1

source_name: AtIPT8/pga22, estradiol, 24h


title: 1-14_Z24h_Rep2_ATH1


title: HOXB4 Overexpressing Clone B-4

description: Gene expression analysis of HOXB4 overexpressing EML cells

source_name: EML cells transduced to overproduce HOXB4

value: HOXB4 Overexpressing


title: 1-11_E24h_Rep1_ATH1


title: HOXB4 Overexpressing Clone B-11


title: Control Clone M-1


title: HOXB4 Overexpressing  Clone B4-17


title: 1-9_K24h_Rep1_ATH1

source_name: AtIPT8/pga22, control, 24h

value: untreated


title: 1-10_K24h_Rep2_ATH1


title: 1-8_Z12h_Rep2_ATH1

source_name: AtIPT8/pga22, zeatin, 12h


title: 1-7_Z12h_Rep1_ATH1


title: Control Clone M-14


title: 1-4_E12h_Rep1_ATH1


title: NonTFH_Rep2


title: 1-2_K12h_Rep2_ATH1

source_name: AtIPT8/pga22, control, 12h


title: 1-1_K12h_Rep1_ATH1


title: VHL null MEFs, biological rep2

status: Public on Apr 17 2010

last: Zhang

address: 9500 Gilman Drive

institute: UCSD

description: Gene expression data in VHL null MEFs

hyb_protocol: Hybridization was performed in Hybridization Oven 320. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data were analyzed with Microarray Suite version 5.0 (MAS 5.0).

source_name: VHL null MEFs

label_protocol: It was performed according to the standard Affymetrix protocol.

growth_protocol: MEFs were cultured under normoxia (21% O2) in the standard tissue culture incubator (37C, 5% CO2) with growth medium (high glucose DMEM supplemented with 10% FBS and antibiotics).

extract_protocol: Total RNA was extracted by using Rneasy kit (Qiagen).

tag: cell type

value: embryonic fibroblasts (MEFs)

tag: genotype

value: VHL null


title: VHL/FIH null MEFs, biological rep1

description: Gene expression data in VHL/FIH null MEFs

source_name: VHL/FIH null MEFs

value: VHL/FIH null


title: Wild-type MEFs, biological rep2

description: Gene expression data in wild-type MEFs

source_name: wildtype MEFs

value: wild type


title: condition B, independent labeling 3, technical replicate beta

status: Public on Apr 15 2010

type: other

city: Buffalo

first: Qianqian

last: Zhu

state: NY

address: 701 Ellicott St.

department: Biochemistry

institute: State University of New York at Buffalo

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

B3beta

hyb_protocol: Roughly 3.9 μg cRNA was hybridized to each array following standard Affymetrix protocols.

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

data_processing: Over 40,000 analysis routes were assessed for detecting differentially expressed genes.

molecule: other

organism: Drosophila melanogaster

source_name: spiked-in Drosophila cDNAs

label_protocol: Biotin-labeled cRNAs were generated from each pool using the Ambion MEGAscript kit with T7 or SP6 polymerase.

extract_protocol: PCR products from cDNA clones.

tag: cdna clones

value: Drosophila Gene Collection


title: condition B, independent labeling 2, technical replicate gamma

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

B2gamma


title: condition B, independent labeling 2, technical replicate alpha

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

B2alpha


title: condition B, independent labeling 1, technical replicate gamma

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

B1gamma


title: condition B, independent labeling 2, technical replicate beta

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

B2beta


title: condition B, independent labeling 3, technical replicate gamma

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

B3gamma


title: condition B, independent labeling 3, technical replicate alpha

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

B3alpha


title: rosettes_myoox_drought_rep1

status: Public on Apr 21 2010

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Biological replicate 1 of 2.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm.

data_processing: The data was analysed using Affyminer. Arrays were normalised via RMA, and all treatments were compared to the control watered wildtype.  A p-value of 0.05 was taken as significance cutoff, and a 1.5 log2ratio cutoff was also applied.

source_name: vegetative rosettes, myoox, water deficit

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Soil water deficit stress was imposed on four week old plants by withholding water until plants reached a relative water content (RWC) of 65%.

tag: mutant

value: MYO-OX


title: 1-3_K12h_Rep3_ATH1


title: VHL null MEFs, biological rep1

description: Gene expression data in VHL null MEFs


title: SAPKO_CXCR5_Positive_Rep2

source_name: mouse SAP-/- CXCR5+ CD4 T cells


title: condition B, independent labeling 1, technical replicate beta

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

B1beta


title: condition A, independent labeling 3, technical replicate alpha

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

A3alpha


title: FIH null MEFs, biological rep1

description: Gene expression data in FIH null MEFs

source_name: FIH null MEFs

value: FIH null


title: condition A, independent labeling 3, technical replicate gamma

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

A3gamma


title: condition B, independent labeling 1, technical replicate alpha

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

B1alpha


title: condition A, independent labeling 2, technical replicate gamma

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

A2gamma


title: condition A, independent labeling 2, technical replicate alpha

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

A2alpha


title: VHL/FIH null MEFs, biological rep2


title: condition A, independent labeling 1, technical replicate gamma

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

A1gamma


title: condition A, independent labeling 3, technical replicate beta

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

A3beta


title: FIH null MEFs, biological rep2

description: Gene expression data in FIH null MEFs


title: dorsal skin of bitransgenic animal, biological rep2

status: Public on Apr 16 2010

city: BUFFALO

first: SATRAJIT

last: SINHA

address: 701 ELLICOTT STREET

institute: SUNY AT BUFFALO

description: gene expression data from BG skin tissue

hyb_protocol: Biotinylated cRNA were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays.

data_processing: MAS5.0 algorithm in the Affy package of Bioconductor in the R statistical computing enviroment was used to generate expression summary values, followed by trimmed mean global normalization.

source_name: mouse skin p16

label_protocol: Total RNA was subjected to the standard Affymetrix labeling protocol to obtain biotinylated cRNA.

extract_protocol: Total RNA was extracted from wild type and BG skin using TRIzol (Invitrogen, Carlsbad, CA) and then purified using the RNeasy Mini kit (Qiagen, Valencia, CA).

value: dorsal skin from deltaNp63alpha overexpressing animals


title: condition A, independent labeling 2, technical replicate beta

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

A2beta


title: dorsal skin of wild type animal, biological rep1

description: gene expression data from norrmal skin tissue

value: dorsal skin from wildtype


title: dorsal skin of bitransgenic animal, biological rep1


title: condition A, independent labeling 1, technical replicate beta

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

A1beta


title: Wild-type MEFs, biological rep1

description: Gene expression data in wild-type MEFs


title: condition A, independent labeling 1, technical replicate alpha

description:
PCR-amplified Drosophila cDNAs spiked in at defined relative concentrations. See 'GSE21344_allclones_fcvalue.txt', which is linked to the Series GSE21344 record as a supplementary file, for the relative amounts of the cDNA clones in samples A and B.

Conditions "A" and "B" in the spike-in dataset represent two different biological conditions in real experiments.

A1alpha


title: dorsal skin of wild type animal, biological rep2


title: 292FW19

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

hyb_protocol: Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer  (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC

scan_protocol: Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400.  Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).

data_processing: Affymetrix Microarray Suite version 5.0

source_name: native fetal RPE

label_protocol: Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24  primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).

growth_protocol: Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.

extract_protocol: Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA).  Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA).  cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY).  Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.

value: native fetal RPE

tag: gestational age

value: 18 weeks


title: 292FW23

description: Adult native RPE (anRPE) were collected from donors of Caucasian decent and total RNA was extracted right after.

source_name: adult native RPE

value: adult native RPE from 89 y.o. donor


title: 292FW18

description: Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.


title: 292FW12

source_name: fetal RPE cultures

value: fetal RPE

value: 17 weeks


title: 292FW14

value: 16 weeks


title: 292FW2


title: 292FW21

source_name: adult choroid from 76 y.o. donor

value: adult choroid from 76 y.o. donor


title: 292FW13


title: 292FW10


title: 292FW9


title: 292FW20

value: adult native RPE from 76 y.o. donor


title: 292FW22

value: adult native RPE from 78 y.o. donor


title: 292FW8


title: 292FW11


title: 292FW17


title: 292FW7


title: 292FW4


title: 292FW1


title: C032 Gprc5a wild type mouse normal lung epithelial cell replicate 1

status: Public on Apr 13 2010

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description: This sample is a normal, non-tumorigenic murine cell line derived from trachea of a three week old Gprc5a wild type mouse.

