title: ALL cells from pediatric diagnostic bone marrow 12

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD543-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 20

status: Public on Aug 16 2009

type: RNA

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

country: USA

institute: St Jude Childrens Research Hospital

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0020-ALL-v5-U133A

hyb_protocol: Following fragmentation, 15ugs of cRNA were hybridized for 16hr at 45C on the Human Genome U133A GeneChip Array. GeneChips were washed and stained using the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Leukemic blasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Leukemic blast cells were enriched from bone marrow aspirates by centrifugation on a Ficoll gradient.

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

tag: disease status

value: acute lymphoblastic leukemia

tag: developmental stage

value: pediatric

tag: tissue

value: diagnostic bone marrow

tag: cell type

value: leukemic blast cells


title: ALL cells from pediatric diagnostic bone marrow 24

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0041-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 15

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD612-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 25

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0063-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 6

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD166-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 19

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0017-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 26

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0064-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 21

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0023-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 13

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD544-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 11

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD514-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 22

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0031-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 17

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0010-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 16

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD619-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 18

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0011-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 9

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD375-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 14

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD611-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 7

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD280-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 10

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD485-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 8

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD283-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 5

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD163-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 2

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD083-v5-U133A


title: Cancer mammospheres, biological rep9

status: Public on Aug 15 2009

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: cells obtained from primary breast cancers were grown as mammosphere and compared with the primary cancers

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized on U133 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-2v4.

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

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

source_name: mammospheres derived from human breast tumors

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

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

tag: Cancer mammosphere


title: ALL cells from pediatric diagnostic bone marrow 1

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD013-v5-U133A


title: primary breast cancer, patient 7

source_name: human breast tumors

tag: human breast tumor


title: Cancer mammospheres, biological rep13


title: ALL cells from pediatric diagnostic bone marrow 3

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD085-v5-U133A


title: Cancer mammospheres, biological rep11


title: Cancer mammospheres, biological rep10


title: Cancer mammospheres, biological rep15


title: Cancer mammospheres, biological rep7


title: primary breast cancer, patient 10


title: Cancer mammospheres, biological rep8


title: Cancer mammospheres, biological rep6


title: primary breast cancer, patient 6


title: ALL cells from pediatric diagnostic bone marrow 4

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD-ALD112-v5-U133A


title: Cancer mammospheres, biological rep12


title: primary breast cancer, patient 8


title: Cancer mammospheres, biological rep14


title: primary breast cancer, patient 4


title: primary breast cancer, patient 5


title: primary breast cancer, patient 11


title: primary breast cancer, patient 9


title: Cancer mammospheres, biological rep4


title: non-CD44+/CD24- flow sorted cells, biological rep13

description: cells from primary breast cancers were flow sorted to select for CD44+/CD24- cells and compare with the rest of the cells

source_name: human breast tumor, flow sorted

tag: cells other than CD44+/CD24-


title: Cancer mammospheres, biological rep5


title: CD44+/CD24- flow sorted cells, biological rep14


title: primary breast cancer, patient 2


title: CD44+/CD24- flow sorted cells, biological rep11


title: non-CD44+/CD24- flow sorted cells, biological rep7


title: Cancer mammospheres, biological rep1


title: non-CD44+/CD24- flow sorted cells, biological rep11


title: non-CD44+/CD24- flow sorted cells, biological rep15


title: non-CD44+/CD24- flow sorted cells, biological rep8


title: Cancer mammospheres, biological rep2


title: non-CD44+/CD24- flow sorted cells, biological rep14


title: Cancer mammospheres, biological rep3


title: non-CD44+/CD24- flow sorted cells, biological rep12


title: CD44+/CD24- flow sorted cells, biological rep12


title: non-CD44+/CD24- flow sorted cells, biological rep9


title: CD44+/CD24- flow sorted cells, biological rep10


title: CD44+/CD24- flow sorted cells, biological rep13


title: non-CD44+/CD24- flow sorted cells, biological rep6


title: primary breast cancer, patient 1


title: non-CD44+/CD24- flow sorted cells, biological rep3


title: non-CD44+/CD24- flow sorted cells, biological rep1


title: non-CD44+/CD24- flow sorted cells, biological rep5


title: non-CD44+/CD24- flow sorted cells, biological rep2


title: non-CD44+/CD24- flow sorted cells, biological rep4


title: non-CD44+/CD24- flow sorted cells, biological rep10


title: CD44+/CD24- flow sorted cells, biological rep9


title: CD44+/CD24- flow sorted cells, biological rep7


title: primary breast cancer, patient 3


title: CD44+/CD24- flow sorted cells, biological rep8


title: CD44+/CD24- flow sorted cells, biological rep5


title: LAME 5

city: Jouy-en-Josas

first: Olivier

last: Sandra

address: Domaine de Vilvert

department: UMR BDR

country: France

institute: INRA

hyb_protocol: Samples were then combined according to their fluorescent intensity(picomoles), denatured 2 min at 95°C, and co hybridized on the 13 257 oligoarray at 42°C for 16 to 18 hr using the Corning Pronto!TM Universal Microarray Kits according to the manufacturer~s recommendations (Fischer Scientific Bioblock, Illkirsch, France). After stringent washes to remove unbound cDNA, slides were scanned using a GenePix 4000B scanner (Axon instrument, France) and features were analysed with GenePix Pro Version 4.0 software (Axon Instrument).

scan_protocol: Feature extraction software : Genepix Pro - Scanner : Genepix 4000B

data_processing: Varmixt normalization Data were normalized by a global loess regression

organism: Bos taurus

source_name: caruncle B7 - cycle

label_protocol: Twenty microg of each RNA sample was converted into aminoallyl-labelled cDNA with oligo-dT primers, amino-allyl-dUTP (Sigma, Saint-Quentin-Fallavier, France) and superscript II Reverse Transcriptase (Invitrogen, Cergy-Pontoise, France). The cDNA was purified on a Microcon PCR column according to the manufacturer's protocol (Millipore, St-Quentin-en-Yvelines, France) and added to an aliquot of fluorescent dye (Cy3 or Cy5: GE HealthCare, Vélizy, France). Unused reactive sites were blocked by hydroxylamine 4M, and fluorescent probes were purified on QiaQuick columns according to the manufacturer's recommendations (Qiagen, Courtaboeuf, France). Every probe was quantified using Nanodrop spectrophotometer and quality was assessed on an agarose gel electrophoresis 1% TAE 1X. The mean lengths of the fluorescent probes were analyzed by the Typhoon Imaging system scanner (GE HealthCare, Vélizy, France).

extract_protocol: Total RNA from frozen tissue was isolated by homogenization using Trizol Reagent (Invitrogen, Cergy-Pontoise, France) according to the manufacturer's recommendations. All RNA samples were purified on Qiagen columns according to the manufacturer's protocol (RNeasy Mini kit, Qiagen, Courtaboeuf, France). Quality and integrity of total extracted and purified RNA were determined by Agilent 2100 bio analyser (Massy, France). The RIN of each RNA sample was between 7.5 to 9.5 (84).

tag: Area

value: Caruncular

source_name: intercaruncle B7 - cycle

value: Intercaruncular


title: CD44+/CD24- flow sorted cells, biological rep4


title: CD44+/CD24- flow sorted cells, biological rep1


title: LAME 24

source_name: caruncle B98095 - pregnant

source_name: intercaruncle B98095 - pregnant


title: CD44+/CD24- flow sorted cells, biological rep2


title: LAME 4

source_name: intercaruncle B8 - cycle

source_name: caruncle B8 - cycle


title: CD44+/CD24- flow sorted cells, biological rep6


title: LAME 28

source_name: intercaruncle B2 - pregnant

source_name: caruncle B2 - pregnant


title: LAME 25

source_name: caruncle B1 - pregnant

source_name: intercaruncle B1 - pregnant


title: LAME 6


title: LAME 23


title: LAME 27


title: LAME 26


title: CD44+/CD24- flow sorted cells, biological rep3


title: LAME 22

source_name: intercaruncle B98114 - pregnant

source_name: caruncle B98114 - pregnant


title: LAME 15

source_name: caruncle B9114 - cycle

source_name: intercaruncle B9114 - cycle


title: LAME 20

source_name: intercaruncle B99035 - pregnant

source_name: caruncle B99035 - pregnant


title: LAME 16


title: LAME 3


title: LAME 78

source_name: Pregnancy B1; Area: Caruncular

source_name: Cycle B857; Area: Caruncular


title: LAME 21


title: LAME 77

source_name: Pregnancy B3; Area: Caruncular


title: LAME 14

source_name: intercaruncle B9105 - cycle

source_name: caruncle B9105 - cycle


title: LAME 13


title: LAME 61

source_name: Cycle B5; Area: Intercaruncular

source_name: Pregnancy B2; Area: Intercaruncular


title: lame 51

source_name: Pregnancy B98095; Area: Intercaruncular

source_name: Cycle B9114; Area: Intercaruncular


title: LAME 80

source_name: Pregnancy B2; Area: Caruncular

source_name: Cycle B808; Area: Caruncular


title: LAME 19


title: LAME 74

source_name: Cycle B9090; Area: Caruncular

source_name: Pregnancy B9098; Area: Caruncular


title: LAME 9

source_name: caruncle B9090 - cycle

source_name: intercaruncle B9090 - cycle


title: LAME 79


title: LAME 81

source_name: Cycle B4; Area: Caruncular


title: LAME 10


title: LAME 83

source_name: Cycle B5; Area: Caruncular

source_name: Pregnancy B714; Area: Caruncular


title: LAME 82


title: LAME 84

source_name: Pregnancy B732; Area: Caruncular


title: LAME 73

source_name: Cycle B9114; Area: Caruncular


title: LAME 72

source_name: Pregnancy B98104; Area: Caruncular


title: LAME 71

source_name: Cycle B9105; Area: Caruncular


title: LAME 76

source_name: Pregnancy B3; Area: Caruncular

source_name: Cycle B7; Area: Caruncular


title: LAME 69

source_name: Pregnancy B98095; Area: Caruncular

source_name: Cycle B9115; Area: Caruncular


title: LAME 70


title: LAME 65

source_name: Cycle B857; Area: Intercaruncular

source_name: Pregnancy B4; Area: Intercaruncular


title: lame 68

source_name: Pregnancy B98114; Area: Caruncular


title: LAME 66

source_name: Pregnancy B3; Area: Intercaruncular


title: LAME 64

source_name: Cycle B808; Area: Intercaruncular


title: lame 67

source_name: Cycle B9090; Area: Caruncular


title: LAME 62

source_name: Pregnancy B6; Area: Intercaruncular

source_name: Cycle B5; Area: Intercaruncular


title: lame 56

source_name: Cycle B9090; Area: Intercaruncular

source_name: Pregnancy B99035; Area: Intercaruncular


title: LAME 58

source_name: Cycle B9105; Area: Intercaruncular

source_name: Pregnancy B9109; Area: Intercaruncular


title: LAME 63


title: LAME 59

source_name: Cycle B7; Area: Intercaruncular


title: LAME 57


title: LAME 75

source_name: Pregnancy B732; Area: Caruncular


title: LAME 60

source_name: Pregnancy B2; Area: Intercaruncular


title: lame 52

source_name: Cycle B9064; Area: Intercaruncular

source_name: Pregnancy B98095; Area: Intercaruncular


title: lame 54

source_name: Cycle B9115; Area: Intercaruncular

source_name: Pregnancy B98070; Area: Intercaruncular


title: VentralSkin_K14WT_rep3

city: Philadelphia

first: Lewis

last: Chodosh

state: PA

address: 612 BRB II/III 421 Curie Blvd

institute: University of Pennsylvania

description:
WT murine embryonic ventral skin. Used in comparison with K14-PTHrP murine embryonic ventral skin.
K14WTS3

hyb_protocol: Affymetrix generic hybridization.

