title: RNA PolII in HeLa cell, 30 minutes - rep2 of 3

description: Genome-wide location analysis of RNA polymerase II binding using RenLab ENCODE PCR tiling array. Array ID is ENC795. Replicate 2 of 3.

source_name: Chromatin immunoprecipitated DNA using RNA polymersase II antibody


title: TAF1 in HeLa cell, 30 minutes - rep1 of 3

status: Public on Jun 10 2005

type: genomic

city: San Diego

first: Chunxu

last: Qu

state: CA

department: Gene Regulation

country: USA

institute: Ludwig Institute for Cancer Research

description: Genome-wide location analysis of TAF1 binding using RenLab ENCODE PCR tiling array. Array ID is ENC635B. Replicate 1 of 3.

molecule: genomic DNA

organism: Homo sapiens

source_name: Chromatin immunoprecipitated DNA using TAF1 antibody

source_name: input DNA


title: RNA PolII in HeLa cell, 30 minutes - rep3 of 3

description: Genome-wide location analysis of RNA polymerase II binding using RenLab ENCODE PCR tiling array. Array ID is ENC797. Replicate 3 of 3.


title: TAF1 in HeLa cell, 0 minute - rep3 of 3

description: Genome-wide location analysis of TAF1 binding using RenLab ENCODE PCR tiling array. Array ID is ENC488. Replicate 3 of 3.


title: TAF1 in HeLa cell, 0 minute - rep1 of 3

description: Genome-wide location analysis of TAF1 binding using RenLab ENCODE PCR tiling array. Array ID is ENC631B. Replicate 1 of 3.


title: RNA PolII in HeLa cell, 30 minutes - rep1 of 3

description: Genome-wide location analysis of RNA polymerase II binding using RenLab ENCODE PCR tiling array. Array ID is ENC737. Replicate 1 of 3.


title: SM22-tet-BMPR2delx4+ 8 weeks no dox

type: RNA

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

description: These mice have normal right ventricular pressures by heart catheter, of 30 +/- 3 mm Hg

data_processing: dChip 2004 with PM/MM odel

label: biotinylation

molecule: total RNA

organism: Mus musculus

source_name: whole lung

tag: mixed pool of whole lung RNA from 4 male and female SM22-tet-BMPR2delx4+ mice on fvb/n background 8 weeks old, transgene never activated (no dox)


title: rectal14_tumor_2x

status: Public on Jun 07 2005

city: Leiden

first: Elza

middle: C

last: de Bruin

country: Netherlands

institute: Leiden University Medical Center

description: for all information: http://microarray.nki.nl

scan_protocol: Of each slide, two images were scanned using the GeneTac LSIV laser scanner (Genomic Solutions, Ann Arbor, MI) at different gain settings, one at which hardly any of the spots were saturated and one with a higher gain to obtain data from lowly expressed genes.

data_processing: Spots were quantified by using GenePix Pro 4.1 software (Axon Instruments Inc., Union City, CA). For spot selection an MS-Excel macro was used. Briefly: spots were corrected for local background noise. Per dye, the intensity of each spot was normalized to the median of all spots on the array and for each spot, the ratio of the sample to the reference was calculated. Because arrays were scanned at two different settings, ratios from high gain-saturated spots were used from the low gain scans, while lowly expressed genes were used from the high gain scans. Genes saturated in both gains were rejected from analysis. For other spots, the mean of the ratios of the two scans was calculated. Finally, ratios were log10 transformed. Because the goal of this study was to analyze the effects of macro- and microdissection on overall gene expression profiles and not to select specific genes, only qualified genes that were present on all arrays (2358 genes) were selected for analyses.

molecule: polyA RNA

source_name: rectal carcinoma sample #14, microdissected tumor epithelium and twice-amplified

tag: Tissue

value: rectal carcinoma

source_name: pooled cell lines

tag: pooled cell lines


title: rectal14_stroma_2x2

source_name: rectal carcinoma sample #14, microdissected stroma and twice-amplified, labelling duplicate


title: rectal13_tumor_2x

source_name: rectal carcinoma sample #13, microdissected tumor epithelium and twice-amplified


title: rectal14_macro_2x

source_name: rectal carcinoma sample #14, macrodissected and twice-amplified


title: rectal14_stroma_2x

source_name: rectal carcinoma sample #14, microdissected stroma and twice-amplified


