title: sfl1-sok2 rep2

description: Gene expression from yeast cells


title: Pre Irradiation patient 24

status: Public on Mar 01 2007

type: RNA

city: Durham

first: Holly

middle: Kloos

last: Dressman

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

country: USA

institute: Duke University Medical Center

description: No treatment

data_processing: Data was analysed with GeneSpring 7 data software package (Silicon Genetics). Each data set filtered out probes that were below 1.5X background was normalised using  Lowess intensity-dependent normalisation, then data was put into PAM and missing values were imputed.

molecule: total RNA

organism: Homo sapiens

source_name: Pre Irradiation patient

growth_protocol: no growth protocol

extract_protocol: Briefly, 5 x 106 MNCs were pelleted and total RNA was isolated using the RNAeasy minispin column

treatment_protocol: no IR treatment

tag: Mononuclear cells (MNCs) were collected from each patient’s PB and RNA extracted via Qiagen RNAeasy kits

source_name: Stratagene Universal Human reference

treatment_protocol: No treatment


title: Pre Irradiation patient 23

description: No treatment


title: cup9-skn7 rep1

city: Bar Harbor

first: Gregory

last: Carter

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Gene expression from yeast cells

data_processing: Data was normalized using BioConductor RMA

label: biotin

organism: Saccharomyces cerevisiae

source_name: Yeast colonies after 10 hr growth

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

growth_protocol: 10hr growth on Synthetic low-ammonium dextrose media (SLAD) with uracil and histidine

tag: Genotype

value: G85 with cup9::bcKanMX4 skn7::bcKanMX4


title: Pre Irradiation patient 25

description: No treatment


title: Pre Irradiation patient 26

description: No treatment


title: Pre Irradiation patient 27

description: No treatment


title: Pre Irradiation patient 28

description: No treatment


title: cup9-skn7 rep3

description: Gene expression from yeast cells


title: Pre Irradiation patient 20

description: No treatment


title: Pre Irradiation patient 22

description: No treatment


title: cup9-skn7 rep2

description: Gene expression from yeast cells


title: Pre Irradiation patient 21

description: No treatment


title: Pre Irradiation patient 19

description: No treatment


title: normal plasma cells (NPC 547)

city: Salamanca

first: Norma

middle: Carmen

last: Gutierrez

department: Hematology

country: Spain

institute: University Hospital

hyb_protocol: Hybridizations were performed according to protocols from Affymetrix. Labeled RNA was hybridized to Human Genome U133A microarray (Affymetrix), after quality checking on GeneChips Test 3 Arrays.

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix Inc.).

data_processing:
Expression value for each probe set was calculated using
RMAExpress program that uses RMA (robust multi-array
average) algorithm For a first supervised analysis,
gene-filtering methods were applied following the detection
calls calculated using MAS 5.0 algorithm (Affymetrix). Probe sets
with absent calls as well as those showing minimal variation
across all samples (maximum–minimum log2 variation < 2.5)
were filtered out. In a second, more exhaustive analysis, the
complete set of microarrays without gene filtering was
introduced in a multivariable matrix where each of the six cell
states (NBL, WM-BL, CLL-BL, NPC, WM-PC and MM-PC) were
introduced to perform the differential expression analyses.

label: BIOTIN

source_name: Bone marrow

label_protocol:
Labeling were performed according to protocols from Affymetrix.
Briefly,100 ng of total RNA was amplified and labeled using the
GeneChip two-cycle cDNA synthesis kit and GeneChip IVT
labeling kit (Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol:
Total RNA was extracted from purified cell
populations using the RNeasy Mini Kit (Qiagen, Valencia, CA,
USA) according to the manufacturer’s instructions. The RNA
integrity was assessed using Agilent 2100 Bioanalyzer (Agilent,
Palo Alto, CA, USA).

tag: PC from healthy donors, isolated using CD38-APC.


title: cup9-sok2 rep2

description: Gene expression from yeast cells

value: G85 with cup9::bcKanMX4 sok2::bcKanMX4


title: normal plasma cells (NPC 642)


title: normal plasma cells (NPC 389)


title: cup9-sok2 rep3

description: Gene expression from yeast cells


title: normal B lymphocytes (NBL 534)

source_name: Peripheral blood

tag: BL from healthy donors, isolated using CD19-PE-Cy7.


title: normal plasma cells (NPC 545)


title: Pre Irradiation patient 18

description: No treatment


title: normal plasma cells (NPC 625)


title: cup9-sok2 rep1

description: Gene expression from yeast cells


title: cup9-sfl1 rep3

description: Gene expression from yeast cells

value: G85 with cup9::bcKanMX4 sfl1::bcKanMX4


title: cup9-sfl1 rep2

description: Gene expression from yeast cells


title: Pre Irradiation patient 16

description: No treatment


title: tec1-skn7 rep3

description: Gene expression from yeast cells

value: G85 with tec1::bcKanMX4 skn7::bcKanMX4


title: Pre Irradiation patient 17

description: No treatment


title: cup9-sfl1 rep1

description: Gene expression from yeast cells


title: Pre Irradiation patient 13

description: No treatment


title: Pre Irradiation patient 11

description: No treatment


title: tec1-skn7 rep2

description: Gene expression from yeast cells


title: tec1-skn7 rep1

description: Gene expression from yeast cells


title: normal B lymphocytes (NBL 531)


title: normal B lymphocytes (NBL 002)


title: normal B lymphocytes (NBL 533)


title: tec1-sok2 rep3

description: Gene expression from yeast cells

value: G85 with tec1::bcKanMX4 sok2::bcKanMX4


title: tec1-sok2 rep2

description: Gene expression from yeast cells


title: tec1-sok2 rep1

description: Gene expression from yeast cells


title: normal B lymphocytes (NBL 006)


title: Pre Irradiation patient 14

description: No treatment


title: Waldenström’s macroglobulinemia (WM-PC 33325)

tag: PC from WM patient, isolated using Kappa or Lambda-fluorescein isothiocyanate, CD10-PE, CD38-PerCPCy5.5,CD19-PE-Cy7, CD34-APC and CD45-APC-Cy7.


title: Waldenström’s macroglobulinemia (WM-PC 33161)


title: normal B lymphocytes (NBL 004)


title: Pre Irradiation patient 10

description: No treatment


title: Pre Irradiation patient 8

description: No treatment


title: normal B lymphocytes (NBL 001)


title: Pre Irradiation patient 12

description: No treatment


title: normal B lymphocytes (NBL 005)


title: Waldenström’s macroglobulinemia (WM-PC 32833)


title: Pre Irradiation patient 15

description: No treatment


title: Pre Irradiation patient 9

description: No treatment


title: Pre Irradiation patient 7

description: No treatment


title: tec1-sfl1 rep3

description: Gene expression from yeast cells

value: G85 with tec1::bcKanMX4 sfl1::bcKanMX4


title: tec1-sfl1 rep2

description: Gene expression from yeast cells


title: tec1-sfl1 rep1

description: Gene expression from yeast cells


title: Pre Irradiation patient 5

description: No treatment


title: Pre Irradiation patient 3

description: No treatment


title: Waldenström’s macroglobulinemia (WM-PC 32395)


title: tec1-cup9 rep3

description: Gene expression from yeast cells

value: G85 with tec1::bcKanMX4 cup9::bcKanMX4


title: skn7 rep2

description: Gene expression from yeast cells

value: G85 with skn7::bcKanMX4


title: skn7 rep3

description: Gene expression from yeast cells


title: Pre Irradiation patient 4

description: No treatment


title: Waldenström’s macroglobulinemia (WM-PC 30639)


title: tec1-cup9 rep1

description: Gene expression from yeast cells


title: tec1-cup9 rep2

description: Gene expression from yeast cells


title: Pre Irradiation patient 6

description: No treatment


title: Waldenström’s macroglobulinemia (WM-PC 32131)


title: Pre Irradiation patient 2

description: No treatment


title: Waldenström’s macroglobulinemia (WM-PC 31098)


title: Waldenström’s macroglobulinemia (WM-PC 30866)


title: skn7 rep1

description: Gene expression from yeast cells


title: sok2 rep3

description: Gene expression from yeast cells

value: G85 with sok2::bcKanMX4


title: Waldenström’s macroglobulinemia (WM-PC 31489)


title: Waldenström’s macroglobulinemia (WM-BL 33325)

tag: BL from WM patient, isolated using Kappa or Lambda-fluorescein isothiocyanate, CD10-PE, CD38-PerCPCy5.5,CD19-PE-Cy7, CD34-APC and CD45-APC-Cy7.