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

data_processing:
Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.

Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.

organism: Mus musculus

source_name: WT ventral skin

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

extract_protocol: Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.

tag: strain

value: Embryonic ventral skin

tag: age

tag: group


title: VentralSkin_K14-PTHrP_rep3

description:
K14-PTHrP murine embryonic ventral skin.
K14S3

source_name: K14-PTHrP ventral skin


title: Leafy spurge, Xam inoculated, 7 DAI, rep2, CY3

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

hyb_protocol: Arrays were pre-hybridized with a soln. of BSA, SDS and Dehardts. Arrays were then rinsed in 2XSSC/2%SDS, then water, and then 100 EtOH before being spun dry. Labeled cDNAs were mixed in a volume of 26.4 ul water, 7.65 ul 2XSSC, 7.2 ul 2%SDS, and 3.75 ul tRNA (10 mg/ml). cDNA was heated to 95 C for 5 minutes, spun down and placed on the array under a cover slip. Arrays were hybridized ON at 60 C. Washing was done by consecutive 5 minute rinses in 2XSSC/2%SDS, 1XSSC/0.2%SDS, 1XSSC/0.2%SDS again, 0.1XSSC, 0.1XSSC again, and spun dry.

scan_protocol: Arrays were scanned using a Genepix 4000b under default conditions for normalizing signal intensities.

data_processing: Raw signal intensities of all DNA-containing spots were up-loaded as single color files into GeneMaths XT microarray data analysis program. Intensity data was log transformed, and normalized between arrays using default parameters.

organism: Euphorbia esula

source_name: Leafy spurge, Xam inoculated, 7 DAI

label_protocol: Total RNA was reverse transcribed and labeled with Invitrogen alexaflour 555 or 647 dyes using the two-step method suggested by the manufacturer.

growth_protocol: Plants were grown from shoot cuttings in the greenhouse with mix of artificial and natural lighting under a 16 hr day at 23-25 C in 1 x 8 inch cone-tainers in peat soil mix until 3 MO old. Plants were then moved to a growth chamber with mixed fluorescent and incandescent lighting at 23 C under a 16 hr day.

extract_protocol: Leaves were harvested and placed in liquid nitrogen and ground to a fine powder. The Pine Tree extraction procedure (Chang S, Puryear, J. and Cairney, J. : A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 1993, 11:113-116.) was used to isolate total RNA.

treatment_protocol: Greenhouse grown plants were moved into a growth chamber set at 16hr day lengths and 23 C. Plants were inoculated (or mock inoculated) by puncturing several leaves and the stem midway down the plant with a toothpick dipped in either an ON culture of Xanthomonas axonopodis pv. manihotis in LB broth or with sterile LB broth. Leaves at or above the site of inoculation were harvested at various times following inoculation.

value: 3 month old

tag: environment

value: greenhouse grown

value: single stem


title: lame 55


title: VentralSkin_K14WT_rep2

description:
WT murine embryonic ventral skin. Used in comparison with K14-PTHrP murine embryonic ventral skin.
K14WTS2


title: Leafy spurge, Xam inoculated, 7 DAI, rep2, CY5


title: Leafy spurge, Xam inoculated, 7 DAI, rep3, CY3


title: VentralSkin_K14-PTHrP_rep1

description:
K14-PTHrP murine embryonic ventral skin.
K14S1


title: LAME 49

data_processing: Varmixt normalization data were normalized by a global loess regression

source_name: Pregnancy B98114; Area: Intercaruncular


title: Leafy spurge, Xam inoculated, 7 DAI, rep1, CY5


title: Leafy spurge, Xam inoculated, 7 DAI, rep3, CY5


title: VentralSkin_WT_rep2

description:
WT murine embryonic ventral skin.
WTS2

value: WT


title: VentralSkin_K14WT_rep1

description:
WT murine embryonic ventral skin. Used in comparison with K14-PTHrP murine embryonic ventral skin.
K14WTS1


title: VentralSkin_WT_rep3

description:
WT murine embryonic ventral skin.
WTS3


title: VentralSkin_K14-PTHrP_rep2

description:
K14-PTHrP murine embryonic ventral skin.
K14S2


title: lame 53


title: Leafy spurge, Xam inoculated, 7 DAI, rep1, CY3


title: VentralSkin_WT_rep1

description:
WT murine embryonic ventral skin.
WTS1


title: Leafy spurge, Xam inoculated, 1 DAI, rep3, CY3

source_name: Leafy spurge, Xam inoculated, 1 DAI


title: Buds_PTHrP-KO_rep1

description:
PTHrP-/- murine embryonic mammary buds.
KOB1

source_name: PTHrP-/- mammary buds

value: Embryonic mammary buds

value: PTHrP-/-


title: Leafy spurge, Xam inoculated, 1 DAI, rep1, CY3


title: Leafy spurge, Xam inoculated, 1 DAI, rep3, CY5


title: Leafy spurge, Xam inoculated, 1 DAI, rep1, CY5


title: Buds_PTHrP-KO_rep2

description:
PTHrP-/- murine embryonic mammary buds.
KOB2


title: Buds_PTHrP-KO_rep3

description:
PTHrP-/- murine embryonic mammary buds.
KOB3


title: Leafy spurge, Xam inoculated, 21 DAI, rep2, CY5

source_name: Leafy spurge, Xam inoculated, 21 DAI


title: Leafy spurge, Xam inoculated, 21 DAI, rep3, CY3


title: Leafy spurge, Xam inoculated, 1 DAI, rep2, CY5


title: Leafy spurge, Xam inoculated, 1 DAI, rep2, CY3


title: Buds_WT_rep3

description:
WT murine embryonic mammary buds.
WTB3

source_name: WT mammary buds


title: Leafy spurge, Xam inoculated, 21 DAI, rep2, CY3


title: Leafy spurge, Xam inoculated, 21 DAI, rep3, CY5


title: HDL_GSK4.Starved.replicate2

city: RTP

first: Joan

last: Stuart

address: 5 Moore Drive

institute: GSK

hyb_protocol: Fragmented cRNA was then hybridized to Affymetrix MOE430_2 chips according to standard procedures. Samples were randomized in the labeling and hybridizing process.

scan_protocol: Hybridized chips were washed and then scanned on an Affymetrix GeneChip 3000 scanner according to the Affymetrix expression analysis technical manual.

data_processing: Gene expression signals were extracted from the scanned microarrays by the MAS 5.0 software provided by Affymetrix.

source_name: bTC3 insulinoma cell line

label_protocol: One μg of total RNA material was amplified and labeled with biotin according to Affymetrix protocols using the Enzo kit (Affymetrix; catalog n° 900182) for in vitro transcription.

growth_protocol: βTC3 cells were grown for 2 days in complete medium prior to being subjected to the indicated experimental conditions.

extract_protocol: Cells were washed, lysed using RLT buffer (Qiagen; catalog n° 79216) and scraped off the dishes using a rubber policeman. Lysates were then added to a QIAshredder column (Qiagen kit for the isolation of total RNA from animal cells; catalog n° 74104) and spun at maximum speed in an Eppendorf centrifuge for 2 minutes at room temperature. The lysate was then frozen at -80°C. The QIAshredder unit is used to homogenize lysates and to reduce viscosity caused by high molecular weight cellular components and cell debris. RNA was then isolated and purified using the RNeasy column (Qiagen; catalog n° 74104). Total RNA was checked for quality on an RNA Nano labChip using the Bioanalyzer system (Agilent Technologies).

treatment_protocol:
Starvation medium: RPMI (Gibco, catalog n° 61870) supplemented with sodium pyruvate (1mM) (without FCS).
HDL concentration: 1 mM

value: pancreas

value: beta cells

tag: cell line

value: bTC3 insulinoma cell line

tag: hdl preparation


title: HDL_GSK4.Starved.replicate3


title: V_GSK4.Starved.replicate3

treatment_protocol:
Starvation medium: RPMI (Gibco, catalog n° 61870) supplemented with sodium pyruvate (1mM) (without FCS).
Vehicle: dialysis medium that is used during the HDL preparation.


title: Buds_WT_rep2

description:
WT murine embryonic mammary buds.
WTB2


title: Leafy spurge, Xam inoculated, 21 DAI, rep1, CY3


title: V_GSK4.Starved.replicate2


title: Buds_WT_rep1

description:
WT murine embryonic mammary buds.
WTB1


title: L. infantum Sb2000.1 vs WT_replicate 5

city: Québec

first: Philippe

last: Leprohon

state: Québec

address: 2705 boulevard Laurier

department: Centre hospitalier de l'Université Laval

country: Canada

institute: Université Laval

description: Biological replicate 5 of 5

hyb_protocol: Prehybridization and hybridization were performed at 42°C. Washes for pre-hyb and hyb were as follows: 2X5min in 50ml 2X SSC, 0.1%SDS at 42oC; 3min in 50ml 1X SSC at room temperature; 3min in 50ml 0.2X SSC at room temperature and 3 min in 50ml 0.05X SSC at room temperature. Slides were prehybridized in 5X Denhardt, 30% formamide, 6X SSPE, 0,5% SDS, 100µg/ml salmon sperm DNA. Then, slides were washed. For hybridization, labelled cDNA probes were independently dried and resuspended in 2,5X Denhardt, 30% formamide, 6X SSPE, 0,5% SDS, 100µg/ml salmon sperm DNA, 750µg/ml Yeast tRNA and pooled. Pooled probes were applied on the array under a lifterslip. Hybridization was performed for 16h and then slides were washed.

scan_protocol: The Perkin Elmer ScanArray 4000XL Scanner was used for image acquisition. GenePix Pro 6.0 image analysis software (Axon Instruments) was used to quantify the fluorescence signal intensities of the array features

data_processing:
Raw data from GenePix were imported in R 2.2.1.  Normalization and statistical analyses were performed using the LIMMA (version 2.7.3) package.
Intra-array normalization was carried out using the ‘print-tip loess’ statistical method and inter-array normalization was done using the ‘quantiles of A’ method for each array (Yang, 2003). A blank VALUE in the Sample table below indicates a spot which has been flagged out and not considered in the analysis.
Multiple testing corrections were done using the FDR method with a threshold p-value of 0.05. Only genes statistically significant with an absolute log ratio greater than 0.58 (log2 1.5) were considered as differentially expressed

organism: Leishmania infantum

source_name: wild-type strain

label_protocol: 10 µg of RNA were converted to aminoallyl-dUTP incorporated cDNA using random hexamers (Roche) and the SuperScript III RNase H- Reverse Transcriptase (Invitrogen). Probes were thereafter coupled to the fluorescent dye Alexa Fluor555 or Alexa Fluor647 (Invitrogen) following manufacturer recommendations. Fluorescent probes were then purified with MinElute Spin Columns (QIAGEN) and quantified spectrophotometrically.

growth_protocol: All cells were grown in SDM-79 medium supplemented with 10% heat-inactivated fetal bovine serum and 5 µg/ml hemin at 25 °C. When needed, the appropriate concentration of trivalent antimony was added.  The antimony resistant strain was grown in presence of 2000 micromolar of drug.