title: rectal12_tumor_2x

source_name: rectal carcinoma sample #12, microdissected tumor epithelium and twice-amplified


title: rectal14_macro_1x

source_name: rectal carcinoma sample #14, macrodissected and once-amplified


title: rectal13_macro_1x

source_name: rectal carcinoma sample #13, macrodissected and once-amplified


title: rectal12_macro_1x

source_name: rectal carcinoma sample #12, macrodissected and once-amplified


title: rectal11_macro_2x2

scan_protocol: Of each slide, two images were scanned using the GeneTAC LSIV laser scanner (Genomic Solutions, Ann Arbor, MI) at different gain settings, one at which hardly any of the spots were saturated and one with a higher gain to obtain data from lowly expressed genes.

source_name: rectal carcinoma sample #11, macrodissected and twice-amplified, labelling duplicate


title: rectal13_macro_1x2

source_name: rectal carcinoma sample #13, macrodissected and once-amplified, amplification duplicate


title: rectal11_stroma_2x

source_name: rectal carcinoma sample #11, microdissected stroma and twice-amplified


title: rectal11_tumor_2x

source_name: rectal carcinoma sample #11, microdissected tumor epithelium and twice-amplified


title: C57bl6 CL 316234 1 day

city: Detroit

last: Granneman

state: MI

institute: Wayne State University

description: EWAT RNA pooled from 3-4 month-old male C57 BL6 mice treated for 1 day with 3nmol/hr CL 316243.

source_name: Mouse epididymal white adipose tissue


title: RNA PolII in HeLa cell, 0 minute - rep2 of 3

description: Genome-wide location analysis of RNA polymerase II binding using RenLab ENCODE PCR tiling array. Array ID is ENC796. Replicate 2 of 3.

source_name: Chromatin immunoprecipitated DNA using RNA polymersase II antibody

source_name: input DNA


title: C57bl6 Control

description: Control EWAT RNA pooled from 3-4 month-old male C57 BL6 mice.


title: rectal11_macro_2x

source_name: rectal carcinoma sample #11, macrodissected and twice-amplified


title: rectal10_tumor_2x

source_name: rectal carcinoma sample #10, microdissected tumor epithelium and twice-amplified

source_name: pooled cell lines


title: rectal11_macro_1x

source_name: rectal carcinoma sample #11, macrodissected and once-amplified


title: rectal9_tumor_2x

source_name: rectal carcinoma sample #9, microdissected tumor epithelium and twice-amplified


title: rectal10_macro_1x

source_name: rectal carcinoma sample #10, macrodissected and once-amplified


title: rectal10_macro_2x

source_name: rectal carcinoma sample #10, macrodissected and twice-amplified


title: rectal9_macro_1x

source_name: rectal carcinoma sample #9, macrodissected and once-amplified


title: SM22-tet-BMPR2delx4+ 8 weeks dox

description: These mice had elevated right ventricular pressures by heart catheter, of 50+/- 8 mm Hg

data_processing: dChip2004 with PM/MM model

source_name: whole lung

tag: mixed pool of whole lung RNA from 4 male and female SM22-tet-BMPR2delx4+ mice on fvb/n background with doxycycline 8 weeks from birth


title: rectal8_tumor_2x

source_name: rectal carcinoma sample #8, microdissected tumor eptihelium and twice-amplified


title: RNA PolII in HeLa cell, 0 minute - rep3 of 3

description: Genome-wide location analysis of RNA polymerase II binding using RenLab ENCODE PCR tiling array. Array ID is ENC798. Replicate 3 of 3.


title: rectal8_stroma_2x

source_name: rectal carcinoma sample #8, microdissected stroma and twice-amplified


title: rectal7_macro_1x2

source_name: rectal carcinoma sample #7, macrodissected and once-amplified, labelling duplicate


title: rectal7_macro_1x

source_name: rectal carcinoma sample #7, macrodissected and once-amplified


title: RNA PolII in HeLa cell, 0 minute - rep1 of 3

description: Genome-wide location analysis of RNA polymerase II binding using RenLab ENCODE PCR tiling array. Array ID is ENC738. Replicate 1 of 3.


title: rectal8_macro_2x

source_name: rectal carcinoma sample #8, macrodissected and twice-amplified


title: rectal7_tumor_2x

source_name: rectal carcinoma sample #7, microdissected tumor epithelium and twice-amplified


title: acetylated histone H4 in HeLa cell, 30 minutes - rep3 of 3

description: Genome-wide location analysis of acetylated histone H4 binding using RenLab ENCODE PCR tiling array. Array ID is ENC813. Replicate 3 of 3.

