title: Blastemal_Component_Wilms_Tumor_4_rep2

description: Patient had surgery as first treatment. Blastema component was scalpel microdissected / polyA RNA was amplified.

source_name: Blastemal Component 4

value: 31 months, Blastema component from Wilms tumor predominatly blastemal, stage II


title: Epithelial_Component_Wilms_Tumor_18_rep1

status: Public on Aug 01 2006

type: other

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

description: Epithelial component was scalpel microdissected / polyA RNA was amplified.

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 4 ug Cot1 DNA; 5X Denhardt´s ; 10 ug Salmon sperm, Deyonized formamide 25%, 20 mg BSA / Temperature:42oC / Time:16-20hrs / Touch Down: 70oC-55oC-42oC Washing - Round 1 - Solution: SSC2X / Temperature:42ºC / Time:15' / Washing Number: 1 Washing - Round 2 - Solution: SSC0,1X-SDS0,1% / Temperature:42ºC / Time:15' / Washing Number: 2 Washing - Round 3 - Solution: SSC0,1X / Temperature:42ºC / Time:15' / Washing Number: 2

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing: Lowesss

molecule: other

organism: Homo sapiens

source_name: Epithelial Component 18

tag: unknown

source_name: Reference

tag: Pool of 6 mature kidneys


title: Blastemal_Component_Wilms_Tumor_39_rep1

description: Patient had chemotherapy as first treatment. Blastema component was laser microdissected / polyA RNA was amplified.

source_name: Blastemal Component 39

tag: Gender male, Age

value: 132 months, Blastema component from Wilms tumor predominatly blastemal, stage IV


title: Stromal_Component_Wilms_Tumor_7_rep1

description: Patient had surgery as first treatment. Stromal component was scalpel microdissected / polyA RNA was amplified.

source_name: Stromal Component 7

value: 29 months, Stromal component from Wilms tumor predominatly blastemal, stage


title: Blastemal_Component_Wilms_Tumor_4_rep1

tag: Gender female, Age


title: Blastemal_Component_Wilms_Tumor_20_rep2

description: Patient had chemotherapy as first treatment. Blastema component was scalpel microdissected / polyA RNA was amplified.

source_name: Blastemal Component 20

value: 38 months, Blastema component from Wilms tumor predominatly stromal, stage IV


title: Blastemal_Component_Wilms_Tumor_20_rep1


title: Blastemal_Component_Wilms_Tumor_2_rep1

source_name: Blastemal Component 2

value: 51 months, Blastema component from Wilms tumor predominatly blastemal, stage I


title: Blastemal_Component_Wilms_Tumor_2_rep2


title: Blastemal_Component_Wilms_Tumor_11_rep2

source_name: Blastemal Component 11

value: 15 months, Blastema component from Wilms tumor predominatly blastemal


title: Blastemal_Component_Wilms_Tumor_16_rep1

description: Patient had surgery as first treatment. Blastema component was laser microdissected / polyA RNA was amplified.

source_name: Blastemal Component 16

value: 9 months, Blastema component from Wilms tumor triphasic, stage II


title: Mature_kidney2_rep1

description: Histological mature normal kidney / polyA RNA was amplified.

source_name: Histological normal mature kidney 1

value: 51 months


title: Blastemal_Component_Wilms_Tumor_1_rep1

source_name: Blastemal Component 1

value: 5 months, Tissue:blastemal component of a Wilms Tumor predominantly blastema stage I


title: Mature_kidney2_rep2


title: Pool_of_fetal_kidneys_rep2

description: Pool of fetal kidney poly A RNA from Clontech cat#6526-1 / polyA RNA was amplified.

tag: Pool f 6 mature kidneys

source_name: Pool of fetal kidneys

tag: Pool of 16 fetal kidneys, age 16 to 32 weeks


title: Pool_of_fetal_kidneys_rep5

description: Pool of fetal kidney poly A RNA from Clontech cat#6526-1 / polyA RNA was amplified


title: Blastemal_Component_Wilms_Tumor_1_rep2


title: Mature_kidney15_rep1

source_name: Histological normal mature kidney 15

tag: Gender Male, Age

value: 25 months


title: Blastemal_Component_Wilms_Tumor_11_rep1


title: Mature_kidney15_rep2


title: Pool_of_fetal_kidneys_rep6

tag: Pool of fetal kidney poly A RNA from Clontech cat#6526-1


title: Pool_of_fetal_kidneys_rep1


title: Mature_kidney1_rep2

value: 5 months,


title: Pool_of_fetal_kidneys_rep3


title: Pool_of_fetal_kidneys_rep4


title: Mature_kidney1_rep1


title: MPI-084

status: Public on Jun 07 2006

type: RNA

city: Berlin

first: Michael

last: Hummel

address: Hindenburgdamm 30

department: Institute of Pathology

country: Germany

institute: Universitätsmedizin Berlin, Campus Benjamin Franklin

description: Mature aggressive B-cell lymphoma

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536).  Probe-set summarization was performed using the median polish method on the normalized data (Irrizary et al. Nucleic Acids Research 2003, PMID: 12582260).