hyb_protocol: Fragmented cRNAs were then hybridized to GeneChip® Mouse Genome 430 2.0 arrays (Affymetrix), according to the manufacturer’s instructions.

scan_protocol: The arrays were scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image files were converted to probe set data (*.CEL files), using the Affymetrix GeneChip® Operating Software.

data_processing: robust multi-chip analysis was used for normalization of this sample with other samples and with a statistical test of a p<0.01 of significance of difference across the samples (n=6).

source_name: cell line derived from trachea of three week old Gprc5a wild type mouse

label_protocol: Biotin-labeled cRNAs were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was isolated and purified using RNeasy columns (Qiagen, Valencia, CA).  The cells were washed twice with ice-cold PBS, lysed with the RLT buffer, incubated with DNase I for RNA isolation according to the manufacturer’s instructions.  RNA quality based on the 28S/18S ribosomal RNA ratio (>1.5) was assessed using the RNA 6000 Nano Lab-On-chip and Agilent 2100 Bioanalyzer device (Agilent Technologies, Palo Alto, CA).

value: lung epithelial cells from tracheas of Gprc5a wild type

tag: age

value: three week old


title: HT1080-RECK/4NQ

status: Public on Apr 14 2010

city: wako

first: Satoshi

last: Takagi

state: Saitama

department: ASI

country: Japan

institute: RIKEN

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 h at 45°C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

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.

source_name: RECK/4NQ-overexpressing HT1080 cells (in which four N-glycosylation asparagine residues of RECK were replaced with glutamine residues)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8.1 to 15 ug total RNA using GeneChip IVT Labeling Kit.

growth_protocol: HT1080 cells were cultured in DMEM (SIGMA) containing 10% FCS (SIGMA) and 50 ug/mL Zeocin (Invitrogen) under 5% CO2, 37°C condition.

extract_protocol: ISOGEN (Nippongene) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Permanent cell lines expressing RECK protein were established by transfecting pZeoSV2(+)-RECK or pZeoSV2(+)-RECK/4NQ into HT1080 cells followed by 50 µg/mL Zeocin (Invitrogen) selection.

value: HT1080 fibrosarcoma

tag: agent

value: RECK/4NQ-overexpressing (in which four N-glycosylation asparagine residues of RECK were replaced with glutamine residues)


title: C036 Gprc5a knockout mouse normal lung epithelial cell replicate 2

description: This sample is a normal, non-tumorigenic murine cell line derived from trachea of a three week old Gprc5a knockout mouse.

source_name: cell line derived from trachea of three week old Gprc5a knockout mouse

value: lung epithelial cells from tracheas of Gprc5a knockout mouse


title: C037 Gprc5a knockout mouse normal lung epithelial cell replicate 3


title: C034 Gprc5a wild type mouse normal lung epithelial cell replicate 3


title: C033 Gprc5a wild type mouse normal lung epithelial cell replicate 2


title: HT1080-Zeo

source_name: mock-transfected HT1080 cells

value: mock-transfected


title: Control, replicate 1

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: Control, replicate 1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on Mouse430_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10% of intensity values

source_name: mouse uterus, wild-type SmoM2

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

growth_protocol: Mice were maintained in the designated animal care facility at Baylor College of Medicine according to the institutional guidelines for the care and use of laboratory animals.  SmoM2-YFP mice were obtained from Dr. Andrew P. McMahon.  We generated mice with constitutive activation of Smo in the uterus by crossing SmoM2 mice with the PR-cre mouse model.  These mice have Smo activated in all PR-positive cells which includes all compartments of the uterus.  Because the SmoM2 allele was fused to YFP, we could use detection of YFP to validate activation of the SmoM2 allele.  Immunofluorescence for YFP demonstrated that Smo was activated in the stroma of SmoM2 uteri but not in control uteri.

tag: mouse type

value: SmoM2 (control)

tag: tissue

value: uterus


title: SmoM2, replicate 3

description: SmoM2, replicate 3

source_name: mouse uterus, mutant SmoM2

value: Mutant SmoM2


title: C035 Gprc5a knockout mouse normal lung epithelial cell replicate 1


title: SmoM2, replicate 2

description: SmoM2, replicate 2


title: HT1080-RECK

source_name: RECK-overexpressing HT1080 cells

tag: cell line

value: RECK-overexpressing


title: SmoM2, replicate 1

description: SmoM2, replicate 1


title: Control, replicate 3

description: Control, replicate 3


title: Control, replicate 2

description: Control, replicate 2


title: ERRa KO biological replicate 1

status: Public on Apr 11 2010

city: Montreal

first: Vincent

last: Giguere

state: Quebec

address: 1160 Pine avenue West

country: Canada

institute: McGill University

hyb_protocol: Standard protocols were performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.

scan_protocol: Arrays were scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the array. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.

data_processing: The data were analyzed with Genespring GX (Agilent) using RMA normalization method and statistical analysis was done using unpaired Students' t-test and asymptotic p-value computation.

source_name: ERRa KO kidneys

label_protocol: Target RNA was reverse transcribed into cDNA, and in-vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA was stained with streptavidin phycoerythrin. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.

growth_protocol: Mice were housed in standard conditions (12h light-dark, ad libitum standard diet and water).

extract_protocol: RNeasy midi RNA extraction kit was used according to manufacturer protocol.

treatment_protocol: Left and right kidneys were removed, snap frozen in liquid nitrogen and stored at -80C. Before RNA isolation, both kidneys were ground together in liquid nitrogen using a frozen mortar and pestle.

tag: gender

value: male

value: 2-3 months

value: kidney

value: ERRa KO


title: TGFb-1

status: Public on Apr 09 2010

city: Birmingham

first: Rosa

last: Serra

state: AL

address: 1918 University Blvd. 660 MCLM

department: Cell Biology

institute: University of Alabama at Birmingham

hyb_protocol: The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).

scan_protocol: Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).

data_processing: The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used. Baseline transformation to median was used.

source_name: Sclerotome in micromass culture, TGFb treated.

label_protocol: Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).  Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions.  After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed.  Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.

growth_protocol: Sclerotome cultures were set up using a method similar to that used for limb micromass cultures.  Briefly, after removal of the notochord, sclerotome ventral to the neural tube was isolated from E11.5 day mouse embryos.  Mesenchymal cells were dissociated into a single cell suspension with incubation in 1mg/ml collagenase D at 37 °C for 30 minutes and reconstituted at a density of 1 X 107 cells / ml.  Twenty microliters of cell suspension was dropped into each well of a 24 well plate.  After a pre-incubation time of 1 h at 37°C to allow cells to attach, the cultures were then flooded with F-12:DMEM (3:2) containing 10 % FBS, 50 µg/ml ascorbic acid, 10 mM ß-glycerolphosphate, 2 mM glutamine, antibiotics with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems).  Cultures were incubated at 37 °C in CO2 incubator.

extract_protocol: RNA was extracted from the cells in culture using the standard Trizol method.  RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.

treatment_protocol: After overnight culture, cells were treated with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems) for 8 hours.

value: TGFb


title: BMP-1

source_name: Sclerotome in micromass culture, BMP treated.

value: BMP


title: BMP-2


title: ERRa KO biological replicate 2


title: WT biological replicate 3

source_name: WT kidneys

value: WT


title: TGFb-3


title: WT biological replicate 1


title: WT biological replicate 2


title: TGFb-2


title: Untreated-3

source_name: Sclerotome in micromass culture, untreated.


title: BMP-3


title: ERRa KO biological replicate 3


title: Intervertebral disc-mutant-4

description: Intervertebral disc-mutant-4

hyb_protocol: Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day.

scan_protocol: Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console).

source_name: IVD E13.5 days, mutant

growth_protocol: Mouse embryos, embryonic day E13.5 day.

extract_protocol: E13.5 day control and mutant mouse embryos were rinsed in DEPC treated PBS, embedded into OCT and frozen for sectioning.  Using a cryostat, 8-12um sagittal cut frozen sections were collected and placed on PALM PEN-Membrane Slides (P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany). The frozen sections were then quickly dehydrated (70 to 100% EtOH) and stored in Xylene prior to LCM.  Laser Capture Microdissection (LCM) was carried out by using a Zeiss/ PALM Microbeam Instrument (Microdissection System; Carl Zeiss Microimaging GmbH, Munchen, Germany). The presumptive IVD from the lumbar region were collected into RNase/DNase free special PALM AdhesiveCaps (P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany).  After IVDs were collected, the adjacent presumptive vertebrae were collected into a separate adhesive cap.  Collected sample tubes are stored at -80C until RNA was isolated.  RNA was isolated using Ambion RNAqueous – Micro Kit (Austin, TX). The optional DNase treatment step was included.