data_processing: Single-Array Error Model

source_name: Chromatin immunoprecipitated DNA using acetylated histone H4 antibody

tag: input DNA


title: rectal8_macro_1x

source_name: rectal carcinoma sample #8, macrodissected and once-amplified


title: rectal6_tumor_2x

source_name: rectal carcinoma sample #6, microdissected tumor epithelium and twice-amplified


title: rectal5_macro_2x

source_name: rectal carcinoma sample #5, macrodissected and twice-amplified


title: rectal5_tumor_2x

source_name: rectal carcinoma sample #5, microdissected tumor epithelium and twice-amplified

source_name: pooled cell lines


title: rectal6_tumor_2x2

source_name: rectal carcinoma sample #6, microdissected tumor epithelium and twice-amplified, labelling duplicate


title: rectal4_macro_1x

source_name: rectal carcinoma sample #4, macrodissected and once-amplified


title: rectal5_macro_1x

source_name: rectal carcinoma sample #5, macrodissected and once-amplified


title: rectal2_tumor_2x

source_name: rectal carcinoma sample #2, microdissected tumor epithelium and twice-amplified


title: rectal6_macro_1x

source_name: rectal carcinoma sample #6, macrodissected and once-amplified


title: rectal3_tumor_2x2

source_name: rectal carcinoma sample #3, microdissected tumor epithelium and twice-amplified, labelling duplicate


title: rectal3_macro_1x

source_name: rectal carcinoma sample #3, macrodissected and once-amplified


title: rectal4_tumor_2x

source_name: rectal carcinoma sample #4, microdissected tumor epithelium and twice-amplified


title: rectal2_stroma_2x

source_name: rectal carcinoma sample #2, microdissected stroma and twice-amplified


title: rectal2_macro_1x

description: For all information: http://microarray.nki.nl

source_name: rectal carcinoma sample #2, macrodissected and once-amplified


title: rectal2_macro_2x

source_name: rectal carcinoma sample #2, macrodissected and twice-amplified


title: rectal3_tumor_2x

source_name: rectal carcinoma sample #3, microdissected tumor epithelium and twice-amplified


title: rectal1_tumor_2x

source_name: rectal carcinoma sample #1, microdissected tumor epithelium and twice-amplified


title: rectal1_macro_1x

source_name: rectal carcinoma sample #1, macrodissected and once-amplified


title: NIH 3T3 cells transfected with pHA-CMV-ATCE1-C-del

city: Ramat-Gan

first: Stelzer

last: Gil

address: Ramat-Gan

country: Israel

institute: Bar-Ilan University

description: pHA-CMV-ATCE1-C-del expressed a C-terminal deleted form of ATCE1

label: biotin

source_name: NIH 3T3 cell line transfected with pHA-CMV-ATCE1-C-del

growth_protocol: Cells were grown on DMEM according to ATCC instructions

extract_protocol: Total RNA was extracted 48 hours after transfection.  According to Affymetrix GeneChip Expression Manual

treatment_protocol: Cells were transfected with the pHA-CMV-ATCE1-C-del plasmid using Lipofectamine reagent

tag: NIH 3T3 cell line


title: NIH 3T3 cells transfected with pHA-CMV

description: pHA-CMV is an empty vector (clontech) that was used as a control

source_name: NIH 3T3 cell line transfected with pHA-CMV

label_protocol: According to Affymetrix GeneChip Expression Manual and using recomended reagents

extract_protocol: Total RNA was extracted 48 hours after transfection. According to Affymetrix GeneChip Expression Manual

treatment_protocol: Cells were transfected with the pHA-CMV plasmid using Lipofectamine reagent


title: Affy 1x Tumor Sample 3

status: Public on Jun 03 2005

city: Rochester

first: Chin-Yi

last: Chu

state: NY

address: 75 Elmwood Avenue

department: Environmental Medicine

institute: University of Rochester

description:
This sample is part of a study that compares small sample amplification technologies.  The analysis looks at differential gene expression when compared to one round of T7 amplification.  A tumor cell line was used in comparison to a human reference RNA in this study.
Keywords = amplification
Keywords = small sample
Keywords = Affymetrix