title: Healthy donor 18

description: No treatment

source_name: Healthy donor


title: Waldenström’s macroglobulinemia (WM-BL 33161)


title: Waldenström’s macroglobulinemia (WM-PC 30381)

tag: PC from WM patient, isolated using Kappa or Lambda-fluorescein isothiocyanate, CD10-PE,CD38-PerCPCy5.5,CD19-PE-Cy7, CD34-APC and CD45-APC-Cy7.


title: Healthy donor 17

description: No treatment


title: sok2 rep2

description: Gene expression from yeast cells


title: sok2 rep1

description: Gene expression from yeast cells


title: Pre Irradiation patient 1

description: No treatment


title: Waldenström’s macroglobulinemia (WM-BL 32833)


title: Healthy donor 15

description: No treatment


title: sfl1 rep3

description: Gene expression from yeast cells

value: G85 with sfl1::bcKanMX4


title: cup9 rep4

description: Gene expression from yeast cells

value: G85 with cup9::bcKanMX4


title: Healthy donor 12

description: No treatment


title: Waldenström’s macroglobulinemia (WM-BL 32395)


title: cup9 rep5

description: Gene expression from yeast cells


title: Waldenström’s macroglobulinemia (WM-BL 31489)


title: Healthy donor 16

description: No treatment


title: Healthy donor 14

description: No treatment


title: sfl1 rep1

description: Gene expression from yeast cells


title: Healthy donor 13

description: No treatment


title: cup9 rep3

description: Gene expression from yeast cells


title: Waldenström’s macroglobulinemia (WM-BL 32131)

tag: from WM patient, isolated using Kappa or Lambda-fluorescein isothiocyanate, CD10-PE, CD38-PerCPCy5.5,CD19-PE-Cy7, CD34-APC and CD45-APC-Cy7.


title: cup9 rep2

description: Gene expression from yeast cells


title: Waldenström’s macroglobulinemia (WM-BL 31098)


title: Healthy donor 7

description: No treatment


title: Healthy donor 10

description: No treatment


title: Waldenström’s macroglobulinemia (WM-BL 30639)


title: Healthy donor 11

description: No treatment


title: Healthy donor 8

description: No treatment


title: sfl1 rep2

description: Gene expression from yeast cells


title: Healthy donor 9

description: No treatment


title: Waldenström’s macroglobulinemia (WM-BL 30381)


title: Waldenström’s macroglobulinemia (WM-BL 30866)


title: multiple myeloma (MM 517)

data_processing:
Expression value for each probe set was calculated using
RMAExpress program that uses RMA (robust multi-array
average) algorithm. For a first supervised analysis,
gene-filtering methods were applied following the detection
calls calculated using MAS 5.0 algorithm (Affymetrix). Probe sets
with absent calls as well as those showing minimal variation
across all samples (maximum–minimum log2 variation < 2.5)
were filtered out. In a second, more exhaustive analysis, the
complete set of microarrays without gene filtering was
introduced in a multivariable matrix where each of the six cell
states (NBL, WM-BL, CLL-BL, NPC, WM-PC and MM-PC) were
introduced to perform the differential expression analyses.

extract_protocol:
Total RNA was extracted from purified cell populations using the RNeasy Mini Kit (Qiagen, Valencia, CA,USA) according to the manufacturer’s instructions. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent,
Palo Alto, CA, USA).

tag: PC from MM patient, isolated using CD38-APC.


title: cup9 rep1

description: Gene expression from yeast cells


title: multiple myeloma (MM 513)


title: tec1 rep5

description: Gene expression from yeast cells

value: G85 with tec1::bcKanMX4


title: Healthy donor 6

description: No treatment


title: tec1 rep4

description: Gene expression from yeast cells


title: multiple myeloma (MM 501)


title: Healthy donor 3

description: No treatment


title: Healthy donor 4

description: No treatment


title: Healthy donor 5

description: No treatment


title: Wild-type filamentous form rep3

description: Gene expression from yeast cells


title: tec1 rep1

description: Gene expression from yeast cells


title: Wild-type filamentous form rep1

description: Gene expression from yeast cells


title: Wild-type filamentous form rep2

description: Gene expression from yeast cells


title: multiple myeloma (MM 409)


title: multiple myeloma (MM 500)

tag: PC from MM patient, isolated using CD38-APC


title: multiple myeloma (MM 412)


title: Wild-type yeast form rep5

description: Gene expression from yeast cells

growth_protocol: 10hr growth on Synthetic complete dextrose media (SCD)


title: Healthy donor 2

description: No treatment


title: multiple myeloma (MM 410)


title: multiple myeloma (MM 158)

source_name: Bone marrow.


title: multiple myeloma (MM 370)


title: tec1 rep3

description: Gene expression from yeast cells


title: Wild-type yeast form rep4

description: Gene expression from yeast cells


title: tec1 rep2

description: Gene expression from yeast cells


title: Wild-type yeast form rep3

description: Gene expression from yeast cells


title: multiple myeloma (MM 36)

tag: PC from MM patient,isolated using CD38-APC.


title: chronic lymphocytic leukemia (CLL 68148)

tag: BL from CLL patient, isolated using CD19-PE and CD5-APC.


title: Wild-type yeast form rep1

description: Gene expression from yeast cells


title: multiple myeloma (MM 199)


title: Wild-type yeast form rep2

description: Gene expression from yeast cells


title: chronic lymphocytic leukemia (CLL 35513)


title: exposed to uva, rep=1

status: Public on Feb 22 2007

city: Bunkyo-ku

first: Saneyuki

last: Kawabata

state: Tokyo

address: 1-1-1 Yayoi

country: Japan

institute: University of Tokyo

description: The swollen hypocotyls of Red turnip 'Tsuda' was exposed to blue light for 24 hours.

hyb_protocol: According to the manufacturer’s instruction of an Expression Array Detection Kit for Microarray, Cy3/Cy5, 3DNA Array 900 (Genisphere).

scan_protocol: The microarray slides were scanned at 5 μm resolution, using a ScanArray Express scanner (Perkin-Elmer).

data_processing: Spots with foreground signal below 3 times background signal in more than 25% arrays were flagged as low quality spots and excluded. Background correction was not carried out. Spatial normalization was applied to the M values (location smoothing, span=0.5) and then to the absolute M values (scale smoothing, span=0.75). After print-tip loess normalization (span = 0.75), within slide replicates was collapsed by calculating arithmetic average of replicate spots for each probe.

molecule: polyA RNA

organism: Brassica rapa subsp. rapa

source_name: Brassica rapa subsp rapa, exposed to uva, 24 hours

extract_protocol: Total RNA was extracted from the peeled surface tissue with approximately 1-2 mm thickness by using Trizol . The mRNA was purified by using Oligo(dT)-Cellulose Type 7  (GE Healthcare).

tag: Brassica rapa subsp rapa 'Tsuda'; epidermal tissue of the swollen hypocotyl; two months after sowing; exposed to UV-A for 24 hours.

source_name: Brassica rapa subsp rapa, kept in darkness

tag: Brassica rapa subsp rapa 'Tsuda'; epidermal tissue of the swollen hypocotyl; two months after sowing; kept in darkness.


title: exposed to uva, rep=2

source_name: Brassica rapa subsp rapa, exposed to UV-A, 24 hours

label_protocol: According to the manufacturer’s instruction of an Expression Array Detection Kit for Microarray, Cy3/Cy5, 3DNA Array 900 (Genisphere).


title: exposed to uvb, rep=1

source_name: Brassica rapa subsp rapa, exposed to UV-B, 24 hours

tag: Brassica rapa subsp rapa 'Tsuda'; epidermal tissue of the swollen hypocotyl; two months after sowing; exposed to UV-B for 24 hours.


title: exposed to uvb, rep=3

source_name: Brassica rapa subsp rapa, exposed to UV-B, 24 hours.


title: exposed to uvb, rep=2

source_name: Brassica rapa subsp rapa, kept in darkness.


title: exposed to blue, rep=1

source_name: Brassica rapa subsp rapa, exposed to blue, 24 hours

tag: Brassica rapa subsp rapa 'Tsuda'; epidermal tissue of the swollen hypocotyl; two months after sowing; exposed to blue light for 24 hours.