treatment_protocol: Comparison of control and Col2aCre;Tgfbr2 deleted mice.

value: Intervertebral disc (IVD)


title: Intervertebral disc-mutant-1

description: Intervertebral disc-mutant-1


title: Intervertebral disc-mutant-2

description: Intervertebral disc-mutant-2


title: Vertebrae-mutant-2

source_name: Vertebrae E13.5 days, mutant

value: Vertebrae


title: Untreated-2


title: Vertebrae-mutant-1


title: Intervertebral disc-control-2

description: Intervertebral disc-control-2

source_name: IVD E13.5 days, control


title: Intervertebral disc-mutant-3

description: Intervertebral disc-mutant-3


title: Vertebrae-mutant-3


title: Intervertebral disc-control-1

description: Intervertebral disc-control-1


title: Untreated-1


title: Vertebrae-control-2

source_name: Vertebrae E13.5.days, control


title: Intervertebral disc-control-3

description: Intervertebral disc-control-3


title: Vertebrae-control-3


title: Vertebrae-control-1


title: 292FW3

description: Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.

source_name: fetal RPE cultures

value: fetal RPE

value: 16 weeks


title: 1D 0uM_Signal

status: Public on Apr 06 2010

city: Daejeon

first: Kyu-Sun

last: Lee

address: 111 Gwahangno Yuseong-gu

department: Aging Research Center

country: South Korea

institute: KRIBB

description: Gene expression data from aged and curcumin feeding.

hyb_protocol: Fifteen micrograms of the purified cRNA of each sample was fragmented and hybridized to arrays for 16 h at 45℃. Biotinylated cRNA probes were hybridized to the high density Drosophila GeneChip 2.0 oligonucleotide microarrays (Affymetrix, Inc., Santa Clara, CA, USA) and visualized with a streptavidin-phycoerythrin conjugate.

scan_protocol: All arrays were washed and stained automatically by using a fluidics Station 450 (Affymetrix, U.S.A.) and scanned by GeneChip® scanner 3000 (Affymetrix, Inc, U.S.A.).

source_name: young flies without curcumin-feeding

label_protocol: Synthesis of cDNA and biotin-labeled cRNA, fragmentation, hybridization, washing, and scanning were performed according to the Affymetrix GeneChip Expression Analysis Technical Manual (2005). Double-stranded cDNA was synthesized from 5 ug of template total RNA using One-Cycle cDNA Synthesis kit (Affymetrix, U.S.A.), and biotin labeled cRNA was synthesized using IVT Labeling kit (Affymetrix, U.S.A.). The labeled cRNA was purified with GeneChip® Sample Cleanup Module (Affymetrix, U.S.A.). The quality and quantity of the cRNA was checked by conducting gel electrophoresis and NanoDrop® ND-1000 (NanoDrop, U.S.A.), respectively.

growth_protocol: Larvae of the Canton-S strain were grown on standard CSY medium [5.2 g cornmeal, 11 g sucrose, 11 g nutritional yeast (MP Biomedicals, Solon, OH), 1.1 mL of 20% tegosept, 0.79 g agar per 100 ml in water] supplemented with several grains of live yeast.

extract_protocol: Total RNA was extracted from each sample using Trizol (Invitrogen) according to the manufacturer’s protocol. For clean-up the RNA samples, the RNA was subjected to purify using the RNeasy Maxi Kit (Qiagen, Valencia, CA) according to the manufacturer's directions. The quality and yield of the preparation was assessed throughout processing and labeling using a 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: Stock solutions of curcumin from Agros (Geel, Belgium) were prepared and added to the fly food and all feeding assays were performed in 500 mL cages under 12 hour light/dark cycle. Assays were performed in 50% humidity and 25 °C. Adult sucrose-yeast diets were prepared with 10 g sucrose, 10 g yeast, 1.1 mL of 20% tegosept (w:v in ethanol), and 0.79 g agar per 100 ml in water. After boiling, media was cooled to 60 °C and curcumin stock solution, or ethanol alone, was added by volume of 19:1. Then 5 ml of media was distributed into 10 X 75 mm shell vials, stored at 4 °C and used within two to three weeks.

value: no curcumin

value: 1 to 3 day aged adult

tag: strain

value: Canton-S

value: 30 male and 30 female


title: 40D 0uM_Signal

source_name: old flies without curcumin-feeding

value: 40 day aged adult


title: 40D 100uM_Signal

source_name: old flies fed with 100uM curcumin

value: curcumin


title: Normal luminal YAP knock down cell pmig-YAP/pRS-IRES-GFP-YAP rep2

status: Public on Apr 08 2010

city: london

first: Subham

last: Basu

address: Charterhouse Square

department: Molecular Oncology Unit

institute: Cancer Research UK

description: gene expression data from stable normal breast luminal cell with YAP gene knock down

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: RMA robust multi-array analysis using R

source_name: normal breast 1089 luminal cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: MBA MB231 was maintained in DMEM with 10% FBS. Normal luminal cell was cultured in the medium for luminal cell.

treatment_protocol: cells were grown to 70-80% before RNA extraction.

tag: stable normal luminal cell with YAP gene knock down


title: Normal luminal  control cell pmig/pRS-IRES-GFP  rep2

description: gene expression data from stable normal breast luminal cell with control vector

tag: stable normal luminal cell with control vector


title: Normal luminal  control cell pmig/pRS-IRES-GFP  rep1


title: 1D 100uM_Signal

source_name: young flies fed with 100uM curcumin


title: wild-type rostral forebrain at E10.5

status: Public on Apr 02 2010

city: Nagoya

first: Masahiko

last: Hibi

state: Aichi

address: Furocho, Chikusaku

department: Bioscience and Biotechnology Center

institute: Nagoya University

description: Gene expression data from rostral forebrain of E10.5 wild-type mice

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 raw data were summarized with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Mouse rostral forebrain

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

growth_protocol: Mice were housed in an environmentally controlled room at the Animal Facility of the RIKEN Center for Developmental Biology (CDB) under the institutional guidelines for animal and recombinant DNA experiments.

extract_protocol: Total RNA was isolated by Sepasol-RNA I (Nacalai Tesque) according to the manufacturer's instructions.

treatment_protocol: Forebrain rostral to the caudal limit of the lateral ventricle was isolated manually from E9.5, E10.5, and E12.5 wild-type and Fezf1-/- Fezf2-/- mice.

value: wild type

value: Embryonic day 10.5


title: wild-type rostral forebrain at E12.5

description: Gene expression data from rostral forebrain of E12.5 wild-type mice

value: Forebrain rostral to the caudal limit of the lateral ventricle

value: Embryonic day 12.5


title: Normal luminal YAP knock down cell pmig-YAP/pRS-IRES-GFP-YAP rep1


title: Fezf1Fezf2KO rostral forebrain at E12.5

description: Gene expression data from rostral forebrain of E12.5 Fezf1-/- Fezf2-/- mice

value: Fezf1-/- Fezf2-/-


title: MDA MB231 YAP knock down cell pmig-YAP/pRS-IRES-GFP-YAP rep2

description: gene expression data from MDA MB231 pmig-YAP/pRS-IRES-GFP-YAP

source_name: breast cancer cell line MDA MB231

tag: stable breast cancer cell line MDA MB231with YAP gene knock down


title: Fezf1Fezf2KO rostral forebrain at E10.5

description: Gene expression data from rostral forebrain of E10.5 Fezf1-/- Fezf2-/- mice


title: Normal luminal  control cell pmig/pRS-IRES-GFP  rep3


title: MDA MB231 control cell pmig/pRS-IRES-GFP  rep2

description: gene expression data from MDA MB231 pmig/pRS-IRES-GFP

tag: stable breast cancer cell line MDA MB231 with control vector


title: MDA MB231 control cell pmig/pRS-IRES-GFP  rep1


title: Normal luminal YAP knock down cell pmig-YAP/pRS-IRES-GFP-YAP rep3


title: MDA MB231 YAP knock down cell pmig-YAP/pRS-IRES-GFP-YAP rep1


title: MouseLiver_Fas_KO

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

description: Mouse Fas knock-out liver tissue

hyb_protocol: Affymetrix hybridization protocol

scan_protocol: Affymetrix scan protocol

data_processing: MAS5.0 transformation algorithm

source_name: Mouse Fas knock-out liver tissue

label_protocol: Affymetrix labeling protocol

extract_protocol: Qiagen miRNeasy Mini Kit

tag: genotype/variation

value: Fas knock-out

value: male

value: 2 months

value: liver


title: MouseLiver_WT

description: Mouse wild type normal liver tissue

source_name: Mouse wild type normal liver tissue


title: Fezf1Fezf2KO rostral forebrain at E9.5

description: Gene expression data from rostral forebrain of E9.5 Fezf1-/- Fezf2-/- mice