source_name: Total RNA from Breast Adenocarcinoma Cell Line


title: Affy 1x Tumor Sample 2


title: Affy 1x Control Sample 3

source_name: Total RNA from Stratagene Human Reference RNA


title: Affy 1x Control Sample 2


title: Affy 1x Control Sample 1


title: Ppara KO control

description: Ppara KO Control

source_name: Mouse epididymal white adipose tissue


title: Affy 1x Tumor


title: CIN3 #15

city: Atlanta

first: Martin

last: Steinau

state: GA

institute: CDC

description: cDNA from cervical exfol cells - severe dysplasia

data_processing: We used sARM values (artifact removed density minus the background density) of each feature for statistical analysis and a signal to noise ratio (S/N = sARM, divided by the SD of the background density) of 1.5 as the cut-off for detection of gene expression.

source_name: cervical exfoliated cells

tag: see description


title: CIN3 #14


title: NuGEN Control Sample 2


title: NuGEN Control Sample 1


title: CIN3 #13


title: CIN3 #12


title: NuGEN Tumor Sample 2


title: NuGEN Tumor Sample 3


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B1T4_PBclassic

status: Public on Jun 04 2005

city: New Haven

first: Olof

last: Emanuelsson

state: CT

address: 260 Whitney Avenue

institute: Yale University

description:
Poly(A)+ RNA human placenta tissue pooled from 2-3 individuals was obtained from Ambion (Austin, TX). First strand cDNA was generated from 5µg RNA for each reaction with (RnaseH-)M-MLV reverse transcriptase, primed with equimolar concentrations of oligo(dT)18 and random decamers. The reactions were carried out at 42°C for 2 hours in the presence of 0.5mM dATP, 0.5mM dCTP, 0.5mM dGTP, 0.15mM dTTP and 0.15mM amino allyl dUTP to facilitate the secondary labeling of an amine reactive fluorescent conjugate.
Following reverse transcription the products were heated at 95°C for 5 minutes to denature the RNA:DNA hybrids and heat inactivate the reverse transcriptase, after which the RNA template was hydrolysed by incubating in 0.2M NaOH at 65°C for 15 minutes. The reaction was then neutralized in 0.3M HEPES (pH 7.0). Reverse transcription products from 10 separate reactions were produced in  this manner and pooled to reduce technical variability between samples. The cDNAs were precipitated in ethanol with 3M sodium acetate and resuspended in 0.1m NaHCO3 to facilitate coupling reactive groups of the amino allyl dUTPs. Following incubation at room temperature for 2 hours, the labeled cDNAs were purified with CyScribe GFX glass fiber spin columns (Amersham Bioscience, Piscataway, NJ) and isopropanol precipitated.
Microarrays were  hybridized with 2-3µg labeled cDNA in 360µl hybridization buffer (50mM MES, 0.5M NaCl, 10mM EDTA and 0.005% {V/V} Tween 20) for 20 hours at 50°C. Hybridizations were performed in disposable adhesive chambers (Grace Biolabs, Bend, OR) in a hybridization oven with constant agitation. After hybridization, the arrays were washed on an orbital platform in nonstringent buffer (6X SSPE, 0.01%[V/V] Tween-20) for 10 minutes at room temperature and then washed in a stringent buffer (100mM MES, 0.1M NaCl, 0.01% tween-20) for 30 minutes at 45°C. This was followed by a 5 minute wash in the  non-stringent buffer and a 4 minute wash in 0.2X SSC. The arrays were then dried with an air duster. Fluorescence micrographs were acquired with an Axon 4200B laser scanner at 5µm resolution.
Keywords = placenta poly(A)+ RNA, ENCODE, tiling array, maskless photolithography, transcription mapping