title: multiple myeloma (MM 48)


title: exposed to uva, rep=3


title: exposed to blue, rep=3

source_name: Brassica rapa subsp rapa, exposed to blue, 24

tag: Brassica rapa subsp rapa 'Tsuda'; epidermal tissue of the swollen hypocotyl; two months after sowing; exposed to blue light for 24


title: Wild-type yeast form rep6

description: Gene expression from yeast cells

tag: Wild-type yeast form rep6


title: Healthy donor 1

description: No treatment

tag: Mononuclear cells (MNCs) were collected from each patient’s PB and RNA extracted via Qiagen RNAeasy kits


title: chronic lymphocytic leukemia (CLL 528)


title: chronic lymphocytic leukemia (CLL 532)

source_name: Bone Marrow.


title: chronic lymphocytic leukemia (CLL 13651)

tag: BL from CLL patient, isolated using CD19-PE and CD5-APC


title: chronic lymphocytic leukemia (CLL 34297)


title: chronic lymphocytic leukemia (CLL 45205)


title: chronic lymphocytic leukemia (CLL 32489)


title: chronic lymphocytic leukemia (CLL 525)


title: exposed to blue, rep=2


title: chronic lymphocytic leukemia (CLL 26212)


title: chronic lymphocytic leukemia (CLL 529)


title: SDC-3 IP2 array2

status: Public on Feb 11 2007

type: genomic

city: Chapel Hill

first: Jason

middle: D

last: Lieb

address: 408 Fordham Hall, CB# 3280

department: Biology

institute: University of North Carolina at Chapel Hill

description: see NimbleGen website

hyb_protocol: see NimbleGen website

scan_protocol: see NimbleGen website

data_processing: autosomal spot normalized and median centered log2 ratios (see publication)

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: IP performed with SDC-3 antibody

label_protocol: see NimbleGen website

extract_protocol: Extract was prepared from formaldehyde fixed N2 embryos by dounce homogenization followed by sonication. (see publication for details)

tag: IP performed with SDC-3 antibody in mixed embryos obtained from N2 hermaphrodites.

source_name: Input as reference

tag: Input as reference


title: No Antibody control IP2 array2

description: see NimbleGen website

source_name: IP performed with no antibody as control

tag: IPs performed without antibody in mixed embryos obtained from N2 hermaphrodites.

extract_protocol: Extract was prepared from formaldehyde fixed N2 embryos by dounce homogenization followed by sonication.


title: SDC-3 IP1 array 2

description: see NimbleGen website

tag: IPs performed with SDC-3 antibody in mixed embryos obtained from N2 hermaphrodites.


title: No Antibody control IP 3 array2

description: see NimbleGen website

source_name: No Antibody IP3 array2

tag: IP performed without antibody in mixed embryos obtained from N2 hermaphrodites.


title: SDC-3 IP3 array2

description: see NimbleGen website


title: SDC-3 IP2 array1

description: see NimbleGen website


title: DPY-27 IP3 array 2

description: see NimbleGen website

source_name: IP performed with DPY-27 antibody

tag: IP performed with DPY-27 antibody in mixed embryos obtained from N2 hermaphrodites.


title: DPY-27 IP2 array2

description: see NimbleGen website

tag: IPs performed with DPY-27 antibody in mixed embryos obtained from N2 hermaphrodites.


title: No Antibody control IP1 array2

description: see NimbleGen website

tag: IP performed with No Antibody as control in mixed embryos obtained from N2 hermaphrodites.

tag: Inputs as reference


title: mouse hippocampus, cox-2 heterozygous, rep2

status: Public on Feb 05 2007

city: Bethesda

first: Christopher

middle: Dennis

last: Toscano

state: MD

address: 9 Memorial Drive Room 1S126

department: National Institute on Aging

institute: National Institutes of Health

description: mouse hippocampus from COX-2 heterozygous

hyb_protocol: Samples were hybridized to custom nylon cDNA array. Details of hybridization protocol can be found at http://www.grc.nia.nih.gov/branches/rrb/dna/dna.htm

scan_protocol: Arrays apposed to phosphoimager plate and scanned according to protocol found at  http://www.grc.nia.nih.gov/branches/rrb/dna/dna.htm

data_processing: The data were analyzed as described at http://www.grc.nia.nih.gov/branches/rrb/dna/dna.htm. Data are presented as z-ratios

organism: Mus musculus

source_name: Hippocampus COX-2 Hetero

label_protocol: P33 labelled cDNA was prepared as described using the protocol found at http://www.grc.nia.nih.gov/branches/rrb/dna/dna.htm

growth_protocol: 12/12 light cycle, ad libitum food

extract_protocol: Extraction of total RNA was performed using the Qiagen Rneasy Lipid tissue extraction kit according to the manufacturer's instructions.

treatment_protocol: Mice were euthanized with pentobarbital overdose, decapitated and brain was frozen on dry ice after dissection into Cerebral cortex and hippocampus. Samples were stored at -80C until usage

tag: Genotype

value: COX-2 Hetero

tag: Age

value: 12 weeks of age


title: SDC-3 IP3 array1

description: see NimbleGen website


title: mouse hippocampus, cox-2 heterozygous, rep3


title: SDC-3 IP1 array1

description: see NimbleGen website


title: mouse hippocampus, cox-2 knockout, rep2

description: mouse hippocampus from COX-2 knockout

source_name: Hippocampus COX-2 KO

value: COX-2 KO


title: WI38 cells_ChIP H3-K4me2_Replicate1

status: Public on Feb 15 2007

city: Basel

first: Michaël

last: Weber

address: Maulbeerstrasse 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institute

description: No description

hyb_protocol: Hybridization performed according to standard procedures by Nimblegen

scan_protocol: Scanning performed according to standard procedures by Nimblegen

data_processing: No normalization

source_name: Cy5, total input sample from WI38 cells

label_protocol: Labeling performed according to standard procedures by Nimblegen

extract_protocol: Genomic DNA prepared from sonicated input chromatin and amplified by ligation-mediated PCR

tag: WI38 primary fibroblasts

tag: Gender

value: female

source_name: Cy3, ChIP H3-K4me2 from WI38 cells

extract_protocol: Genomic DNA bound to H3-K4me2 prepared by ChIP and amplified by ligation-mediated PCR


title: DPY-27 IP1 array2

description: see NimbleGen website


title: No Antibody control IP2 array1

description: see NimbleGen website


title: DPY-27 IP3 array1

description: see NimbleGen website

source_name: IP performed with DPY-27 antibod


title: No Antibody control IP-1 array1

description: see NimbleGen website

extract_protocol: Extract was prepared from formaldehyde fixed N2 embryos by dounce homogenization followed by sonication. IP was performed without antibody.

tag: IPs performed with No Antibody as control in mixed embryos obtained from N2 hermaphrodites.

source_name: Inputs as reference


title: WI38 cells_ChIP H3-K4me2_Replicate3

description: No description

source_name: Cy5, ChIP H3-K4me2 from WI38 cells

source_name: Cy3, total input sample from WI38 cells


title: mouse hippocampus, cox-2 heterozygous, rep1


title: human sperm cells_MeDIP_Replicate2

description: No description

source_name: Cy5, total input sonicated DNA from human sperm cells

extract_protocol: Total genomic DNA sonicated to give fragments between 200bp and 1000bp

tag: Sperm samples were from normospermic males attending Nijmegen Medical Center. Samples were purified by density gradient centrifugation (Pure Sperm, Nidacom, Sweden) during 20 minutes (2000 rpm). This procedure was repeated twice to avoid contamination with other cell types.