value: Embryonic day 9.5


title: wild-type rostral forebrain at E9.5

description: Gene expression data from rostral forebrain of E9.5 wild-type mice


title: late at day 2, BMP4, biological rep1

status: Public on Apr 01 2010

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

institute: University of British Columbia

description: Gene expression data from cultured forelimb proximal mesenchyal cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse transcriptome arrays (MOE430 2.0) . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

source_name: forelimb proximal mesenchymal cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Limb mesenchymal cultures from CD-1 embryonic age (E) E11.5 mouse limb buds were established as previously described (Hoffman et al., 2006).  E10.5 ELM cultures were established from microdissection of E10.5 fore and hind limbs.  After proteolytic digestion, cells were filtered through a Cell Strainer (40 uM; Falcon) to obtain a single cell suspension and resuspended at a density of 2 X 10^7/ml.  For microarray analyses, 5 X 10 ul aliquots of this suspension were plated into a Nunc 35 mm tissue culture dish and allowed to adhere for 1 hr.  Following this period, 2 mls of culture medium consisting of 60% F12, 40% DMEM and 10% FBS (Qualified-Invitrogen) — this time was considered time 0 (T=0).

extract_protocol: To eliminate the need for amplification prior to microarray analyses, > 1 ug of RNA was collected from cultures derived from ~280 embryos.  RNA was harvested from primary cultures using RNAeasy (Qiagen) according to the manufacturer’s instructions as described previously (Hoffman et al., 2006).  Following isolation, RNA was diluted to 125 ng/ul, the expression of Sox9 and Col2b were measured using real-time PCR and RNA quality was examined on a Bioanalyzer 2100 (Agilent).

treatment_protocol: Culture medium with or without 20 ng/ml BMP4 (R & D Systems) was added at time 0.

tag: embryonic age

tag: cell type

value: forelimb proximal mesenchymal cells


title: early at day 2, BMP4, biological rep1

description: Gene expression data from cultured hindlimb distal mesenchymal cells

source_name: hindlimb distal mesenchymal cells

value: hindlimb distal mesenchymal cells


title: early at day 2, control, biological rep1


title: late at day 2, control, biological rep1


title: early at day 2, control, biological rep2


title: early at day 2, BMP4, biological rep2


title: late at day 2, control, biological rep2


title: late at day 2, BMP4, biological rep2


title: intermediate at day 2, control, biological rep2

description: Gene expression data from cultured forelimb distal mesenchymal cells

source_name: forelimb distal mesenchymal cells

value: forelimb distal mesenchymal cells


title: early at day 1, BMP4, biological rep2


title: late at day 1, BMP4, biological rep1


title: late at day 1, BMP4, biological rep2


title: intermediate at day 2, BMP4, biological rep1


title: early at day 1, BMP4, biological rep1


title: early at day 1, control, biological rep2


title: intermediate at day 2, BMP4, biological rep2


title: early at day 1, control, biological rep1


title: late at day 1, control, biological rep1


title: intermediate at day 2, control, biological rep1


title: intermediate at day 1, BMP4, biological rep1


title: late at day 1, control, biological rep2


title: intermediate at day 1, control, biological rep1


title: late at day 0, control, biological rep2


title: late at day 0, control, biological rep1


title: intermediate at day 1, control, biological rep2


title: intermediate at day 1, BMP4, biological rep2


title: early at day 0, control, biological rep2


title: early at day 0, control, biological rep1


title: intermediate at day 0, control, biological rep2


title: intermediate at day 0, control, biological rep1


title: FGF2 treated replicate 1

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description: Total RNA isolated from 10e9 cells following 48hrs treatment

hyb_protocol: Affymetrix EukGE-WS2v4 Protocol

scan_protocol: Standard Affymetrix Genechip 7G Scanner

data_processing: MAS5/GCOS Image Analysis

label: Biotin cRNA

source_name: NS5 neural stem cells

label_protocol: Affymetrix standard 1 cycle

extract_protocol: RNeasy (Qiagen)

tag: treatment protocol

value: neural stem cells

value: brain


title: FGF2 treated replicate 2


title: Ethanol and TGF-beta1 treated replicate 2

value: Ethanol and TGF-beta1


title: LECs from healthy tissue, biological replicate 2

city: Zurich

first: milica

last: Nikolic

department: DCHAB

country: Switzerland

institute: ETH

description: mRNA was subjected to 1 round of Ribo-Spia amplification prior to microarray analysis

hyb_protocol: Following fragmentation, 3 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 450.

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

data_processing: The data were analyzed with robust multi-array average (RMA) statistics using Affymetrix default analysis settings.

source_name: LECs from healthy mammary skin of balb-c/nude mice

label_protocol: Biotinylated cRNA were prepared according to the FL-Ovation cDNA Biotin Module V2 from Nugen  from 3 ug amplified cDNA.

growth_protocol: MDA-MB-435 xenografts were injected subcutaneously and were excised 8 weeks after injection

extract_protocol: Qiagen RNeasy Plus Micro

treatment_protocol: Tissue sections of healthy skin and tumors were briefly immunostained for the LEC marker LYVE-1 before isolating LECs by means of Laser Capture microdissection

value: normal LECs


title: TGF-beta1 treated replicate 2


title: TGF-beta1 treated replicate 1


title: tumor-associated LECs, biological replicate 3

source_name: LECs from MDA-MB-435 tumor xenografts (8 weeks after injection)

value: tumor-associated LECs


title: tumor-associated LECs, biological replicate 2


title: LECs from healthy tissue, biological replicate 3


title: tumor-associated LECs, biological replicate 1


title: Ethanol and FGF2 treated replicate 1

value: Ethanol and FGF2


title: Cbfb-/-, technical replicate 3

status: Public on Mar 31 2010

first: Christopher

last: Pan

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

hyb_protocol: The hybridization cocktail containing the fragmented and Biotin labeled cDNAs was hybridized to The Affymetrix Mouse 430 2.0 GeneChip. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip® Command Console® Software (AGCC) and Expression Console™ Software. RMA normalziation was performed to generate the CHP files. Genesifter software and Pairwise comparisons were perfomed with Benjamini and Hochberg correction.

source_name: peripheral blood from E12.5 Cbfb-/-  embryos

label_protocol: Per RNA labeling, 5 micrograms  of total RNA was used in conjunction with the Affymetrix recommended protocol One-Cycle Target Labeling and Control Reagents(Catalog# 900493 ).

extract_protocol:
Embryos were dissected and peripheral blood was collected
RNA-Stat 60 extraction of total RNA was performed according to the manufacturer's instructions.

value: peripheral blood from 8-10 E12.5 embryos

tag: genotype

value: Cbfb-/-

tag: progeny from cross

value: Cbfb+/- x Cbfb+/-


title: Cbfb+/+, technical replicate 2

source_name: peripheral blood from E12.5 Cbfb+/+  embryos

value: Cbfb+/+


title: Cbfb+/+, technical replicate 3


title: Ethanol and TGF-beta1 treated replicate 1

tag: age


title: Cbfb-/-, technical replicate 2


title: Cbfb+/+, technical replicate 1


title: WT, technical replicate 3

value: Cbfb+/MYH11 x C57/Bl6


title: WT, technical replicate 4


title: Ethanol and FGF2 treated replicate 2


title: LECs from healthy tissue, biological replicate 1


title: Cbfb-/-, technical replicate 1


title: Cbfb+/MYH11, technical replicate 2

source_name: peripheral blood from E12.5 Cbfb+/MYH11  embryos


title: WT, technical replicate 2


title: WT, technical replicate 1


title: Cbfb+/MYH11, technical replicate 3


title: Cbfb+/MYH11, technical replicate 4


title: LLC-PSF1P-EGFP_low, biological rep1

city: Suita

first: Nobuyuki

last: Takakura

state: Osaka

address: Yamada-oka 3-1

department: Signal Transduction

institute: The Research Institute for Microbial Disease, Osaka university

description: Gene expression data from sorted PSF1 low expression cells of LLC-PSF1P-EGFP

hyb_protocol: Following fragmentation,10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AFFYMETRIX GeneChip Scanner 7G

data_processing: The data were analyzed with RMA using R/Bioconductor and global scaling as normalization method.

