title: Reselected MA high line D1 (2487.VD1-3)

description: Gene expression data from wing discs.

source_name: Wing discs MA D1 line

tag: Reselected Massachussetts high angular offset


title: High selected line CA (2533.CF1-3)

status: Public on Jan 02 2008

type: RNA

city: San Diego

first: Ralph

middle: J

last: Greenspan

state: CA

address: 10640 John Jay Hopkins Dr.

country: USA

institute: The Neurosciences Institute

description: Gene expression data from wing discs.

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 using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 2500.

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

source_name: Wing discs CA high line

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

growth_protocol: Lines H and L were derived from a wild Massachusetts population sample by 20 generations of divergent selection, then isogenized.  H and L were then crossed to make hybrid populations A-D.  After 34 generations of genomic mingling, hybrid lines were divergently selected for 25 generations, then inbred for 10.  The California lines were selected from a separate population.  Flies were cultured at 20ºC on cornmeal agar medium.

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

treatment_protocol: Larvae were dissected in 30 μl drops of cold PBS on siliconized slides, with needle-tip tweezers where wing disks were rapidly excised and cleaned with tungsten wire needles.  Each pair of disks was then transferred from the needle tip to the bottom of a 0.5 ml microcentrifuge tube in dry ice, where 100 disks were collected in single microcentrifuge tubes.

tag: California high angular offset

tag: Age

value: 3rd instar larvae median age 6.2 hr prior to pupariation.


title: Reselected MA low line C2 (2484.VC2-3)

description: Gene expression data from wing discs.

source_name: Wing discs MA C2 line

tag: Reselected Massachussetts low angular offset


title: Reselected MA low line D2 (2489.VD2-2)

description: Gene expression data from wing discs.

source_name: Wing discs MA D2 line


title: Low selected line CA (2536.CF2-3)

description: Gene expression data from wing discs.

source_name: Wing discs CA low line

tag: California low angular offset


title: Reselected MA high line C1 (2479.VC1-1)

description: Gene expression data from wing discs.

source_name: Wing discs MA C1 line


title: Reselected MA low line D2 (2488.VD2-1)

description: Gene expression data from wing discs.


title: CP16AA_subject 16

status: Public on Jan 03 2008

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: Gene expression data from subject at time 0h exposed to 200ug diesel exhaust

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133plus2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 scanner

data_processing: The data were analyzed with BioConductor GCRMA using the gcrma package.

organism: Homo sapiens

source_name: healthy human subject

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle protocol from 50ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Residual phenol were removed using Qiagen's spin columns.


title: Reselected MA high line D1 (2485.VD1-1)

description: Gene expression data from wing discs.


title: Reselected MA high line C1 (2480.VC1-2)

description: Gene expression data from wing discs.


title: Reselected MA low line C2 (2482.VC2-1)

description: Gene expression data from wing discs.


title: CP10BA_subject 10


title: Low selected line CA (2534.CF2-1)

description: Gene expression data from wing discs.


title: Reselected MA high line C1 (2481.VC1-3)

description: Gene expression data from wing discs.


title: Reselected MA high line D1 (2486.VD1-2)

description: Gene expression data from wing discs.


title: Reselected MA low line B2 (2477.VB2-2)

description: Gene expression data from wing discs.

source_name: Wing discs MA B2 line


title: Reselected MA low line B2 (2478.VB2-3)

description: Gene expression data from wing discs.


title: Reselected MA low line C2 (2483.VC2-2)

description: Gene expression data from wing discs.


title: Reselected MA low line B2 (2476.VB2-1)

description: Gene expression data from wing discs.


title: Reselected MA high line B1 (2475.VB1-3)

description: Gene expression data from wing discs.

source_name: Wing discs MA B1 line


title: Reselected MA high line B1 (2474.VB1-2)

description: Gene expression data from wing discs.


title: Reselected MA high line A1 (2468.VA1-2)

description: Gene expression data from wing discs.

source_name: Wing discs MA A1 line


title: KO_RA+LIF_72hr_rep2

city: New York

first: Simne

last: Langton

state: NY

address: 1300 York Ave, E405

department: Pharmacology

institute: Weill Cornell Medical College

description: After biotin-labeling, the GeneChip Sample Cleanup Module was used to prepare the biotinylated cRNA for hybridization.  Following the standard protocol, the biotinylated cRNA was also fragmented prior to hybridization.

hyb_protocol: The hybridization steps were performed by the Microarray Core Facility of Weill Medical College of Cornell University, using the Affymetrix platform (Hyb Oven 640)

scan_protocol: The scanning was performed by the Microarray Core Facility of Weill Medical College of Cornell University, using the Affymetrix platform (7G 3000 and Fluidics Station).

data_processing: MAS 5.0

organism: Mus musculus

source_name: CYP26A1-/- ES cells, 100 nM RA +LIF, 72hr

label_protocol: The IVT labeling kit (part of the One-Cycle cDNA Synthesis Kit) was used to biotin-label the cRNA.

extract_protocol: Total RNA was extracted using RNA-STAT-60 (Tel-test, #Cs-112).  The GeneChip Expression 3'-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431) was used subsequently to generate cDNA from the total RNA.  The cDNA was used for in vitro transcription to form complementary RNA (cRNA), which was then labeled with biotin.

tag: CYP26A1-/- AB1 murine embryonic stem cells


title: Reselected MA low line A2 (2470.VA2-1)

description: Gene expression data from wing discs.

source_name: Wing discs MA A2 line


title: KO_RA+LIF_8hr_rep3

source_name: CYP26A1-/- ES cells, 100 nM RA +LIF, 8hr

tag: CYP26A1-/- AB1 murine ES cells


title: KO_RA+LIF_8h_rep2

description: The biotinylated-cRNA was prepared using the GeneChip Cleanup Module.  Prior to hybridization, the biotinylated-cRNA was also fragmented.

hyb_protocol: The hybridization steps were performed by the Microarray Core Facility at Weill Medical College of Cornell University, using the Affymetrix platform (Hyb Oven 640).

scan_protocol: The scanning as performed by the Microarray Core Facility at Weill Medical College of Cornell University, using the Affymetrix platform (7G 3000 and Fluidics Station).

label_protocol: The cRNA was biotin-labeled using the IVT kit according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using RNA-Stat-60.  The One-Cycle cDNA Synthesis kit was used to generate cDNA and cRNA.

tag: CYP26A1-/- AB1 ES cells


title: Reselected MA low line A2 (2471.VA2-2)

description: Gene expression data from wing discs.


title: Wt_Control+LIF_8hr_rep3

source_name: Wt AB1 murine ES cells, Control +LIF, 8hr

tag: Wt AB1 murine embryonic stem cells


title: KO_Control+LIF_8hr_rep3

source_name: CYP26A1-/- ES cells, Control+LIF, 8hr


title: Reselected MA high line B1 (2473.VB1-1)

description: Gene expression data from wing discs.


title: Reselected MA high line A1 (2469.VA1-3)

description: Gene expression data from wing discs.


title: KO_Control+LIF_8h_rep2

source_name: CYP26A1-/- ES cells, Control +LIF, 8hr


title: Wt_RA+LIF_72hr_rep2

source_name: Wt AB1 ES cells, 100 nM RA +LIF, 72hr, rep2

tag: Wt AB1 ES cells


title: KO_RA+LIF_72h

source_name: CYP26A1-/- AB1 murine ES cells, 100 nM RA +LIF, 72h


title: Wt_RA+LIF_8hr_rep3

source_name: Wt AB1 ES cells, 100 nM RA +LIF, 8hr


title: Reselected MA low line A2 (2472.VA2-3)

description: Gene expression data from wing discs.


title: Sample from retroviral MSCV-D1b infected cyclin D1 knockout 3T3 cells (line 12).

status: Public on Jan 07 2008

city: Philadelphia

first: Mathew

last: Casimiro

state: PA

address: 1035 BLSB, 233 South 10th street

department: Cancer Biology

institute: Thomas Jefferson University

description: Gene expression data from cyclin D1 knockout 3T3s (cell line 12) infected with a cyclin D1 splice variant (variant D1b) using Murine Stem Cell Virus (MSCV) system.

hyb_protocol: The hybridization protocol was followed for single probe array 49 format (standard)/64 format array outlined in genechip expression analysis technical manual provided by Affymetrix. This was also true for washing, staining and scanning procedures.

scan_protocol: Mouse 430 2.0 chips scanned using Gene chip scanner 3000 with autoloader following Affymetrix guidelines. Image aquired using Gene Chip Operating Sofware version 1.4.

data_processing: The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm.

label: Biotin

source_name: 3T3 cells from cyclin D1KO mice infected with MSCV-D1b.

label_protocol: Total RNA (5µg of RNeasy purified) was reverse transcribed using Superscript III First-Strand Synthesis System (Invitrogen) using a HPLC purified T7-dT24 primer (Sigma Genosys) which contains the T7 polymerase promoter sequence. The single stranded cDNA was converted to double stranded cDNA using DNA polymerase I (promega) and purified by cDNA spin column purification using GeneChip Sample Cleanup Module (Affymetrix). The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix). 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module.

growth_protocol: Cells maintained in DMEM supplemented with 10% fetal bovine serum/ 100u/ml of Penicillin-Streptomycin and cultured at 37oC in 5% carbon dioxide.

extract_protocol: Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.

treatment_protocol: Cell strain 12 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV-D1b murine stem cell virus.

tag: Strain

tag: Retrovirus


title: Wt_RA+LIF_8hr

source_name: Wt AB1 ES cells, 100 nM RA, 8hr


title: KO_Control_minusLIF_8hr

source_name: CYP26A1-/- AB1 murine ES cells, Control (-LIF), 8hr


title: Reselected MA high line A1 (2467.VA1-1)

description: Gene expression data from wing discs.


title: KO_RA+LIF_8hr

source_name: CYP26A1-/- AB1 ES cells, 100 nM RA +LIF, 8hr


title: Low selected line MA  (2530.L3)

description: Gene expression data from wing discs.

source_name: Wing discs MA L line

tag: Original Massachussetts low angular offset


title: Low selected line MA  (2529.L2)

description: Gene expression data from wing discs.


title: High selected line MA  (2527.H3)

description: Gene expression data from wing discs.

source_name: Wing discs MA H line

tag: Original Massachussetts high angular offset


title: Low selected line MA  (2528.L1)

description: Gene expression data from wing discs.


title: WtES_RA+LIF_8hr

source_name: Wt AB1 murine embryonic stem cells, 100 nM RA, +LIF, 8hr

tag: Wt, AB1, murine Embryonic stem cells


title: Wt_Control+LIF_8hr

source_name: Wt AB1 ES cells, Control+LIF, 8hr


title: High selected line MA (2525.H1)

description: Gene expression data from wing discs.


title: WtES_RA+LIF_72hr

source_name: Wt AB1 ES cells, 100 nM RA +LIF, 72hr


title: High selected line MA  (2526.H2)

description: Gene expression data from wing discs.