source_name: Cy3, methylated DNA from human sperm cells enriched by MeDIP

extract_protocol: Methylated DNA purified from total sonicated DNA by MeDIP


title: DPY-27 IP2 array1

description: see NimbleGen website


title: DPY-27 IP1 array1

description: see NimbleGen website


title: mouse hippocampus, cox-2 WT, rep2

description: mouse hippocampus from COX-2 WT

source_name: Hippocampus COX-2 WT

value: COX-2 WT


title: mouse hippocampus, cox-2 knockout, rep3

description: mouse hippocampus from COX-2 knockout


title: mouse hippocampus, cox-1 knockout, rep3

description: mouse hippocampus from COX-1 Knockout

source_name: Hippocampus COX-1 KO

value: COX-1 KO


title: No Antibody control IP 3 array1

description: see NimbleGen website

source_name: No Antibody IP3 array1


title: mouse hippocampus, cox-1 knockout, rep2

description: mouse hippocampus from COX-1 Knockout


title: WI38 cells_ChIP H3-K4me2_Replicate2

description: No description


title: mouse hippocampus, cox-2 WT, rep1

description: mouse hippocampus from COX-2 WT


title: mouse hippocampus, cox-2 knockout, rep1

description: mouse hippocampus from COX-2 knockout


title: WI38 cells_MeDIP_Replicate1

description: No description

source_name: Cy5, total input sonicated DNA from WI38 cells

label_protocol: Labeling performed by Nimblegen

source_name: Cy3, methylated DNA from WI38 cells enriched by MeDIP


title: WI38 cells_ChIP RNA Pol2_Replicate1

description: No description

source_name: Cy3, ChIP RNA Pol2 from WI38 cells

extract_protocol: Genomic DNA bound to RNA polymerase 2 prepared by ChIP and amplified by ligation-mediated PCR


title: WI38 cells_MeDIP_Replicate2

description: No description

source_name: Cy5, methylated DNA from WI38 cells enriched by MeDIP

source_name: Cy3, total input sonicated DNA from WI38 cells


title: mouse hippocampus, cox-1 WT, rep3

description: mouse hippocampus from COX-1 WT

source_name: Hippocampus COX-1 WT

value: COX-1 WT


title: mouse hippocampus, cox-1 WT, rep2

description: mouse hippocampus from COX-1 WT


title: human sperm cells_MeDIP_Replicate1

description: No description


title: mouse hippocampus, cox-1 WT, rep1

description: mouse hippocampus from COX-1 WT


title: mouse cerebral cortex, cox-2 heterozygous, rep1

description: mouse cerebral cortex from COX-2 heterozygous

source_name: Cerebral Cortex COX-2 Hetero


title: mouse cerebral cortex, cox-2 heterozygous, rep3


title: mouse hippocampus, cox-1 knockout, rep1

description: mouse hippocampus from COX-1 Knockout


title: mouse cerebral cortex, cox-2 heterozygous, rep2


title: WI38 cells_ChIP RNA Pol2_Replicate3

description: No description

source_name: Cy5, ChIP RNA Pol2 from WI38 cells


title: mouse cerebral cortex, cox-2 knockout, rep3

description: mouse cerebral cortex from COX-2 knockout

source_name: Cerebral Cortex COX-2 KO


title: mouse cerebral cortex, cox-2 WT, rep3

description: mouse cerebral cortex from COX-2 WT

source_name: Cerebral Cortex COX-2 WT


title: WI38 cells_ChIP RNA Pol2_Replicate2

description: No description

source_name: Cy5, total input sample from WI38 cells


title: mouse cerebral cortex, cox-2 WT, rep2

description: mouse cerebral cortex from COX-2 WT


title: mouse cerebral cortex, cox-1 knockout, rep3

description: mouse cerebral cortex from COX-1 Knockout

source_name: Cerebral Cortex COX-1 KO


title: mouse cerebral cortex, cox-1 knockout, rep2


title: mouse hippocampus, cox-2 WT, rep3

description: mouse hippocampus from COX-2 WT


title: mouse cerebral cortex, cox-1 knockout, rep1


title: mouse cerebral cortex, cox-2 WT, rep1

description: mouse cerebral cortex from COX-2 WT


title: mouse cerebral cortex, cox-1 WT, rep1

description: mouse cerebral cortex from COX-1 WT

source_name: Cerebral Cortex COX-1 WT


title: mouse cerebral cortex, cox-1 WT, rep3

description: mouse cerebral cortex from COX-1 WT


title: mouse cerebral cortex, cox-1 WT, rep2

description: mouse cerebral cortex from COX-1 WT


title: human sperm cells_MeDIP_Replicate3

description: No description

source_name: Cy5, methylated DNA from human sperm cells enriched by MeDIP

source_name: Cy3, total input sonicated DNA from human sperm cells


title: HeLa, mock vs. HeLa, miR_106b-2-OME, 200 nM, 24 hr

status: Public on Feb 01 2007

city: Boston

first: Julja

last: Burchard

state: MA

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

description: Linsley PS, Schelter J, Burchard J, Kibukawa M, Martin MM, Bartz SR, Johnson JM, Cummins JM, Raymond CK, Dai H, Chau N, Cleary M, Jackson AL, Carleton M, and Lim L.  MCB (2007).

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: HeLa

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: HeLa, mock

tag: HeLa, miR_106b-2-OME, 200 nM, 24 hr


title: HeLa, mock vs. HeLa, miR_106b, 200 nM, 24 hr

tag: HeLa, miR_106b, 200 nM, 24 hr


title: HeLa, mock vs. HeLa, Luc, 200 nM, 24 hr

tag: HeLa, Luc, 200 nM, 24 hr


title: HeLa, mock vs. HeLa, miR_16, 200 nM, 24 hr

tag: HeLa, miR_16, 200 nM, 24 hr


title: TUBB antibody

type: protein

first: Uma

middle: T

last: Shankavaram

address: 9000 Rockville Pike

department: NCI

institute: NIH

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40564

hyb_protocol: Each slide was washed manually with deionized water to remove urea. Then, in an Autostainer universal staining system (DAKO), it was blocked with I-block. Also in autostainer, it was incubated with strpetavidin-biotin complex, biotynyl tyramide(for amplification) for 15 min, streptavidin-peroxidase for 15 min, 3,3'-diaminobenzidine-tetrahydrochloride chromagen for 5 min. For detection of total protein, arrays were stained with SYPRO ruby protein blot stain.

scan_protocol: ProteinChips were scanned with Perfection 1200S scanner (Epson America) with a 256-shade gray scale at 600 dots per inch. Total protein stained with SYPRO ruby was scanned with Fluoriamger SI (Amersham Pharmacia Biotech) at 100-um resolution.

data_processing: The data were analyzed with dose interpolation (DI) algorithm.

label: Streptavidin-biotin complex

molecule: protein

source_name: specific primary antibody. Antibody description: Tubulin-beta Ab-3, Batch number: 16, AbIDNumber: 214

tag: Each of 176 specific primary antibodies was prescreened to give highest quality by western analysis.


title: HeLa, mock vs. HeLa, miR_16-2-OME, 200 nM, 24 hr

tag: HeLa, miR_16-2-OME, 200 nM, 24 hr


title: TYR antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40606

source_name: specific primary antibody. Antibody description: Tyrosinase Ab-1, Batch number: 19, AbIDNumber: 256


title: YWHAG antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26603

source_name: specific primary antibody. Antibody description: 14.3.3 gamma (Ab-2), Batch number: 20, AbIDNumber: 304


title: TUBAB antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54337

source_name: specific primary antibody. Antibody description: Tubulin Ab-4, Batch number: 22, AbIDNumber: 4


title: VASP antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26573

source_name: specific primary antibody. Antibody description: VASP, Batch number: 13, AbIDNumber: 203


title: VIL1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8966

source_name: specific primary antibody. Antibody description: Villin NovoCastra, Batch number: 6, AbIDNumber: 135


title: VIL2 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40608

source_name: specific primary antibody. Antibody description: Ezrin/p81/80K/Cytovillin Ab-1, Batch number: 19, AbIDNumber: 258


title: TP53_26_GBL00064 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00064

source_name: specific primary antibody. Antibody description: p53 Ab-3, Batch number: 26, AbIDNumber: 136


title: TP53_26_GBL00063 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00063

source_name: specific primary antibody. Antibody description: p53 Ab-2, Batch number: 26, AbIDNumber: 137


title: TRADD antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8978

source_name: specific primary antibody. Antibody description: TRADD, Batch number: 6, AbIDNumber: 85


title: TP53_20_26604 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26604

source_name: specific primary antibody. Antibody description: p53 Ab-5, Batch number: 20, AbIDNumber: 316


title: TP53_20_26607 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26607

source_name: specific primary antibody. Antibody description: p53, Batch number: 20, AbIDNumber: 319


title: TP53_10_24342 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 24342

source_name: specific primary antibody. Antibody description: p53 Ab-6, Batch number: 10, AbIDNumber: 68