extract_protocol: Total RNA was isolated from 10e8 Leishmania cells during the mid-log phase using RNeasy Plus Mini Kit (QIAGEN) as described by the manufacturer. The RNA preparation was treated with TURBO DNase (Ambion) to avoid any genomic contamination

value: wild-type

tag: antimony tolerance

value: sensitive

source_name: Sb2000.1 strain

value: resistant


title: Leafy spurge, Xam inoculated, 21 DAI, rep1, CY5


title: Leafy spurge, mock inoculated, 7 DAI, rep3, CY3

source_name: Leafy spurge, mock inoculated, 7 DAI


title: HDL_GSK4.CM.replicate3

treatment_protocol:
Control medium: RPMI (Gibco, catalog n° 61870) supplemented with 10% FCS and sodium pyruvate (1mM).
HDL concentration: 1 mM


title: L. infantum Sb2000.1 vs WT_replicate 4 (dyeswap)

description: Biological replicate 4 of 4. Dye-swap samples for which the labelling has been inverted to avoid any bias.


title: Leafy spurge, mock inoculated, 7 DAI, rep1, CY3


title: L. infantum Sb2000.1 vs WT_replicate 1

description: Biological replicate 1 of 4


title: Leafy spurge, mock inoculated, 7 DAI, rep2, CY5


title: HDL_GSK4.CM.replicate2


title: V_GSK4.CM.replicate2

treatment_protocol:
Control medium: RPMI (Gibco, catalog n° 61870) supplemented with 10% FCS and sodium pyruvate (1mM).
Vehicle: dialysis medium that is used during the HDL preparation.


title: HDL_GSK4.CM.replicate1


title: L. infantum Sb2000.1 vs WT_replicate 3

description: Biological replicate 3 of 4


title: Leafy spurge, mock inoculated, 7 DAI, rep1, CY5


title: V_GSK4.CM.replicate3


title: Leafy spurge, mock inoculated, 7 DAI, rep2, CY3


title: L. infantum Sb2000.1 vs WT_replicate 2 (dyeswap)

description: Biological replicate 2 of 4. Dye-swap samples for which the labelling has been inverted to avoid any bias.


title: V_GSK4.CM.replicate1


title: HDL_GSK4.Starved.replicate1


title: Leafy spurge, mock inoculated, 1 DAI, rep2, CY3

source_name: Leafy spurge, mock inoculated, 1 DAI


title: Leafy spurge, mock inoculated, 1 DAI, rep3, CY3


title: Leafy spurge, mock inoculated, 7 DAI, rep3, CY5


title: Leafy spurge, mock inoculated, 1 DAI, rep1, CY3


title: Leafy spurge, mock inoculated, 1 DAI, rep2, CY5


title: Leafy spurge, mock inoculated, 21 DAI, rep2, CY3

source_name: Leafy spurge, mock inoculated, 21 DAI


title: HDL_GSK3.Starved.replicate3


title: V_GSK3.Starved.replicate3


title: HDL_GSK3.Starved.replicate1


title: Leafy spurge, mock inoculated, 21 DAI, rep3, CY3


title: V_GSK3.Starved.replicate2


title: Leafy spurge, mock inoculated, 21 DAI, rep1, CY3


title: Leafy spurge, mock inoculated, 1 DAI, rep3, CY5


title: Leafy spurge, mock inoculated, 1 DAI, rep1, CY5


title: HDL_GSK3.CM.replicate2


title: V_GSK3.Starved.replicate1


title: HDL_GSK3.CM.replicate1


title: HDL_GSK3.Starved.replicate2


title: HDL_GSK3.CM.replicate3


title: V_GSK3.CM.replicate3


title: PNT2-siGFP, rep3

city: Iowa City

first: Yi

last: Xing

state: IA

address: 3294 CBRB, 285 Newton Rd

department: Internal Medicine, Biomedical Engineering

institute: University of Iowa

description: RNA (6874) EGFP3 HuEx

hyb_protocol: The labeling assay yielded labeled single-stranded DNA that was fragmented and hybridized to Affymetrix Human Exon 1.0 ST Arrays (exon arrays) according to manufacturer’s protocols at the Penn Microarray Core Facility.

scan_protocol: Hybridized Affymetrix Human Exon 1.0 ST Arrays (exon arrays) were scanned following the manufacturer’s protocols at the Penn Microarray Core Facility.

data_processing: Raw image files were processed using Affymetrix Genechip Command Console (AGCC) to generate CEL data files. Exon array expression indexes were calculated using the GeneBASE program (Kapur et al., 2007, Genome Biol 8:R82). Briefly, the program employs a sequence-specific background model to correct background intensities of exon-array probes (Kapur et al., 2007, Genome Biol 8:R82), followed by an iterative probe selection procedure (Xing et al., 2006, PLoS ONE 1:e88) that selects a subset of highly correlated probes of a gene for expression index computation. Differential splicing events were detected using the MADS algorithm (Xing et al., 2008).

source_name: human PNT2 prostatic epithelium cells, control

label_protocol: Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).  Ribosomal RNA reduction was performed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01).

growth_protocol: PNT2 cells were grown in RPMI1640 media supplemented with 10% FBS (Thermo Scientific) and Glutamax (Invitrogen).

extract_protocol: Total RNA was collected from adherent tissue culture cells using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA was quantified (A260) using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies).

treatment_protocol: Short interfering RNA knockdown of ESRP1 and ESRP2 in human PNT2 cells was performed as described before (Warzecha et al., 2009, Molecular Cell 33:591-601). The efficiency of ESRP1 and ESRP2 knockdown was monitored by quantitative RT-PCR as described before (Warzecha et al., 2009, Molecular Cell 33:591-601).  In all cases the efficiency of the knockdown was close to 80%.

value: prostatic epithelium cells

tag: sirna

value: GFP


title: PNT2-siESRP, rep3

description: RNA (6878) RBM3 HuEx

source_name: human PNT2 prostatic epithelium cells, siESRP

value: ESRP1, ESRP2


title: Leafy spurge, mock inoculated, 21 DAI, rep3, CY5


title: PNT2-siGFP, rep4

description: RNA (6875) EGFP4 HuEx


title: PNT2-siGFP, rep1

description: RNA (6872) EGFP1 HuEx


title: Leafy spurge, mock inoculated, 21 DAI, rep2, CY5


title: PNT2-siESRP, rep2

description: RNA (6877) RBM2 HuEx


title: V_GSK3.CM.replicate2


title: V_GSK3.CM.replicate1


title: leafy spurge, mock inoculated, 21 DAI, rep 1

source_name: leafy spurge, mock inoculated, 21 DAI


title: Spurp_CO2_Hyb11_B3O3

status: Public on Aug 14 2009

city: San Francisco

first: Anne

last: Todgham

state: CA

address: 1600 Holloway Ave

department: Biology

institute: San Francisco State University

hyb_protocol: Samples were hybridized following Agilent’s Protocol for Two-Color Microarray-Based Gene Expression Analysis (version 5.5, pages 24-35).  The cDNA samples were quantified using a NanoDrop 1000 UV/visible spectrophotometer (Thermo Scientific, Wilmington, DE, USA) to ensure high quality cDNA synthesis and dye incorporation before continuing on to the slide hybridization.  If the cDNA yield of a particular sample was <600 ηg and the specific activity was <8.0 ρmol dye per μg cDNA, cDNA synthesis and labeling was repeated.  Prior to slide hybridization, cDNA samples were fragmented following Agilent’s Gene Expression Hybrization Kit for 4x44K slides.  Briefly, 600ηg of Alexafluor 555-labeled cDNA, 600ηg of Alexafluor 647-labeled cDNA, 11 μL of 10X Blocking Agent and 2.2 μL of 25X Fragmentation Buffer were mixed to a total volume of 55 μL with nuclease-free water and incubated at 60°C for 30 min.  To each array mixture 55 μL of 2X GE Hybridization Buffer HI-RPM was added and then the sample was applied to the microarray slides.  Hybridizations were conducted overnight (~17 h) at 65°C in Agilent Microarray Hybridization Chambers with the hybridization oven rotisserie set at 10rpm.  Following hybridization, the slides were washed in Agilent’s Gene Expression Wash Buffers following manufacturer’s instructions.

scan_protocol: The slides were scanned at 5μm on a GenePix 4000B microarray scanner (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA).  Data from the microarrays were extracted using GenePix Pro 4.0 software (Axon Instruments).

data_processing: Normalization and data analysis were completed using R (R Development Core Team 2008) with the limma software package (Smyth 2005). To avoid violating assumptions of the number or degree of symmetry of differentially expressed genes, a global normalization for dye-bias was applied on a probe-by-probe basis, after averaging over log-ratios from replicate probes within arrays, by including a dye-effect in the linear model.

label: Alexafluor 647

organism: Strongylocentrotus purpuratus

source_name: S. purpuratus, prism, 1020ppm CO2, rep3

label_protocol: Indirect coupling of dye following cDNA synthesis with amino-allyl dUTP. cDNA was incubated with 1 μL of either Alexafluor 555 or 647 dye for 1h at room temperature in the dark.

extract_protocol: Total RNA was extracted from a pooled sample of approximate 60,000 prism stage urchin larvae.  Total RNA was isolated using TRIzol® Reagent following manufacturer’s instructions (Invitrogen, Carlsbad, CA, USA). RNA was then processed through an additional column clean-up step to remove tRNA and small-sized RNA degradation products.

tag: Species

value: Strongylocentrotus purpuratus,

tag: Developmental stage

value: prism,

tag: Age

value: 40 hours post-fertilization,

tag: CO2 treatment

tag: Replicate culture

label: Alexafluor 555

source_name: S. purpuratus, prism, 380ppm CO2, rep3

value: 380 ppm CO2,


title: PNT2-siESRP, rep1

description: RNA (6876) RBM1 HuEx

tag: cell type


title: H37Rv Ctrl vs 2 ug/ml garlic extract 6hrs rep2

city: Rockville

first: Helena

middle: I

last: Boshoff

state: MD

address: 12441 Parklawn Drive

department: LIG

institute: NIAID/ NIH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84514.gif

hyb_protocol: not provided

scan_protocol: not provided

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

organism: Mycobacterium tuberculosis

source_name: Control exposed to DMSO for 6hrs

label_protocol: Amount of extract labeled = 4 ug of RNA; Type of label = Cy3

extract_protocol: Extraction method = Trizol; Extracted molecule = RNA

treatment_protocol: Time = 6hrs; Compound Based Treatment = "Control, exposed to DMSO"

tag: treatment

value: Control exposed to DMSO for 6hrs

source_name: Treated with 2 ug/ml garlic (Allium stipitatum) extract for 6hrs

label_protocol: Amount of extract labeled = 4 ug of RNA; Type of label = Cy5

growth_protocol: Growth Temperature = 37oC; Media = "Middlebrook 7H9 supplemented with 0.2% glycerol, 0.5% BSA fraction V, 0.05% Tween 80, 0.08% NaCl and 0.2% glucose"

treatment_protocol: Time = 6hrs; Compound Based Treatment = Treated with 2ug/ml garlic extract


title: Spurp_CO2_Hyb12_O3B3


title: H37Rv Ctrl vs 10 ug/ml garlic extract 6hrs

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84515.gif

source_name: Treated with 10 ug/ml garlic (Allium stipitatum) extract for 6hrs

treatment_protocol: Time = 6hrs; Compound Based Treatment = Treated with 10ug/ml garlic extract


title: PNT2-siESRP, rep4

description: RNA (6879) RBM4 HuEx


title: H37Rv Ctrl vs 2 ug/ml garlic extract 6hrs rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84513.gif

value: Treated with 2 ug/ml garlic (Allium stipitatum) extract for 6hrs


title: C57 at 6hr after APAP treatment_237

city: Palo Alto

first: Hong-Hsing

last: Liu

address: S3-115E, 3431 Hillview Ave.

institute: Roche Palo Alto

description: gene expression data from C57 train at 6hr after APAP treatment

hyb_protocol: The labeled samples were applied to the Affymetrix Murine Genome MOE430v2 chip and processed according to the manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: C57237 at 6hr after APAP treatment

label_protocol: Aliquots of  RNAs were purified using RNeasy columns (Qiagen) and 10 μg of each purified total RNA served as template for reverse transcription using a T7-promoter coupled oligo(dT) primer, followed by an in vitro transcription reaction (Affymetrix, version 2.03).

growth_protocol: All animal experiments followed protocols that were approved by Roche Palo Alto Institutional Animal Care and Use Committee. The mice were housed in a pathogen-free environment with a 12h:12h light:dark cycle and had access to food and water ad libitum. Before APAP exposure, mice were fasted overnight (>16h) to uniformly deplete hepatic glutathione stores.