title: KO_Control+LIF_8hr

source_name: CYP26A1-/- AB1 murine ES cells, Control +LIF, 8hr

tag: CYP26A1-/- ES cells


title: WtES_Control_minusLIF_8hr

hyb_protocol: The hybridization and washing and staining steps were performed by the Microarray Core Facility of Weill Medical College of Cornell University, using the Affymetrix platform (Hyb Oven 640)

source_name: AB1 murine ES cells, control, -LIF, 8hr

tag: Wild-type, AB1, murine embryonic stem cells


title: human MSC transduced with the empty vector without the triple reporters_rep 2

status: Public on Jan 01 2008

city: Cleveland

first: Fangjing

last: Wang

state: OH

address: Bishop building, Room s731, UH

department: Biomedical Engineering

institute: case Western Reserve University

description: Gene expression data for hMSCs that were transduced with virus containing only the virus backbone without the triple reporter

hyb_protocol: After purification and fragmentation, 15 ug of biotin-labeled cRNA was used in a 300 ul hybridization cocktail containing spiked transcript controls.200 ul of cocktail was loaded onto Affymetrix RAE230 microarrays (Santa Clara, CA) and hybridized for 16 hr at 45o C with agitation.

scan_protocol: Standard post-hybridization washes and double-stain protocols used an Affymetrix GeneChip Fluidics Station 450. Arrays were scanned using the high resolution Gene Array scanner 3000.

data_processing: the hybridization results for each transduced/untransduced sample pair were first analyzed using GCOS 1.2 from Affymetrix (Santa Clara, CA). The genes that were differentially expressed in all the sample pairs were considered, and were further analyzed by SAM (developed by the Stanford University). A fold change of 2.0 and delta value above 1.0 was used as the criteria for SAM analysis.

source_name: human mesenchymal stem cells

label_protocol: 3 ug of RNA was used in a reverse transcription reaction (SuperScript II; Life Technologies, Rockville, MD) to generate first strand cDNA.  After second strand synthesis, double stranded cDNA was used in an in vitro transcription (IVT) reaction to generate biotinylated cRNA.

growth_protocol: culutred in normal MSC medium

extract_protocol: Qiagen RNeasy Midi Kit  according to the protocols provided by the supplier

treatment_protocol: Cells were transduced with lentivirus  containing only the backbone of the virus without the triple vector.

tag: passage <6


title: hMSCs transduced with the empty vector (only the backbone of the virus)_rep 1


title: human MSC cells control_rep 2

description: Gene expression data for hMSCs as controls

treatment_protocol: Cells were not transduced with lentivirus

tag: < 6 passages


title: transduced human MSC with lentivirus containing the triple reporters, high signal fraction_rep 2

description: Gene expression data for hMSCs that were transduced with virus, those cells have lower intensity (MRFP FL8 >10^3 under flow cytometry)

treatment_protocol: Cells were transduced with lentivirus containing luciferase, mono red fluoroscence protein and thymidine kinase gene at an MOI of 16 and incubation for 36 hours, and then sorted by FACS. The sorted cells were culutred for one passage


title: transduced human MSC with lentivirus containing the triple reporter genes, low signal fraction_rep 2

description: Gene expression data for hMSCs that were transduced with virus, those cells have lower intensity (MRFP FL8 <10^3 under flow cytometry)

tag: passage < 6


title: transduced hMSC with lentivirus containing the triple reporters, high signal fraction_rep 1


title: transduced human MSC with lentivirus containing the triple reporter genes, low signal fraction_rep 1


title: human MSC cells control_rep 1

description: Gene expression data for hMSCs that were not transduced with virus

growth_protocol: culutre in normal MSC medium

extract_protocol: Qiagen RNeasy Midi Kit

treatment_protocol: no treatment

tag: <passage 6


title: wild-type tumor #3152

city: La Jolla

first: Maria

last: Hedlund

address: 9500 Gilman Dr CMM-E #1087

institute: UCSD

description: Six PyV-mT St6gal1 null and wild-type tumor pairs were used, in four independent pools of three tumors each.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Murine Genome 430 2.0 Array GeneChip. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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.

label: Biotin (Affymetrix IVT)

source_name: PyV-mT wild-type tumor

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

extract_protocol: The tumor tissue (100 mg) was homogenized in Ultraspec (Biotecx Labs, Houston, TX), and total RNA was extracted according to the manufacturer's protocol.

tag: Gender

value: female

tag: Age

value: 110 days

tag: Tissue

value: mammary tumor

tag: Days after tumor onset

value: 14 days


title: Undifferentiated Dicer -/- (27H) ES cell line transfected with siRL replicate_1

city: Basel

first: Lasse

last: Sinkkonen

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

description:
ES cells deficient of Dicer_transfected with siRNA agains Renilla luciferase
_date of analysis 01072007

hyb_protocol: 20 µg of biotinylated cRNA was fragmented by heating in the presence of Mg2+ (as per Affymetrix’s instructions) and 15 µg of fragmented cRNA was hybridized to Mouse MOE430 v2.0 GeneChips™

scan_protocol: standard Affymetrix procedures

data_processing: Quality control and background normalization were performed using Refiner from Genedata AG (Basel, Switzerland). All arrays were condensed together using the GC-RMA algorithm with quantile normalization composed of 100 bins using Genedata’s Refiner application. Per chip normalization was performed by scaling the median of the genes called present (detection p-value < 0.04) to a value of 500. Per chip normalized data are referred to as “raw” expression values.

label: biotinylated cRNA

source_name: Embryonic stem cell transfected with siRL

label_protocol: cRNA was produced by in vitro transcription (IVT) by T7 RNA polymerase, using the Affymetrix IVT kit as per manufacturer’s instructions.

extract_protocol: Absolutely RNA Miniprep Kit (Stratagene)

tag: Undifferentiated Dicer -/- ES cell line, passage 22, transfected with siRNA against Renilla luciferase


title: wild-type tumor #3375


title: Undifferentiated Dicer -/- (27H) ES cell line transfected with siRL replicate_2


title: Undifferentiated Dicer -/- (27H) ES cell line transfected with miR-290 cluster replicate_2

description: ES cells deficient of Dicer_transfected with miRNA mimics (Dharmacon) of mmu-miR-290 cluster_date of analysis 01072007

source_name: Embryonic stem cell transfected with miR-290 cluster

tag: Undifferentiated Dicer -/- ES cell line, passage 22, transfected with miRNA mimics (Dharmacon) of mmu-miR-290 cluster.


title: St6gal1-/- tumor #3376

source_name: PyV-mT St6gal1-/- tumor

tag: Strain


title: WtES_Control+LIF_8hr

hyb_protocol: The hybridization and washing and staining steps were performed by the Microarray Core Facility of Weill Medical College of Cornell University, using the Affymetrix platform.

scan_protocol: The scanning was performed by the Microarray Core Facility of Weill Medical College of Cornell University, using the Affymetrix platform and the 7G 3000 and Fluidics Station.

source_name: Wt AB1 murine embryonic stem cells

tag: wild-type


title: Undifferentiated Dicer -/- (27H) ES cell line transfected with miR-290 cluster replicate_1


title: Undifferentiated Dicer -/- (27H) ES cell line transfected with siRL replicate_3


title: Undifferentiated Dicer -/- (27H) ES cell line transfected with miR-290 cluster replicate_3


title: 2098_n_r3

city: Gainesville

first: Brian

last: Harfe

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: gene expression from cells outside of the ZPA

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on Mu430 2.0 A Array. GeneChips were processed on GeneChip fluidics station F450.

data_processing: The data were analyzed with GCOS 1.3 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: E10.5 mouse limb bud

label_protocol: Biotinylated cRNA was prepared according to the two-cycle Affymetrix protocol from 50ng total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).

growth_protocol: Shhgfpcre heterozygotes were harvested at E10.5.

extract_protocol: Qiagen RNeasy according to manufacturer's instructions

treatment_protocol: After dissociating the limbs into single cell suspensions, GFP-positive (ZPA) and GFP-negative (rest of the limb) cells were purified by FACS.

tag: GFP-negative, rest of limb


title: HeLa shLuc+ 90min 2

first: Fumiko

last: Iwamoto

institute: FMI

description: This is the sample of HeLa-shLuc cells with expression of short hairpin RNA, 90 min incubation with ActD

hyb_protocol: 15 μg of fragmentated cRNA was hybridized to Human U133 plus 2.0 GeneChipsTM

scan_protocol: The chips were scanned using an Affymetrix 7G scanner.

data_processing: GC-RMA expression values and detection P-values were estimated using Refiner 4.0 from Genedata AG (Basel, Switzerland). Data analysis was performed using Analyst 4.0 from Genedata AG (Basel, Switzerland). The chip distributions were standardized by quantile normalization and they were scaled to make the median expression value 500. For the analysis of steady-state RNA levels, genes were required to have a detection p-value < 0.04 (Affymetrix default) in at least two replicates of any one condition.The objective was to exclude genes that are not expressed in any condition. They were then subjected to a student t-test (P<0.05) and have a median fold change of 1.5 or 2 greater between samples dox+ and dox- or with and without starvation.

source_name: HeLa shLuc+ 90min 2

label_protocol: Total RNA (5 μg) from each replicate was reverse transcribed and labelled using the Affymetrix 1-cycle labelling kit as per manufacturer’s instructions. Biotinylated cRNA (20 μg) was fragmented by heating with magnesium (as per Affymetrix’s instructions)

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen).

value: HeLa

value: Female


title: HeLa shLuc+ 60min 1

description: This is the sample of HeLa-shLuc cells with expression of short hairpin RNA, 60 min incubation with ActD

source_name: HeLa shLuc+ 60min 1


title: HeLa shLuc+ 120min 2

description: This is the sample of HeLa-shLuc cells with expression of short hairpin RNA, 120 min incubation with ActD

source_name: HeLa shLuc+ 120min 2


title: 2089_n_r1


title: 2100_n_r4


title: St6gal1-/- tumor #3151


title: 2091_n_r2


title: HeLa shLuc+ 120min 1

source_name: HeLa shLuc+ 120min 1


title: HeLa shLuc+ 30min 2

description: This is the sample of HeLa-shLuc cells with expression of short hairpin RNA, 30 min incubation with ActD

source_name: HeLa shLuc+ 30min 2


title: HeLa shLuc+ 90min 1

source_name: HeLa shLuc+ 90min 1


title: 2097_z_r3

description: gene expression from ZPA cells

tag: GFP-positive, ZPA


title: HeLa shLuc+ 30min 1

source_name: HeLa shLuc+ 30min 1


title: HeLa shLuc- 120min 2

description: This is the sample of HeLa-shLuc cells without expression of short hairpin RNA, 120 min incubation with ActD

source_name: HeLa shLuc- 120min 2


title: 2week old smoke exposed lung 5

city: Baltimore

first: Sharon

last: McGrath-Morrow

state: MD

address: 200 N.Wolfe St.

department: Pediatrics

institute: Johns Hopkins

description: B6 Lung gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 10 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)

scan_protocol: Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.

data_processing: Data extraction was processed by Affy GeneChip® Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  6 sets B6 1smoke exposed (2 weeks) x 4 sets B6 age-matched controls (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons). Also, ABS |FC - FC SEM| >= 1.5

source_name: B6 2wk-smoke lung

label_protocol: cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).