title: TP53_1_5429 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 24337

source_name: specific primary antibody. Antibody description: p53, Batch number: 10, AbIDNumber: 129


title: TUBA antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26533

source_name: specific primary antibody. Antibody description: Tubulin-alpha Ab-2, Batch number: 14, AbIDNumber: 213


title: TP53_20_26606 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26606

source_name: specific primary antibody. Antibody description: p53, Batch number: 20, AbIDNumber: 318


title: TP53_10_24337 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 5429

source_name: specific primary antibody. Antibody description: p53 tumor suppressor protein Ab-8, Batch number: 1, AbIDNumber: 1


title: TGFB1I1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26572

source_name: specific primary antibody. Antibody description: Hic-5, Batch number: 13, AbIDNumber: 201


title: TNFSF6 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00071

source_name: specific primary antibody. Antibody description: Fas Ligand/CD95L, Batch number: 26, AbIDNumber: 82


title: STAT6_9 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26608

source_name: specific primary antibody. Antibody description: Anti-STAT6, Batch number: 20, AbIDNumber: 327


title: STAT5A_22 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8921

source_name: specific primary antibody. Antibody description: Stat5, Batch number: 9, AbIDNumber: 96


title: STAT6_20 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8922

source_name: specific primary antibody. Antibody description: Stat6, Batch number: 9, AbIDNumber: 97


title: STAT5A_9 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54352

source_name: specific primary antibody. Antibody description: Stat5, Batch number: 22, AbIDNumber: 96


title: STAT3_22 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26612

source_name: specific primary antibody. Antibody description: Stat3, Batch number: 20, AbIDNumber: 333


title: STAT3_20 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8920

source_name: specific primary antibody. Antibody description: Stat3, Batch number: 9, AbIDNumber: 92


title: STAT3_9 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54351

source_name: specific primary antibody. Antibody description: Stat3, Batch number: 22, AbIDNumber: 92


title: SMARCB1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00161

source_name: specific primary antibody. Antibody description: BAF47, Batch number: 30, AbIDNumber: 540


title: SEC8 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54308

source_name: specific primary antibody. Antibody description: Sec8, Batch number: 21, AbIDNumber: 360


title: STAT1_20 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8919

source_name: specific primary antibody. Antibody description: Stat1 (C-terminus), Batch number: 9, AbIDNumber: 90


title: RNASEH2A antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00157

source_name: specific primary antibody. Antibody description: RNase HI, Batch number: 30, AbIDNumber: 467


title: RELA_12 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 24315

source_name: specific primary antibody. Antibody description: NF-kappaB p65, Batch number: 11, AbIDNumber: 74


title: RIPK1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8977

source_name: specific primary antibody. Antibody description: RIP, Batch number: 6, AbIDNumber: 84


title: RELA_14 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26558

source_name: specific primary antibody. Antibody description: NF-kappaB p65, Batch number: 13, AbIDNumber: 74


title: RELA_6 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26528

source_name: specific primary antibody. Antibody description: NF-kappaB p65, Batch number: 14, AbIDNumber: 74


title: STAT1_22 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26610

source_name: specific primary antibody. Antibody description: Stat1 (C-terminus), Batch number: 20, AbIDNumber: 331


title: RELA_13 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26540

source_name: specific primary antibody. Antibody description: NF-kappaB p65, Batch number: 12, AbIDNumber: 74


title: RELA_11 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 24330

source_name: specific primary antibody. Antibody description: NF-kappaB p65, Batch number: 10, AbIDNumber: 74


title: RB1_2 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 24344

source_name: specific primary antibody. Antibody description: Rb, Batch number: 10, AbIDNumber: 130


title: RB1_10 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8427

source_name: specific primary antibody. Antibody description: Retinoblastoma (Rb) Suppressor Protein Ab-1, Batch number: 2, AbIDNumber: 14


title: RELA_10 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8970

source_name: specific primary antibody. Antibody description: NF-kappaB p65, Batch number: 6, AbIDNumber: 74


title: PTPN11 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54307

source_name: specific primary antibody. Antibody description: PTP1D/SHP2, Batch number: 21, AbIDNumber: 355


title: PTPN6 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54306

source_name: specific primary antibody. Antibody description: PTP1C/SHP1, Batch number: 21, AbIDNumber: 354


title: PRKCA antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26561

source_name: specific primary antibody. Antibody description: PKCa, Batch number: 13, AbIDNumber: 159


title: STAT1_9 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54350

source_name: specific primary antibody. Antibody description: Stat1 (C-terminus), Batch number: 22, AbIDNumber: 90


title: PKAR2A antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26544

source_name: specific primary antibody. Antibody description: PKARIIa, Batch number: 12, AbIDNumber: 147


title: PRKCB1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26562

source_name: specific primary antibody. Antibody description: PKCb, Batch number: 13, AbIDNumber: 160


title: PRSS8 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00156

source_name: specific primary antibody. Antibody description: Prostasin, Batch number: 30, AbIDNumber: 464


title: PRKCH antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26565

source_name: specific primary antibody. Antibody description: PKCl, Batch number: 13, AbIDNumber: 167


title: PRKCI antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00061

source_name: specific primary antibody. Antibody description: PKCi, Batch number: 26, AbIDNumber: 166


title: PKAR1A antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00065

source_name: specific primary antibody. Antibody description: PKARIa, Batch number: 26, AbIDNumber: 146


title: NCAM1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40574

source_name: specific primary antibody. Antibody description: CD56/NCAM-1 Ab-5, Batch number: 16, AbIDNumber: 239


title: MVP antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8223

source_name: specific primary antibody. Antibody description: LRP/MVP (Major Vault Protein) Ab-1, Batch number: 5, AbIDNumber: 45


title: NME1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8914

source_name: specific primary antibody. Antibody description: Nm23, Batch number: 9, AbIDNumber: 128


title: PCNA antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8433

source_name: specific primary antibody. Antibody description: Proliferating Cell Nuclear Antigen (PCNA) Ab-1, Batch number: 2, AbIDNumber: 12


title: MU18 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00014

source_name: specific primary antibody. Antibody description: Munc-18, Batch number: 24, AbIDNumber: 367


title: MGMT_9 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8913

source_name: specific primary antibody. Antibody description: MGMT Ab-1, Batch number: 9, AbIDNumber: 9


title: MLH1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00060

source_name: specific primary antibody. Antibody description: MLH1, Batch number: 26, AbIDNumber: 172


title: MSH6 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8924

source_name: specific primary antibody. Antibody description: MSH6/GTBP, Batch number: 9, AbIDNumber: 118


title: MCC antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00062

source_name: specific primary antibody. Antibody description: MCC, Batch number: 26, AbIDNumber: 127


title: MCM7_22 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8044

source_name: specific primary antibody. Antibody description: CDC47/MCM7 (Proliferation Marker) Ab-2, Batch number: 4, AbIDNumber: 38


title: MSN_4 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8046

source_name: specific primary antibody. Antibody description: Moesin Ab-1, Batch number: 4, AbIDNumber: 42


title: MSN_9 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8908

source_name: specific primary antibody. Antibody description: Moesin Ab-1, Batch number: 9, AbIDNumber: 42


title: MCM7_4 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54339

source_name: specific primary antibody. Antibody description: CDC47/MCM7 (Proliferation Marker) Ab-2, Batch number: 22, AbIDNumber: 38


title: MSH2 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8923

source_name: specific primary antibody. Antibody description: MSH2, Batch number: 9, AbIDNumber: 117


title: PGR antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8226

source_name: specific primary antibody. Antibody description: Progesterone Receptor (PgR) Ab-2, Batch number: 5, AbIDNumber: 48


title: MGMT_2 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8432

source_name: specific primary antibody. Antibody description: MGMT Ab-1, Batch number: 2, AbIDNumber: 9


title: MCP antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8042

source_name: specific primary antibody. Antibody description: CD46 (Mambrane Cofactor Protein) Ab-2, Batch number: 4, AbIDNumber: 36


title: MAP2K2_3 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 6386

source_name: specific primary antibody. Antibody description: MEK2, Batch number: 3, AbIDNumber: 24


title: MAPK1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8425

source_name: specific primary antibody. Antibody description: ERK2, Batch number: 2, AbIDNumber: 16


title: MAP2K2_8 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8882

source_name: specific primary antibody. Antibody description: MEK2, Batch number: 8, AbIDNumber: 24