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

treatment_protocol: Acetaminophen (Voigt Global Distribution INC) was dissolved in heat and was administered by i.p. bolus injection to mice at 300mg/kg.

tag: tissue

value: Liver

tag: agent

value: APAP

tag: time


title: PNT2-siGFP, rep2

description: RNA (6873) EGFP2 HuEx


title: Spurp_CO2_Hyb10_O2B2

source_name: S. purpuratus, prism, 380ppm CO2, rep2

source_name: S. purpuratus, prism, 1020ppm CO2, rep2


title: Spurp_CO2_Hyb5_B3G3

source_name: S. purpuratus, prism, 540ppm CO2, rep3

value: 540 ppm CO2,


title: Spurp_CO2_Hyb6_G3B3


title: Spurp_CO2_Hyb9_B2O2


title: Spurp_CO2_Hyb8_O1B1

source_name: S. purpuratus, prism, 380ppm CO2, rep1

source_name: S. purpuratus, prism, 1020ppm CO2, rep1


title: Spurp_CO2_Hyb3_B2G2

source_name: S. purpuratus, prism, 540ppm CO2, rep2


title: Spurp_CO2_Hyb7_B1O1


title: C57 at 6hr after APAP treatment_236

source_name: C57236 at 6hr after APAP treatment

tag: strain


title: C57 at 3hr after APAP treatment_231

description: gene expression data from C57 train at 3hr after APAP treatment

source_name: C57231 at 3hr after APAP treatment


title: C57 at 6hr after APAP treatment_233

source_name: C57233 at 6hr after APAP treatment


title: C57 at 3hr after APAP treatment_226

source_name: C57226 at 3hr after APAP treatment


title: C57 at 0hr_181

description: gene expression data from C57 strain at 0hr (pre-dose)


title: Spurp_CO2_Hyb2_G1B1

source_name: S. purpuratus, prism, 540ppm CO2, rep1


title: C57 at 3hr after APAP treatment_230

source_name: C57230 at 3hr after APAP treatment


title: Spurp_CO2_Hyb4_G2B2


title: LAME 50

source_name: Cycle B9114; Area: Intercaruncular

tag: Area

value: Intercaruncular

source_name: Pregnancy B98114; Area: Intercaruncular


title: Spurp_CO2_Hyb1_B1G1


title: DBA at 6hr after APAP treatment_168

description: gene expression data from DBA train at 6hr after APAP treatment

source_name: DBA168 at 6hr after APAP treatment

value: DBA


title: DBA at 3hr after APAP treatment_160

description: gene expression data from DBA train at 3hr after APAP treatment

source_name: DBA160 at 3hr after APAP treatment


title: normal renal cortical tissue_3

city: Toronto

first: York

middle: PC

last: Pei

state: Ontario

address: 8N838, 585 University Avenue

department: Department of Medicine

institute: University of Toronto

description: normal control tissue

hyb_protocol: Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.

data_processing: Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.

source_name: Non-cancerous renal cortical tissue from nephrectomized kidney with isolated renal cell carcinoma of patient 3

label_protocol: cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.

growth_protocol: The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.

extract_protocol: Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination.  The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.

treatment_protocol: All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer

tag: PKD1 patient


title: DBA at 6hr after APAP treatment_166

source_name: DBA166 at 6hr after APAP treatment


title: DBA at 3hr after APAP treatment_158

source_name: DBA158 at 3hr after APAP treatment


title: DBA at 3hr after APAP treatment_159

source_name: DBA159 at 3hr after APAP treatment


title: DBA at 6hr after APAP treatment_169

source_name: DBA169 at 6hr after APAP treatment


title: DBA at 0hr_114

description: gene expression data from DBA strain at 0hr (pre-dose)

source_name: DBA114 at 0hr


title: C57 at 0hr_180


title: DBA at 0hr_115

source_name: DBA115 at 0hr


title: SMJ at 6hr after APAP treatment_102

description: gene expression data from SMJ train at 6hr after APAP treatment

source_name: SMJ102 at 6hr after APAP treatment

value: SMJ


title: minimally cystic tissue_5

description: PKD1 control tissue

source_name: Minimally cystic tissue from PKD1 patient


title: minimally cystic tissue_4

description: PKD1 control tissue


title: normal renal cortical tissue_2

description: normal control tissue

source_name: Non-cancerous renal cortical tissue from nephrectomized kidney with isolated renal cell carcinoma of patient 2


title: DBA at 0hr_113

source_name: DBA113 at 0hr


title: SMJ at 6hr after APAP treatment_103

source_name: SMJ103 at 6hr after APAP treatment


title: normal renal cortical tissue_1

description: normal control tissue

source_name: Non-cancerous renal cortical tissue from nephrectomized kidney with isolated renal cell carcinoma of patient 1


title: V_GSK4.Starved.replicate1

source_name: bTC3 insulinoma cell line

value: pancreas

value: beta cells

tag: cell line

value: bTC3 insulinoma cell line


title: SMJ at 6hr after APAP treatment_101

source_name: SMJ101 at 6hr after APAP treatment


title: minimally cystic tissue_3

description: PKD1 control tissue


title: minimally cystic tissue_2

description: PKD1 control tissue


title: SMJ at 0hr_58

description: gene expression data from SMJ strain at 0hr (pre-dose)

source_name: SMJ58 at 0hr


title: SMJ at 0hr_57

source_name: SMJ57 at 0hr


title: PKD1 renal cyst, large cyst_1, 60 ml

description: PKD1 renal cyst

source_name: Renal cyst from PKD1 patient, large single cyst


title: PKD1 renal cyst, large cyst_3, 100 ml

description: PKD1 renal cyst


title: SMJ at 3hr after APAP treatment_96

description: gene expression data from SMJ train at 3hr after APAP treatment

source_name: SMJ96 at 3hr after APAP treatment


title: PKD1 renal cyst, large cyst_2, 50 ml

description: PKD1 renal cyst


title: PKD1 renal cyst, medium cyst_4, 15 ml

description: PKD1 renal cyst

source_name: Renal cyst from PKD1 patient, medium single cyst


title: SMJ at 0hr_56

source_name: SMJ56 at 0hr


title: SMJ at 3hr after APAP treatment_98

source_name: SMJ98 at 3hr after APAP treatment


title: PKD1 renal cyst, medium cyst_5, 19 ml

description: PKD1 renal cyst


title: SJL at 3hr after APAP treatment_42

description: gene expression data from SJL train at 3hr after APAP treatment

source_name: SJL42 at 3hr after APAP treatment

value: SJL


title: minimally cystic tissue_1

description: PKD1 control tissue


title: PKD1 renal cyst, medium cyst_3, 11 ml

description: PKD1 renal cyst


title: SJL at 6hr after APAP treatment_45

description: gene expression data from SJL train at 6hr after APAP treatment

source_name: SJL45 at 6hr after APAP treatment


title: SMJ at 3hr after APAP treatment_95

source_name: SMJ95 at 3hr after APAP treatment


title: PKD1 renal cyst, medium cyst_1, 23 ml

description: PKD1 renal cyst


title: SJL at 6hr after APAP treatment_48

source_name: SJL48 at 6hr after APAP treatment


title: SJL at 6hr after APAP treatment_44

source_name: SJL44 at 6hr after APAP treatment


title: PKD1 renal cyst, medium cyst_2, 20 ml

description: PKD1 renal cyst


title: GM06990 Pool_101

status: Public on Aug 13 2009

city: Woodbury

first: Chris

last: Zaleski

state: NY

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Labs

description: single chip, 1 replicate

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

scan_protocol: Arrays were scanned on Affymetrix GCS3000 scanner

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

label: Biotin

molecule: polyA RNA

source_name: BD SMARTTM RACE cDNA – GM06990

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

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

extract_protocol: see Kapranov, et al Science 2002

value: GM06990 cell line


title: GM06990 Pool_102

description: single chip, 1 replicate


title: GM06990 Pool_98

description: single chip, 1 replicate


title: GM06990 Pool_99

description: single chip, 1 replicate


title: GM06990 Pool_97

description: single chip, 1 replicate


title: PKD1 renal cyst, small cyst_3, < 1ml

description: PKD1 renal cyst

source_name: Renal cyst from PKD1 patient, pooled from 4 different small cysts


title: SJL at 0hr_1

description: gene expression data from SJL strain at 0hr (pre-dose)

source_name: SJL1 at 0hr


title: SJL at 0hr_2

source_name: SJL2 at 0hr


title: GM06990 Pool_96

description: single chip, 1 replicate


title: PKD1 renal cyst, small cyst_5, < 1ml

description: PKD1 renal cyst


title: PKD1 renal cyst, small cyst_2, < 1ml

description: PKD1 renal cyst


title: H37Rv Ctrl vs 5 ug/ml garlic extract 6hrs

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84517.gif

source_name: Control exposed to DMSO for 6hrs

source_name: Treated with 5 ug/ml garlic (Allium stipitatum) extract for 6hrs

treatment_protocol: Time = 6hrs; Compound Based Treatment = Treated with 5ug/ml garlic extract


title: GM06990 Pool_94

description: single chip, 1 replicate


title: GM06990 Pool_95

description: single chip, 1 replicate


title: SJL at 3hr after APAP treatment_40

source_name: SJL40 at 3hr after APAP treatment


title: SJL at 3hr after APAP treatment_39

source_name: SJL39 at 3hr after APAP treatment


title: PKD1 renal cyst, small cyst_4, < 1ml

description: PKD1 renal cyst


title: GM06990 Pool_100

description: single chip, 1 replicate


title: GM06990 Pool_93

description: single chip, 1 replicate


title: SJL at 0hr_4

source_name: SJL4 at 0hr


title: GM06990 Pool_92

description: single chip, 1 replicate


title: PKD1 renal cyst, small cyst_1, < 1ml

description: PKD1 renal cyst


title: GM06990 Pool_90

description: single chip, 1 replicate


title: GM06990 Pool_89

description: single chip, 1 replicate


title: AGMPED_Blood_1 2005020

status: Public on Aug 21 2009

city: Pittsburgh

first: Anna

middle: J

last: Jasinska

address: 3550 Terrace Street

department: School of Medicine

institute: University of Pittsburgh

description: Illumina_project_number: 2008-036

hyb_protocol: Illumina Beadstation, standard Illumina protocol

data_processing: Raw signal was background corrected in BeadStudio. VST transformation and RSN normalization was performed using Lumi package.

organism: Chlorocebus sabaeus

source_name: blood

label_protocol: cDNA was synthesized and in vitro transcribed into biotinylated cRNA using the Illumina Totalprep RNA amplification kit, following the manufacturer’s instructions (Ambion)

extract_protocol: Total RNA was extracted from brain tissues with PefectPure RNA Cell and Tissue Kit (5 Prime) and from peripheral blood collected to PaxGene RNA blood tubes using PAXgene Blood RNA Kit (PreAnalyticX).