label: Biotin

molecule: total RNA

source_name: Frozen tissue

tag: Relapse

value: unk

tag: Age

tag: Sex

value: male

value: BL

value: present

value: absent

value: IG-MYC

tag: Lesions

tag: Radiotherapy

tag: RITUXIMAB

tag: Chemotherapy

value: mBL

value: GCB

value: Training

value: yes


title: MPI-043

description: Mature aggressive B-cell lymphoma

value: no

value: atypical BL

value: II

value: nodal + extranodal

value: dead

value: ALL-like


title: Zebrafish_MZ Dicer_Rep2

status: Public on Feb 17 2006

city: New Haven

first: Antonio

middle: J.

last: Giraldez

state: CT

address: 333 Cedar Street

department: Genetics

country: USA

institute: Yale University

hyb_protocol: 10 micrograms of labeled and fragmented cRNA were hybridized to GeneChip at 45 degrees C for 16 hours. Post hybridization staining and washing were performed according to the manufacturer (Affymetrix).

scan_protocol: GeneChips were scanned with a high-numerical Aperture and flying objective (FOL) lens in a GS3000 scanner (Affymetrix).

data_processing: normalization of all arrays was performed by dChip v.3.1.  The values were then calculated using dChip's PM/MM difference model (www.dchip.org)

label: biotin

organism: Danio rerio

source_name: MZ Dicer mutant embryos_9 hours post fertilization

label_protocol: 2 micrograms of total RNA was used for cDNA synthesis using an oligo(dT)-T7 primer and the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen).  Synthesis, linear amplification, and labeling of cRNA were accomplished by in vitro transcription using the MessageAmp aRNA Kit (Ambion) and biotinylated nucleotides(Enzo Diagnostics).

growth_protocol:
embryos were collected and grown in egg water (Stock salts: 40 g "Instant Ocean" Sea Salts added to 1 L distilled water
Egg water = 1.5 ml stock salts added to 1 L distilled water = 60 µg/ml final concentration) at 28 degrees Celcius prior to RNA extraction

extract_protocol: RNA was isolated from 20 embyros using Trizol (Invitrogen).  20-50 ng of sample was quality checked using the RNA 6000 NanoAssay and Bioanalyzer 2100 (Agilent).  Samples with a 28S/18S ribosomal peak ratio of 1.8-2.0 were labled.

tag: maternal zygotic dicer mutants

tag: embryos collected 9 hours post fertilization


title: Zebrafish_Wild Type_Rep1

source_name: wild type embryos_9 hours post fertilization

tag: TLAB wild type embryos

tag: 9 hours post fertilization


title: Zebrafish_Wild Type_Rep2

tag: TLAB (wild type) embryos collected 9 hours post fertilization


title: Zebrafish_Wild Type_miR-430 injected_Rep2

source_name: Wild Type embryos_miR-430 injected

treatment_protocol: injected with miR-430 microRNA at the one cell stage

tag: TLAB (wild type) embryos, 9 hours post fertilization


title: Zebrafish_Wild Type_miR-430 injected_Rep1

tag: TLAB (wild type) embryos

tag: injected with miR-430 microRNA at the one cell stage

tag: collected 9 hours post fertilization


title: Zebrafish_MZ Dicer_Rep3

source_name: MZ Dicer mutants_9 hours post fertilization

tag: maternal zygotic dicer mutant embryos


title: Zebrafish_MZ Dicer_miR-430 injected_Rep2

hyb_protocol: 10 micrograms of labeled and fragmented cRNA were hybridized to GeneChip at 45 degrees C for 16 hours. Post hybridization staining and washing were performed according to the manufacturer (Affymetrix)

source_name: MZ Dicer mutants injected with miR-430

treatment_protocol: injected at the one cell stage with miR-430 micro-RNA

tag: Maternal Zygotic dicer mutants

tag: embryos collected 9 hours post

tag: fertilization


title: Zebrafish_Wild Type_Rep3

source_name: wild type embryos, 9 hours post fertilization

tag: TLAB wild type embryos collected 9 hour post fertilization


title: Zebrafish_Wild Type_miR-430 injected_Rep3


title: Zebrafish Embryo_50% epiboly

hyb_protocol: 10 micrograms of labeled and fragmented cRNA were hybridized to GeneChip at 45 degrees C for 16 hours.  Post hybridization staining and washing were performed according to the manufacturer (Affymetrix).

source_name: zebrafish at 50% epiboly stage

growth_protocol: embryos were collected and grown in egg water (Stock salts: 40 g

treatment_protocol: no treatment

tag: strain

value: TLAB (Wild Type)

tag: stage

value: 50% epiboly


title: Zebrafish_MZ Dicer_miR-430 injected_Rep3

tag: Maternal zygotic Dicer mutants


title: Zebrafish_MZ Dicer_miR-430 injected_Rep1

source_name: MZ_Dicer mutants_injected with miR-430

tag: maternal zygotic (MZ) dicer mutants

tag: injected with miR-430 at the one cell stage


title: Zebrafish Embryo_16 cell stage_Rep2

source_name: zebrafish_16 cell stage

value: TLAB (wild type)

tag: embryos

value: 16 cell stage


title: Zebrafish Embyro_16cell stage_Rep1

description: This array data is obtained from zebrafish embryos at the 16 cell stage (Replicate 1).