title: mouse cerebral cortex, cox-2 knockout, rep2

description: mouse cerebral cortex from COX-2 knockout

source_name: Cerebral Cortex COX-2 KO


title: MAP2K1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8883

source_name: specific primary antibody. Antibody description: MEK1, Batch number: 8, AbIDNumber: 23


title: KRT19 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40565

source_name: specific primary antibody. Antibody description: Keratin 19 Ab-1, Batch number: 16, AbIDNumber: 219


title: KRT8 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8429

source_name: specific primary antibody. Antibody description: Keratin 8 Ab-3, Batch number: 2, AbIDNumber: 8


title: KRT7 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40568

source_name: specific primary antibody. Antibody description: Keratin 7 Ab-1, Batch number: 16, AbIDNumber: 224


title: KRT6 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40567

source_name: specific primary antibody. Antibody description: Keratin 6 Ab-1, Batch number: 16, AbIDNumber: 223


title: KRT20 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8437

source_name: specific primary antibody. Antibody description: Keratin 20 Ab-1 (Clone Ks20.8), Batch number: 2, AbIDNumber: 2


title: KRT18 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 5431

source_name: specific primary antibody. Antibody description: Keratin 18 Ab-1, Batch number: 1, AbIDNumber: 43


title: JAK1_6 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00067

source_name: specific primary antibody. Antibody description: JAK1, Batch number: 26, AbIDNumber: 89


title: KLK3 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00153

source_name: specific primary antibody. Antibody description: Prostate Specific Antigen (PSA) Ab-1, Batch number: 30, AbIDNumber: 250


title: JAK1_22 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8980

source_name: specific primary antibody. Antibody description: JAK1, Batch number: 6, AbIDNumber: 89


title: IRS1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26547

source_name: specific primary antibody. Antibody description: IRS-1, Batch number: 12, AbIDNumber: 152


title: JAK1_26 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54349

source_name: specific primary antibody. Antibody description: JAK1, Batch number: 22, AbIDNumber: 89


title: ISGF3G_9 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00072

source_name: specific primary antibody. Antibody description: ISGF3g, Batch number: 26, AbIDNumber: 88


title: GRB2 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00013

source_name: specific primary antibody. Antibody description: GRB2, Batch number: 24, AbIDNumber: 350


title: HSPA4 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40578

source_name: specific primary antibody. Antibody description: Heat Shock Protein 70 (HSP70), Batch number: 16, AbIDNumber: 248


title: GSTP1_13 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26569

source_name: specific primary antibody. Antibody description: GST-p, Batch number: 13, AbIDNumber: 176


title: HSPD1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54338

source_name: specific primary antibody. Antibody description: Heat Shock Protein 60 (hsp60) Ab-1, Batch number: 22, AbIDNumber: 7


title: GSTP1_14 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26532

source_name: specific primary antibody. Antibody description: GSTpi, Batch number: 14, AbIDNumber: 209


title: HRAS antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00066

source_name: specific primary antibody. Antibody description: Ras, Batch number: 26, AbIDNumber: 111


title: GTF2B antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00039

source_name: specific primary antibody. Antibody description: TFIIB, Batch number: 25, AbIDNumber: 477


title: FADD_9 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00070

source_name: specific primary antibody. Antibody description: FADD, Batch number: 26, AbIDNumber: 80


title: ISGF3G_26 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8918

source_name: specific primary antibody. Antibody description: ISGF3g, Batch number: 9, AbIDNumber: 88


title: FADD_26 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8974

source_name: specific primary antibody. Antibody description: FADD, Batch number: 6, AbIDNumber: 80


title: FN1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8435

source_name: specific primary antibody. Antibody description: Fibronectin Ab-1, Batch number: 2, AbIDNumber: 6


title: GSK3B antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8915

source_name: specific primary antibody. Antibody description: GSK-3b, Batch number: 9, AbIDNumber: 150


title: ESR1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40607

source_name: specific primary antibody. Antibody description: Estrogen Receptor Ab-15, Batch number: 19, AbIDNumber: 257


title: FADD_6 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8916

source_name: specific primary antibody. Antibody description: FADD, Batch number: 9, AbIDNumber: 80


title: EP300_9_8925 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00163

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 30, AbIDNumber: 311


title: ERBB2 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8424

source_name: specific primary antibody. Antibody description: c-erbB-2/HER-2/neu Oncoprotein Ab-8, Batch number: 2, AbIDNumber: 19


title: G22P1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8222

source_name: specific primary antibody. Antibody description: Ku (p70) Ab-4, Batch number: 5, AbIDNumber: 44


title: EP300_8_8881 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00052

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 26, AbIDNumber: 312


title: EP300_30_GBL00163 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00049

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 25, AbIDNumber: 312


title: EP300_2_8439 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00023

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 24, AbIDNumber: 311


title: EP300_9_8907 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00152


title: EP300_30_GBL00152 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00046

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 25, AbIDNumber: 311


title: EP300_2_8430 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00002

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 24, AbIDNumber: 312


title: EP300_8_8884 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00073

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 26, AbIDNumber: 311


title: EP300_2_8423 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54312

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 21, AbIDNumber: 311


title: EP300_25_GBL00049 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26599

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 20, AbIDNumber: 311


title: EP300_26_GBL00073 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54296


title: EP300_25_GBL00046 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40619

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 19, AbIDNumber: 311


title: EP300_24_GBL00023 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40603


title: EP300_26_GBL00052 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26615


title: EP300_1_5433 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26560

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 13, AbIDNumber: 311


title: EP300_21_54296 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26534

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 14, AbIDNumber: 311


title: EP300_21_54312 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40563

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 16, AbIDNumber: 311


title: EP300_24_GBL00002 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40579


title: EP300_20_26599 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26576


title: EP300_19_40619 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26542

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 12, AbIDNumber: 311


title: EP300_16_40579 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 24332

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 10, AbIDNumber: 11


title: EP300_16_40563 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8925

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 9, AbIDNumber: 11


title: EP300_20_26615 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26530


title: EP300_14_26534 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8907


title: EP300_14_26530 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8881

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 8, AbIDNumber: 11


title: EP300_13_26576 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8884


title: EP300_19_40603 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 24347

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 10, AbIDNumber: 311


title: EP300_12_26542 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8430

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 2, AbIDNumber: 11


title: ENAH antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26574

source_name: specific primary antibody. Antibody description: Mena, Batch number: 13, AbIDNumber: 207


title: EP300_13_26560 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8423


title: EP300_10_24332 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 5433

source_name: specific primary antibody. Antibody description: p300/CBP Ab-1, Batch number: 1, AbIDNumber: 11


title: EMS1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54311

source_name: specific primary antibody. Antibody description: Cortactin, Batch number: 21, AbIDNumber: 379


title: DSG1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54302

source_name: specific primary antibody. Antibody description: Desmoglein, Batch number: 21, AbIDNumber: 347


title: EP300_10_24347 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8439


title: CTNNG antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54301

source_name: specific primary antibody. Antibody description: g-Catenin, Batch number: 21, AbIDNumber: 346


title: CTNNB1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54300

source_name: specific primary antibody. Antibody description: b-Catenin, Batch number: 21, AbIDNumber: 345


title: mouse cerebral cortex, cox-2 knockout, rep1

description: mouse cerebral cortex from COX-2 knockout

source_name: Cerebral Cortex COX-2 KO


title: CRK antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00012

source_name: specific primary antibody. Antibody description: Crk, Batch number: 24, AbIDNumber: 349


title: CDK7 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40615

source_name: specific primary antibody. Antibody description: cdk7 / p40MO15 / CAK Ab-1, Batch number: 19, AbIDNumber: 280


title: CDKN2A antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 24333

source_name: specific primary antibody. Antibody description: p16 INK4a/MTS1 Ab-4, Batch number: 10, AbIDNumber: 29


title: CDRO antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40573

source_name: specific primary antibody. Antibody description: CDRO (T-cell Marker) Ab-1, Batch number: 16, AbIDNumber: 238


title: CDK5 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40614

source_name: specific primary antibody. Antibody description: Cdk5 Ab-4 (cocktail), Batch number: 19, AbIDNumber: 279


title: CDK6 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8045

source_name: specific primary antibody. Antibody description: Cdk6 (Cyclin-Dependent Kinase 6) Ab-3, Batch number: 4, AbIDNumber: 41