tag: ucla animal id


title: GM06990 Pool_86

description: single chip, 1 replicate


title: GM06990 Pool_85

description: single chip, 1 replicate


title: GM06990 Pool_88

description: single chip, 1 replicate


title: GM06990 Pool_87

description: single chip, 1 replicate


title: GM06990 Pool_84

description: single chip, 1 replicate


title: GM06990 Pool_83

description: single chip, 1 replicate


title: GM06990 Pool_91

description: single chip, 1 replicate


title: GM06990 Pool_77

description: single chip, 1 replicate


title: GM06990 Pool_81

description: single chip, 1 replicate


title: GM06990 Pool_76

description: single chip, 1 replicate


title: GM06990 Pool_80

description: single chip, 1 replicate


title: GM06990 Pool_73

description: single chip, 1 replicate


title: GM06990 Pool_74

description: single chip, 1 replicate


title: GM06990 Pool_75

description: single chip, 1 replicate


title: GM06990 Pool_72

description: single chip, 1 replicate


title: GM06990 Pool_82

description: single chip, 1 replicate


title: GM06990 Pool_78

description: single chip, 1 replicate


title: GM06990 Pool_79

description: single chip, 1 replicate


title: GM06990 Pool_71

description: single chip, 1 replicate


title: GM06990 Pool_69

description: single chip, 1 replicate


title: GM06990 Pool_70

description: single chip, 1 replicate


title: GM06990 Pool_68

description: single chip, 1 replicate


title: GM06990 Pool_66

description: single chip, 1 replicate


title: GM06990 Pool_67

description: single chip, 1 replicate


title: GM06990 Pool_64

description: single chip, 1 replicate


title: GM06990 Pool_63

description: single chip, 1 replicate


title: GM06990 Pool_65

description: single chip, 1 replicate


title: GM06990 Pool_62

description: single chip, 1 replicate


title: GM06990 Pool_61

description: single chip, 1 replicate


title: GM06990 Pool_59

description: single chip, 1 replicate


title: GM06990 Pool_53

description: single chip, 1 replicate


title: GM06990 Pool_57

description: single chip, 1 replicate


title: GM06990 Pool_55

description: single chip, 1 replicate


title: GM06990 Pool_56

description: single chip, 1 replicate


title: GM06990 Pool_51

description: single chip, 1 replicate


title: GM06990 Pool_49

description: single chip, 1 replicate


title: GM06990 Pool_47

description: single chip, 1 replicate


title: GM06990 Pool_58

description: single chip, 1 replicate


title: GM06990 Pool_48

description: single chip, 1 replicate


title: GM06990 Pool_50

description: single chip, 1 replicate


title: GM06990 Pool_46

description: single chip, 1 replicate


title: GM06990 Pool_45

description: single chip, 1 replicate


title: GM06990 Pool_44

description: single chip, 1 replicate


title: GM06990 Pool_42

description: single chip, 1 replicate


title: GM06990 Pool_43

description: single chip, 1 replicate


title: GM06990 Pool_41

description: single chip, 1 replicate


title: GM06990 Pool_52

description: single chip, 1 replicate


title: GM06990 Pool_38

description: single chip, 1 replicate


title: GM06990 Pool_40

description: single chip, 1 replicate


title: C57 at 0hr_182


title: GM06990 Pool_60

description: single chip, 1 replicate


title: GM06990 Pool_39

description: single chip, 1 replicate


title: GM06990 Pool_36

description: single chip, 1 replicate


title: GM06990 Pool_29

description: single chip, 1 replicate


title: GM06990 Pool_31

description: single chip, 1 replicate


title: GM06990 Pool_26

description: single chip, 1 replicate


title: GM06990 Pool_35

description: single chip, 1 replicate


title: GM06990 Pool_25

description: single chip, 1 replicate


title: GM06990 Pool_30

description: single chip, 1 replicate


title: GM06990 Pool_28

description: single chip, 1 replicate


title: GM06990 Pool_27

description: single chip, 1 replicate


title: GM06990 Pool_24

description: single chip, 1 replicate


title: GM06990 Pool_22

description: single chip, 1 replicate


title: GM06990 Pool_37

description: single chip, 1 replicate


title: GM06990 Pool_23

description: single chip, 1 replicate


title: GM06990 Pool_20

description: single chip, 1 replicate


title: GM06990 Pool_21

description: single chip, 1 replicate


title: GM06990 Pool_16

description: single chip, 1 replicate


title: GM06990 Pool_18

description: single chip, 1 replicate


title: GM06990 Pool_15

description: single chip, 1 replicate


title: GM06990 Pool_14

description: single chip, 1 replicate


title: GM06990 Pool_19

description: single chip, 1 replicate


title: GM06990 Pool_17

description: single chip, 1 replicate


title: GM06990 Pool_33

description: single chip, 1 replicate


title: GM06990 Pool_34

description: single chip, 1 replicate


title: GM06990 Pool_13

description: single chip, 1 replicate


title: GM06990 Pool_12

description: single chip, 1 replicate


title: AGMPED_Blood_1 2001073

description: Illumina_project_number: 2008-036

scan_protocol: Illumina Beadstation, standard Illumina protocol


title: GM06990 Pool_11

description: single chip, 1 replicate


title: GM06990 Pool_8

description: single chip, 1 replicate


title: GM06990 Pool_10

description: single chip, 1 replicate


title: GM06990 Pool_7

description: single chip, 1 replicate


title: GM06990 Pool_3

description: single chip, 1 replicate


title: GM06990 Pool_6

description: single chip, 1 replicate


title: GM06990 Pool_4

description: single chip, 1 replicate


title: Ovary Placenta Pool_102

description: single chip, 1 replicate

source_name: BD Clontech – Ovary, Placenta polyA RNA

value: ovary, placental


title: GM06990 Pool_9

description: single chip, 1 replicate


title: GM06990 Pool_5

description: single chip, 1 replicate


title: GM06990 Pool_1

description: single chip, 1 replicate


title: Ovary Placenta Pool_97

description: single chip, 1 replicate


title: Ovary Placenta Pool_100

description: single chip, 1 replicate


title: Ovary Placenta Pool_101

description: single chip, 1 replicate


title: Ovary Placenta Pool_96

description: single chip, 1 replicate


title: Ovary Placenta Pool_98

description: single chip, 1 replicate


title: Ovary Placenta Pool_95

description: single chip, 1 replicate


title: Ovary Placenta Pool_99

description: single chip, 1 replicate


title: Ovary Placenta Pool_89

description: single chip, 1 replicate


title: Ovary Placenta Pool_91

description: single chip, 1 replicate


title: GM06990 Pool_2

description: single chip, 1 replicate


title: Ovary Placenta Pool_92

description: single chip, 1 replicate


title: Ovary Placenta Pool_94

description: single chip, 1 replicate


title: Ovary Placenta Pool_88

description: single chip, 1 replicate


title: Ovary Placenta Pool_87

description: single chip, 1 replicate


title: Ovary Placenta Pool_85

description: single chip, 1 replicate


title: Ovary Placenta Pool_90

description: single chip, 1 replicate


title: GM06990 Pool_32

description: single chip, 1 replicate


title: Ovary Placenta Pool_79

description: single chip, 1 replicate


title: Ovary Placenta Pool_82

description: single chip, 1 replicate


title: Ovary Placenta Pool_81

description: single chip, 1 replicate


title: Ovary Placenta Pool_93

description: single chip, 1 replicate


title: Ovary Placenta Pool_84

description: single chip, 1 replicate


title: Ovary Placenta Pool_78

description: single chip, 1 replicate


title: Ovary Placenta Pool_80

description: single chip, 1 replicate


title: Ovary Placenta Pool_73

description: single chip, 1 replicate


title: Ovary Placenta Pool_83

description: single chip, 1 replicate


title: Ovary Placenta Pool_76

description: single chip, 1 replicate


title: Ovary Placenta Pool_77

description: single chip, 1 replicate


title: Ovary Placenta Pool_69

description: single chip, 1 replicate


title: Ovary Placenta Pool_75

description: single chip, 1 replicate


title: GM06990 Pool_54

description: single chip, 1 replicate


title: Ovary Placenta Pool_67

description: single chip, 1 replicate


title: Ovary Placenta Pool_72

description: single chip, 1 replicate


title: Ovary Placenta Pool_66

description: single chip, 1 replicate


title: Ovary Placenta Pool_71

description: single chip, 1 replicate


title: Ovary Placenta Pool_63

description: single chip, 1 replicate


title: Ovary Placenta Pool_70

description: single chip, 1 replicate


title: Ovary Placenta Pool_68

description: single chip, 1 replicate


title: Ovary Placenta Pool_65

description: single chip, 1 replicate


title: Ovary Placenta Pool_64

description: single chip, 1 replicate


title: Ovary Placenta Pool_74

description: single chip, 1 replicate


title: Ovary Placenta Pool_62

description: single chip, 1 replicate


title: Ovary Placenta Pool_57

description: single chip, 1 replicate


title: Ovary Placenta Pool_59

description: single chip, 1 replicate


title: Ovary Placenta Pool_60

description: single chip, 1 replicate


title: Ovary Placenta Pool_56

description: single chip, 1 replicate


title: Ovary Placenta Pool_58

description: single chip, 1 replicate


title: Ovary Placenta Pool_52

description: single chip, 1 replicate


title: Ovary Placenta Pool_55

description: single chip, 1 replicate


title: Ovary Placenta Pool_54

description: single chip, 1 replicate


title: Ovary Placenta Pool_50

description: single chip, 1 replicate


title: Ovary Placenta Pool_53

description: single chip, 1 replicate


title: Ovary Placenta Pool_51

description: single chip, 1 replicate


title: Ovary Placenta Pool_48

description: single chip, 1 replicate


title: Ovary Placenta Pool_46

description: single chip, 1 replicate


title: Ovary Placenta Pool_45

description: single chip, 1 replicate


title: Ovary Placenta Pool_43

description: single chip, 1 replicate


title: Ovary Placenta Pool_41

description: single chip, 1 replicate


title: Ovary Placenta Pool_40

description: single chip, 1 replicate


title: Ovary Placenta Pool_44

description: single chip, 1 replicate


title: Ovary Placenta Pool_42

description: single chip, 1 replicate


title: Ovary Placenta Pool_35

description: single chip, 1 replicate


title: Ovary Placenta Pool_38

description: single chip, 1 replicate


title: Ovary Placenta Pool_32

description: single chip, 1 replicate


title: Ovary Placenta Pool_39

description: single chip, 1 replicate


title: Ovary Placenta Pool_34

description: single chip, 1 replicate


title: Ovary Placenta Pool_33

description: single chip, 1 replicate


title: Ovary Placenta Pool_36

description: single chip, 1 replicate


title: Ovary Placenta Pool_37

description: single chip, 1 replicate


title: Ovary Placenta Pool_30

description: single chip, 1 replicate


title: Ovary Placenta Pool_31

description: single chip, 1 replicate


title: Ovary Placenta Pool_25

description: single chip, 1 replicate


title: Ovary Placenta Pool_27

description: single chip, 1 replicate


title: Ovary Placenta Pool_23

description: single chip, 1 replicate


title: Ovary Placenta Pool_21

description: single chip, 1 replicate


title: Ovary Placenta Pool_24

description: single chip, 1 replicate


title: Ovary Placenta Pool_17

description: single chip, 1 replicate


title: Ovary Placenta Pool_22

description: single chip, 1 replicate


title: Ovary Placenta Pool_19

description: single chip, 1 replicate


title: Ovary Placenta Pool_26

description: single chip, 1 replicate