source_name: zebrafish_16cell stage


title: Zebrafish_MZ Dicer_Rep1

source_name: MZ_dicer embryos_9 hours post fertilization

tag: maternal zygotic dicer mutants

tag: embryos collected 9 hours post fertilization


title: DUSP1-/- LPS replicate 1

status: Public on Dec 15 2005

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

description: three mice per group were used; the spleen from an individual mice was extracted and homogenized in TriFast; 5 µg total RNA were labeledand hybridized to MOE430A 2.0 GeneChips

data_processing: RMA normalized CEL file

organism: Mus musculus

source_name: spleen

label_protocol: Affymetrix One Cycle Kit

treatment_protocol: 6h after LPS 10 µg/g body weight i.p.

tag: spleens from mice on C57/Bl6 x 129 Sv background


title: DUSP1-/- control replicate 3


title: DUSP1+/+ LPS replicate 3


title: DUSP1+/+ LPS replicate 2


title: DUSP1+/+ control replicate 1


title: DUSP1-/- LPS replicate 3


title: DUSP1-/- control replicate 2


title: DUSP1+/+ LPS replicate 1


title: DUSP1+/+ control replicate 3


title: DUSP1+/+ control replicate 2


title: DUSP1-/- LPS replicate 2


title: 12209751

status: Public on Dec 07 2005

description:
Human mammary gland ductal carcinome invasive
Invasive breast cancer was histopathologically confirmed on 47 samples obtained by core or incisional biopsy. Total RNAs from frozen specimens were isolated using Trizol reagent (Invitrogen Corporation, Carlsbad, CA) according to the manufacturer protocol. RNA quality was verified by electrophoresis through agarose gel upon visualization with ethidium bromide and only RNA samples with a ratio >1 for 28S/18S ribosomal RNA were further processed.
A two-round RNA amplification procedure was carried out by combining antisense RNA amplification with a template-switching effect. HB4A normal epithelial mammary cell line was used as reference for hybridizations. These cells were processed in the same manner as tumor samples. Three to 5 µg of amplified RNA (aRNA) were then used in a transcriptase reverse reaction into cDNA in the presence of 2µl of Cy3- or Cy5-labeled dCTP (Amersham, Biosciences), 25 mM dGTP, 25 mM dATP, 25 mM dTTP and 10 mM dCTP and 2 µl of SuperScript II (Invitrogen-Life Technology) for 2h at 42°C. After hydrolysis of RNA in 1 M NaOH and 0.5 M EDTA for 20 min at 70°C, the reaction was neutralized with HCl 1M and purified by Autoseq G50 columns following the fabricant`s instructions.
The cDNA from test samples aRNA and the cDNA from reference aRNA were mixed. After that, were added 2 µl of poly A DNA (2 µg/µl), 2 µl of Cot1 DNA (2µg/µl) and 2 µl BSA (10 mg/ml). The volume was dried in Speed vacuum and resuspended in 12.25 µl of ddH20 and added 47.5 µl of pre-heating hybridization buffer (10 X SSC, 02% SDS), 23.75 µl of deionized formamide, 9.5 µl of Denhardt`s solution 50X and 2 µl sonicated salmon sperm DNA (5µ/µl) for hybridization against the cDNA microarray slides for 20 hours at 42°C.
Fluorescent array images of Breast Normal and Tumor tissue of different clinical stages  were collected for both Cy3 and Cy5 with a confocal laser scanner (Arrayexpress, Packard Bioscience) using identical photomultiplicatior voltage for all slides and data recovered by QuantArray software (Packard Bioscience). After background correction, image acquisition and quantification, saturated spots (signal intensity higher than 63,000) as well as unreliable low intensity spots, defined as those within the 95% percentile of intensity distribution of known empty spots, were removed from the analysis. The validated values were log base 2 expression ratios transfomred and normalized by Lowess (linear transformed).
Keywords = Breast Normal and Tumor tissue of different clinical stage, were collected for both Cy3 and Cy5 with a Perkinelmer fluorescent scanner and image intensity data were extracted and analyzed with QuantArray analysis software. After background correction.