growth_protocol: no growth protocol

treatment_protocol: one-day old neonatal mouse  placed in smoke chamber with mother for 1hr/day  for first 7 days, then 2hrs/day for 7 days, cigarette were smoked with standard puffs of 35ml volume of 2-sec duration.  Average total particulate matter in chamber 90mg/m3.

tag: C57BL/6J mouse strain (Jackson Lab)  gender- unknown, age- 2 weeks, n = 1, # of tissue = 1 tissue

value: Lung


title: 2088_z_r1

description: gene expression from ZPA cells


title: HeLa shLuc+ 60min 2

source_name: HeLa shLuc+ 60min 2


title: HeLa shLuc- 60min 2

description: This is the sample of HeLa-shLuc cells without expression of short hairpin RNA, 60 min incubation with ActD

source_name: HeLa shLuc- 60min 2


title: HeLa shLuc- 90min 1

description: This is the sample of HeLa-shLuc cells without expression of short hairpin RNA, 90 min incubation with ActD

source_name: HeLa shLuc- 90min 1


title: HeLa shLuc- 60min 1

source_name: HeLa shLuc- 60min 1


title: 2099_z_r4

description: gene expression from ZPA cells


title: 2week old smoke exposed lung 6

description: B6 Lung gene expression

label: ENZO BioArray HighYield RNA Transcript Labeling Kit


title: 2week old smoke exposed lung 3

description: B6 Lung gene expression


title: 2week old smoke exposed lung 2

description: B6 Lung gene expression

label_protocol: cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External  controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).


title: HeLa shLuc- 120min 1

source_name: HeLa shLuc- 120min 1


title: 2week old smoke exposed lung 4

description: B6 Lung gene expression


title: HeLa shLuc- 90min 2

source_name: HeLa shLuc- 90min 2


title: 2week old smoke exposed lung 1

description: B6 Lung gene expression


title: HeLa shLuc+ STV 3

description: This is the sample of HeLa-shLuc cells with expression of short hairpin RNA, cultured 24 hrs in serum-depleted medium

source_name: HeLa shLuc+ STV 3


title: 2 week old C57BL6 control lung 4

description: B6 Lung gene expression

data_processing: Data extraction was processed by Affy GeneChip® Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets B6 18/26 months x 3 sets B6 2 months comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons). Also, ABS |FC - FC SEM| >= 1.5

source_name: B6 2 week control lung

treatment_protocol: mice kept in air filtered environment away from the experimental group


title: HeLa shLuc+ 0min 3

description: This is the sample of HeLa-shLuc cells with expression of short hairpin RNA

source_name: HeLa shLuc+ 0min 3


title: HeLa shLuc- 30min 2

description: This is the sample of HeLa-shLuc cells without expression of short hairpin RNA, 30 min incubation with ActD

source_name: HeLa shLuc- 30min 2


title: 2 week old C57BL6 control lung 1

description: B6 Lung gene expression


title: HeLa shLuc- 30min 1

source_name: HeLa shLuc- 30min 1


title: 2 week old C57BL6 control lung 3

description: B6 Lung gene expression


title: HeLa shLuc- 0min 3

description: This is the sample of HeLa-shLuc cells without expression of short hairpin RNA

source_name: HeLa shLuc- 0min 3


title: HeLa shLuc- STV 3

description: This is the sample of HeLa-shLuc cells without expression of short hairpin RNA, cultured 24 hrs in serum-depleted medium

source_name: HeLa shLuc- STV 3


title: HeLa shLuc+ 0min 2

source_name: HeLa shLuc+ 0min 2


title: HeLa shLuc+ STV 2

source_name: HeLa shLuc+ STV 2


title: Undifferentiated Dicer -/- (27H) ES cell line replicate_1

description: ES cells deficient of Dicer_date of analysis 16082006

source_name: Embryonic stem cell

tag: Undifferentiated Dicer -/- ES cell line, passage 18


title: Undifferentiated Dicer +/- (D4) ES cell line replicate_3

description: ES cells heterozygous for Dicer_date of analysis 16082006

tag: Undifferentiated Dicer +/- ES cell line, passage 20


title: Undifferentiated Dicer -/- (27H) ES cell line replicate_2


title: HeLa shLuc+ 0min 1

source_name: HeLa shLuc+ 0min 1


title: HeLa shLuc- 0min 1

source_name: HeLa shLuc- 0min 1


title: Undifferentiated Dicer +/- (D4) ES cell line replicate_2


title: Undifferentiated Dicer -/- (27H) ES cell line replicate_3


title: HeLa shRHAU+ 0min 3

description: This is the sample of HeLa-shRHAU cells with expression of short hairpin RNA

source_name: HeLa shRHAU+ 0min 3


title: HeLa shRHAU+ 90min 2

description: This is the sample of HeLa-shRHAU cells with expression of short hairpin RNA, 90 min incubation with ActD

source_name: HeLa shRHAU+ 90min 2


title: HeLa shLuc- 0min 2

source_name: HeLa shLuc- 0min 2


title: HeLa shLuc- STV 2

source_name: HeLa shLuc- STV 2


title: HeLa shRHAU+ STV 3

description: This is the sample of HeLa-shRHAU cells with expression of short hairpin RNA, cultured 24 hrs in serum-depleted medium

source_name: HeLa shRHAU+ STV 3


title: 2 week old C57BL6 control lung 2

description: B6 Lung gene expression


title: HeLa shRHAU- STV 3

description: This is the sample of HeLa-shRHAU cells without expression of short hairpin RNA, cultured 24 hrs in serum-depleted medium

source_name: HeLa shRHAU- STV 3


title: HeLa shLuc+ STV 1

source_name: HeLa shLuc+ STV 1


title: HeLa shRHAU+ 30min 2

description: This is the sample of HeLa-shRHAU cells with expression of short hairpin RNA, 30 min incubation with ActD

source_name: HeLa shRHAU+ 30min 2


title: HeLa shRHAU+ 60min 2

description: This is the sample of HeLa-shRHAU cells with expression of short hairpin RNA, 60 min incubation with ActD

source_name: HeLa shRHAU+ 60min 2


title: HeLa shRHAU- 90min 2

description: This is the sample of HeLa-shRHAU cells without expression of short hairpin RNA, 90 min incubation with ActD

source_name: HeLa shRHAU- 90min 2


title: HeLa shRHAU- 60min 2

description: This is the sample of HeLa-shRHAU cells without expression of short hairpin RNA, 60 min incubation with ActD

source_name: HeLa shRHAU- 60min 2


title: HeLa shRHAU+ STV 2

source_name: HeLa shRHAU+ STV 2


title: Undifferentiated Dicer +/- (D4) ES cell line replicate_1


title: HeLa shRHAU+ 120min 2

description: This is the sample of HeLa-shRHAU cells with expression of short hairpin RNA, 120 min incubation with ActD

source_name: HeLa shRHAU+ 120min 2


title: HeLa shRHAU+ 0min 2

source_name: HeLa shRHAU+ 0min 2


title: HeLa shRHAU- 120min 2

description: This is the sample of HeLa-shRHAU cells without expression of short hairpin RNA, 120 min incubation with ActD

source_name: HeLa shRHAU- 120min 2


title: HeLa shRHAU- 0min 2

description: This is the sample of HeLa-shRHAU cells without expression of short hairpin RNA,

source_name: HeLa shRHAU- 0min 2


title: HeLa shRHAU- STV 2

source_name: HeLa shRHAU- STV 2


title: HeLa shRHAU+ 120min 1

source_name: HeLa shRHAU+ 120min 1


title: HeLa shRHAU- 30min 2

description: This is the sample of HeLa-shRHAU cells without expression of short hairpin RNA, 30 min incubation with ActD

source_name: HeLa shRHAU- 30min 2


title: HeLa shRHAU+ 90min 1

source_name: HeLa shRHAU+ 90min 1


title: HeLa shRHAU- 0min 3

description: This is the sample of HeLa-shRHAU cells without expression of short hairpin RNA

source_name: HeLa shRHAU- 0min 3


title: HeLa shRHAU+ 60min 1

source_name: HeLa shRHAU+ 60min 1


title: HeLa shRHAU- 90min 1

source_name: HeLa shRHAU- 90min 1


title: HeLa shRHAU+ 0min 1

source_name: HeLa shRHAU+ 0min 1


title: HeLa shRHAU+ STV 1

source_name: HeLa shRHAU+ STV 1


title: HeLa shRHAU- 120 min 1

source_name: HeLa shRHAU- 120 min 1


title: Single cell profile of retinal progenitor cell E14.5 B1

status: Public on Dec 31 2007

city: Boston

first: jeffrey

last: trimarchi

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Retinas were dissociated to individual cells using papain and single cells were harvested using a capillary pipette drawn into a fine needle. The isolated single cells were lysed, the RNA reverse transcribed, and the resulting cDNAs subjected to a 35 cycle RT-PCR based protocol that was previously shown to generate a sufficient amount of cDNA (10-20 ug) for hybridization on Affymetrix microarrays.

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The MAS5.0 algorithm was used with the data normalized by scaling all probe sets to 500.

source_name: E14.5 single retinal progenitor cell B1

label_protocol: Ten micrograms of each single cell cDNA was digested with DNase I for 13 minutes at 37C, heated to 99C for 15 minutes and biotin labeled using Biotin N6 ddATP (Enzo Biosciences) and TdT (Roche) at 37C for 1.5 hours.

extract_protocol: Single retinal cells were isolated, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified. Individual retinal cells were harvested using a mouth pipette and were expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40). The total single cell RNA was reverse transcribed using Superscript II (Invitrogen) combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

tag: cell type

value: retinal progenitor

tag: background strain

tag: developmental stage

value: embryonic day 14.5 (E14.5)


title: Single cell profile of retinal progenitor cell F3

source_name: P0 single retinal progenitor cell F3

tag: Single cells were harvested from a dissociated CD1 mouse retina at postnatal day 0 (P0).


title: Single cell profile of adult rod photoreceptor 1

source_name: Adult single rod photoreceptor 1

tag: Single cells were harvested from a dissociated adult CD1 mouse retina.


title: HeLa shRHAU- 30min 1

source_name: HeLa shRHAU- 30min 1

tag: Gender


title: Single cell profile of retinal progenitor cell E12.5 G2

source_name: E12.5 single retinal progenitor cell G2

value: embryonic day 12.5 (E12.5)


title: Single cell profile of retinal ganglion cell F6

source_name: E12.5 single retinal ganglion cell F6

value: retinal ganglion


title: Single cell profile of retinal progenitor cell E12.5 E5

source_name: E12.5 single retinal progenitor cell E5


title: sidroshaC-transfected sample

first: John

middle: C

last: Newman

address: 1959 NE Pacific St.

department: Biochemistry

description: Gene expression data from HeLa cells 72 hours following transfection with anti-Drosha retroviral siRNA expression vector sidroshaC

hyb_protocol: Following cRNA preparation and fragmentation according to Affymetrix protocol, cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChip Operayting Software (GCOS) 1.4 using Affymetrix default analysis settings and global scaling to an arbitrary mean value of 800 as normalization method.