title: Ovary Placenta Pool_28

description: single chip, 1 replicate


title: Ovary Placenta Pool_20

description: single chip, 1 replicate


title: Ovary Placenta Pool_12

description: single chip, 1 replicate


title: Ovary Placenta Pool_15

description: single chip, 1 replicate


title: Ovary Placenta Pool_18

description: single chip, 1 replicate


title: Ovary Placenta Pool_7

description: single chip, 1 replicate


title: Ovary Placenta Pool_13

description: single chip, 1 replicate


title: Ovary Placenta Pool_11

description: single chip, 1 replicate


title: Ovary Placenta Pool_86

description: single chip, 1 replicate


title: Ovary Placenta Pool_14

description: single chip, 1 replicate


title: Ovary Placenta Pool_5

description: single chip, 1 replicate


title: Ovary Placenta Pool_8

description: single chip, 1 replicate


title: Ovary Placenta Pool_10

description: single chip, 1 replicate


title: Ovary Placenta Pool_6

description: single chip, 1 replicate


title: Testis, Prostate  Pool_102

description: single chip, 1 replicate

source_name: BD Clontech – Testis, Prostate  polyA RNA

value: testis, prostate


title: Ovary Placenta Pool_2

description: single chip, 1 replicate


title: Ovary Placenta Pool_1

description: single chip, 1 replicate


title: Testis, Prostate  Pool_101

description: single chip, 1 replicate


title: Testis, Prostate  Pool_100

description: single chip, 1 replicate


title: Ovary Placenta Pool_3

description: single chip, 1 replicate


title: Testis, Prostate  Pool_99

description: single chip, 1 replicate


title: Ovary Placenta Pool_9

description: single chip, 1 replicate


title: Ovary Placenta Pool_47

description: single chip, 1 replicate


title: Testis, Prostate  Pool_97

description: single chip, 1 replicate


title: Testis, Prostate  Pool_96

description: single chip, 1 replicate


title: Testis, Prostate  Pool_94

description: single chip, 1 replicate


title: Testis, Prostate  Pool_95

description: single chip, 1 replicate


title: Ovary Placenta Pool_49

description: single chip, 1 replicate


title: Testis, Prostate  Pool_89

description: single chip, 1 replicate


title: Testis, Prostate  Pool_93

description: single chip, 1 replicate


title: Testis, Prostate  Pool_91

description: single chip, 1 replicate


title: Testis, Prostate  Pool_80

description: single chip, 1 replicate


title: Testis, Prostate  Pool_81

description: single chip, 1 replicate


title: Testis, Prostate  Pool_88

description: single chip, 1 replicate


title: Testis, Prostate  Pool_86

description: single chip, 1 replicate


title: Testis, Prostate  Pool_79

description: single chip, 1 replicate


title: Testis, Prostate  Pool_90

description: single chip, 1 replicate


title: Testis, Prostate  Pool_83

description: single chip, 1 replicate


title: Testis, Prostate  Pool_84

description: single chip, 1 replicate


title: Testis, Prostate  Pool_92

description: single chip, 1 replicate


title: Testis, Prostate  Pool_82

description: single chip, 1 replicate


title: Ovary Placenta Pool_61

description: single chip, 1 replicate


title: Testis, Prostate  Pool_78

description: single chip, 1 replicate


title: Testis, Prostate  Pool_76

description: single chip, 1 replicate


title: Testis, Prostate  Pool_85

description: single chip, 1 replicate


title: Testis, Prostate  Pool_77

description: single chip, 1 replicate


title: Testis, Prostate  Pool_75

description: single chip, 1 replicate


title: Testis, Prostate  Pool_73

description: single chip, 1 replicate


title: Testis, Prostate  Pool_71

description: single chip, 1 replicate


title: Ovary Placenta Pool_16

description: single chip, 1 replicate


title: Testis, Prostate  Pool_72

description: single chip, 1 replicate


title: Testis, Prostate  Pool_70

description: single chip, 1 replicate


title: Testis, Prostate  Pool_68

description: single chip, 1 replicate


title: Testis, Prostate  Pool_65

description: single chip, 1 replicate


title: Testis, Prostate  Pool_60

description: single chip, 1 replicate


title: Testis, Prostate  Pool_66

description: single chip, 1 replicate


title: Testis, Prostate  Pool_69

description: single chip, 1 replicate


title: Testis, Prostate  Pool_61

description: single chip, 1 replicate


title: Testis, Prostate  Pool_74

description: single chip, 1 replicate


title: Testis, Prostate  Pool_62

description: single chip, 1 replicate


title: Testis, Prostate  Pool_67

description: single chip, 1 replicate


title: Testis, Prostate  Pool_59

description: single chip, 1 replicate


title: Testis, Prostate  Pool_58

description: single chip, 1 replicate


title: Ovary Placenta Pool_4

description: single chip, 1 replicate


title: Testis, Prostate  Pool_64

description: single chip, 1 replicate


title: Testis, Prostate  Pool_57

description: single chip, 1 replicate


title: Testis, Prostate  Pool_56

description: single chip, 1 replicate


title: Testis, Prostate  Pool_98

description: single chip, 1 replicate


title: Ovary Placenta Pool_29

description: single chip, 1 replicate


title: Testis, Prostate  Pool_63

description: single chip, 1 replicate


title: Testis, Prostate  Pool_55

description: single chip, 1 replicate


title: Testis, Prostate  Pool_47

description: single chip, 1 replicate


title: Testis, Prostate  Pool_51

description: single chip, 1 replicate


title: Testis, Prostate  Pool_54

description: single chip, 1 replicate


title: Testis, Prostate  Pool_52

description: single chip, 1 replicate


title: Testis, Prostate  Pool_46

description: single chip, 1 replicate


title: Testis, Prostate  Pool_48

description: single chip, 1 replicate


title: Testis, Prostate  Pool_50

description: single chip, 1 replicate


title: Testis, Prostate  Pool_45

description: single chip, 1 replicate


title: Testis, Prostate  Pool_39

description: single chip, 1 replicate


title: Testis, Prostate  Pool_44

description: single chip, 1 replicate


title: Testis, Prostate  Pool_41

description: single chip, 1 replicate


title: Testis, Prostate  Pool_36

description: single chip, 1 replicate


title: Testis, Prostate  Pool_40

description: single chip, 1 replicate


title: Testis, Prostate  Pool_38

description: single chip, 1 replicate


title: Testis, Prostate  Pool_37

description: single chip, 1 replicate


title: Testis, Prostate  Pool_35

description: single chip, 1 replicate


title: Testis, Prostate  Pool_43

description: single chip, 1 replicate


title: Testis, Prostate  Pool_32

description: single chip, 1 replicate


title: Testis, Prostate  Pool_53

description: single chip, 1 replicate


title: Testis, Prostate  Pool_33

description: single chip, 1 replicate


title: Testis, Prostate  Pool_31

description: single chip, 1 replicate


title: Testis, Prostate  Pool_42

description: single chip, 1 replicate


title: Testis, Prostate  Pool_28

description: single chip, 1 replicate


title: Testis, Prostate  Pool_27

description: single chip, 1 replicate


title: Testis, Prostate  Pool_23

description: single chip, 1 replicate


title: Testis, Prostate  Pool_29

description: single chip, 1 replicate


title: Testis, Prostate  Pool_24

description: single chip, 1 replicate


title: Testis, Prostate  Pool_21

description: single chip, 1 replicate


title: Testis, Prostate  Pool_22

description: single chip, 1 replicate


title: Testis, Prostate  Pool_30

description: single chip, 1 replicate


title: Testis, Prostate  Pool_26

description: single chip, 1 replicate


title: Testis, Prostate  Pool_25

description: single chip, 1 replicate


title: Testis, Prostate  Pool_17

description: single chip, 1 replicate


title: Testis, Prostate  Pool_20

description: single chip, 1 replicate


title: Testis, Prostate  Pool_18

description: single chip, 1 replicate


title: Testis, Prostate  Pool_13

description: single chip, 1 replicate


title: Testis, Prostate  Pool_15

description: single chip, 1 replicate


title: Testis, Prostate  Pool_10

description: single chip, 1 replicate


title: Testis, Prostate  Pool_14

description: single chip, 1 replicate


title: Testis, Prostate  Pool_16

description: single chip, 1 replicate


title: Testis, Prostate  Pool_5

description: single chip, 1 replicate


title: Testis, Prostate  Pool_8

description: single chip, 1 replicate


title: Testis, Prostate  Pool_7

description: single chip, 1 replicate


title: Testis, Prostate  Pool_11

description: single chip, 1 replicate


title: Testis, Prostate  Pool_12

description: single chip, 1 replicate


title: Testis, Prostate  Pool_6

description: single chip, 1 replicate


title: Testis, Prostate  Pool_3

description: single chip, 1 replicate


title: HepG2 Pool_100

description: single chip, 1 replicate

source_name: BD SMARTTM RACE cDNA – HepG2

value: HepG2 cell line


title: Testis, Prostate  Pool_19

description: single chip, 1 replicate


title: Testis, Prostate  Pool_9

description: single chip, 1 replicate


title: Testis, Prostate  Pool_2

description: single chip, 1 replicate


title: Testis, Prostate  Pool_4

description: single chip, 1 replicate


title: HepG2 Pool_102

description: single chip, 1 replicate


title: HepG2 Pool_93

description: single chip, 1 replicate


title: HepG2 Pool_95

description: single chip, 1 replicate


title: HepG2 Pool_96

description: single chip, 1 replicate


title: HepG2 Pool_101

description: single chip, 1 replicate


title: HepG2 Pool_92

description: single chip, 1 replicate


title: Testis, Prostate  Pool_1

description: single chip, 1 replicate


title: HepG2 Pool_98

description: single chip, 1 replicate


title: HepG2 Pool_97

description: single chip, 1 replicate


title: HepG2 Pool_94

description: single chip, 1 replicate


title: HepG2 Pool_99

description: single chip, 1 replicate


title: HepG2 Pool_86

description: single chip, 1 replicate


title: Testis, Prostate  Pool_34

description: single chip, 1 replicate


title: HepG2 Pool_90

description: single chip, 1 replicate


title: HepG2 Pool_84

description: single chip, 1 replicate


title: HepG2 Pool_89

description: single chip, 1 replicate


title: HepG2 Pool_88

description: single chip, 1 replicate


title: HepG2 Pool_85

description: single chip, 1 replicate


title: HepG2 Pool_83

description: single chip, 1 replicate


title: HepG2 Pool_76

description: single chip, 1 replicate


title: Testis, Prostate  Pool_87

description: single chip, 1 replicate


title: HepG2 Pool_81

description: single chip, 1 replicate


title: HepG2 Pool_79

description: single chip, 1 replicate


title: HepG2 Pool_74

description: single chip, 1 replicate


title: HepG2 Pool_87

description: single chip, 1 replicate


title: HepG2 Pool_71

description: single chip, 1 replicate


title: HepG2 Pool_78

description: single chip, 1 replicate


title: HepG2 Pool_77

description: single chip, 1 replicate


title: HepG2 Pool_73

description: single chip, 1 replicate


title: HepG2 Pool_68

description: single chip, 1 replicate


title: HepG2 Pool_75

description: single chip, 1 replicate


title: HepG2 Pool_80

description: single chip, 1 replicate


title: AGMPED_Blood_1 2004052

description: Illumina_project_number: 2008-063


title: HepG2 Pool_66

description: single chip, 1 replicate


title: HepG2 Pool_72

description: single chip, 1 replicate


title: HepG2 Pool_69

description: single chip, 1 replicate


title: HepG2 Pool_82