title: 12209759


title: 12209755


title: DUSP1-/- control replicate 1


title: 12209209


title: 12209737


title: 12209208


title: 12209736


title: 12209206


title: 12209205


title: 12209174


title: 12209732

description:
Human mammary gland normal tissue
Invasive breast cancer was histopathologically confirmed on 47 samples obtained by core or incisional biopsy. Total RNAs from frozen specimens were isolated using Trizol reagent (Invitrogen Corporation, Carlsbad, CA) according to the manufacturer protocol. RNA quality was verified by electrophoresis through agarose gel upon visualization with ethidium bromide and only RNA samples with a ratio >1 for 28S/18S ribosomal RNA were further processed.
A two-round RNA amplification procedure was carried out by combining antisense RNA amplification with a template-switching effect. HB4A normal epithelial mammary cell line was used as reference for hybridizations. These cells were processed in the same manner as tumor samples. Three to 5 µg of amplified RNA (aRNA) were then used in a transcriptase reverse reaction into cDNA in the presence of 2µl of Cy3- or Cy5-labeled dCTP (Amersham, Biosciences), 25 mM dGTP, 25 mM dATP, 25 mM dTTP and 10 mM dCTP and 2 µl of SuperScript II (Invitrogen-Life Technology) for 2h at 42°C. After hydrolysis of RNA in 1 M NaOH and 0.5 M EDTA for 20 min at 70°C, the reaction was neutralized with HCl 1M and purified by Autoseq G50 columns following the fabricant`s instructions.
The cDNA from test samples aRNA and the cDNA from reference aRNA were mixed. After that, were added 2 µl of poly A DNA (2 µg/µl), 2 µl of Cot1 DNA (2µg/µl) and 2 µl BSA (10 mg/ml). The volume was dried in Speed vacuum and resuspended in 12.25 µl of ddH20 and added 47.5 µl of pre-heating hybridization buffer (10 X SSC, 02% SDS), 23.75 µl of deionized formamide, 9.5 µl of Denhardt`s solution 50X and 2 µl sonicated salmon sperm DNA (5µ/µl) for hybridization against the cDNA microarray slides for 20 hours at 42°C.
Fluorescent array images of Breast Normal and Tumor tissue of different clinical stages  were collected for both Cy3 and Cy5 with a confocal laser scanner (Arrayexpress, Packard Bioscience) using identical photomultiplicatior voltage for all slides and data recovered by QuantArray software (Packard Bioscience). After background correction, image acquisition and quantification, saturated spots (signal intensity higher than 63,000) as well as unreliable low intensity spots, defined as those within the 95% percentile of intensity distribution of known empty spots, were removed from the analysis. The validated values were log base 2 expression ratios transfomred and normalized by Lowess (linear transformed).
Keywords = Breast Normal and Tumor tissue of different clinical stage, were collected for both Cy3 and Cy5 with a Perkinelmer fluorescent scanner and image intensity data were extracted and analyzed with QuantArray analysis software. After background correction.


title: 12209177


title: 12209750


title: 12209758


title: 12209656


title: BF-FN5b (rep1)

status: Public on Sep 10 2006

description: HB4A was used as reference

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 4 ug Cot1 DNA; 5X Denhardt´s ; 10 ug Esperma de salmão,  Formamida 25%. / Temperature:14 a 24 hs / Time:42 C / Touch Down: Washing - Round 1 - Solution: 0,1 X SSC / Temperature:sol 42C / Lavagem TA / Time:5 min / Washing Number: 1 Washing - Round 2 - Solution: 0,1 X SSC / Temperature:sol 42C / Lavagem TA / Time:10 min / Washing Number: 2 Washing - Round 3 - Solution: 0,1 X SSC / Temperature:sol 42C / Lavagem TA / Time:2,5 min / Washing Number: 2