title: CDK4 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00155

source_name: specific primary antibody. Antibody description: Cdk4, Batch number: 30, AbIDNumber: 421


title: CDH2_26 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00053

source_name: specific primary antibody. Antibody description: N-Cadherin, Batch number: 26, AbIDNumber: 341


title: CDH2_24 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00010

source_name: specific primary antibody. Antibody description: N-Cadherin, Batch number: 24, AbIDNumber: 341


title: CDH3 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00011

source_name: specific primary antibody. Antibody description: P-Cadherin, Batch number: 24, AbIDNumber: 342


title: CDH2_1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 5436

source_name: specific primary antibody. Antibody description: N-Cadherin, Batch number: 1, AbIDNumber: 73


title: CDH1_9 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54297

source_name: specific primary antibody. Antibody description: E-Cadherin, Batch number: 21, AbIDNumber: 339


title: CDH1_6 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8909

source_name: specific primary antibody. Antibody description: E-Cadherin, Batch number: 9, AbIDNumber: 72


title: IP- GFP cy5 vs B52 cy3 rep.2

city: Montpellier

first: johann

last: Soret

address: 1919, route de Mende

department: Institut de Genetique Moleculaire

country: France

institute: CNRS

description: Identification of B52 potential target mRNAs in the Drosophila developing eye

data_processing: ArrayVision software

organism: Drosophila melanogaster

source_name: mRNA immunoprecipitated from GMR X GFP-NLS transgenic larvae

extract_protocol: Anterior quarters of 600 3rd instar larvae were dissected in cold PBS 1x, pooled in 1 ml of cold NETN buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM MgCl2, 0.25% NP40, 0.5% Triton X100) completed with 400 µg tRNA from E. coli (Roche), 20 µl RNAsin (Promega) and 100 µl protease inhibitors cocktail (Complete, EDTA-free, Roche). Tissue extracts were homogenized with a plastic pestle in a 1.5-ml microfuge tube and sonicated twice for 5 seconds. The homogenates were centrifuged at 3500 rpm at 4°C for 5 minutes. Protein G sepharose beads (Amersham Biosciences) were pre-saturated by incubating with NETN buffer with BSA 1% during 1 hour at 4°C on a rotator and sequentially washed with coating buffer (50 mM Tris pH 7.5, 150 mM NaCl). 100 µl of protein G sepharose beads were then coated with 15 µl of monoclonal anti-GFP antibody (Roche) in 500 µl of coating buffer with BSA 1% for 1 hour at RT on a rotator, and washed successively 3 times with coating buffer and NETN buffer. Coated beads were incubated up to 2 hours at 4°C with the supernatants complemented with 5µl RNAsin, 6 µl DTT 100 mM, 18 µl EDTA 0.5 M, 60 µl of protease inhibitors cocktail (Roche). Following centrifugation 5 min at 3500 rpm, the supernatant was removed. The beads were washed 6 times in cold NETN buffer and resuspended in 100µl of RNAse free water. The beads were then treated with proteinase K, and immunoprecipitated RNAs were isolated following phenol/chloroform extraction and precipitation.

tag: mRNA immunoprecipitated from anterior quarters of GMR X GFP-NLS transgenic 3rd instar larvae

source_name: mRNA immunoprecipitated from GMR X GFP-B52 transgenic larvae

tag: mRNA immunoprecipitated from anterior quarters of GMR X GFP-B52 transgenic 3rd instar larvae


title: CDC2 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40577

source_name: specific primary antibody. Antibody description: cdk1/p34cdc2 Ab-2, Batch number: 16, AbIDNumber: 246


title: IP- GFP cy3 vs B52 cy5 rep.2


title: CD45RB antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40572

source_name: specific primary antibody. Antibody description: CD45RB Ab-1, Batch number: 16, AbIDNumber: 237


title: CCNE antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8230

source_name: specific primary antibody. Antibody description: Cyclin E (G1- & S-phase Cyclin) Ab-2, Batch number: 5, AbIDNumber: 57


title: IP- GFP cy3 vs B52 cy5 rep.1


title: CDH1_21 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8969

source_name: specific primary antibody. Antibody description: E-Cadherin, Batch number: 6, AbIDNumber: 72


title: IP- GFP cy5 vs B52 cy3 rep.1


title: IP- GFP cy5 vs ASF cy3 rep.1

description: Identification of dASF/SF2 potential target mRNAs in the Drosophila developing eye

source_name: mRNA immunoprecipitated from GMR X GFP-dASF/SF2 transgenic larvae

tag: mRNA immunoprecipitated from anterior quarters of GMR X GFP-dASF/SF2 transgenic 3rd instar larvae


title: CD4+CD25+ vs. NKT spleen Sort II

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description:
Antibodies
Antibodies against murine CD4, FasL, IL-4, IFN, TNF, CXCR4, Mac-1, B220, CD11c and CD8 were isolated from hybridoma cell lines. The alpha-GalCer tetramers were produced as previously described. Antibodies against murine NK1.1, CD3, CD25, LFA-1 and Streptavidin-PE-Cy7 were obtained from BD Bioscience (Heidelberg, Germany)
Isolation and purification of cells by MACS and FACS sorting
Isolation of spleen and liver lymphocytes, red blood cell lysis and tetramer stainings were performed as described elsewhere [28]. Magnetic cell sorting (MACS) with MicroBeads (Miltenyi Biotec, Bergisch Gladbach, Germany) was performed according to manufacturer’s protocol to enrich cell populations by positive selection. Subsequently, enriched cells were sorted using a FACS-Diva (BD Bioscience, Heidelberg, Germany). All manipulations were performed at 4°C. Cells were sorted into tubes containing cold PBS, 0.1% BSA to avoid activation of cells. Viable cells were detected by staining with PI (propidium iodid) or DAPI (Diamidino-phenylindol). The purity of sorted fractions was verified visually and by FACS reanalysis. At least 5 × 105 cells were isolated by FACS sorting and further used for microarray analysis. FACS sorts were repeated four times and duplicate samples of each sorted cell type were used for two independent microarray studies.
Preparation of RNA from single cell suspension
Total RNA was isolated by the TRIzol® Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany). Briefly, cells were resuspended immediately after FACS sorting in 500 µl TRIzol, shock frozen and stored at –80°C. Cells were thawed and further processed for total RNA isolation as described by the manufacturer. The amount of RNA was determined by OD260/280 nm measurement and total RNA was purified by RNeasy (Qiagen, Hilden, Germany). The RNA integrity and the amount of total RNA were measured with a Bioanalyzer 2100 (Agilent Technologies, Waldbronn, Germany).

hyb_protocol: Agilent Technologies

scan_protocol: Agilent Technologies

data_processing: Features were extracted with an image analysis tool version A.6.1.1 (Agilent Technologies) using default settings. Data analysis was carried out on the Rosetta Inpharmics platform Resolver Version 5.0. Ratio profiles were combined in an error-weighted fashion with Resolver to create ratio experiments. A two fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis set highly significant (P-value > 0.05), robust and reproducible.

label_protocol: Agilent Technologies fluorescent linear amplification reaction

extract_protocol: Trizol isolation + RNeasy purification

source_name: NKT spleen

tag: C57BL/6 NKT spleen


title: CCNB1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8228

source_name: specific primary antibody. Antibody description: Cyclin B1 (G2- & M-phase cyclin) Ab-1, Batch number: 5, AbIDNumber: 52


title: IP- GFP cy3 vs ASF cy5 rep.2


title: GMR X GFP cy3 vs GMR X ASFcy5

description: Trancriptome comparison between GMR-GFP-NLS (control) and GMR-GFP-dASF/SF2 transgenic larvae.