source_name: LLC-PSF1P-EGFP xenograft tumor

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

growth_protocol: LLC-PSF1P-EGFP or colon26-PSF1P-EGFP were innocuated into s.c. of mice and disected after 4(LLC-PSF1P-EGFP) or 2(colon26-PSF1P-EGFP) weeks after innocuation

value: lewis lung carcinoma (LLC)

tag: psf1 expression

value: low

tag: biological replicate

tag: tumor stage

value: 4 weeks after innocuation

tag: innocuation site


title: colon26-PSF1P-EGFP_low, biological rep2

source_name: colon26-PSF1P-EGFP xenograft tumor

tag: cell line

value: colon cancer (colon26)

value: 2 weeks after innocuation


title: LLC-PSF1P-EGFP_high, biological rep1

description: Gene expression data from sorted PSF1 high expression cells of LLC-PSF1P-EGFP

value: high


title: Cbfb+/MYH11, technical replicate 1

tag: tissue


title: LLC-PSF1P-EGFP_high, biological rep2


title: colon26-PSF1P-EGFP_high, biological rep1


title: colon26-PSF1P-EGFP_high, biological rep2


title: LLC-PSF1P-EGFP_low, biological rep2


title: colon26-PSF1P-EGFP_low, biological rep1


title: Threat pool 2 (PFC)

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

description: Affymetrix MOE430 2.0

hyb_protocol: Standard Affymetrix hybridization protocol for gene expression profiling (carried out in UCLA DNA Microarray Core).

scan_protocol: Standard Affymetrix scan protocol for gene expression profiling (carried out in UCLA DNA Microarray Core).

data_processing: RMA (RMAExpress) processing of Affymetrix .CEL files generated by UCLA DNA Microarray Core.

source_name: Prefrontal cortex

label_protocol: Standard Affymetrix probe synthesis for gene expression profiling (carried out in UCLA DNA Microarray Core).

extract_protocol: Primary prefrontal cortex tissues were isolated and homogenized, and total RNA was extracted using Qiagen RNEasy.

value: Prefrontal cortex

tag: environment

value: HighThreat


title: Threat pool 2 (SpleenCD11b)

description: Affymetrix MOE430 2.0

source_name: CD11b+ splenocytes

extract_protocol: Primary CD11b+ splenocytes were isolated and total RNA was extracted using Qiagen RNEasy.

value: CD11b+ splenocytes


title: Control pool 1 (PFC)

description: Affymetrix MOE430 2.0

value: LowThreat


title: Threat pool 1 (PFC)

description: Affymetrix MOE430 2.0


title: Threat pool 1 (SpleenCD11b)

description: Affymetrix MOE430 2.0


title: Control pool 1 (SpleenCD11b)

description: Affymetrix MOE430 2.0


title: Control pool 2 (PFC)

description: Affymetrix MOE430 2.0


title: Control pool 2 (SpleenCD11b)

description: Affymetrix MOE430 2.0


title: Wild Type Lung at 1 day, biological rep3

city: Rochester

first: Soumyaroop

last: Bhattacharya

address: 601 Elmwood Avenue Box 850

department: Pediatrics

institute: University of Rochester Medical Center

description: Gene expression data from lung of 8 day old mouse.

hyb_protocol: Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix.

data_processing: The data were analyzed with RMAExpress.

source_name: Mouse Lung from 1 day old animal

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

growth_protocol: Double mutants (FGFR3 /FGFR4) and age-matched C57BL6 mice were used and tissues harvested from animals at various ages and frozen in liquid nitrogen.

extract_protocol:
DNAase reated RNA was extracted by homogenization. RNA was isolated by protocol recommended by kit manufacturer.
For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).

value: Lung

value: Wild Type

value: 8 Days


title: Compound Knock-out Lung at 8 day, biological rep1

description: Gene expression data from lung of 1 day old mouse.

source_name: Mouse Lung from 8 day old animal

treatment_protocol: DNAase reated RNA was extracted by homogenization. RNA was isolated by protocol recommended by kit manufacturer.

value: Double Knock Out

value: 1 Day


title: Wild Type Lung at 1 day, biological rep2


title: Wild Type Lung at 8 day, biological rep1


title: Wild Type Lung at 8 day, biological rep2


title: Compound Knock-out Lung at 1 day, biological rep3


title: Compound Knock-out Lung at 1 day, biological rep1


title: Compound Heterozygous Lung at 1 day, biological rep3

value: Double Heterozygous


title: Compound Knock-out Lung at 8 day, biological rep2


title: Compound Knock-out Lung at 8 day, biological rep3


title: Compound Heterozygous Lung at 28 day, biological rep2

description: Gene expression data from lung of 4 week old mouse.

source_name: Mouse Lung from 28 day old animal

value: 28 Days


title: Compound Heterozygous Lung at 1 day, biological rep1


title: Compound Heterozygous Lung at 8 day, biological rep2


title: Compound Heterozygous Lung at 1 day, biological rep2


title: Wild Type Lung at 1 day, biological rep1


title: Wild Type Lung at 28 day, biological rep1


title: Wild Type Lung at 8 day, biological rep3


title: Compound Knock-out Lung at 1 day, biological rep2


title: Compound Heterozygous Lung at 8 day, biological rep3


title: Compound Knock-out Lung at 28 day, biological rep3


title: Compound Heterozygous Lung at 28 day, biological rep3


title: Compound Knock-out Lung at 28 day, biological rep1


title: Compound Knock-out Lung at 28 day, biological rep2


title: Compound Heterozygous Lung at 28 day, biological rep1


title: Wild Type Lung at 28 day, biological rep2


title: Compound Heterozygous Lung at 8 day, biological rep1


title: Ski6 depleted, biological rep2

city: Cleveland

first: Daniel

middle: Louis

last: Kiss

state: OH

address: 2109 Adelbert Road

department: Molceular Biology and Microbiology

institute: Case Western Reserve University

description: Gene expression data from S2 cells treated with indicated dsRNA

hyb_protocol: Samples were hybridized using Genechip Drosophila_2 microarrays (Affymetrix), washed, and data acquired via GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and default normalization methods. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Drosophila S2 cells treated with Ski6 dsRNA (Day 5)

growth_protocol: S2 Cells were grown in HyQ CCM3 media at 27 degrees

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

treatment_protocol: Cells were grown in 25 cm2 flasks, treated with dsRNAs (30µg/ml) on days 0, 1, and 3, resuspended by pipetting each time dsRNA was added, and lysed using TRIzol on day 5.

tag: agent

value: Ski6 dsRNA

value: S2 tissue culture cells


title: Rrp47 depleted, biological rep1

source_name: Drosophila S2 cells treated with Rrp47 dsRNA (Day 5)

value: Rrp47 dsRNA


title: Rrp47 depleted, biological rep2


title: Ski6 depleted, biological rep1


title: Rrp46 depleted, biological rep2

source_name: Drosophila S2 cells treated with Rrp46 dsRNA (Day 5)

value: Rrp46 dsRNA


title: Rrp4 depleted, biological rep4

source_name: Drosophila S2 cells treated with Rrp4 dsRNA (Day 5)

value: Rrp4 dsRNA


title: Dis3 depleted, biological rep2

source_name: Drosophila S2 cells treated with Dis3 dsRNA (Day 5)

value: Dis3 dsRNA


title: Rrp4 depleted, biological rep3


title: GFP dsRNA treated control 1

source_name: Drosophila S2 cells treated with GFP dsRNA (Day 5)

value: GFP dsRNA


title: Mtr3 depleted, biological rep1

source_name: Drosophila S2 cells treated with Mtr3 dsRNA (Day 5)

value: Mtr3 dsRNA


title: Rrp4 depleted, biological rep2


title: Rrp6 depleted, biological rep2

source_name: Drosophila S2 cells treated with Rrp6 dsRNA (Day 5)

value: Rrp6 dsRNA


title: Rrp40 depleted, biological rep2

source_name: Drosophila S2 cells treated with Rrp40 dsRNA (Day 5)

value: Rrp40 dsRNA


title: Csl4 depleted, biological rep1

source_name: Drosophila S2 cells treated with Csl4 dsRNA (Day 5)

value: Csl4 dsRNA


title: Rrp40 depleted, biological rep1


title: Rrp6 depleted, biological rep1


title: Rrp46 depleted, biological rep1


title: GFP dsRNA treated control 2


title: Rrp4 depleted, biological rep1


title: Dis3 depleted, biological rep1


title: Double mutant, after heat shock, biological rep 3

city: Lincoln

first: Jaime

last: Davila

address: 1901 Vine Street

department: Plant Science Innovation Center

institute: University of Nebraska

description: Gene expression from double mutant plants, after heat shock

hyb_protocol: RNA was hybridized to individual Affymetrix GeneChip oligonucleotide ATH1 array using manufacturers instructions

scan_protocol: According to Affymetrix instructions

data_processing: Expression data from Affymetrix genechips were normalized using the Robust Multichip Average (RMA) method using Bioconductor’s affy package in the R language

source_name: Arabidopsis, double mutant plants after heat shock for two hours

label_protocol: According to Affymetrix instructions

growth_protocol: Cold treated seeds were sown directly on soil (Metro Mix 360) and kept in growth chambers at 8- hour daylength at 24°C for 8 weeks and then transferred to a growth chamber with 16-hour daylength at 24°C.