source_name: Benign Breast disease

tag: female

source_name: HB4A Luminal mammary epithelial cell line


title: 12209171


title: 12209172


title: 12209753


title: 12209001


title: 12208953


title: 12208962


title: 12208993


title: 12205870


title: 12208926


title: 12209207


title: 12208925


title: 12205786


title: 12205849


title: 12205785


title: 12204803


title: 12205869


title: 12204799


title: 12148428


title: 12204800


title: 12148430


title: 12148427


title: 12148325


title: 12204802


title: 12148145


title: 12148426


title: 12205871


title: 12148329


title: 12148108


title: 12148429


title: 12148107


title: 12148332


title: 12148086


title: 12148085


title: 12148063


title: 12147996


title: 12148062


title: 12148080


title: 12148083


title: 12147995


title: 12147984


title: 12147978


title: 12147836


title: 12147999


title: 12147977


title: 12147979


title: 12147838


title: 12147837


title: 12147840


title: 12147980


title: 12147975


title: 12147983


title: 12147976


title: 12147651


title: 12147654


title: 12139231


title: 12147652


title: 12147650


title: 12147839


title: 12139230


title: 12139177


title: 12139182


title: 12147653


title: 12139166


title: 12139175


title: 12139176


title: 12139173


title: 12139178


title: 12139159


title: 12139115


title: 12139117


title: 12139010


title: 12139113


title: 12139111


title: 12139011


title: 12139104


title: 12139007


title: 12139106


title: 12139172


title: 12138976


title: 12138975


title: 12138973


title: 12138972


title: 12138977


title: 12138968


title: 12138939


title: 12138938


title: 12138974


title: 12138890


title: 12139009


title: 12139008


title: 12138886


title: 12138847


title: 12138887


title: 12138873


title: 12138879


title: 12138876


title: 12138819


title: 12138818


title: 12138814


title: 12138875


title: 12138817


title: 12138872


title: 12138815


title: 12210371

status: Public on May 09 2005

description: Patients were recruited at the Departments of Abdominal Surgery and Endoscopy of the Hospital do Cancer AC Camargo (São Paulo/Brazil) during a 4-year period (2001 to 2004). All patients signed a pre-informed consent and the study was approved by the internal ethics committee. Tissue samples were either snap frozen in liquid nitrogen (when obtained by surgery) or collected in RNAlaterTM (Ambion®, Austin, Texas USA, when obtained by biopsy).  For all samples, diagnosis was confirmed by H&E staining at the time of RNA extraction. Biopsy samples of the esophageal and gastric mucosa obtained by endoscopy had information of the correct anatomical location using a standard diagram. Frozen samples were dissected and only those having at least 70% of tumor cells were processed. A total of 71 samples were analyzed: 39 esophagus and esophagogastric junction samples (9 normal mucosa, 6 esophagitis mucosa, 10 Barretts mucosa  4 for the long type and 6 for the short type, and 14 tumor samples of adenocarcinoma) and 32 stomach samples (6 normal body and antrum mucosa, 5 normal cardiac mucosa, 9 intestinal metaplasia mucosa, 7 samples of intestinal type adenocarcinoma and 5 samples of diffuse type carcinoma). For Barretts samples, diagnosis required evidence of intestinal metaplasia together with tongues or segments of red columnar-appearing epithelium extending upwards from the esophagogastric junction. A long Barretts esophagus was defined as longer 3cm and a short Barretts esophagus by 3cm of columnar epithelium (Spechler, 2004). The tumor samples of esophagus and esophagogastric junction were not differentiated. For the gastric adenocarcinoma samples were used the Lauréns classification (Laurén, 1965) and the others gastric sample were previously described (Meireles et al, 2003).

source_name: Normal mucosa of esophagus


title: 12210174


title: 12205610


title: 12209778


title: 12205762


title: 12210249


title: 12210243


title: 12205833


title: 12209795


title: 12205321


title: 12210177


title: 12209567


title: 12210248


title: 12209781


title: 12205474


title: 12205747


title: 12205511


title: 12210597


title: 12205741


title: 12205763


title: 12205317


title: 12210226


title: 12210050


title: 12205830


title: 12205829


title: 12209568


title: 12210327


title: 12205343

description:
Post-surgical samples of normal thyroid tissue, adenoma and follicular carcinoma were obtained from Hospital do Câncer A.C. Camargo, São Paulo, Hospital Araújo Jorge, Goiânia, and Instituto de Enfermedades Neoplásicas-INEN, Lima, Peru. All patients signed an informed consent and the study was approved by the Internal Review Board from all institutions. Excess of tissue not used for histopathology was immediately transferred to liquid nitrogen and kept frozen at -140oC until RNA extraction. Before RNA extraction histopathological diagnosis was re-confirmed, all samples were dissected in order to enrich for the appropriated tissue and only tissues with at least 70% of the corresponding alteration and no visible infiltrating inflammatory cells were used. Morphologically disease-free tissue obtained from surgical margins was considered as normal.
RNA extraction was performed using TRIZOL (Life Technologies) and a mechanical tissue homogenizer (Polytron). The samples with OD260/280 ratio of at least 1.7 were evaluated by agarose gel with ethidium bromide staining. A total of 24 samples were analyzed: 12 adenomas and 12 follicular carcinomas. All RNAs were amplified based on the procedure previously described by Wang and co-workers with modifications described by Gomes and co-workers. The procedure was optimized for 1.5 µg of total RNA as starting material.

source_name: pool of 4 thyroid tissues


title: 12210004


title: 12205342


title: 12205503


title: 12205494


title: 12209338


title: 12205724


title: 12205204


title: 12205501


title: 12210453


title: 12205846


title: 12218413


title: 12210007


title: 12205223


title: 12205524


title: 12205715


title: 12210002


title: 12209904


title: 12210535


title: 12210451


title: 12205718


title: 12210455


title: 12210539


title: 12209951


title: 12205134


title: 12210217


title: 12205219


title: 12205131


title: 12210452


title: 12210218


title: 12210211


title: 12210210


title: 12218415


title: 12218414


title: 12209335


title: 12210509


title: 12209336


title: 12218417


title: 12205717


title: 12205504


title: 12210221


title: 12210508


title: 12205523


title: 12209897

description: Laryngeal and hypopharyngeal squamous cell carcinoma was histopathologically confirmed on 35 samples obtained by incisional biopsy. Total RNAs from frozen specimens were isolated using Trizol reagent (Invitrogen Corporation, Carlsbad, CA) according to the manufacturer protocol. RNA quality was verified by electrophoresis through agarose gel upon visualization with ethidium bromide and only RNA samples with a ratio >1 for 28S/18S ribosomal RNA were further processed.  A two-round RNA amplification procedure was carried out. Normal larynx and hypopharynx samples was used as reference for hybridizations, these samples were processed in the same manner as tumor samples. Amplified RNA were then used in a transcriptase reverse reaction into cDNA in the presence of Cy3- or Cy5-labeled dCTP