source_name: HeLa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HeLa cells grown in DMEM+10% FBS at 37degC

treatment_protocol: HeLa cells at 50% confluence were infected with retroviral supernatants; at 24 hrs split and puromycin selected (1 ug/mL); at 72 hrs harvested at 50-80% confluence

tag: sidroshaC-transfected sample


title: Single cell profile of retinal progenitor cell B1

source_name: E12.5 single retinal progenitor cell B1


title: HeLa shRHAU- 0min 1

description: This is the control sample without expression of the short hairpin shRHAU at actinomycin time zero

hyb_protocol: 15 μg of fragmentated cRNA was hybridized to Human U133 plus 2.0 GeneChipsTM.

scan_protocol: The chip was scanned using an Affymetrix 7G scanner

data_processing: GC-RMA expression values and detection P-values were estimated using Refiner 4.0 from Genedata AG (Basel, Switzerland). Data analysis was performed using Analyst 4.0 from Genedata AG (Basel, Switzerland). The chip distributions were standardized by quantile normalization and they were scaled to make the median expression value 500. For the analysis of steady-state RNA levels, genes were required to have a detection p-value < 0.04 (Affymetrix default) in at least two replicates of any one condition. The objective was to exclude genes that are not expressed in any condition. They were then subjected to a student t-test (P<0.05) and have a median fold change of 1.5 or 2 greater between samples dox+ and dox- or with and without starvation.

source_name: HeLa shRHAU- 0min 1

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen)


title: siGFP-transfected sample 2

description: Gene expression data from HeLa cells 72 hours following transfection with anti-GFP retroviral siRNA expression vector, sample 2

tag: siGFP-transfected sample 2


title: siGFP-transfected sample 1

description: Gene expression data from HeLa cells 72 hours following transfection with anti-GFP retroviral siRNA expression vector, sample 1

tag: siGFP-transfected sample 1


title: HeLa shRHAU+ 30min 1

source_name: HeLa shRHAU+ 30min 1


title: Single cell profile of retinal progenitor cell B4

source_name: E12.5 single retinal progenitor cell B4


title: Single cell profile of retinal ganglion cell F1

source_name: P0 single retinal ganglion cell F1


title: HeLa shRHAU- STV 1

source_name: HeLa shRHAU- STV 1


title: Single cell profile of retinal amacrine cell B1

source_name: P0 single retinal amacrine cell B1


title: Single cell profile of retinal progenitor cell G2

source_name: P0 single retinal progenitor cell G2

value: postnatal day 0 (P0)


title: Single cell profile of retinal ganglion cell A6

source_name: P0 single retinal ganglion cell A6


title: Single cell profile of retinal progenitor cell E13.5 A8

source_name: E13.5 single retinal progenitor cell A8

value: embryonic day 13.5 (E13.5)


title: HeLa shRHAU- 60min 1

source_name: HeLa shRHAU- 60min 1


title: Single cell profile of retinal amacrine cell G3

source_name: P0 single retinal amacrine cell G3


title: Single cell profile of retinal amacrine cell F6

source_name: P0 single retinal amacrine cell F6


title: Single cell profile of retinal progenitor cell B3

source_name: E13.5 single retinal progenitor cell B3


title: sidroshaB-transfected sample

description: Gene expression data from HeLa cells 72 hours following transfection with anti-Drosha retroviral siRNA expression vector sidroshaB

tag: sidroshaB-transfected sample


title: Single cell profile of retinal progenitor cell E16.5 E5

source_name: E16.5 single retinal progenitor cell E5

value: embryonic day 16.5 (E16.5)


title: Single cell profile of retinal progenitor cell E1

source_name: E12.5 single retinal progenitor cell E1


title: Single cell profile of retinal progenitor cell E16.5 D5

source_name: E16.5 single retinal progenitor cell D5


title: Single cell profile of retinal ganglion cell E13.5 A3

source_name: E13.5 single retinal ganglion cell A3

tag: Single cells were harvested from a dissociated CD1 mouse retina at embryonic day 13.5 (E13.5).


title: Single cell profile of retinal ganglion cell B1

source_name: E15.5 single retinal ganglion cell B1

value: embryonic day 15.5 (E15.5)


title: Single cell profile of retinal ganglion cell C7

source_name: E15.5 single retinal ganglion cell C7

tag: Single cells were harvested from a dissociated CD1 mouse retina at embryonic day 15.5 (E15.5).


title: Single cell profile of retinal progenitor cell D6

source_name: E16.5 single retinal progenitor cell D6


title: Single cell profile of retinal progenitor cell E16.5 E3

source_name: E16.5 single retinal progenitor cell E3


title: Single cell profile of retinal progenitor cell A6

source_name: E13.5 single retinal progenitor cell A6


title: Single cell profile of retinal progenitor cell E2

source_name: P0 single retinal progenitor cell E2


title: Single cell profile of retinal ganglion cell B5

source_name: E15.5 single retinal ganglion cell B5


title: Single cell profile of retinal progenitor cell C5

source_name: P0 single retinal progenitor cell C5


title: Single cell profile of retinal ganglion cell C6

source_name: P0 single retinal ganglion cell C6


title: Single cell profile of retinal ganglion cell A3

source_name: P0 single retinal ganglion cell A3


title: Single cell profile of retinal photoreceptor cell E1

source_name: P0 single retinal photoreceptor cell E1

value: retinal photoreceptor


title: HeLa shLuc- STV 1

description: This is the sample of HeLa-shLuc cells without expression of short hairpin RNA, cultured 24 hrs in serum-depleted medium

source_name: HeLa shLuc- STV 1

tag: Strain


title: Single cell profile of retinal progenitor cell B5

source_name: P0 single retinal progenitor cell B5


title: Single cell profile of retinal progenitor cell J1

source_name: E16.5 single retinal progenitor cell J1


title: Single cell profile of retinal progenitor cell J2

source_name: E16.5 single retinal progenitor cell J2


title: Single cell profile of retinal progenitor cell H2

source_name: P0 single retinal progenitor cell H2


title: Single cell profile of retinal amacrine cell J6

source_name: E16.5 single retinal amacrine cell J6

value: retinal amacrine


title: Single cell profile of retinal progenitor cell H3

source_name: P0 single retinal progenitor cell H3


title: Single cell profile of retinal progenitor cell C8

source_name: P0 single retinal progenitor cell C8


title: Single cell profile of retinal progenitor cell B6

source_name: P0 single retinal progenitor cell B6


title: Single cell profile of retinal amacrine cell D1

source_name: P0 single retinal amacrine cell D1


title: Single cell profile of retinal progenitor cell B7

source_name: E15.5 single retinal progenitor cell B7


title: Single cell profile of retinal progenitor cell F1

source_name: E16.5 single retinal progenitor cell F1


title: Single cell profile of retinal progenitor cell E8

source_name: E16.5 single retinal progenitor cell E8


title: Single cell profile of retinal ganglion cell E4

source_name: E12.5 single retinal ganglion cell E4


title: Single cell profile of retinal photoreceptor cell H1

source_name: P0 single retinal photoreceptor cell H1


title: Single cell profile of retinal progenitor cell E3

source_name: E12.5 single retinal progenitor cell E3


title: Single cell profile of retinal progenitor cell P0 E6

source_name: P0 single retinal progenitor cell E6


title: Single cell profile of retinal progenitor cell D7

source_name: E14.5 single retinal progenitor cell D7


title: Single cell profile of retinal ganglion cell D8

source_name: E14.5 single retinal ganglion cell D8


title: Single cell profile of retinal progenitor cell C1

source_name: P0 single retinal progenitor cell C1


title: Single cell profile of retinal progenitor cell F4

source_name: E16.5 single retinal progenitor cell F4


title: Single cell profile of retinal progenitor cell A5

source_name: E13.5 single retinal progenitor cell A5


title: Single cell profile of retinal progenitor cell E5

source_name: P0 single retinal progenitor cell E5


title: Single cell profile of retinal ganglion cell F3

source_name: E12.5 single retinal ganglion cell F3


title: Single cell profile of retinal ganglion cell E1

source_name: E14.5 single retinal ganglion cell E1


title: Single cell profile of retinal progenitor cell J4

source_name: E16.5 single retinal progenitor cell J4


title: Single cell profile of retinal progenitor cell A8

source_name: P0 single retinal progenitor cell A8


title: Single cell profile of retinal progenitor cell F2

source_name: E12.5 single retinal progenitor cell F2


title: Single cell profile of retinal progenitor cell E6

source_name: E12.5 single retinal progenitor cell E6


title: Single cell profile of retinal progenitor cell F5

source_name: E16.5 single retinal progenitor cell F5


title: Single cell profile of retinal amacrine cell A4

source_name: P0 single retinal amacrine cell A4


title: Single cell profile of retinal progenitor cell A4

description: Retinas were dissociated to individual cells using papain and single cells were harvested using a capillary pipette drawn into a fine needle.   The isolated single cells were lysed, the RNA reverse transcribed, and the resulting cDNAs subjected to a 35 cycle RT-PCR based protocol that was previously shown to generate a sufficient amount of cDNA (10-20 ug) for hybridization on Affymetrix microarrays.

source_name: E12.5 single retinal progenitor cell A4

extract_protocol: Single retinal cells were isolated, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified.  Individual retinal cells were harvested using a mouth pipette and were expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40).  The total single cell RNA was reverse transcribed using Superscript II (Invitrogen) combined with an oligo dT primer.  This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.


title: Forebrain P17 (35h)

city: Stanford

last: Cahoy

address: 299 Campus Drive

department: Department of Neurobiology

institute: Stanford University

description: John_35H-P17-cortex_Mouse430 _2

hyb_protocol: Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility

scan_protocol: Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility

data_processing: Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files.  Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated.  Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20).  Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percentage present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency.  In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.;  CEL data files were also independently analyzed using the dChip algorithm.  Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).

source_name: Postnatal age day 17 Forebrain Forebrain

label_protocol: Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 30-50 ng total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).