extract_protocol: total RNA was extracted from above-ground parts of 8-week-old Col-0 plants and msh1 recA3 double mutant plants (Col-0 background) using TRIzol (Invitrogen) extraction procedure followed by purification on Rneasy columns (Qiagen).

treatment_protocol: For heat treatment experiments, 8-week-old plants were first transferred to a chamber (Percival Scientific) where they were subjected to heat stress at 37oC for approximately 24 hours.

value: above-ground parts

value: 8-week-old plants

value: msh1/msh1-recA3/recA3 double mutant


title: Double mutant, untreated, biological rep 2

description: Gene expression from double mutant plants, under normal conditions

source_name: Arabidposis, double mutant plants under normal conditions


title: Double mutant, after heat shock, biological rep 1


title: Double mutant, untreated, biological rep 3


title: Wild type, after heat shock, biological rep 1

description: Gene expression from wild type plants, after heat shock

source_name: Arabidopsis, col-0 plants after heat shock for two hours

value: wild type


title: Double mutant, after heat shock, biological rep 2


title: Mtr3 depleted, biological rep2


title: Double mutant, untreated, biological rep 4


title: Wild type, after heat shock, biological rep 2


title: Wild type, after heat shock, biological rep 3


title: Wild type untreated, biological rep 2

description: Gene expression from wild type plants, under normal conditions

source_name: Arabidposis, col-0 plants under normal conditions


title: Double mutant, untreated, biological rep 1


title: Csl4 depleted, biological rep2


title: Leaves-cs26-SD-REP2

city: Sevilla

first: Cecilia

last: Gotor

address: Avda. Américo Vespucio, 49

country: Spain

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

description: Gene expression data from leaves (cs26)

hyb_protocol: Following fragmentation, 15 µg of biotinylated cRNA were hybridized to Affymetrix chips (GeneChip Arabidopsis ATH1 Genome Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDT

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

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

source_name: Leaves, cs26 mutant, Short Day

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis thaliana (accession Col-0) and the cs26 mutant (SALK_034133) were grown in soil supplemented with Hoagland media. Plants were grown under a long-day photoperiod of 16 h of white light at 20ºC/8 h in the dark at 18ºC, or under a short-day photoperiod of 8 h of white light at 20ºC/16 h in the dark at 18ºC. The light intensity ranged from 140 – 160 E m-2 s-1.

extract_protocol: The leaves of 3-week-old plants grown under identical LD conditions, and the leaves of 5-week-old plants grown under identical SD conditions were collected and RNA extracted from each sample. Total RNA was isolated with Trizol reagent (Invitrogen) followed by cleaning with the RNeasy Plant Mini Kit (Qiagen).

value: cs26 mutant

tag: photoperiod

value: Short day


title: Leaves-cs26-SD-REP1

description: Gene expression data from leaves (cs26)


title: Leaves-WildType-SD-REP2

description: Gene expression data from leaves (wild type)

source_name: Leaves, Wild Type, Short Day

value: Wild Type


title: Wild type untreated, biological rep 1


title: Leaves-cs26-LD-REP1

description: Gene expression data from leaves (cs26)

source_name: Leaves, cs26 mutant, Long Day

value: Long day


title: Leaves-WildType-SD-REP3


title: Leaves-cs26-LD-REP2

description: Gene expression data from leaves (cs26)


title: Leaves-WildType-LD-REP1

source_name: Leaves, Wild Type, Long Day


title: Leaves-WildType-LD-REP3


title: Leaves-WildType-SD-REP1


title: Leaves-cs26-LD-REP3

description: Gene expression data from leaves (cs26)


title: Leaves-WildType-LD-REP2


title: Leaves-cs26-SD-REP3

description: Gene expression data from leaves (cs26)


title: IL6_1h3_MOE430_2

status: Public on Mar 24 2010

city: Munich

first: Andreas

last: Roller

address: Max-Lebsche-Platz 31

country: Germany

institute: Munich Leukemia Laboratory

description:
GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).
Frahm_250406_2303_IL6_1h3_MOE430_2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16h at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Fluorescence intensities of the hybridized arrays were acquired with the GeneChip Scanner 3000 and the operating software GCOS (Affymetrix).

data_processing: Data processing was performed using the Limma toolbox (Smyth et al., 2005) provided by Bioconductor (Gentleman et al., 2004). The RMA approach was used for normalization and background correction. In addition, probe sets were filtered out by the genefilter package.

source_name: hepatocytes, Il-6, 1h

label_protocol: Biotinylated cRNA were prepared according to the One-Cycle Target Labeling Assay from 2.5ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Primary hepatocytes were isolated and cultivated as described previously (Klingmüller et al., 2006).

extract_protocol: The quality of total RNA samples extracted from 2x 10^6 primary mouse hepatocytes was assessed with the Bioanalyzer 2100 (Agilent) to ensure that 28S/18S rRNA ratios were in the range of 1.5 to 2.0 and concentrations were comparable between samples. For each time point, 4 μg of total RNA were used for the hybridization procedure using the One-Cycle Target Labeling Kit (Affymetrix).

treatment_protocol: Primary hepatocytes were serum starved as described before (Klingmüller et al., 2006). After 5 hours of starvation, cells were stimulated with 1nM IL-6 for 0, 1, 2, or 4 hours.

value: primary mouse hepatocytes

tag: treatment

tag: time

value: 1 h


title: IL6_0h3_MOE430_2

description:
GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).
Frahm_250406_2303_IL6_0h3_MOE430_2

source_name: hepatocytes, 0h

value: unstimulated

value: 0 h


title: IL6_1h1_MOE430_2

description:
GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).
Frahm_250406_2303_IL6_1h1_MOE430_2


title: IL6_2h1_MOE430_2

description:
GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).
Frahm_250406_2303_IL6_2h1_MOE430_2

source_name: hepatocytes, Il-6, 2h

value: 2 h


title: IL6_4h1_MOE430_2

description:
GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).
Frahm_250406_2303_IL6_4h1_MOE430_2

source_name: hepatocytes, Il-6, 4h

value: 4 h


title: IL6_4h2_MOE430_2

description:
GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).
Frahm_250406_2303_IL6_4h2_MOE430_2


title: IL6_4h3_MOE430_2

description:
GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).
Frahm_250406_2303_IL6_4h3_MOE430_2


title: IL6_1h2_MOE430_2

description:
GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).
Frahm_250406_2303_IL6_1h2_MOE430_2


title: IL6_0h2_MOE430_2

description:
GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).
Frahm_250406_2303_IL6_0h2_MOE430_2


title: IL6_0h1_MOE430_2

description:
GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).
Frahm_250406_2303_IL6_0h1_MOE430_2


title: IL6_2h2_MOE430_2

description:
GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).
Frahm_250406_2303_IL6_2h2_MOE430_2


title: IL6_2h3_MOE430_2

description:
GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).
Frahm_250406_2303_IL6_2h3_MOE430_2


title: BCB two-cell embryos, Sample3

status: Public on Mar 22 2010

city: Philadelphia

first: Zhiming

last: Han

state: PA

address: 3307 North Broad Street, AHB 561

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: Microarray Analysis Suite 5.0 (MAS, Affymetrix) was used to quantify the microarray signals with default analysis parameters and global scaling to target a mean equal to 150 signal units.

source_name: Mouse two-cell embryos, BCB, untreated

label_protocol: ENZO RNA labelling kit.