source_name: Alexa 555 labeled cDNA derived from human placenta poly(A)+ RNA


title: CIN3 #11


title: CIN3 #10


title: CIN3 #9


title: NuGEN Control Sample 3


title: Total RNA from Human cell line NB4; Sample B3T1

description:
Total RNA was isolated from NB4 human cell line by Rneasy Mini kit using manufacturer's protocol (Qiagen). The first strand cDNA was generated from 10µg of total RNA/reaction in a 20µl reaction volume with 600U Superscript II (Life technologies), 1µg of Oligo (dT)24-T7[5'GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG(dt)24-3'] in the presence of 10mM of each dNTP and 0.1M DTT. The reactions were carried out at 42°C for one hour.
Second strand cDNA was carried out in a 150µl final reaction volume containing 40U DNA polymerase I, 2U of Escgerichia coli Rnase H, 10mM of each dNTP and 10U of Escherichia coli DNA ligase in 5X second strand buffer (Life Technologies) by adding 130µl of ice cold second strand synthesis premix to the 20µl RT reaction and incubated at 16°C for 2 hours. The double strand DNA synthesis was terminated by adding 10U of T4 DNA polymerase and incubating for 5minutes at 16°C This facilitates the formation of blunt ended double stranded DNA. The cDNA was purified with Phenol/Chloroform/Isoamyl alcohol 25:24:1 (V/V/V) extraction and precipitated with 7.5M Ammonium acetate, absolute ethanol and pellet paint NF co-precipitant (Novagen).
Transcription of double stranded DNA reaction was prepared in a 20µl volume at 37°C for 5 hours using MEGA script T7 transcription kit (Ambion) in the presence of 10mM-Biotin-11-CTP and 10mM Biotin-16-UTP. In vitro transcribed biotin labeled RNA was purified on RNeasy mini columns (Qiagen) according to the manufacturer's protocol. cRNA was quantified by absorbance at 260nm. The purified and labeled cRNA were fragmented from 500bp-2000bp to 50-200bp by incubating in 5X RNA fragmentation buffer (200mM Trisacetate, pH 8.1, 100mM KOAc and 150mM MgOAc) at 95°C for 35 minutes. Fragmented and labeled cRNA of about 10-12µg was heated to 95°C for 5 minutes in 55µl hybridization buffer (40% Formamide, 1mM Tris, 0.1mM EDTA, 5X SSC and 0.1% SDS) and placed in a 45°C heat block until ready for hybridization (5-30minutes).
Hybridization was done using MAUI station at 42°C for 18 hours with a constant agitation. After hybridization, the arrays were washed on an orbital platform in Wash I Buffer (0.2%SDS and 0.2XSSC) for two minutes at 42°C. and then immediately placed in a nonstringent Wash Buffer (6X SSPE, 0.01%{V/V}Tween-20) until ready for the second wash in Wash Buffer II (0.2X SSC) at room temperature for one minute. The arrays were then stained in a staining container (Cy3-Streptavidin stain, 2X stain buffer and water) for 25 minutes. This was followed by a quick wash in wash buffer II and  signals were amplified by placing in antibody amplification mix for 25 minutes. The arrays were then given  another wash in Wash Buffer II, stained again for 25 minutes and then amplified for 25 minutes. The slides were then placed in a nonstringent holding buffer until all arrays were ready for  wash in Wash Buffer II for one minute followed by 30 seconds wash in Wash Buffer III (0.05X SSC). The arrays were dried with an air duster. Fluorescence micrographs were acquired with an Axon 4200 laser scanner at 5µm resolution.
Keywords = NB4 cell line total RNA, ENCODE, tiling array, maskless photolithography, transcription mapping

source_name: Cy3 Streptavidin linked and biotin labeled cRNA derived from Human cell line NB4 total RNA