growth_protocol: Preparation Of Mouse Astroglia: Preparation of astroglia cultures was as follows.  Cortices were isolated by crude dissection of six P1 mice from a S100β-EGFP transgenic litter, meninges were removed, and the tissue was chopped using a curved-blade surgical scalpel.  This tissue was enzymatically dissociated to make a suspension of single cells.  Briefly, the tissue was incubated at 33 °C for 75 minutes in 20 ml of a papain solution prepared in dissociation buffer containing EDTA and L-cysteine.;  After papain treatment the tissue was washed with 3 x 4 ml of DPBS containing BSA (1.5 mg/ml), ovomucoid (1.5 mg/ml), and DNase (125U/ml) (ovomucoid inhibitor).  The tissue was then mechanically dissociated by gentle sequential trituration using a 5 ml pipette with 5 x 4 ml fresh ovomucoid inhibitor to yield a suspension of single cells.  Dissociated cells were harvested by centrifugation at 220 x g for 10 minutes.  Cells were resuspended in 12 ml of concentrated ovomucoid inhibitor (5 mg/ml BSA and 5 mg/ml ovomucoid) and harvested by centrifugation.  Dissociated cells were resuspended in 15 ml of astroglia media and plated in 75 cm2 tissue culture flasks (BD Falcon, 353136) that were pre-coated with PDL (10 μg/ml in water, Sigma, P6407) at a density of 25-30 million cells per flask.  Astroglia media contained Dulbecco's modified eagle medium (DMEM, Invitrogen, 11960-044), 10% fetal bovine serum (FBS, Invitrogen, 10437-028), 2 mM glutamine (Invitrogen, 25030-081), 1 mM Na pyruvate (Invitrogen, 11360-070), 5 μg/ml N-Acetyl-L-cysteine (NAC, Sigma, A8199), 5 μg/ml insulin (Sigma, I6634), 100 U/ml penicillin-streptomycin (Invitrogen, 15140-122), and 10 μM hydrocortisone (Sigma, H0888).  When plated under these conditions most cells including neurons and mature astrocytes die, but a small percentage of immature cells are able to survive and proliferate.;  After 3 days the astroglia layer was confluent and the flask was rinsed once with DPBS and then shaken 3 times with DPBS containing phenol red to remove contaminating OL progenitor cells (OPCs), and fresh astroglia media was added.  OPCs grow on top of the single cell monolayer of astroglia, so they can be removed by vigorous shaking of the sealed tissue culture flask.  After 2 days, 10 μM cytosine arabinoside (AraC, Sigma, C1768) was added to kill dividing cells such as fibroblasts and microglia; the underlying monolayer of astrocytes is not affected by the antimitotic because astroglia divide slowly in dense cultures due to contact inhibition.  After 48 hours the astroglia were trypsinized off and plated onto PDL-coated 15 cm tissue culture dishes at 2 million cells per dish in astroglia media.;  For preparation of astroglia grown in serum free media, confluent cultures of astroglia prepared as described above were washed three times with DPBS and 20 ml serum-free media was added.  Serum-free medium, modified from Bottenstein and Sato (1979), contained neurobasal (Invitrogen, 21103-049), bovine serum albumin (100 μg/ml, BSA, Sigma, A4161), selenium (40 ng/ml, Sigma, S5261), putrescine (16 μg/ml, Sigma, P5780), transferrin (100 μg/ml, Sigma, T1147), progesterone (60 ng/ml, Sigma, P8783), triiodo-thyronine (40 ng/ml, Sigma, T6397), penicillin-streptomycin (100U/ml), insulin (5 μg/ml) NAC (5 μg/ml), pyruvate (1 mM), and glutamine (2 mM).

extract_protocol: Total RNA was isolated from acutely purified cells with the RNeasy micro kit (Qiagen, Valencia, CA) using Qiashredder columns for cell lysis and Qiagen on-column DNase treatment to remove any contaminating genomic DNA.  The integrity of RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara , CA), and RNA concentration was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Rockland, DE).

treatment_protocol: The purification procedures are based on previously described dissociation (Huettner and Baughman, 1986; Segal et al., 1998) and immunopanning purification protocols for other cell types (Barres et al., 1988; Barres et al., 1992; Meyer-Franke et al., 1995).  All aspects of the panning and FACS purification procedures are summarized below.;  Preparation Of Mouse Forebrain Cell Suspensions: Six to eight mice from a wild-type litter (C57BL/6, Charles River, Wilmington, MA) or S100β-EGFP transgenic litter (C57BL/6 x DBA (F1), Kosmos line, Zuo et al., 2004) were used.  The forebrain was isolated by removal of the olfactory lobes, cerebellum, and midbrain/hindbrain structures by crude dissection, and the tissue was diced with a curved-blade surgical scalpel (Feather, Osaka, Japan, GRF-2976 #10).  To isolate cerebral cortical gray matter astrocytes, the brain was sliced in 2-3 mm coronal sections and the cerebral cortex was carefully dissected away from the ventral white matter tracks.  This tissue was enzymatically dissociated to make a suspension of single cells, essentially as described by Huettner and Baughman (Huettner and Baughman, 1986; Segal et al., 1998).  Briefly, the tissue was incubated at 33 °C for 80 minutes (90 minutes for animals P16 and older) in 20 ml of a papain solution (20 U/ml, Worthington, Lakewood, NJ, LS03126) prepared in dissociation buffer with EDTA (0.5 mM), and L-cysteine-HCl (necessary to activate the papain, 1 mM, Sigma, St. Louis, MO, C7880).  The dissociation buffer contained Earle’s balanced salts (EBSS, Sigma, E7510), D(+)-glucose (22.5 mM), NaHCO3 (26 mM), and DNase (125U/ml, Worthington, LS002007) and requires careful equilibration with 5% CO2 and 95% O2 gas before use and during papain treatment.  When dissociation buffer is exposed to room air during trituration, minimizing surface area and avoiding bubbles is essential to maintain the proper pH and cell health.;  After papain treatment to loosen contacts in the extracellular matrix, the tissue was washed with 3 x 4 ml dissociation buffer containing BSA (1.0 mg/ml, Sigma, A-8806) and ovomucoid (also known as Trypsin Inhibitor, 1.0 mg/ml, Roche Diagnostics Corporation, Indianapolis, IN, 109878) (inhibitor solution) and then mechanically dissociated by gentle sequential trituration using a 5 ml pipette with 5 x 4 ml fresh inhibitor solution to yield a suspension of single cells.  Dissociated cells were layered on top of 12 ml of concentrated inhibitor solution (5 mg/ml BSA and 5 mg/ml ovomucoid) and harvested by centrifugation (140 x g for 5 minutes, 220 x g for 10 minutes when purifying OL lineage cells).  This method routinely yielded ~15-20 million cells per mouse pup forebrain, with excellent cell health as determined by morphology and viability (>90% by trypan blue exclusion).

tag: C57BL/6 x DBA (F1)


title: Single cell profile of retinal progenitor cell D5

source_name: E12.5 single retinal progenitor cell D5


title: Neurons P7n (38B)

description: John_38B NegB P7_Mouse430 _2

source_name: Postnatal age day 7 Neg (Bsl1) Neurons


title: Cultured Astroglia (41FCS)

description: John_41FCS Cult_Mouse430 _2

source_name: Culture day 28 Culture Cultured Astroglia Astroglia


title: Astros P1 (34a)

description: John_34A-P1-pos_Mouse430 _2

source_name: Postnatal age day 1 Positive Astrocytes


title: Myelin OLs (30q)

description: John_30Q MOQ_Mouse430 _2

source_name: Postnatal age day 17 MOG Myelin Oligodendrocytes


title: Astros P17g (36g)

description: John_jlz5-36G-P17_Mouse430 _2

source_name: Postnatal age day 17 Gray Astrocytes


title: Astros P30 (33a)

description: John_33A-P30-pos_Mouse430 _2

source_name: Postnatal age day 30 Positive Astrocytes


title: OLs (30p)

description: John_30P GC_Mouse430 _2

source_name: Postnatal age day 17 GC Oligodendrocytes


title: Astros P17 (32a)

description: Lu_32A_Mouse430 _2

source_name: Postnatal age day 17 Positive Astrocytes


title: OPCs (30o)

description: John_30O PDGFRa_Mouse430 _2

source_name: Postnatal age day 17 PDGFRa OPCs


title: Astros P17 (24a)

description: John_24A P17_Mouse430 _2


title: Astros P17 (22a)

description: John_22A P17_Mouse430 _2


title: Cultured FACS Pos (19c)

description: John_19C_Mouse430 _2

source_name: Culture day 12 FACS pos Cultured Astroglia FACS Pos


title: Cultured Astroglia (19e)

description: John_19E_Mouse430 _2

source_name: Culture day 12 Culture Cultured Astroglia Astroglia


title: Astros P17g (25g)

description: John_25G P17G_Mouse430 _2

source_name: Postnatal age day 17 Gray-single Astrocytes


title: Cultured FACS All (19d)

description: John_19D_Mouse430 _2

source_name: Culture day 12 FACS all Cultured Astroglia FACS All


title: Cultured FACS All (14d)

description: John_14D_Mouse430 _2

source_name: Culture day 9 FACS all Cultured Astroglia FACS All


title: Cultured Astroglia (23e)

description: John_23E Cult_Mouse430 _2

source_name: Culture day 33 Culture Cultured Astroglia Astroglia


title: Cultured Astroglia (14f)

description: John_14F_Mouse430 _2

source_name: Culture day 9 Culture Cultured Astroglia Astroglia


title: Cultured FACS Pos (14c)

description: John_14C_Mouse430 _2

source_name: Culture day 9 FACS pos Cultured Astroglia FACS Pos


title: Neurons P7 (6b)

source_name: Postnatal age day 7 Negative Neurons


title: Neurons P26 (18b)

description: John_18B_Mouse430 _2

source_name: Postnatal age day 26 Negative Neurons


title: Neurons P16 (13b)

description: John_13B_Mouse430 _2

source_name: Postnatal age day 16 Negative Neurons


title: Astros P7 (6a)

source_name: Postnatal age day 7 Positive Astrocytes


title: Neurons P7 (5b)


title: Neurons P16n (11d)

source_name: Postnatal age day 16 Neg (Bsl1) Neurons


title: Neurons P7 (8b)


title: Astros P7 (5a)


title: OPCs (PDGF_c)

description: Ben_PDGF_c_Mouse430 _2

source_name: Postnatal age day 16 PDGFRa OPCs


title: Myelin OLs (MOG_c)

description: Ben_MOG_c_Mouse430 _2

source_name: Postnatal age day 16 MOG Myelin Oligodendrocytes


title: Neurons P16 (10d)


title: Myelin OLs (MOG_b)

description: Ben_Emery_MOG_b_Mouse430 _2


title: OLs (GC_b)

description: Ben_Emery_GC_b_Mouse430 _2

source_name: Postnatal age day 16 GC Oligodendrocytes


title: Myelin OLs (MOG_a2)

description: Ben_MOG_a2_Mouse430 _2


title: OLs (GC_a3)

description: Ben_GC_a3_Mouse430 _2


title: Expression data from Cas exon 2-homo deficient primary fibroblast2

city: Hiroshima

first: Eiso

last: Hiyama

state: Hiroshima

address: 1-2-3, Kasumi, Minami-ku

department: Natural Science Center for Basic Research and Deve

country: Japan

institute: Hiroshima University

description: Cas exon 2+/∆ mice were intercrossed and embryos at 12.5 dpc were collected. Heads and inner organ tissues were used for genotyping and primary embryonic fibroblasts were isolated from the remaining of embryos and cultured

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 degree 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 GeneChip Scanner 3000.

data_processing: The data were analyzed using GeneSpring (Agilent Technologies).

source_name: MEF38 homo

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

growth_protocol: Cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal calf serum (FCS), penicillin and streptomycin at 37 degree with 5% CO2.

treatment_protocol: Embryos at 12.5 dpc were collected and primary embryonic fibroblasts were isolated from them.