extract_protocol: Picopure RNA extraction kit.

tag: strain of maternal pronucleus

tag: strain of paternal pronucleus

tag: strain of ooplasm

tag: developmental stage

value: two-cell embryos

value: untreated


title: BBB two-cell embryos, Sample3

source_name: Mouse two-cell embryos, BBB, untreated


title: BCB two-cell embryos, Sample4


title: BCB two-cell embryos, Sample1


title: BBB two-cell embryos, Sample1


title: BCB two-cell embryos, Sample2


title: BBB two-cell embryos, Sample4


title: osteoclasts

city: Shinjuku-ku

first: Takeshi

last: Miyamoto

state: Tokyo

address: 35 Shinanomachi

department: School of Medicine

institute: Keio University

description: Gene expression data from osteoclasts

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip®Mouse Genome 430 2.0 Array. GeneChip® Arrays were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneChip®Operating Software using Affymetrix default analysis settings.

source_name: osteoclasts cultured in the presence of M-CSF plus RANKL for six days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol, one-cycle, from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Bone marrow cells were isolated from 8 weeks old mouse and cultured in the presence of M-CSF for three days. Then M-CSF-dependent adherent cells were harvested as macrophage and osteoclast common progenitor cells.

extract_protocol: RLT extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: Common progenitor cells were cultured with M-CSF alone for macrophages and M-CSF plus RANKL for osteoclasts, respectively. After six days of cultivation, cells were lysed in RLT solution (RNeasy, QIAGEN).

tag: cell type

value: Bone marrow derived osteoclasts

tag: strain


title: BBB two-cell embryos, Sample2


title: CD34-4

status: Public on Mar 20 2010

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

institute: CIEMAT

description: RNA integrity tested with Bioanalyzer (Agilent)

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: RMA normalization, log2 transformed

label_protocol: Affymetrix protocol

extract_protocol: miRNeasy Mini Kit from QIAGEN

value: C57 DBA

value: skin

tag: sample

value: CD34- cells using MACS


title: CD34-6


title: Skin_ K5IKKb_1

first: Manuel

last: Navarro

address: Av. Complutense 40

department: Molecular Oncology

description: no additional information

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array, according to Affymetrix protocol.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and GCOS software

data_processing: The data were analyzed with R/Bioconductor. Data were normalized with RMA.

source_name: mouse back skin, K5-IKKbeta transgenic

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

extract_protocol: Total RNA was extracted with Trizol followed by RNAeasy columns (Qiagen) according to the manufacturer's instructions.

tag: genotype/variation

value: K5-IKKbeta transgenic

tag: age

value: 32 days

tag: sex

value: male

value: C57BL6 X DBA2


title: Skin_ K5IKKb_2

description: no additional information


title: Skin_WT_2

description: no additional information

source_name: mouse back skin, wild type

value: control


title: Mouse primary megakaryocytes, NF-E2p45-deficient

city: Sendai

first: Hozumi

last: Motohashi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Center for Radioisotope Science

institute: Tohoku University Graduate School of Medicine

description: Gene expression in primary megakaryocytes cultured from NF-E2p45-null fetal livers.

hyb_protocol: 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual.  Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.

scan_protocol: Scanning was performed in an Affymetrix GeneChip® Scanner 3000. Chip analysis was performed using the Affymetrix GeneChip® Operating Software v1.3.

data_processing: Signal intensity was calculated by MAS5-method (target intensity=100).

source_name: Primary megakaryocytes cultured from NF-E2p45-null fetal liver at E14.5

label_protocol: 1µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Affymetrix).  Double-stranded cDNA was cleaned up by using the GeneChip® Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: Whole livers were recovered from mouse fetuses at E14.5 and single cell suspensions were prepared by successive passage through 25-gauge needles. Fetal liver cells were maintained in RPMI1640 (Wako) supplemented with 20% charcoal-stripped fetal bovine serum, 50 units/ml penicillin, 50 µg/ml streptomycin, and 50 ng/ml of recombinant human thrombopoietin (TPO; generously provided by Kirin). CD41+ cells were selected from a 4 day primary culture of E14.5 fetal liver cells using a MACS magnetic system (Miltenyi Biotec). The fetal liver culture with TPO described above was incubated with FITC-conjugated anti-CD41 antibody (BD Pharmingen, clone MWReg30) followed by incubation with anti-FITC microbeads. Subsequently, the microbeads were selected magnetically through MACS large cell columns (Miltenyi Biotec).

extract_protocol: Total RNA was extracted from the CD41+ cells using Isogen (Nippon Gene). RNA was further purified using an RNeasy Mini Kit (Qiagen).

treatment_protocol: None.

tag: genotype

value: mixed background

tag: gender

value: female and male

value: primary megakaryocytes


title: Skin_WT_1

description: no additional information

tag: tissue


title: CD34-3


title: Mouse primary megakaryocytes, wild type

description: Gene expression in primary megakaryocytes cultured from wild type fetal livers.

source_name: Primary megakaryocytes cultured from wild type fetal liver at E14.5

value: wild type


title: CD34-1


title: CD34+5

value: CD34+ cells using MACS


title: CD34+1


title: CD34+4


title: CD34-5


title: CD34+2


title: CD34+6


title: CD34+3


title: CD62Llo PSGL1lo, technical replicate 3

status: Public on Mar 18 2010

city: New Haven

first: Amanda

last: Poholek

state: CT

address: 300 Cedar St. TAC S530

institute: Yale University

description: Gene expression data from CD62Llo PSGL1lo effector (CD44hi) CD4 T cells

hyb_protocol: Fragmented cRNA was hybridized to the Affymetrix 430 2.0 mouse array for 16 hours at 45C. The array is then washed and stained with streptavidin-phycoerythrin (SAPE) using the fluidics station.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The normalization algorithm used was MAS5. Additional normalization using a GeneSpring GX Analysis Platform (Agilent Technologies) used all default settings. Genes that were differentially expressed (p value ≤ 0.05) among CD62Llo PSGL1lo, CD62Llo PSGL1hi, CD62Lhi PSGL1hi, and naïve subsets (n = 3) were identified using 2-way ANOVA.

source_name: TCRb+ CD4+ B220- CD44+ splenocytes isolated from aged mice

label_protocol:
Single stranded cDNA is synthesized by reverse transcription using the poly (A) RNA present in the starting total RNA sample. Single stranded cDNA is then converted into double stranded cDNA and purified using the Affymetrix Cleanup Module.
An in vitro transcription (IVT) reaction is then carried out overnight in the presence of biotinylated UTP and CTP to produce biotin-labeled cRNA from the double stranded cDNA. The resulting cRNA is fragmented in the presence of heat and Mg+2 before hybridization to the test array.

extract_protocol: Extraction of total RNA was performed using the Qiagen RNAeasy kit according to the manufacturer's instructions.

value: spleen

value: MRL/Faslpr

value: 16-24 weeks


title: CD62Llo PSGL1hi, technical replicate 2

description: Gene expression data from CD62Lhi PSGL1lo effector (CD44hi) CD4 T cells


title: CD62Llo PSGL1hi, technical replicate 3


title: CD62Lhi, CD44lo technical replicate 3

description: Gene expression data from naïve (CD62Lhi CD44lo) CD4 T cells

source_name: TCRb+ CD4+ B220-  splenocytes isolated from young mice

value: 6-8 weeks


title: CD62Lhi, CD44lo technical replicate 1


title: CD62Lhi, CD44lo technical replicate 2


title: CD62Llo PSGL1lo, technical replicate 2


title: CD62Lhi PSGL1hi, technical replicate 3

description: Gene expression data from CD62Lhi PSGL1hi effector (CD44hi) CD4 T cells


title: CD34-2

value: C57 DBA


title: Ezh2-Vec1

status: Public on Mar 19 2010

city: Bethesda

first: Lifeng

last: Wang

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

description: Gene expression data from Ezh2+/+ brwon preadipocytes

hyb_protocol: standard Affymetrix hyb protocol

scan_protocol: standard Affymetrix scan protocol

data_processing: The data were normalized by the  methods Microarray Suite version 5.0 (MAS 5.0)

source_name: immortalized mouse brown preadipocyte

label_protocol: standard Affymetrix label protocol

growth_protocol: All cells were routinely cultured in DMEM plus 10% FBS (Hyclone). For selection, count cells and plate 5x105/10cm, add 150ug/ml Hygromycin for 2~3days. Repeat the selection one more time.