description: single chip, 1 replicate


title: HepG2 Pool_70

description: single chip, 1 replicate


title: HepG2 Pool_67

description: single chip, 1 replicate


title: HepG2 Pool_62

description: single chip, 1 replicate


title: HepG2 Pool_59

description: single chip, 1 replicate


title: HepG2 Pool_57

description: single chip, 1 replicate


title: HepG2 Pool_63

description: single chip, 1 replicate


title: HepG2 Pool_56

description: single chip, 1 replicate


title: HepG2 Pool_54

description: single chip, 1 replicate


title: HepG2 Pool_64

description: single chip, 1 replicate


title: HepG2 Pool_58

description: single chip, 1 replicate


title: HepG2 Pool_55

description: single chip, 1 replicate


title: HepG2 Pool_52

description: single chip, 1 replicate


title: HepG2 Pool_65

description: single chip, 1 replicate


title: HepG2 Pool_53

description: single chip, 1 replicate


title: HepG2 Pool_49

description: single chip, 1 replicate


title: HepG2 Pool_48

description: single chip, 1 replicate


title: HepG2 Pool_44

description: single chip, 1 replicate


title: HepG2 Pool_43

description: single chip, 1 replicate


title: HepG2 Pool_46

description: single chip, 1 replicate


title: HepG2 Pool_45

description: single chip, 1 replicate


title: HepG2 Pool_91

description: single chip, 1 replicate


title: HepG2 Pool_40

description: single chip, 1 replicate


title: HepG2 Pool_41

description: single chip, 1 replicate


title: HepG2 Pool_47

description: single chip, 1 replicate


title: HepG2 Pool_38

description: single chip, 1 replicate


title: HepG2 Pool_51

description: single chip, 1 replicate


title: Testis, Prostate  Pool_49

description: single chip, 1 replicate


title: HepG2 Pool_37

description: single chip, 1 replicate


title: HepG2 Pool_39

description: single chip, 1 replicate


title: HepG2 Pool_36

description: single chip, 1 replicate


title: HepG2 Pool_35

description: single chip, 1 replicate


title: HepG2 Pool_34

description: single chip, 1 replicate


title: HepG2 Pool_33

description: single chip, 1 replicate


title: HepG2 Pool_30

description: single chip, 1 replicate


title: HepG2 Pool_31

description: single chip, 1 replicate


title: HepG2 Pool_32

description: single chip, 1 replicate


title: HepG2 Pool_28

description: single chip, 1 replicate


title: HepG2 Pool_29

description: single chip, 1 replicate


title: HepG2 Pool_27

description: single chip, 1 replicate


title: HepG2 Pool_50

description: single chip, 1 replicate


title: HepG2 Pool_26

description: single chip, 1 replicate


title: HepG2 Pool_24

description: single chip, 1 replicate


title: HepG2 Pool_25

description: single chip, 1 replicate


title: HepG2 Pool_23

description: single chip, 1 replicate


title: HepG2 Pool_18

description: single chip, 1 replicate


title: HepG2 Pool_20

description: single chip, 1 replicate


title: HepG2 Pool_22

description: single chip, 1 replicate


title: HepG2 Pool_19

description: single chip, 1 replicate


title: HepG2 Pool_17

description: single chip, 1 replicate


title: HepG2 Pool_21

description: single chip, 1 replicate


title: HepG2 Pool_61

description: single chip, 1 replicate


title: HepG2 Pool_11

description: single chip, 1 replicate


title: HepG2 Pool_12

description: single chip, 1 replicate


title: HepG2 Pool_15

description: single chip, 1 replicate


title: HepG2 Pool_13

description: single chip, 1 replicate


title: HepG2 Pool_16

description: single chip, 1 replicate


title: HepG2 Pool_10

description: single chip, 1 replicate


title: HepG2 Pool_14

description: single chip, 1 replicate


title: HepG2 Pool_9

description: single chip, 1 replicate


title: HepG2 Pool_6

description: single chip, 1 replicate


title: HepG2 Pool_8

description: single chip, 1 replicate


title: HepG2 Pool_7

description: single chip, 1 replicate


title: HepG2 Pool_5

description: single chip, 1 replicate


title: HepG2 Pool_4

description: single chip, 1 replicate


title: HepG2 Pool_2

description: single chip, 1 replicate


title: HepG2 Pool_1

description: single chip, 1 replicate


title: HeLaCIS3 Pool_96

description: single chip, 1 replicate

source_name: BD SMARTTM RACE cDNA – HeLaS3

value: HeLaS3 cell line


title: HeLaCIS3 Pool_97

description: single chip, 1 replicate


title: HeLaCIS3 Pool_98

description: single chip, 1 replicate


title: HeLaCIS3 Pool_99

description: single chip, 1 replicate


title: HeLaCIS3 Pool_101

description: single chip, 1 replicate


title: HeLaCIS3 Pool_102

description: single chip, 1 replicate


title: HeLaCIS3 Pool_95

description: single chip, 1 replicate


title: HeLaCIS3 Pool_92

description: single chip, 1 replicate


title: HeLaCIS3 Pool_89

description: single chip, 1 replicate


title: HeLaCIS3 Pool_93

description: single chip, 1 replicate


title: HeLaCIS3 Pool_90

description: single chip, 1 replicate


title: HeLaCIS3 Pool_85

description: single chip, 1 replicate


title: HepG2 Pool_42

description: single chip, 1 replicate


title: HeLaCIS3 Pool_87

description: single chip, 1 replicate


title: HeLaCIS3 Pool_83

description: single chip, 1 replicate


title: HeLaCIS3 Pool_100

description: single chip, 1 replicate


title: HepG2 Pool_3

description: single chip, 1 replicate


title: HeLaCIS3 Pool_84

description: single chip, 1 replicate


title: HeLaCIS3 Pool_88

description: single chip, 1 replicate


title: HeLaCIS3 Pool_80

description: single chip, 1 replicate


title: HeLaCIS3 Pool_81

description: single chip, 1 replicate


title: HeLaCIS3 Pool_76

description: single chip, 1 replicate


title: HeLaCIS3 Pool_77

description: single chip, 1 replicate


title: HeLaCIS3 Pool_82

description: single chip, 1 replicate


title: HeLaCIS3 Pool_78

description: single chip, 1 replicate


title: HeLaCIS3 Pool_94

description: single chip, 1 replicate


title: HeLaCIS3 Pool_86

description: single chip, 1 replicate


title: HeLaCIS3 Pool_79

description: single chip, 1 replicate


title: HeLaCIS3 Pool_75

description: single chip, 1 replicate


title: HeLaCIS3 Pool_70

description: single chip, 1 replicate


title: HeLaCIS3 Pool_73

description: single chip, 1 replicate


title: HeLaCIS3 Pool_74

description: single chip, 1 replicate


title: HeLaCIS3 Pool_71

description: single chip, 1 replicate


title: HeLaCIS3 Pool_72

description: single chip, 1 replicate


title: HeLaCIS3 Pool_64

description: single chip, 1 replicate


title: HeLaCIS3 Pool_65

description: single chip, 1 replicate


title: HeLaCIS3 Pool_69

description: single chip, 1 replicate


title: HeLaCIS3 Pool_62

description: single chip, 1 replicate


title: HeLaCIS3 Pool_63

description: single chip, 1 replicate


title: HeLaCIS3 Pool_58

description: single chip, 1 replicate


title: HeLaCIS3 Pool_59

description: single chip, 1 replicate


title: HeLaCIS3 Pool_57

description: single chip, 1 replicate


title: HeLaCIS3 Pool_68

description: single chip, 1 replicate


title: HeLaCIS3 Pool_52

description: single chip, 1 replicate


title: HeLaCIS3 Pool_55

description: single chip, 1 replicate


title: HeLaCIS3 Pool_54

description: single chip, 1 replicate


title: HeLaCIS3 Pool_53

description: single chip, 1 replicate


title: HeLaCIS3 Pool_49

description: single chip, 1 replicate


title: HeLaCIS3 Pool_60

description: single chip, 1 replicate


title: HeLaCIS3 Pool_48

description: single chip, 1 replicate


title: HeLaCIS3 Pool_67

description: single chip, 1 replicate


title: HeLaCIS3 Pool_51

description: single chip, 1 replicate


title: HeLaCIS3 Pool_91

description: single chip, 1 replicate


title: HeLaCIS3 Pool_66

description: single chip, 1 replicate


title: HeLaCIS3 Pool_50

description: single chip, 1 replicate


title: HeLaCIS3 Pool_61

description: single chip, 1 replicate


title: HeLaCIS3 Pool_46

description: single chip, 1 replicate


title: HeLaCIS3 Pool_47

description: single chip, 1 replicate


title: HeLaCIS3 Pool_56

description: single chip, 1 replicate


title: HeLaCIS3 Pool_45

description: single chip, 1 replicate


title: HeLaCIS3 Pool_42

description: single chip, 1 replicate


title: HeLaCIS3 Pool_44

description: single chip, 1 replicate


title: HeLaCIS3 Pool_41

description: single chip, 1 replicate


title: HeLaCIS3 Pool_34

description: single chip, 1 replicate


title: HeLaCIS3 Pool_39

description: single chip, 1 replicate


title: HeLaCIS3 Pool_38

description: single chip, 1 replicate


title: HeLaCIS3 Pool_36

description: single chip, 1 replicate


title: HeLaCIS3 Pool_35

description: single chip, 1 replicate


title: HeLaCIS3 Pool_32

description: single chip, 1 replicate


title: HeLaCIS3 Pool_33

description: single chip, 1 replicate


title: AGMPED_Blood_1 2004057

description: Illumina_project_number: 2008-063


title: HeLaCIS3 Pool_29

description: single chip, 1 replicate


title: HeLaCIS3 Pool_40

description: single chip, 1 replicate


title: HeLaCIS3 Pool_30

description: single chip, 1 replicate


title: HeLaCIS3 Pool_26

description: single chip, 1 replicate


title: HeLaCIS3 Pool_37

description: single chip, 1 replicate


title: HeLaCIS3 Pool_22

description: single chip, 1 replicate


title: HeLaCIS3 Pool_23

description: single chip, 1 replicate


title: HeLaCIS3 Pool_25

description: single chip, 1 replicate


title: HeLaCIS3 Pool_20

description: single chip, 1 replicate


title: HeLaCIS3 Pool_18

description: single chip, 1 replicate


title: HeLaCIS3 Pool_27

description: single chip, 1 replicate


title: HeLaCIS3 Pool_24

description: single chip, 1 replicate


title: HeLaCIS3 Pool_43

description: single chip, 1 replicate


title: HeLaCIS3 Pool_17

description: single chip, 1 replicate


title: HeLaCIS3 Pool_14

description: single chip, 1 replicate


title: HeLaCIS3 Pool_16

description: single chip, 1 replicate


title: HeLaCIS3 Pool_12

description: single chip, 1 replicate


title: HeLaCIS3 Pool_21

description: single chip, 1 replicate


title: HeLaCIS3 Pool_28

description: single chip, 1 replicate


title: HeLaCIS3 Pool_13

description: single chip, 1 replicate


title: HeLaCIS3 Pool_15

description: single chip, 1 replicate


title: HeLaCIS3 Pool_11

description: single chip, 1 replicate


title: HeLaCIS3 Pool_31

description: single chip, 1 replicate


title: HeLaCIS3 Pool_10

description: single chip, 1 replicate


title: HeLaCIS3 Pool_8

description: single chip, 1 replicate


title: HeLaCIS3 Pool_7

description: single chip, 1 replicate


title: HeLaCIS3 Pool_5

description: single chip, 1 replicate


title: TertBJ Pool_102

description: single chip, 1 replicate

source_name: BD SMARTTM RACE cDNA – tert-BJ

value: TertBJ cell line


title: HeLaCIS3 Pool_2

description: single chip, 1 replicate


title: HeLaCIS3 Pool_19

description: single chip, 1 replicate


title: HeLaCIS3 Pool_4

description: single chip, 1 replicate


title: HeLaCIS3 Pool_1

description: single chip, 1 replicate


title: TertBJ Pool_101

description: single chip, 1 replicate


title: TertBJ Pool_98

description: single chip, 1 replicate


title: TertBJ Pool_97

description: single chip, 1 replicate


title: TertBJ Pool_95

description: single chip, 1 replicate


title: TertBJ Pool_90

description: single chip, 1 replicate


title: TertBJ Pool_96

description: single chip, 1 replicate


title: TertBJ Pool_92

description: single chip, 1 replicate


title: TertBJ Pool_91

description: single chip, 1 replicate