value: B6, mouse embryonal fibroblasts, Cas exon 2∆/∆,MEF38 homo


title: Expression data from Cas exon 2-hetero deficient primary fibroblast 1

source_name: MEF33 hetero

value: B6, mouse embrynal fibroblasts, Cas exon 2+/∆,MEF33 hetero


title: Expression data from Cas wild primary fibroblast 2

source_name: MEF32 wild

value: B6, mouse embryonal fibroblasts, Cas exon 2+/+,MEF32 wild


title: Expression data from Cas exon 2-hetero deficient primary fibroblast2

source_name: MEF36 hetero

value: B6, mouse embryonal fibroblasts, Cas exon 2+/∆,MEF36 hetero


title: whole saliva pSS patient 4

city: Los  Angeles

first: david

last: wong

address: 10833 Le Conte ave.

institute: UCLA

description: whole saliva','pSS patient'

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

label: biotinylate

source_name: pSS whole saliva freezed -80 right after colloection

label_protocol: Amplified RNA was labeled at second round of IVT using Gene Chip Expression 3'-Amplification Reagents for IVT labeling according to manusfacturer's instruction (Affymetrix, Santa Clara, CA USA).

extract_protocol: Total RNA was extracted from whole saliva according to the manufacturer's instruction (QIAamp Viral RNA kit, Qiagene, Valencia, CA USA). Isolated RNA was subjected to two round linear amplification using RiboAmp HS RNA Amplification kit (ARCTURUS, Mountain view, CA USA).

tag: gender


title: whole saliva pSS patient 3

description: whole saliva','pSS patient'


title: whole saliva pSS patient 10

description: whole saliva','pSS patient'


title: Expression data from Cas wild primary fibroblasts1

source_name: MEF31 wild

tag: Strain B6, mouse embryonic fibroblasts, Cas exon 2+/+,MEF31 wild


title: whole saliva pSS patient 8

description: whole saliva','pSS patient'


title: Expression data from Cas exon 2-homo deficient primary fibroblast1

source_name: MEF35 homo

value: B6, mouse embryonal fibroblasts, Cas exon 2∆/∆,MEF35 homo


title: whole saliva control 10

description: whole saliva','healthy control'

source_name: whole saliva freezed -80 right after colloection


title: whole saliva control 8

description: whole saliva','healthy control'


title: whole saliva control 9

description: whole saliva','healthy control'


title: OLs (GC_c)

description: Ben_GC_c_Mouse430 _2


title: whole saliva control 7

description: whole saliva','healthy control'


title: whole saliva pSS patient 6

description: whole saliva','pSS patient'


title: whole saliva pSS patient 2

description: whole saliva','pSS patient'


title: whole saliva control 2

description: whole saliva','healthy control'


title: whole saliva pSS patient 5

description: whole saliva','pSS patient'

value: female','age:21','tissue:whole saliva','pSS patient '


title: whole saliva pSS patient 9

description: whole saliva','pSS patient'


title: whole saliva pSS patient 7

description: whole saliva','pSS patient'


title: whole saliva control 3

description: whole saliva','healthy control'


title: Expression analysis of human neuroblastoma (Affymetrix)

description: Affymetrix GeneChipTM Human Genome U133 Plus 2.0 array (~47,000 transcripts, Affymetrix, Santa Clara, CA)

hyb_protocol: After hybridization cocktails preparation, the Human Genome U133 Plus 2.0 Array was hybridized with the fragmented labelled cRNA for 16 h at 45 °C as described in the Affymetrix Technical Analysis Manual.

scan_protocol: Scan protocol GeneChips, bound to streptavidin-phycoerythrin, were processed using the Affymetrix GeneChip Fluidics Station 450 and scanned with an GeneChip Scanner 3000 (Affymetrix).

data_processing: Data were processed using functional ‘ON/OFF’ state of a gene

source_name: human neuroblastoma tissue

label_protocol: Conversion of double stranded cDNA into biotin-labeled cRNA was accomplished using the One-Cycle cDNA Synthesis Kit (T7) (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from tissue specimen using RNA isolation kit according to the manufacturer’s instructions (Stratagene, Agilent techonology, Santa Clara , CA) and purified further using the Rneasy Mini Kit (Invitrogen).

treatment_protocol: At surgery, right adrenal tumor and lymph node metastasis were resected. Then, small peccieces of primary tumor was picked up and frozen immediately until use.

value: female

tag: Age

value: 13 months old

tag: Tissue

value: tumor adrenal grand from time-pregnant rats

tag: Cells

value: neuroblastoma cells


title: whole saliva pSS patient 1

description: whole saliva','pSS patient'


title: whole saliva control 4

description: whole saliva','healthy control'


title: whole saliva control 6

description: whole saliva','healthy control'


title: AWP_AL_Txed_1

city: Memphis

first: Shirlean

middle: B

last: Goodwin

state: TN

address: 3774 Walker Ave

department: Biology

institute: University of Memphis

description: The mRNA levels were measured using Affymetrix ATH1 chips (containing 22,810 probe sets) according to standard GeneChip Expression assay protocol. Total RNA was extracted from 100 pooled  Arabidopsis seedlings for each GeneChip, control and Al-treated.  A total of four chips were used in this experiment, representing two biological replicates to measure expression of whole plant material.

hyb_protocol: Twenty micrograms of the cRNA was fragmented to strands of 35 to 200 bases in length. The fragment cRNA was hybridized to and Affymetrix ATH1 array GeneChip at 450C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320). The GeneChip arrays were washed and stained (streptavidin phycoerythrin) on an Affymetrix Fluidics Station 400, followed by scanning.

scan_protocol: Scanned using Affymetrix 3000 GeneChip scanner

data_processing: After hybridization, the chips were scanned using a GeneChip Scanner and raw hybridization data from microarray experiments were imported directly into Affymetrix GeneChip Operating software (GCOS) v1.2 for normalization and to determine the probe intensities and “Present” (P) or “Absent” (A) calls for each chip. The scanned image results for all 4 chips were quantified and analyzed using, dChip (Li and Wong, 2001) and RMA software (Irizarry et al., 2003). The gene list generated in dchip was uploaded into gene ontology consortium website (http://www.geneontology.org/) to further determine the functional categories of up- and down regulated gene expression.

label: Enzo Biotin-labeled in vitro transcribed (IVT)

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings, removed from agar plates, 16 h treatment

label_protocol: Briefly, total RNA (8 mg) was synthesized to cDNA using the Superscript Double-Stranded cDNA synthesis kit (Invitrogen Corp, Carlsbad, CA) and poly dT-nucleotide primers that contain a sequence recognized by T7 RNA polymerase. The newly synthesized cDNA was used as a template to generate biotin-labeled invitro transcribed (IVT) cRNA using the Bio-Array High Yield RNA transcript labeling kit (Enzo Diagnostics, Inc, Farmingdale, NY).

extract_protocol: 100 seedlings were harvested at following 16 hr Al or mock treatment.Tissue was ground to a fine powder in liquid nitrogen using a pestle and mortar and total RNA was extracted using the following method. Each 0.5 to 1 g of powdered tissue were added to 5 cm3 of STAT-60 (Tel-Test, TX). The mixture was homogenized and stored on ice for 10 min. Chloroform/isoamyl (24:1, v:v) ETOH was added to the homogenate and centrifuged at 12000g for 30 min (40C). Following the transfer of the aqueous phase to a fresh tube, RNA was precipitated with isopropanol overnight at –200C, pelleted by centrifugation at 12000g for 30 min (40C), and resuspended 0.1 cm3 of RNase-free water. Total RNA was quantified using Beckman Spectrophotometer, and qualified by running 1 μg cm-1 of each sample onto a RNA Lab-On-A-Chip using a Agilent Bioanalyzer 2100 (Agilent technologies, Mountain View, CA).

treatment_protocol: Seedlings with 2- to 3 cm root length were removed from agar plates and submerged in 1000 ml flasks containing 500 ml of modified one-sixth MS liquid medium containing 50 micromolar aluminum and 1% sucrose added as a carbon source for 16 hr.

tag: Arabidopsis cv columbia


title: JEKO-1 cell line treated with emetine followed by actinomycin D treatment. Pool of a time course

city: Barcelona

first: Pedro

last: Jares

state: Barcelona

address: c/ Villarroel 170

department: Genomics Unit

country: Spain

institute: IDIBAPS

description: Gene expression data from JEKO-1 cell line treated with emetine

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hours at 45ºC on human 133 Plus 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix 3000 Scanner system

data_processing: The data were analyzed with GCOS 1.4 using the Affymetrix default analysis settings and global scailing as normalization method. The target intensity used was arbitrarily set to 150

label_protocol: Biotynilated cRNA were prepared according to the standard Affymetrix protocol from 2 micrograms Total RNA (Expression Analysis Technical Manual (Affymetrix Inc)

extract_protocol: TRIzol extraction followed by a cleanup using the QUIAGEN RNAesy Mini kit

tag: Mantle Cell Lymphoma cell line


title: Astros P8 (7a)

source_name: Postnatal age day 8 Positive Astrocytes


title: RGCm 8d Astroglia (41NB)

description: John_41NB Cult_Mouse430 _2

source_name: Culture day 28 Cult: serum-free RGCm Astroglia


title: JEKO-1 cell line treated with emetine

source_name: JEKO-1 cell line  treated with emetine


title: AWP_Control_2


title: HBL-2 cell line treated with emetine

description: Gene expression data from HBL-2 cell line treated with emetine

source_name: HBL-2 cell line  treated with emetine


title: whole saliva control 1

description: whole saliva','healthy control'


title: whole saliva control 5

description: whole saliva','healthy control'

scan_protocol: Affymetrix standard ptocol

growth_protocol: Frozen at -80 degree after collection.

extract_protocol: Total RNA was extracted from whole saliva according to the manufacturer's instruction (QIAamp Viral RNA kit, Qiagene, Valencia, CA USA).  Isolated RNA was subjected to two round linear amplification using RiboAmp HS RNA Amplification kit (ARCTURUS, Mountain view, CA USA).


title: JEKO-1 cell line mock treated

description: Gene expression data from JEKO-1 cell line mock treated

source_name: JEKO-1 cell line mock treated


title: Granta-519 cell line mock treated

description: Gene expression data from GRANTA cell line mock treated

source_name: GRANTA-519 cell line mock treated


title: Granta- 519 cell line treated with emetine followed by actinomycin D treatment. Pool of a time course

description: Gene expression data from GRANTA cell line treated with emetine

source_name: Granta-519 cell line treated with emetine followed by actinomycin D treatment. Pool of a time course


title: UPN-1cell line treated with emetine followed by actinomycin D treatment. Pool of a time course

description: Gene expression data from UPN-1 cell line treated with emetine

source_name: UPN-1 cell line treated with emetine followed by actinomycin D treatment. Pool of a time course


title: REC-1cell line treated with emetine

source_name: REC-1 cell line  treated with emetine


title: AWP_Control_1


title: REC-1cell line mock treated

description: Gene expression data from REC-1 cell line mock treated

source_name: REC-1 cell line mock treated


title: Granta-519 cell line treated with emetine

source_name: GRANTA-519 cell line  treated with emetine


title: UPN-1cell line treated with emetine

source_name: UPN-1 cell line  treated with emetine


title: HBL-2 cell line mock treated

description: Gene expression data from HBL-2 cell line mock treated

source_name: HBL-2 cell line mock treated


title: HBL-2 cell line treated with emetine followed by actinomycin D treatment. Pool of a time course


title: UPN-1cell line mock treated

description: Gene expression data from UPN-1 cell line mock treated

source_name: UPN-1 cell line mock treated


title: REC-1cell line treated with emetine followed by actinomycin D treatment. Pool of a time course

description: Gene expression data from Rec-1 cell line treated with emetine

source_name: REC-1 cell line treated with emetine followed by actinomycin D treatment. Pool of a time course


title: activin-knockout granulosa cells replicate 1

status: Public on Dec 28 2007

city: Houston

first: Martin

last: Matzuk

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: No additional descriptions

hyb_protocol: Affymetrix standard

scan_protocol: GeneChip Scanner 3000

data_processing: MAS5 default

source_name: isolated granulosa cells from 21-day female mice

label_protocol: Affymetrix Standard Protocol

extract_protocol: Qiagen RNeasy Mini Prep with on column DNAse treatment

treatment_protocol: granulosa cells collected from 2-3 activin-deficient mutant female mice after 44-46 h PMSG injected i.p.