extract_protocol: Trizol extraction of total RNA followed by Qiagen RNeasy mini kit purification was performed according to the manufacturer's instructions.

value: brown preadipocyte


title: CD62Llo PSGL1hi, technical replicate 1


title: CD62Lhi PSGL1hi, technical replicate 2


title: Ezh2-Cre1

description: Gene expression data from Ezh2-/- brwon preadipocytes


title: Ezh2-Vec2


title: CD62Llo PSGL1lo, technical replicate 1


title: protoplasts at T0, biological rep2 [flg22]

city: Boston

first: Jen

last: Sheen

state: MA

address: 185 Cambridge st. CPZN7620

department: Molecular Biology

institute: Massachusetts General Hospital

description: Gene expression data from Arabidopsis mesophyll protoplasts

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on the Arabidopsis ATH1 GeneChips using the Affymetrix 640 Hybridization Oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 7G with AutoLoader.

data_processing: The data were analyzed in FlexArray with RMA including background correction and normalization.

source_name: Arabidopsis leaves

label_protocol: Total RNA (1.5-4.5 µg) were amplified, biotinylated and fragmented using the BioArrayTM HighYieldTM RNA transcript labelling kit (Enzo) according to the manufacturer’s instructions.

growth_protocol: Arabidopsis plants (Col-0) were grown in a controlled room for 28 days at 22oC, 60% relative humidity, 75 uE light and 12 hr photoperiod.

extract_protocol: Total RNA was extracted using RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol

treatment_protocol: Isolated protoplasts (0.4 million) were incubated in 10 ml 0.5 M mannitol, 4 mM MES pH 5.7 and 20 mM KCl for 4 hr at 28oC before treatment with 100 nM flg22 for 30 min and 60 min.

value: mesophyll protoplasts

value: 28 days, leaf 5-7

tag: agent


title: Ezh2-Cre2


title: protoplasts at T2, biological rep2 [flg22]

description: Gene expression data from Arabidopsis mesophyll protoplasts treated with 100 nM flg22 for 60 min


title: protoplasts at T1, biological rep2 [flg22]

description: Gene expression data from Arabidopsis mesophyll protoplasts treated with 100 nM flg22 for 30 min


title: protoplasts at T2, biological rep1 [flg22]


title: seedlings at T0, biological rep2

description: Gene expression data from Arabidopsis seedlings

source_name: Arabidopsis seedlings

label_protocol: Total RNA (9.0 µg) were amplified, biotinylated and fragmented using the BioArrayTM HighYieldTM RNA transcript labelling kit (Enzo) according to the manufacturer’s instructions.

growth_protocol: Seedlings were grown in walk-in room on the top shelf for 8 days in MS liquid medium

treatment_protocol: Treated with 2nM flg22 for 30 and 60 min.

value: seedlings

value: 8 days, seedlings


title: protoplasts at T1, biological rep1 [flg22]


title: seedlings at T1, biological rep2

description: Gene expression data from Arabidopsis seedlings treated with 2 nM flg22 for 30 min


title: seedlings at T2, biological rep2

description: Gene expression data from Arabidopsis seedlings treated with 2 nM flg22 for 60 min


title: CD62Lhi PSGL1hi, technical replicate 1


title: protoplasts at T1, biological rep1 [CPK]

description: Gene expression data from Arabidopsis mesophyll protoplasts transfected with CPK5ac DNA for 6 hr

label_protocol: Total RNA (10 µg) were amplified, biotinylated and fragmented using the BioArrayTM HighYieldTM RNA transcript labelling kit (Enzo) according to the manufacturer’s instructions.

treatment_protocol: Protoplasts (0.8 - 2 million) were transfected with 1 mg DNA/ml protoplasts using PEG-calcium and incubated in 10 ml 0.5 M mannitol, 4 mM MES pH 5.7 and 20 mM KCl for 6 hr at 25oC.

tag: protocol

value: expression of constitutively active CPK5ac


title: protoplasts at T0, biological rep1 [flg22]

value: control


title: protoplasts at T0, biological rep2 [CPK]

description: Gene expression data from Arabidopsis mesophyll protoplasts transfected with control DNA for 6 hr


title: protoplasts at T2, biological rep1 [CPK]

description: Gene expression data from Arabidopsis mesophyll protoplasts transfected with CPK11ac DNA for 6 hr

value: expression of constitutively active CPK11ac


title: HP1-RNA-1, expression

status: Public on Mar 16 2010

city: Vienna

first: Michaela

last: Schwaiger

address: Althanstr. 14

country: Austria

institute: University of Vienna

description: polydT-primed cDNA from total RNA

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

scan_protocol: GeneChips were scanned on an Affymetrix Scanner 3000 7G.

data_processing: Signal values for Affymetrix expression arrays were estimated using the GC-RMA module from Genedata’s Refiner 4.5 package (Genedata, Basel, Switzerland). Expression data analysis was performed in Genedata’s Analyst 4.5 package. Only those genes which had an Affymetrix detection p-value < 0.05 and signal values > 0.5 were assumed to be expressed.

source_name: Kc cells treated with HP1 dsRNA

growth_protocol: Drosophila Kc cells were kept in HyQ-SFX (Hyclone).

extract_protocol: Trizol extraction of total RNA.

treatment_protocol: Double stranded RNA (dsRNA) was prepared from a PCR product spanning the entire HP1 coding region, generated with primers containing a T7 RNA Polymerase binding site using the MEGASCRIPT T7 In Vitro Transcription Kit (Ambion, Cat.No. AM1334). The RNA was purified and heated to 70○C for 10 minutes and slowly cooled down to room temperature for about 30 minutes to enhance annealing. 50μg of dsRNA was added to 106 cells every 2nd day and 8 days after initial addition of dsRNA cells were harvested and the efficiency of HP1 reduction was estimated by western blot analysis using a monoclonal α-HP1 antibody.

value: female


title: Kc-RNA-5, expression

description: polydT-primed cDNA from total RNA

source_name: Kc cells


title: sorted sox1 neural stem cells

city: Sinjhuang

first: Chi-Chung

address: No. 510, Jhongjheng Rd.,

country: Taiwan

institute: Fu Jen Catholic University

description:
1602
Gene expression data from the sorted sox1 neural stem cells

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

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

data_processing: The data were analyzed with GeneSpring GX software version 7.3 using GCRMA as normalization method.

source_name: sorted sox1 neural stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20-50 ug total RNA .

growth_protocol: HB9-ES cells were maintained on mitomycin C-treated mouse embryonic fibroblast cells in high-glucose DMEM supplemented with 15% fetal bovine serum, 2 mM glutamine, 0.1 mM nonessential amino acids, 1 mM pyruvate, 0.1 mM 2-mercaptoethanol (Sigma-Aldrich), and 1000 U/ml leukemia inhibitory factor (Chemicon). The day on which ES cells were seeded to differentiate is defined as differentiation day 0. Exogenous sonic hedgehog (Shh; 200 uM, R&D Systems), retinoic acid (0.1 uM, Sigma-Aldrich) and purmorphamine (0.2 uM, Tocris) were added into the differentiation medium from day 5 to day 9 and were replaced every other day.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The quality of RNA was carefully evaluated by the electrophoresis and Agilent Bioanalyzer 2100.

treatment_protocol: The HB9-GFP+ cells were sorted and collected on day 8.

value: neural stem cells


title: HP1-RNA-3, expression

description: polydT-primed cDNA from total RNA

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


title: HP1-RNA-4, expression

description: polydT-primed cDNA from total RNA


title: Kc-RNA-4, expression

description: polydT-primed cDNA from total RNA


title: Kc-RNA-1, expression

description: polydT-primed cDNA from total RNA


title: HP1-RNA-5, expression

description: polydT-primed cDNA from total RNA


title: sorted HB9-GFP+ cells

description:
1557
Gene expression data from the sorted HB9-GFP+ cells

source_name: sorted HB9-GFP+ cells

value: HB9 transgenic ES-GFP+ cells


title: Kc-RNA-3, expression

description: polydT-primed cDNA from total RNA


title: Kc-RNA-2, expression

description: polydT-primed cDNA from total RNA


title: HP1-RNA-2, expression

description: polydT-primed cDNA from total RNA


description:
1532
Gene expression data from the mouse cerebellar granule cells on postnatal day 6

value: cerebellar granule cells


title: undifferentiated ES cells

description:
1531
Gene expression data from the undifferentiated ES cells

source_name: undifferentiated ES cells

value: undifferentiated ES cells