source_name: Normal larynx and hypopharynx obtained from surger


title: 12210506


title: 12218416


title: 12205861


title: 12205215


title: 12205579


title: 12205205


title: 12209896


title: 12210005


title: 12205373


title: 12210308


title: 12205224


title: 12210259


title: 12210307


title: 12209115


title: 12210258


title: 12205502


title: 12205721


title: 12209112


title: 12210111


title: 12210427


title: 12210468


title: 12210150


title: 12210184


title: 12205163


title: 12209891


title: 12205376


title: 12210013


title: 12205456


title: 12210183


title: 12205227


title: 12205072


title: 12205699


title: 12210014


title: 12210015


title: 12210017


title: 12210155


title: 12205403


title: 12205068


title: 12209113


title: 12210469


title: 12205159


title: 12210465


title: 12209892


title: 12210467


title: 12210260


title: 12210263


title: 12210466


title: 12205071


title: 12205162


title: 12210187


title: 12210148


title: 12209509


title: 12210151


title: 12204821


title: 12205161


title: 12209124


title: 12209125


title: 12205228


title: 12209510


title: 12205582


title: 12205374


title: 12205372


title: 12209126


title: 12205069


title: 12205577


title: 12210052


title: 12204835


title: 12204822


title: 12205647


title: 12205455


title: 12205377


title: 12204832


title: 12210262


title: 12209507


title: 12204834


title: 12210185


title: 12209520


title: 12205160


title: 12209116


title: 12205767


title: 12210364


title: 12209814


title: 12209779


title: 12209740


title: 12209372


title: 12209816


title: 12205764


title: 12209805


title: 12209804


title: 12205520


title: 12210594


title: 12209741


title: 12205075


title: 12205510


title: 12210365


title: 12205471


title: 12210596


title: 12210230


title: 12210567


title: 12210566


title: 12210598


title: 12110241


title: 12205569


title: 12205257


title: 12210229


title: 12205470


title: 12209373


title: 12205333


title: 12205572


title: 12205573


title: 12205672


title: 12210237


title: 12110572


title: 12110238


title: 12110325


title: 12210482


title: 12210231


title: 12205564


title: 12210233


title: 12209793


title: 12209815


title: 12205671


title: 12218338


title: 12218333


title: 12209561


title: 12205473


title: 12210479


title: 12209560


title: 12205660


title: 12210176


title: 12209993


title: 12209998


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title: pupa vs adult female labeled with Cy3

status: Public on Nov 04 2004

first: Zareen

last: Gauhar

address: 333 Cedar St, 386 NSB

institute: Yale

description: RNA from six developmental stages during the Drosophila life cycle (0-2hr embryos, 3-16hr embryos, larvae, pupae, male and female adults) was isolated, reverse transcribed in the presence of oligodT and random hexamers and the labeled cDNA was hybrid ized to these arrays.Each sample was hybridized four times, twice with Cy5 labeling and twice with Cy3 labeling.

organism: Drosophila melanogaster

source_name: pupa polyA RNA labeled with cy3


title: pupa vs larvae labeled with Cy3

source_name: pupa polyA RNA labeled with cy3.


title: pupa vs larvae labeled with Cy5

source_name: pupa polyA RNA labeled with cy5.


title: pupa vs 3-16hr embryo labeled with Cy5

source_name: pupa polyA RNA labeled with Cy5


title: larvae vs pupa labeled with Cy5

source_name: larvae polyA RNA labeled with cy5.


title: adult male vs larva labeled with Cy5

source_name: adult males polyA RNA labeled with cy5.