tag: KO

value: Inhba flox/-;Inhbb-/-;Amhr2cre/+, Background Strain:C57BL/6J;129S5/SvEvBrd, gender:female, age:21d treated for 44-46h PMSG pooled from 2-3 females, cell type:isolated granulosa cells, gender:female, age:21d treated for 44-46h PMSG pooled from 2-3 females


title: B6.3

status: Public on Dec 27 2007

city: St Louis

first: Daniel

middle: A

last: Peterson

state: MO

address: 4444 Forest Park

department: Molecular Biology and Pharmacology

institute: Center for Genome Sciences

description: Comparison of Wildtype B6 and Rag1 mice colonized for 10 days with Bacteroides thetaiotaomicron

hyb_protocol: Following fragmentation, 40 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430.2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GS300

data_processing: Image files were analyzed in dCHIP06, samples were normalized to the B6.2 chip, using the quartile method.

molecule: polyA RNA

source_name: distal small intestine from Wildtype

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

growth_protocol: Distal Small intestine (Whole intestinal segments 10, 11, 12, and 14 pooled) from mice colonized for 10 days with B. thetaiotaomicron.

extract_protocol: to be added

tag: Wildtype C57Bl/6 mouse colonized for 10 days with B. thetaiotaomicron


title: B6.1


title: C57BL/6J;129S5/SvEvBrd granulosa cell replicate 2

description: No additional descriptions

source_name: 21-day granulosa cells

treatment_protocol: granulosa cells collected from 2-3 female mice after 44-46 h PMSG injected i.p.

value: C57BL/6J;129S5/SvEvBrd, gender:female, age:21d treated for 44-46h PMSG pooled from 2-3 females, cell type:isolated granulosa cells,


title: Rag1.3

source_name: distal small intestine from Rag 1

tag: Rag 1 -/- mouse colonized for 10 days with B. thetatiotaomicron


title: activin-knockout granulosa cells replicate 2

description: No additional descriptions

source_name: isolated granulosa cells

value: Inhba flox/-;Inhbb-/-;Amhr2cre/+, Background Strain:C57BL/6J;129S5/SvEvBrd, gender:female, age:21d treated for 44-46h PMSG pooled from 2-3 females, cell type:isolated granulosa cells


title: C57BL/6J;129S5/SvEvBrd granulosa cell replicate 1

description: No additional descriptions


title: AWP_AL_Txed_2

source_name: Arabidopsis seedlings, removed from agar plates, 16 h treatment


title: BP.3

tag: Rag 1-/- mouse with 225.4 anti-B.thetaiotaomicron specific IgA producing hybridoma growing subcutaneously colonized with B. thetaiotaomicron for 10 days.


title: BP.1


title: B6.2


title: Rag1.1


title: C57BL/6J;129S5/SvEvBrd granulosa cell replicate 3

description: No additional descriptions


title: BP.2


title: Rag1.2


title: Seedling_OETOP6A1_rep1

status: Public on Dec 26 2007

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

description: Arabidopsis 10-day-old transgenic (overexpressing rice OsTOP6A1 cDNA) seedlings grown under normal growth conditions were used for total RNA isolation. The high-quality total RNA (260/280 ratio between 1.9-2.1 and 260/230 ratio >2.0) was used for microarray analysis

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree celsius on Affymetrix ATH1-121501 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using script EukGE-WS2v4.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: Signal intensity was calculated by GCOS1.4 under default parameters with target mean intensity arbitrarily set to 100

source_name: 10-day-old light-grown transgenic Arabidopsis seedlings

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

growth_protocol: Seeds were surface sterilized with 2% sodium hypochlorite and 0.01% triton X-100 for 5 min followed by rinsing in sterile water for 5 times. Seeds were then suspended in 0.1% agar solution and dispensed on 0.8% agar-gelled MS medium containing 2% sucrose. Plates were sealed and shifted to cold room for 72 h to break dormancy and facilitate uniform germination and then transferred to culture room under continuous illumination.

extract_protocol: TRIzol reagent

tag: Ecotype

value: Columbia

value: light-grown seedlings

tag: Stage

tag: Seedlings:from homozygous transgenic Arabidopsis plants overexpressing rice OsTOP6A1 (Oryza sativa topoisomerase 6 subunit A1) cDNA


title: tumor tissue 6 weeks post virus injection mouse 3

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

hyb_protocol: Hybridization as specified by Affymetrix using the DMSO protocol

scan_protocol: Fluidics station 450 used to stain and wash arrays. Chips were scan using GCOS 1.4

data_processing: Array data analysis utilized the BRB array tool (http://linus.nci.nih.gov/BRB-ArrayTools.html) developed by Dr. Richard Simon and Amy Peng Lam at NIH. Data were filtered at intensity >10, excluding absent calls and normalized via median centering. Probes with missing value or notations with absent calls in >50% of the entire experiments were also excluded.

source_name: human breast cancer implant in nude mice

label_protocol: GeneChip® One-Cycle Target Labeling and Control Reagents (Affymetrix) according to manufacturer instructions

growth_protocol: To evaluate the involvement of host mechanisms in the eradication of transplanted xenografts, we implanted human GI-101A cells (5 × 106 in 100 ml of PBS) s.c. on the right hind leg of 6-8-week-old female nude mice.

extract_protocol: Total RNA was extracted from excised tumors using a QIAGEN RNeasy Protect Mini Kit

treatment_protocol: On day 30 after cell implantation, a single dose of virus (5 × 106 pfu of GLV-1h68 in 100 ml of PBS) was delivered via the femoral vein. Four mice per group were killed 3 and 6 weeks following GLV-1h68 injection. An identical number of control mice treated with PBS alone were killed in parallel.

tag: tumor implant 6 weeks post virus injection


title: tumor tissue 6 weeks post virus injection mouse4


title: tumor tissue 6 weeks post virus injection mouse 1


title: Seedling_OETOP6A1_rep2


title: tumor tissue 3 week control (mixed sample from 4 mice)

description: tumor tissue 3 weeks control

tag: tumor implant 3 weeks post PBS injection


title: tumor tissue 6 weeks post virus injection mouse 2


title: tumor tissue 6 week control (mixed sample from 4 mice)

description: tumor tissue 6 weeks control

tag: tumor implant 6 weeks post PBS injection


title: siRNA Stau1 Duplicate 2

city: Montréal

first: Luc

last: DesGroseillers

state: Québec

address: 2900 Edouard Montpetit

department: Biochimie

country: Canada

institute: Université de Montréal

description: Human HeLa cells were transiently transfected with in vitro-synthesized Stau1 siRNA.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: HeLa cells transiently transfected with a Stau1 siRNA

label_protocol: Standard Affymetrix procedures

growth_protocol: Human HeLa cells were propagated in DMEM medium (GIBCO-BRL) containing 10% fetal bovine serum. 2 X 106 HeLa cells were transiently transfected with in vitro-synthesized Stau1 siRNA.

extract_protocol: TriZol reagent


title: tumor tissue 3 weeks post virus injection mouse 4

tag: tumor implant 3 weeks post virus injection


title: tumor tissue 3 weeks post virus injection mouse 3


title: siRNA Stau1

tag: HeLa cells transiently transfected with a Stau1 siRNA.


title: siRNA Stau1 Duplicate 1

tag: HeLa cells transiently transfected with a Stau1 siRNA


title: Seedling_WT_rep3

description: Arabidopsis 10-day-old wild-type seedlings grown under normal growth conditions were used for total RNA isolation. The high-quality total RNA (260/280 ratio between 1.9-2.1 and 260/230 ratio >2.0) was used for microarray analysis

source_name: 10-day-old light-grown wild-type Arabidopsis seedlings

tag: Tissue


title: Seedling_OETOP6A1_rep3


title: Seedling_WT_rep2


title: Seedling_WT_rep1


title: Knockout aortic banded, biological rep1

status: Public on Dec 25 2007

city: Toronto

first: Sara

last: Arab

state: ONT

address: 610 University Avenue

department: Cardiology

institute: Toronto General Hospital

description: Gene Expression data from KO AB

hyb_protocol: Affymetrix strandard protocol

scan_protocol: GeneChip Operating Software (GCOS) 1.4 was used for scanning

data_processing: Data was analysed using GeneSpring 7.0, Agilent

source_name: Heart

label_protocol: Affmetrix standard protocol

extract_protocol: Trizol

treatment_protocol: Aortic banded vs sham

tag: Genotype

value: KO


title: Knockout aortic banded, biological rep2

description: Gene Expression data from KO AB


title: Knockout sham, biological rep1

description: Gene Expression data from KO Sham


title: Knockout sham, biological rep2

description: Gene Expression data from KO Sham


title: Knockout aortic banded, biological rep3

description: Gene Expression data from KO AB


title: tumor tissue 3 weeks post virus injection mouse 1


title: Knockout sham, biological rep3

description: Gene Expression data from KO Sham


title: tumor tissue 3 weeks post virus injection mouse 2


title: Wild type sham, biological rep3

description: Gene Expression data from WT Sham

value: Wild type


title: Wild type sham, biological rep2

description: Gene Expression data from WT Sham


title: siRNA Control

description: Human HeLa cells were transiently transfected with in vitro-synthesized nonspecific control siRNA.

source_name: HeLa cells transiently transfected with a control siRNA

growth_protocol: Human HeLa cells were propagated in DMEM medium (GIBCO-BRL) containing 10% fetal bovine serum. 2 X 106 HeLa cells were transiently transfected with in vitro-synthesized nonspecific control siRNA.

tag: HeLa cells transiently transfected with a nonspecific control siRNA


title: Wild type sham, biological rep1

description: Gene Expression data from WT Sham


title: siRNA Control Duplicate 1


title: Wild type aortic banded, biological rep2

description: Gene Expression data from WT AB


title: Tet integrin alpha7 C2C12 induced rep1

status: Public on Dec 23 2007

city: Urbana

first: Jianming

last: Liu

state: IL

address: B107 CLSL, 601 S. Goodwin Avenue

department: Department of Cell and Developmental Biology

institute: University of Illinois at urbana-champaign

description: Gene expression data from undifferentiated integrin alpha7 inducible C2C12 myoblasts incubated in basal media for 36hr with 1ug/ml tetracycline

hyb_protocol: Following fragmentation,  labeled cRNA were hybridized at 45°C for approximately 16 hr to Gene Chip Mouse Genome 430 2.0 Expression Array (Affymetrix). The arrays were stained on Gene Chip Fluidics Workstation 450.