title: TertBJ Pool_93

description: single chip, 1 replicate


title: TertBJ Pool_99

description: single chip, 1 replicate


title: TertBJ Pool_94

description: single chip, 1 replicate


title: TertBJ Pool_89

description: single chip, 1 replicate


title: TertBJ Pool_100

description: single chip, 1 replicate


title: TertBJ Pool_87

description: single chip, 1 replicate


title: TertBJ Pool_88

description: single chip, 1 replicate


title: HeLaCIS3 Pool_9

description: single chip, 1 replicate


title: HeLaCIS3 Pool_6

description: single chip, 1 replicate


title: TertBJ Pool_86

description: single chip, 1 replicate


title: HeLaCIS3 Pool_3

description: single chip, 1 replicate


title: TertBJ Pool_85

description: single chip, 1 replicate


title: TertBJ Pool_84

description: single chip, 1 replicate


title: TertBJ Pool_82

description: single chip, 1 replicate


title: TertBJ Pool_81

description: single chip, 1 replicate


title: TertBJ Pool_80

description: single chip, 1 replicate


title: TertBJ Pool_78

description: single chip, 1 replicate


title: TertBJ Pool_83

description: single chip, 1 replicate


title: TertBJ Pool_74

description: single chip, 1 replicate


title: TertBJ Pool_76

description: single chip, 1 replicate


title: TertBJ Pool_71

description: single chip, 1 replicate


title: TertBJ Pool_73

description: single chip, 1 replicate


title: TertBJ Pool_75

description: single chip, 1 replicate


title: TertBJ Pool_72

description: single chip, 1 replicate


title: TertBJ Pool_79

description: single chip, 1 replicate


title: TertBJ Pool_69

description: single chip, 1 replicate


title: TertBJ Pool_70

description: single chip, 1 replicate


title: TertBJ Pool_68

description: single chip, 1 replicate


title: TertBJ Pool_67

description: single chip, 1 replicate


title: TertBJ Pool_77

description: single chip, 1 replicate


title: TertBJ Pool_65

description: single chip, 1 replicate


title: TertBJ Pool_64

description: single chip, 1 replicate


title: TertBJ Pool_62

description: single chip, 1 replicate


title: TertBJ Pool_63

description: single chip, 1 replicate


title: TertBJ Pool_59

description: single chip, 1 replicate


title: TertBJ Pool_60

description: single chip, 1 replicate


title: TertBJ Pool_58

description: single chip, 1 replicate


title: TertBJ Pool_57

description: single chip, 1 replicate


title: TertBJ Pool_55

description: single chip, 1 replicate


title: TertBJ Pool_54

description: single chip, 1 replicate


title: TertBJ Pool_66

description: single chip, 1 replicate


title: TertBJ Pool_56

description: single chip, 1 replicate


title: TertBJ Pool_50

description: single chip, 1 replicate


title: TertBJ Pool_51

description: single chip, 1 replicate


title: TertBJ Pool_48

description: single chip, 1 replicate


title: TertBJ Pool_61

description: single chip, 1 replicate


title: TertBJ Pool_47

description: single chip, 1 replicate


title: TertBJ Pool_45

description: single chip, 1 replicate


title: TertBJ Pool_46

description: single chip, 1 replicate


title: TertBJ Pool_42

description: single chip, 1 replicate


title: TertBJ Pool_41

description: single chip, 1 replicate


title: TertBJ Pool_44

description: single chip, 1 replicate


title: TertBJ Pool_40

description: single chip, 1 replicate


title: TertBJ Pool_43

description: single chip, 1 replicate


title: TertBJ Pool_39

description: single chip, 1 replicate


title: TertBJ Pool_52

description: single chip, 1 replicate


title: TertBJ Pool_53

description: single chip, 1 replicate


title: TertBJ Pool_38

description: single chip, 1 replicate


title: TertBJ Pool_36

description: single chip, 1 replicate


title: TertBJ Pool_37

description: single chip, 1 replicate


title: TertBJ Pool_49

description: single chip, 1 replicate


title: TertBJ Pool_35

description: single chip, 1 replicate


title: TertBJ Pool_31

description: single chip, 1 replicate


title: TertBJ Pool_34

description: single chip, 1 replicate


title: TertBJ Pool_28

description: single chip, 1 replicate


title: TertBJ Pool_32

description: single chip, 1 replicate


title: TertBJ Pool_30

description: single chip, 1 replicate


title: TertBJ Pool_27

description: single chip, 1 replicate


title: TertBJ Pool_26

description: single chip, 1 replicate


title: TertBJ Pool_22

description: single chip, 1 replicate


title: TertBJ Pool_24

description: single chip, 1 replicate


title: TertBJ Pool_25

description: single chip, 1 replicate


title: TertBJ Pool_21

description: single chip, 1 replicate


title: TertBJ Pool_20

description: single chip, 1 replicate


title: TertBJ Pool_18

description: single chip, 1 replicate


title: TertBJ Pool_16

description: single chip, 1 replicate


title: TertBJ Pool_33

description: single chip, 1 replicate


title: TertBJ Pool_23

description: single chip, 1 replicate


title: TertBJ Pool_19

description: single chip, 1 replicate


title: TertBJ Pool_14

description: single chip, 1 replicate


title: TertBJ Pool_17

description: single chip, 1 replicate


title: TertBJ Pool_15

description: single chip, 1 replicate


title: TertBJ Pool_13

description: single chip, 1 replicate


title: TertBJ Pool_9

description: single chip, 1 replicate


title: TertBJ Pool_7

description: single chip, 1 replicate


title: TertBJ Pool_29

description: single chip, 1 replicate


title: TertBJ Pool_8

description: single chip, 1 replicate


title: TertBJ Pool_10

description: single chip, 1 replicate


title: TertBJ Pool_11

description: single chip, 1 replicate


title: TertBJ Pool_6

description: single chip, 1 replicate


title: TertBJ Pool_4

description: single chip, 1 replicate


title: TertBJ Pool_5

description: single chip, 1 replicate


title: TertBJ Pool_2

description: single chip, 1 replicate


title: TertBJ Pool_3

description: single chip, 1 replicate


title: TertBJ Pool_1

description: single chip, 1 replicate


title: K562 Pool_98

description: single chip, 1 replicate

source_name: BD SMARTTM RACE cDNA – K562

value: K562 cell line


title: TertBJ Pool_12

description: single chip, 1 replicate


title: K562 Pool_97

description: single chip, 1 replicate


title: K562 Pool_100

description: single chip, 1 replicate


title: K562 Pool_102

description: single chip, 1 replicate


title: K562 Pool_99

description: single chip, 1 replicate


title: K562 Pool_101

description: single chip, 1 replicate


title: K562 Pool_95

description: single chip, 1 replicate


title: K562 Pool_94

description: single chip, 1 replicate


title: K562 Pool_92

description: single chip, 1 replicate


title: K562 Pool_93

description: single chip, 1 replicate


title: K562 Pool_90

description: single chip, 1 replicate


title: K562 Pool_96

description: single chip, 1 replicate


title: K562 Pool_91

description: single chip, 1 replicate


title: K562 Pool_89

description: single chip, 1 replicate


title: K562 Pool_88

description: single chip, 1 replicate


title: K562 Pool_87

description: single chip, 1 replicate


title: K562 Pool_85

description: single chip, 1 replicate


title: K562 Pool_86

description: single chip, 1 replicate


title: K562 Pool_83

description: single chip, 1 replicate


title: K562 Pool_84

description: single chip, 1 replicate


title: K562 Pool_82

description: single chip, 1 replicate


title: K562 Pool_80

description: single chip, 1 replicate


title: K562 Pool_78

description: single chip, 1 replicate


title: K562 Pool_75

description: single chip, 1 replicate


title: K562 Pool_79

description: single chip, 1 replicate


title: K562 Pool_74

description: single chip, 1 replicate


title: K562 Pool_77

description: single chip, 1 replicate


title: K562 Pool_73

description: single chip, 1 replicate


title: K562 Pool_72

description: single chip, 1 replicate


title: K562 Pool_71

description: single chip, 1 replicate


title: K562 Pool_76

description: single chip, 1 replicate


title: K562 Pool_70

description: single chip, 1 replicate


title: K562 Pool_68

description: single chip, 1 replicate


title: baseline_asn_GM18998_rep1

first: Renuka

last: Nayak

address: 3516 Civic Center Blvd

institute: HHMI, University of Pennsylvania

description: Gene expression data at baseline from lymphoblastoid cells of individual GM18998.

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

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

source_name: Lymphoblastoid cell lines derived from GM18998

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

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

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

tag: coriell cell line repository identifier


title: baseline_asn_GM18997_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM18997.

source_name: Lymphoblastoid cell lines derived from GM18997


title: baseline_yri_GM19239_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM19239.

source_name: Lymphoblastoid cell lines derived from GM19239


title: K562 Pool_69

description: single chip, 1 replicate


title: baseline_asn_GM18571_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM18571.

source_name: Lymphoblastoid cell lines derived from GM18571


title: baseline_asn_GM18572_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM18572.

source_name: Lymphoblastoid cell lines derived from GM18572


title: E14 clone with pSicoR-mCherry GFP shRNAi G8

first: Miguel

last: Ramalho-Santos

address: 35 Medical Center Way

department: Eli and Edythe Broad Center of Regeneration Medicine

institute: UCSF

description: Gene expression data of ES cells grown in normal ES cell conditions.

hyb_protocol: According to manufacturer's instructions at the Genomics Core Facility of the Gladstones Institutes.

data_processing: RMA

source_name: ES cells, control

growth_protocol: Cells on gelatin-coated plates with ES cell medium with 15% KSR and recombinant LIF.

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

treatment_protocol: Cells trypsinized with 0.05% Trypsin for 3min at 37C and resuspended in PBS with trypsin inactivator.


title: K562 Pool_66

description: single chip, 1 replicate


title: K562 Pool_67

description: single chip, 1 replicate


title: baseline_yri_GM19223_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM19223.

source_name: Lymphoblastoid cell lines derived from GM19223


title: baseline_asn_GM18951_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM18951.

source_name: Lymphoblastoid cell lines derived from GM18951


title: E14 mouse ES cells (parental cells)

scan_protocol: According to manufacturer's instructions at the Genomics Core Facility of the Gladstones Institutes.

source_name: ES cells, parental


title: E14 clone with pSicoR-mCherry Chd1 shRNAi1 C1i5

source_name: ES cells, Chd1-deficient

label_protocol: According to manufacturer's instructions at the Genomics Core Facility of the Gladstones Institutes.

value: E14 clone C1i5


title: K562 Pool_65

description: single chip, 1 replicate


title: K562 Pool_64

description: single chip, 1 replicate


title: E14 clone with pSicoR-mCherry Chd1 shRNAi1 C1i6

value: E14 clone C1i6


title: baseline_yri_GM19238_rep1

description: Gene expression data at baseline from lymphoblastoid cells of individual GM19238.

source_name: Lymphoblastoid cell lines derived from GM19238


title: E14 clone with pSicoR-mCherry Chd1 shRNAi1 C1i9

value: E14 clone C1i9