title: adult female vs adult female  labeled with Cy5

source_name: adult females polyA RNA labeled with Cy5


title: h2A

status: Public on Jan 31 2004

city: Cambridge

first: Jose

middle: M

last: Ranz

address: Downing

country: United Kingdom

institute: University of Cambridge

description: Strains of Drosophila melanogaster and Drosophila simulans were raised on glucose-cornmeal-yeast medium at 25 C.  Males and virgin females were collected for the interspecific and conspecific crosses. All crosses were performed at 18C using 7-8 individuals from each sex. Virgin females from the parental species as well as hybrid females were stored separately for 5-6 days at room temperature and then snap frozen in liquid nitrogen invariably at the same time of the day in a time window of 2 hours. For each cross, two independent cohorts were used as the source of mRNA. Total RNA was extracted by homogenizing in TRIzol reagent (Invitrogen) followed by a chloroform extraction and isopropanol precipitation.  The resulting pellet was washed with 75% ethanol, air-dried, and resuspended in TE.  Individual extractions were pooled into one common RNA sample for each strain.  Poly-A RNA was purified from total RNA using the Oligotex Direct mRNA kit (Qiagen). mRNA samples were confirmed to be of high quality with a 2100 Bioanalyzer (Agilent).  The production of cDNA and hybridizations were done following a published protocol (Eisen and Brown, Methods in Enzymology 303:179-205).  2 µg of poly-A RNA was used as a template for SuperScript II reverse transcriptase (Invitrogen) in the presence of amino-allyl dUTP (Sigma) with random hexamer and oligo dT primers.  Reverse transcription was done at 42 C for 3 hours, followed by degradation of RNA by the addition of NaOH and EDTA and incubation at 65 C for 15 minutes.  The cDNA was concentrated and purified with Microcon-30 filters (Millipore).   Cyanine-3 or cyanine-5 fluorochromes (Amersham) were incorporated with the addition of 1 M NaHCO3 and a 75 minute incubation at room temperature with the cDNA probe.  The labeled probes were then purified using the QIAquick PCR Purification Kit (Qiagen), concentrated with Microcon-30 filters, and combined into one sample.  25 µL of probe was combined with 22 µg poly(A), 4.4 µL 20X SSC, 0.71 µL 1 M HEPES (pH 7.0), and 0.66 µL 10% SDS.  The probe was boiled at 100 C for 2 minutes and injected under a LifterSlip (Erie Scientific Company) placed over the array.  Slides were placed in a Telechem hybridization chamber with 3X SSC in the chamber wells to prevent drying, sealed, and placed in a 65 C water bath for 12 hours.  After hybridization, slides were washed with two wash solutions (0.6X SSC, 0.025% SDS [solution 1] and 0.05X SSC [solution 2]).  Slides were dried by centrifugation at 1000 rpm for 2 minutes and scanned within an hour of washing.  Fluorescence intensity was measured with Axon GenePix 4000A or 4000B scanners and the data was captured with GenePix 4.0 software. Following exclusion of suboptimal spots, intensity ratios were constructed by subtracting local background from foreground for each spot and normalizing one channel so that the mean foreground fluorescence of both channels across the slide was equal.

source_name: D. melanogaster Canton S adult females

organism: Drosophila simulans

source_name: D. simulans Sim-1 adult females


title: adult male vs 3-16hr embryo labeled with Cy3

source_name: adult males polyA RNA labeled with Cy3


title: h34B

description: Strains of Drosophila melanogaster and Drosophila simulans were raised on glucose-cornmeal-yeast medium at 25 C.  Males and virgin females were collected for the interspecific and conspecific crosses. All crosses were performed at 18C using 7-8 individuals from each sex. Virgin females from the parental species as well as hybrid females were stored separately for 5-6 days at room temperature and then snap frozen in liquid nitrogen invariably at the same time of the day in a time window of 2 hours. For each cross, two independent cohorts were used as a source of mRNA. Total RNA extraction and linear amplification was done as reported in Baugh et al. 2001 (Nucleic Acids Res. 29: E29). Several amplifications using one or two heads each were carried out and pooled. 3 µg of poly-A RNA was used as a template for SuperScript II reverse transcriptase (Invitrogen) in the presence of amino-allyl dUTP (Sigma) with random hexamer and oligo dT primers.  Reverse transcription was done at 42 C for 2 hours, followed by degradation of RNA by the addition of NaOH and EDTA and incubation at 65 C for 15 minutes.  The cDNA was concentrated and purified with Microcon-30 filters (Millipore).   Cyanine-3 or cyanine-5 fluorochromes (Amersham) were incorporated with the addition of 1 M NaHCO3 and a 75 minute incubation at room temperature with the cDNA probe.  The labeled probes were then purified using the QIAquick PCR Purification Kit (Qiagen), concentrated with Microcon-30 filters, and combined into one sample.  30 µL of probe was combined with 26.4 µg poly(A), 5.28 µL 20X SSC, 0.85 µL 1 M HEPES (pH 7.0), and 0.79 µL 10% SDS.  The probe was boiled at 100 C for 2 minutes and injected under a LifterSlip (Erie Scientific Company) placed over the array.  Slides were placed in a Telechem hybridization chamber with 3X SSC in the chamber wells to prevent drying, sealed, and placed in a 65 C water bath for 12 hours.  After hybridization, slides were washed with two wash solutions (0.6X SSC, 0.025% SDS [solution 1] and 0.05X SSC [solution 2]).  Slides were dried by centrifugation at 1000 rpm for 2 minutes and scanned within an hour of washing.  Fluorescence intensity was measured with Axon GenePix 4000A or 4000B scanners and the data was captured with GenePix 4.0 software. Following exclusion of suboptimal spots, intensity ratios were constructed by subtracting local background from foreground for each spot and normalizing one channel so that the mean foreground fluorescence of both channels across the slide was equal.