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B3T2_PBclassic


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B2T1_PBclassic


title: Enzo 2x Control Sample 2


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B1T1

description:
Poly (A)+  RNA human placenta tissue pooled from 2-3 individuals was obtained from Ambion (Austin, TX). The labeling was performed using a standard amplification protocol (Weberman's). The first strand cDNA was generated from 2µg poly(A)+ RNA/reaction in a 20µl reaction volume with 600U Superscript II (Life Technologies), 1µg Oligo(dT)24T7[5'GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG(dt)24-3'] in the presence of 10mM of each dNTP and 0.1M DTT. The reactions were carried out at 42°C for one hour.
Second strand cDNA was carried out in a 150µl final reaction volume containing 40U DNA polymerase I, 2U of Escherichia coli Rnase H, 10mM of each dNTP and 10U of Escherichia coli DNA ligase in 5X second strand buffer (Life Technologies) by adding 130µl of ice cold second strand synthesis premix to the 20µl RT reaction and incubated at 16°C for 2 hours. The double strand DNA synthesis was terminated by adding 10U of T4 DNA polymerase and incubating for 5minutes at 16°C This facilitates the formation of blunt ended double stranded DNA. The cDNA was purified with Phenol/Chloroform/Isoamyl alcohol 25:24:1 (V/V/V) extraction and precipitated with 7.5M Ammonium acetate, absolute ethanol and pellet paint NF co-precipitant(Novagen).
Transcription of double stranded DNA reaction was prepared in a 20µl at 37°C for 5 hours using MEGA script T7 transcription kit (Ambion) in the presence of 10mM-Biotin-11-CTP and 10mM Biotin-16-UTP.  In vitro transcribed biotin labeled RNA was purified on RNeasy mini columns (Qiagen) according to the manufacturer's protocol. cRNA was quantified by absorbance at 260nm. The purified and labeled cRNA were fragmented from 500bp-2000bp to 50-200bp by incubating in 5X RNA fragmentation buffer (200mM Trisacetate, pH 8.1, 100mM KOAc and 150mM MgOAc) at 95°C for 35 minutes. Fragmented and labeled cRNA of about 10-12µg was heated to 95°C for 5 minutes in 55µl hybridization buffer (40% Formamide, 1mM Tris, 0.1mM EDTA, 5X SSC and 0.1% SDS) and placed in a 45°C heat block until ready for hybridization (5-30 minutes).
Hybridization was done using MAUI station at 42°C for 18 hours with constant agitation. After hybridization, the arrays were washed on an orbital platform in Wash I Buffer(0.2%SDS and 0.2XSSC) for two minutes at 42°C, and then immediately  placed in a nonstringent Wash Buffer (6X SSPE, 0.01%{V/V}Tween-20) until ready for the second wash in Wash Buffer II (0.2X SSC) at room temperature for one minute. The arrays were then stained in a staining container (Cy3-Streptavidin stain, 2X stain buffer and water) for 25minutes. This was followed by a quick wash in wash buffer II and signals were amplified by placing in antibody amplification mix for 25minutes. The arrays were given another quick wash in Wash Buffer II, stained  again for 25 minutes and then amplified for 25 minutes.  The arrays were then placed in nonstringent holding buffer until all arrays were ready for wash in Wash Buffer II  for one minute followed by a 30 seconds wash in Wash Buffer III (0.05X SSC). The arrays were then dried with an air duster. Fluorescence micrographs were acquired with an Axon 4200 laser scanner at 5µm resolution.
Keywords = placenta poly(A)+ RNA, ENCODE, tiling array, maskless photolithography, transcription mapping

source_name: Cy3 Streptavidin linked and biotin labeled cRNA derived from human placenta poly(A)+ RNA


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B2T2

description:
Poly (A)+  RNA human placenta tissue pooled from 2-3 individuals was obtained from Ambion (Austin, TX). The labeling was performed using a standard amplification protocol (Weberman's). The first strand cDNA was generated from 2µg poly(A)+ RNA/reaction in a 20µl reaction volume with 600U Superscript II (Life Technologies), 1µg Oligo(dT)24T7[5'GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG(dt)24-3'] in the presence of 10mM of each dNTP and 0.1M DTT. The reactions were carried out at 42°C for one hour.
Second strand cDNA was carried out in a 150µl final reaction volume containing 40U DNA polymerase I, 2U of Escherichia coli Rnase H, 10mM of each dNTP and 10U of Escherichia coli DNA ligase in 5X second strand buffer (Life Technologies) by adding 130µl of ice cold second strand synthesis premix to the 20µl RT reaction and incubated at 16°C for 2 hours. The double strand DNA synthesis was terminated by adding 10U of T4 DNA polymerase and incubating for 5minutes at 16°C This facilitates the formation of blunt ended double stranded DNA. The cDNA was purified with Phenol/Chloroform/Isoamyl alcohol 25:24:1 (V/V/V) extraction and precipitated with 7.5M Ammonium acetate, absolute ethanol and pellet paint NF co-precipitant(Novagen).
Transcription of double stranded DNA reaction was prepared in a 20µl at 37°C for 5 hours using MEGA script T7 transcription kit (Ambion) in the presence of 10mM-Biotin-11-CTP and 10mM Biotin-16-UTP. In vitro transcribed biotin labeled RNA was purified on RNeasy mini columns (Qiagen) according to the manufacturer's protocol. cRNA was quantified by absorbance at 260nm. The purified and labeled cRNA were fragmented from 500bp-2000bp to 50-200bp by incubating in 5X RNA fragmentation buffer (200mM Trisacetate, pH 8.1, 100mM KOAc and 150mM MgOAc) at 95°C for 35 minutes. Fragmented and labeled cRNA of about 10-12µg was heated to 95°C for 5 minutes in 55µl hybridization buffer (40% Formamide, 1mM Tris, 0.1mM EDTA, 5X SSC and 0.1% SDS) and placed in a 45°C heat block until ready for hybridization (5-30 minutes).
Hybridization was done using MAUI station at 42°C for 18 hours with constant agitation. After hybridization, the arrays were washed on an orbital platform in Wash I Buffer(0.2%SDS and 0.2XSSC) for two minutes at 42°C, and then immediately  placed in a nonstringent Wash Buffer (6X SSPE, 0.01%{V/V}Tween-20) until ready for the second wash in Wash Buffer II (0.2X SSC) at room temperature for one minute. The arrays were then stained in a staining container (Cy3-Streptavidin stain, 2X stain buffer and water) for 25minutes. This was followed by a quick wash in wash buffer II and signals were amplified by placing in antibody amplification mix for 25minutes. The arrays were given another quick wash in Wash Buffer II, stained  again for 25 minutes and then amplified for 25 minutes.  The arrays were then placed in nonstringent holding buffer until all arrays were ready for wash in Wash Buffer II  for one minute followed by a 30 seconds wash in Wash Buffer III (0.05X SSC). The arrays were then dried with an air duster. Fluorescence micrographs were acquired with an Axon 4200 laser scanner at 5µm resolution.
Keywords = placenta poly(A)+ RNA, ENCODE, tiling array, maskless photolithography, transcription mapping