scan_protocol: Gene Chips were scanned using the affymetrix GeneArray Scanner 3000.

data_processing: The scanned image was converted into numerical values of the signal intensity (Signal) and into categorical expression level measurement (Absolute Call) using the Affymetrix GCOS V1.1.1 software with default parameters.

source_name: integrin alpha7 C2C12 cells, tetracycline induced

label_protocol: Biotinylated cRNA were prepared according to the manufacturer's instructions (One-Cycle Target Labeling kit, Affymetrix,Inc.)

growth_protocol: integrin alpha7  C2C12 cells were cultured at 37 °C  for 36 hours with 1ug/ml tetracycline

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. total RNA were further subject a a cleanup protocol using a Qiagen Rneasy minikit.

treatment_protocol: integrin alpha7  C2C12 cells were cultured at 37 °C  for 36 hours in Dulbecco's modified Eagle's medium (DMEM) containing 20% FBS, 0.5% chick embryo extract, 2 mM glutamine, 100 units/ml penicillin, 100 µg/ml streptomycin, and 10 µg/ml kanamycin. Tetracycline were used at 1ug/ml to induced integrin alpha7 expression.

tag: Undifferentiated integrin alpha7 inducible C2C12 cell C2C12 myoblasts, generated using invitrogen T-rex system, passage #7, induced with 1ug/ml tetracycline for 36 hours in 5% CO2 humidified incubator before RNA extraction


title: Wild type aortic banded, biological rep3

description: Gene Expression data from WT AB


title: Tet integrin alpha7 C2C12 induced rep2


title: Tet integrin alpha7 C2C12 induced rep3


title: Tet integrin alpha7 C2C12 noninduced rep1

description: Gene expression data from undifferentiated integrin alpha7 inducible C2C12 myoblasts incubated in basal media for 36hr without tetracycline

source_name: integrin alpha7 C2C12 cells, noninduced

growth_protocol: integrin alpha7  C2C12 cells were cultured at 37 °C  for 36 hours without tetracycline

treatment_protocol: integrin alpha7  C2C12 cells were cultured at 37 °C  for 36 hours in Dulbecco's modified Eagle's medium (DMEM) containing 20% FBS, 0.5% chick embryo extract, 2 mM glutamine, 100 units/ml penicillin, 100 µg/ml streptomycin, and 10 µg/ml kanamycin.

tag: Undifferentiated integrin alpha7 inducible C2C12 cell C2C12 myoblasts, generated using invitrogen T-rex system, passage #7, grown for 36 hours in 5% CO2 humidified incubator before RNA extraction


title: Intronic WT control rep2

description: Expression profiles generated from the gastrocnemicus and soleus muscles from wild type control mice for integirn alpha7 transgenic mice

source_name: Gastrocnemius-soleus muscles, basal status, wild type mouse

extract_protocol: Gastrocnemius-soleus muscles were powdered in the liquid nitrogen and Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA were further subject a cleanup protocol using a Qiagen Rneasy minikit.

tag: Gastrocnemius muscle wild-type mouse

value: control mouse for integrin alpha7 overexpressing

tag: Strain

value: SJ6/C57BL6 background

value: wild type

tag: Gender

value: Female

tag: Age

value: 5 week

value: gastrocnemius and soleus muscle

tag: Feeding condition

value: non-fasted


title: Intronic WT control rep1


title: Tet integrin alpha7 C2C12 noninduced rep2


title: Intronic WT control rep3


title: Integrin alpha7 transgenic mouse rep1

description: Expression profiles generated from the gastrocnemicus and soleus muscles from integrin alpha7 transgenic mice

source_name: Gastrocnemius-soleus muscles, basal status, integrin alpha7 transgenic  mouse

tag: Gastrocnemius muscle from integrin alpha7 transgenic mouse

value: integrin alpha7 transgenic


title: Tet integrin alpha7 C2C12 noninduced rep3


title: Integrin alpha7 transgenic mouse rep2

source_name: Gastrocnemius-soleus muscles, basal status, integrin alpha7 transgenic mouse


title: Xenograft Mouse 1 periphery

status: Public on Dec 21 2007

city: Columbus

first: Kevin

middle: R

last: Coombes

state: Ohio

address: 340E Lincoln Tower, 1800 Cannon Drive

department: Biomedical Informatics

institute: Ohio State University Wexner Medical Center

hyb_protocol: The fragmented cRNA was used for hybridization to the U133 Plus 2.0 chip at 42° C for 16 h.

scan_protocol: Scanned and visualized using a GeneArray Scanner (Hewlett-Packard, Palo Alto, CA).

source_name: tumor 1, periphery

label_protocol: Affymetrix GeneChip eukaryotic one-cycle target preparation protocol.

extract_protocol: RNeasy mini kit (Qiagen, Valencia, CA) with on column DNase I treatment.

tag: Human pancreatic tumor cell line L36.pl growing as orthotopic xenograft in male athymic nude mice. Laser capture microdissection from peripheral portion of tumor.  Sample taken from mouse #1.


title: Xenograft Mouse 3 center

source_name: tumor 3, central

tag: Human pancreatic tumor cell line L36.pl growing as orthotopic xenograft in male athymic nude mice. Laser capture microdissection from central portion of tumor.  Sample taken from mouse #3.


title: Xenograft Mouse 2 periphery

source_name: tumor 2, periphery

tag: Human pancreatic tumor cell line L36.pl growing as orthotopic xenograft in male athymic nude mice. Laser capture microdissection from peripheral portion of tumor.  Sample taken from mouse #2.


title: SVEC4-10 cell line, biological rep1

city: New York

first: Levi

last: Ledgerwood

address: One Gustave L. Levy Place

department: Gene and Cell Medicine

institute: Mount Sinai School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GMS fluorescent microarray scanner.

data_processing: The data were analyzed with Gene Chip Operating System software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: SVEC4-10 endothlial cell line

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: MS-1 cells were cultured in DMEM containing 5% FCS. SVEC4-10 cells were cultured in DMEM containing 10% FCS. Cell lines were maintained in culture flasks until reaching confluence, at which time they were treated with trypsin and EDTA (1×) for 2-4 minutes at 37° C and passaged at a 1:6 dilution to new flasks. Cultures were used up to passage five.

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

tag: C3H/HeJ, male

value: derived from axillary lymph node


title: Integrin alpha7 transgenic mouse rep3


title: Xenograft Mouse 3 periphery

source_name: tumor 3, periphery

tag: Human pancreatic tumor cell line L36.pl growing as orthotopic xenograft in male athymic nude mice. Laser capture microdissection from peripheral portion of tumor.  Sample taken from mouse #3.


title: diseased_media

city: cincinnati

first: Marc

middle: E.

last: Rothenberg

address: 3333 burnet avenue

department: Allergy and Immunology

institute: Cincinnati Children's Hospital Medical Center

description: Primary culture of esophageal epithelial cells unstimulated.

hyb_protocol: Full Protocol Description: Create a hybridization cocktail for a single probe array that contains  0.067 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer.  Heat hybridization cocktail to 99?C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45?C for 16 hrs in the Hybridization Oven rotating at 60 rpm.   Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing:
Affymetrix murine HG-U133 plus 2 gene chips were used. GeneChip CEL files were subjected to GC-RMA normalization (get reference) using the GeneSpring GX 7.3.1
Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.3.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering. Samples were normalized pair wise to respective unstimulated controls

source_name: Primary epithelial cell culture from esophageal biopsies

label_protocol: Modified Epicentre protocol (Epicentre biotchnologies) with random primer

extract_protocol:
Total RNA was extracted using Trizol kit (Invitrogen).
Quality control steps: RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used

treatment_protocol: Cells were either left untreated (0) or stimulated with IL-13 (100 ng) for 48h


title: diseased_media 2

tag: diseased cells unstimulated


title: diseased_IL-13 2

description: Primary culture of esophageal epithelial cells stimulated with IL-13 100ng/mL

tag: diseased cells stimulated


title: MS-1 cell line, biological rep1

source_name: MS-1 endothelial cell line

tag: C57BL/6, male

tag: Tissue

value: derived from pancreatic microvasculature


title: Cord blood cells, grown serum-free, CD34 purified, replicate 1

status: Public on Dec 20 2007

city: Cincinnati

first: James

last: Mulloy

address: 3333 Burnet Ave

department: Experimental Hematology

institute: Cincinnati Children's Hospital Research Foundation

description: Gene expression data from long-term serum-free cultures of CD34+ cord blood cells, CD34 selected

hyb_protocol: All hybridization, staining and washing steps were carried out as specified by the Affymetrix technical manual. (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf)

scan_protocol: Affymetrix GeneChip Scanner 3000 7G with GeneChip Operating Software Version 1.4.0.036 (Affymetrix)

data_processing: Data were pre-processed with Microarray Suite version 5.0 function of Bioconductor package (R) using default settings

source_name: Human CD34+ cord blood cells

label_protocol: For cDNA generation, and cRNA labeling we used the ëOne-cycle target labelingí protocol as described by the respective Affymetrix technical manual. (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf)

extract_protocol: total RNA from cells was extracted using the Rneasy Mini Kit (Qiagen)

tag: normal donors


title: AML1-ETO expressing cord blood cell, clone 9 grown serum-free, CD34 purified, replicate 4

description: Gene expression data from long-term serum-free cultures of AML1-ETO-transduced cord blood cells, CD34 selected


title: diseased_media 1


title: Cord blood cells, grown serum-free, CD34 purified, replicate 3


title: diseasedl_IL-13


title: diseased_IL-13 1


title: Wild type aortic banded, biological rep1

description: Gene Expression data from WT AB

tag: Genotype


title: Xenograft Mouse 2 center

source_name: tumor 2, central

tag: Human pancreatic tumor cell line L36.pl growing as orthotopic xenograft in male athymic nude mice. Laser capture microdissection from central portion of tumor.  Sample taken from mouse #2.


title: AML1-ETO expressing cord blood cell, clone 9 grown serum-free, CD34 purified, replicate 2


title: AML1-ETO expressing cord blood cell, clone 13.2 grown serum-free, CD34 purified, replicate 2


title: Xenograft Mouse 1 center

source_name: tumor 1, central

tag: Human pancreatic tumor cell line L36.pl growing as orthotopic xenograft in male athymic nude mice. Laser capture microdissection from central portion of tumor.  Sample taken from mouse #1.


title: Cord blood cells, grown serum-free, CD34 purified, replicate 2


title: AML1-ETO expressing cord blood cell, clone 13.2 grown serum-free, CD34 purified, replicate 1


title: AML1-ETO expressing cord blood cell, clone 9 grown serum-free, CD34 purified, replicate 3