source_name: D. melanogaster Canton S adult females heads only

source_name: D. simulans Sim-1 adult females heads only


title: h36A

source_name: adult hybrid females heads only resulting from the cross D. melanogaster Canton S females x D. simulans Sim-1 males


title: 0-2hr embryo vs 3-16hr embryo labeled with Cy3

source_name: 0-2hr polyA RNA labeled with Cy3


title: h36B


title: adult female vs 0-2hr embryo labeled with Cy3

source_name: adult female polyA RNA labeled with Cy3


title: adult females vs pupa labeled with Cy5

source_name: adult females polyA RNA labeled with Cy5.


title: larvae vs 0-2hr embryo labeled with Cy5

source_name: larvae polyA RNA labeled with Cy5


title: adult male vs adult female  labeled with Cy3

source_name: adult males polyA RNA labeled with cy3.


title: 0-2hr embryo vs 3-16hr embryo labeled with Cy5

source_name: 0-2hr polyA RNA labeled with Cy5


title: larvae vs adult males labeled with Cy3

source_name: larvae polyA RNA labeled with cy3


title: adult female vs adult male   labeled with Cy3

source_name: adult females polyA RNA labeled with Cy3.


title: 3-16hr vs pupa labeled with Cy3

source_name: 3-16hr  polyA RNA labeled with Cy3.


title: h33A


title: 0-2hr embryo vs larvae labeled with Cy5

source_name: 0-2hr polyA RNA labeled with Cy3.


title: adult male vs adult female labeled with Cy5

source_name: adult males polyA RNA labeled with cy5


title: 3-16hr vs 0-2hr embryo labeled with Cy5

source_name: 3-16hr polyA RNA labeled with Cy5


title: 3-16hr vs 0-2hr embryo  labeled with Cy3

source_name: 3-16hr polyA RNA labeled with Cy3


title: 0-2hr embryo vs adult females labeled with Cy5

source_name: 0-2hr polyA RNA labeled with Cy5.


title: 3-16hr vs adult males labeled with Cy5

source_name: 3-16hr  polyA RNA labeled with Cy5.


title: h32B

source_name: D. melanogaster Canton S adult females heads only


title: h34A

source_name: D. simulans Sim-1 adult females heads only


title: h32A

source_name: adult hybrid females heads only resulting from the cross D. melanogaster Canton S females x D. simulans Sim-1 males


title: h37A


title: h17B

source_name: adult hybrid females resulting from the cross D. melanogaster Canton S females x D. simulans Sim-1 males

source_name: D. simulans Sim-1 adult females


title: h33B


title: h37B


title: h1B


title: h14A

source_name: D. melanogaster Canton S adult females


title: larvae vs pupa labeled with Cy3

source_name: larvae polyA RNA labeled with cy3.


title: h14B


title: h3A


title: h1A


title: h35B


title: h15B


title: h4A


title: h18B


title: h8B


title: h5A


title: h3B


title: h4B


title: h16B


title: h16A


title: h6B


title: h17A


title: h15A


title: h18A


title: h35A


title: h2B


title: WT_IL-6_100_rep3

status: Public on Apr 17 2003

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 3 after stimulation for 100 minutes with 10 ng/ml IL-6.

source_name: bone marrow-derived macrophages


title: KO_IL-6_100_rep2

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 2 after stimulation for 100 minutes with 10 ng/ml IL-6.

source_name: bone marrow-derived macropahges


title: KO_IL-6_400_rep3

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 3 after stimulation for 400 minutes with 10 ng/ml IL-6.


title: KO_IL-6_100_rep3

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 3 after stimulation for 100 minutes with 10 ng/ml IL-6.


title: KO_IL-6_400_rep1

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 1 after stimulation for 400 minutes with 10 ng/ml IL-6.


title: KO_IL-6_0_rep3

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 3 unstimulated.


title: KO_IL-6_0_rep1

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 1 unstimulated.


title: WT_IL-6_400_rep2

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 2 after stimulation for 400 minutes with 10 ng/ml IL-6.


title: WT_IL-6_400_rep3

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 3 after stimulation for 400 minutes with 10 ng/ml IL-6.


title: WT_IL-6_400_rep1

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 1 after stimulation for 400 minutes with 10 ng/ml IL-6.


title: KO_IL-6_0_rep2

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 2 unstimulated.


title: WT_IL-6_100_rep2

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 2 after stimulation for 100 minutes with 10 ng/ml IL-6.


title: KO_IL-6_400_rep2

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3-/-embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 2 after stimulation for 400 minutes with 10 ng/ml IL-6.

source_name: boen marrow-derived macrophages


title: WT_IL-6_0_rep1

description:
Effects of SOCS3 on the transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3+/+ embryos were used to reconstitute irradiated mice. Donor derived cells from the bone marrow  were differentiated to macrophages.

Replicate 1 of unstimulated macrophages.

Keywords = macrophage, SOCS3, IL-6, interferon


title: WT_IL-6_0_rep2

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 2 unstimulated.


title: WT_IL-6_100_rep1

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 1 after stimulation for 100 minutes with 10 ng/ml IL-6.


title: KO_IL-6_100_rep1

description:
Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 1 after stimulation for 100 minutes with 10 ng/ml IL-6.

source_name: bone-marrow-derived macrophages