source_name: GMR X GFP-NLS

tag: Anterior quarters of GMR X GFP-NLS 3rd instar larvae

source_name: GMR X GFP-dASF/SF2

tag: Anterior quarters of GMR X GFP-dASF/SF2 3rd instar larvae


title: GMR X GFP cy3 vs GMR X B52 cy5

description: Transcriptome comparison between GMR-GFP-NLS (control) and GMR-GFP-B52 transgenic larvae

data_processing: Array vision software

molecule: cytoplasmic RNA

source_name: GMR X GFP-B52

tag: Anterior quarters of GMR X GFP-B52 3rd instar larvae


title: GMR X GFP cy5 vs GMR X B52 cy3


title: IP- GFP cy3 vs ASF cy5 rep.1


title: GMR X GFP cy5 vs GMR X ASF cy3

description: Transcriptome comparison between GMR-GFP-NLS (control) and GMR-GFP-dASF/SF2 transgenic larvae


title: activated NKT spleen vs. NKT spleen Sort II

source_name: activated NKT

tag: C57BL/6 activated NKT

source_name: NKT

tag: C57BL/6 NKT


title: NKT spleen vs. activated NKT spleen Sort II


title: CCNA2 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8227

source_name: specific primary antibody. Antibody description: Cyclin A (S- & G2-phase Cyclin) Ab-6, Batch number: 5, AbIDNumber: 51


title: IP- GFP cy5 vs ASF cy3 rep.2


title: CASP7_26 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 54342

source_name: specific primary antibody. Antibody description: Caspase-7/MCH-3, Batch number: 22, AbIDNumber: 78


title: CASP7_22 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 40571

source_name: specific primary antibody. Antibody description: Caspase 7 (Mch 3) Ab-1, Batch number: 16, AbIDNumber: 233


title: CASP2_26 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8971

source_name: specific primary antibody. Antibody description: Caspase-2/ICH-1L, Batch number: 6, AbIDNumber: 76


title: CASP7_16 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8973

source_name: specific primary antibody. Antibody description: Caspase-7/MCH-3, Batch number: 6, AbIDNumber: 78


title: CASP2_6 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00068

source_name: specific primary antibody. Antibody description: Caspase-2/ICH-1L, Batch number: 26, AbIDNumber: 76


title: BCAR1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26531

source_name: specific primary antibody. Antibody description: p130Cas, Batch number: 14, AbIDNumber: 208


title: AP2M1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00159

source_name: specific primary antibody. Antibody description: AP50, Batch number: 30, AbIDNumber: 526


title: NKT spleen vs. CD4+CD25+ Sort II


title: ANXA4 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00017

source_name: specific primary antibody. Antibody description: Annexin IV, Batch number: 24, AbIDNumber: 406


title: ANXA2 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00016

source_name: specific primary antibody. Antibody description: Annexin II, Batch number: 24, AbIDNumber: 405


title: ANXA1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00015

source_name: specific primary antibody. Antibody description: Annexin I, Batch number: 24, AbIDNumber: 404


title: NKT spleen vs. activated NKT spleen


title: activated NKT spleen vs. NKT spleen


title: ALDH antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00044

source_name: specific primary antibody. Antibody description: ALDH, Batch number: 25, AbIDNumber: 495


title: ATX2 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00160

source_name: specific primary antibody. Antibody description: Ataxin-2, Batch number: 30, AbIDNumber: 534


title: CD4+CD25- vs. NKT spleen Sort II

description:
Antibodies
Antibodies against murine CD4, FasL, IL-4, IFN, TNF, CXCR4, Mac-1, B220, CD11c and CD8 were isolated from hybridoma cell lines. The alpha-GalCer tetramers were produced as previously described. Antibodies against murine NK1.1, CD3, CD25, LFA-1 and Streptavidin-PE-Cy7 were obtained from BD Bioscience (Heidelberg, Germany)
Isolation and purification of cells by MACS and FACS sorting
Isolation of spleen and liver lymphocytes, red blood cell lysis and tetramer stainings were performed as described elsewhere [28]. Magnetic cell sorting (MACS) with MicroBeads (Miltenyi Biotec, Bergisch Gladbach, Germany) was performed according to manufacturer’s protocol to enrich cell populations by positive selection. Subsequently, enriched cells were sorted using a FACS-Diva (BD Bioscience, Heidelberg, Germany). All manipulations were performed at 4°C. Cells were sorted into tubes containing cold PBS, 0.1% BSA to avoid activation of cells. Viable cells were detected by staining with PI (propidium iodid) or DAPI (Diamidino-phenylindol). The purity of sorted fractions was verified visually and by FACS reanalysis. At least 5 × 105 cells were isolated by FACS sorting and further used for microarray analysis. FACS sorts were repeated four times and duplicate samples of each sorted cell type were used for two independent microarray studies.
Preparation of RNA from single cell suspension
Total RNA was isolated by the TRIzol® Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany). Briefly, cells were resuspended immediately after FACS sorting in 500 µl TRIzol, shock frozen and stored at –80°C. Cells were thawed and further processed for total RNA isolation as described by the manufacturer. The amount of RNA was determined by OD260/280 nm measurement and total RNA was purified by RNeasy (Qiagen, Hilden, Germany). The RNA integrity and the amount of total RNA were measured with a Bioanalyzer 2100 (Agilent Technologies, Waldbronn, Germany).

source_name: NKT spleen


title: NK vs. NKT spleen

source_name: NK

tag: C57BL/6 NK


title: NK vs. NKT spleen Sort II


title: AKAP8 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 24323

source_name: specific primary antibody. Antibody description: AKAP95, Batch number: 11, AbIDNumber: 139


title: AKAP5 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 24322

source_name: specific primary antibody. Antibody description: AKAP79, Batch number: 11, AbIDNumber: 138


title: CD4+CD25+ vs. NKT spleen


title: NKT spleen vs. CD4+CD25- Sort II


title: NKT spleen vs. NK

source_name: NKT


title: NKT spleen vs. CD4+CD25+


title: NKT spleen vs. CD4+CD25-


title: CD4+CD25- vs. NKT spleen


title: AIB1 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00042

source_name: specific primary antibody. Antibody description: AIB-1, Batch number: 25, AbIDNumber: 493


title: NKT spleen vs. NK Sort II


title: CASP7_6 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00069

source_name: specific primary antibody. Antibody description: Caspase-7/MCH-3, Batch number: 26, AbIDNumber: 78


title: ADPRT_6 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number:

source_name: specific primary antibody. Antibody description: PARP, Batch number: , AbIDNumber: 83


title: ACVR2 antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 8041

source_name: specific primary antibody. Antibody description: Activin Receptor, Type II (actRII) Ab-1, Batch number: 4, AbIDNumber: 33


title: ADPRT_22 antibody


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, miR_106b, 100 nM, 24 hr, b

description: Linsley PS, Schelter J, Burchard J, Kibukawa M, Martin MM, Bartz SR, Johnson JM, Cummins JM, Raymond CK, Dai H, Chau N, Cleary M, Jackson AL, Carleton M, and Lim L.  MCB (2007).

source_name: HCT116 Dicer -/- #2

tag: HCT116 Dicer -/- #2, mock


title: ADPE antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00040

source_name: specific primary antibody. Antibody description: Adaptin epsilon, Batch number: 25, AbIDNumber: 489


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, miR_107, 100 nM, 24 hr


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, miR_16, 100 nM, 24 hr, b


title: ADNP antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: GBL00041

source_name: specific primary antibody; Antibody description: ADNP; Batch number: 25; AbIDNumber: 490

tag: Each of the 176 specific primary antibodies was prescreened to give highest quality by western analysis.


title: AACTNN antibody

description: Each array was incubated with a specific primary antibody.  Enables comparison of protein-of-interest across all 60 NCI-60 cell lines.  Experimental slide number: 26609

source_name: specific primary antibody. Antibody description: Anti-a-Actinin, Batch number: 20, AbIDNumber: 328


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, miR_15b, 100 nM, 24 hr


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, miR_195, 100 nM, 10 hr


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, miR_15a, 100 nM, 24 hr, b


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, miR_103, 100 nM, 24 hr


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, Luc, 100 nM, 24 hr, b


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, miR_103, 100 nM, 10 hr


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, miR_107, 100 nM, 10 hr


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, miR_15b, 100 nM, 10 hr


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, miR_15a, 100 nM, 10 hr, b


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, miR_16, 100 nM, 10 hr, b


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, miR_106b, 100 nM, 10 hr, b


title: HCT116 Dicer -/- #2, mock vs. HCT116 Dicer -/- #2, Luc, 100 nM, 10 hr, b


title: HCT116 Dicer -/- #2, mock, 24 hr vs. HCT116 Dicer -/- #2, miR_16_mm2,3, 100 nM, 24 hr

tag: HCT116 Dicer -/- #2, mock, 24 hr


title: HCT116 Dicer -/- #2, mock, 24 hr vs. HCT116 Dicer -/- #2, miR_16_mm4,5, 100 nM, 24 hr