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B1T2


title: NuGEN Tumor Sample 1


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B3T1_PBclassic


title: CIN3 #7


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B2T1


title: CIN3 #6


title: Total RNA from Human cell line NB4; Sample B3T2


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B2T2_PBclassic

description:
Poly(A)+ RNA human placenta tissue pooled from 2-3 individuals was obtained from Ambion (Austin, TX). First strand cDNA was generated from 5µg RNA for each reaction with (RnaseH-)M-MLV reverse transcriptase, primed with equimolar concentrations of oligo(dT)18 and random decamers. The reactions were carried out at 42°C for 2 hours in the presence of 0.5mM dATP, 0.5mM dCTP, 0.5mM dGTP, 0.15mM dTTP and 0.15mM amino allyl dUTP to facilitate the secondary labeling of an amine reactive fluorescent conjugate.
Following reverse transcription the products were heated at 95°C for 5 minutes to denature the RNA:DNA hybrids and heat inactivate the reverse transcriptase, after which the RNA template was hydrolysed by incubating in 0.2M NaOH at 65°C for 15 minutes. The reaction was then neutralized in 0.3M HEPES (pH 7.0). Reverse transcription products from 10 separate reactions were produced in  this manner and pooled to reduce technical variability between samples. The cDNAs were precipitated in ethanol with 3M sodium acetate and resuspended in 0.1m NaHCO3 to facilitate coupling reactive groups of the amino allyl dUTPs. Following incubation at room temperature for 2 hours, the labeled cDNAs were purified with CyScribe GFX glass fiber spin columns (Amersham Bioscience, Piscataway, NJ) and isopropanol precipitated.
Microarrays were  hybridized with 2-3µg labeled cDNA in 360µl hybridization buffer (50mM MES, 0.5M NaCl, 10mM EDTA and 0.005% {V/V} Tween 20) for 20 hours at 50°C. Hybridizations were performed in disposable adhesive chambers (Grace Biolabs, Bend, OR) in a hybridization oven with constant agitation. After hybridization, the arrays were washed on an orbital platform in nonstringent buffer (6X SSPE, 0.01%[V/V] Tween-20) for 10 minutes at room temperature and then washed in a stringent buffer (100mM MES, 0.1M NaCl, 0.01% tween-20) for 30 minutes at 45°C. This was followed by a 5 minute wash in the  non-stringent buffer and a 4 minute wash in 0.2X SSC. The arrays were then dried with an air duster. Fluorescence micrographs were acquired with an Axon 4200B laser scanner at 5µm resolution.

data_processing: not available

label: Cy3 Streptavidin linked and biotin labeled cRNA

tag: placenta poly(A)+ RNA, Sample B2T2, pool from several individuals, ENCODE, tiling array, maskless photolithography, transcription mapping


title: Enzo 2x Control Sample 1


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B1T3


title: CIN3 #5


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B3T2

data_processing: Median fluorescence signal intensity of the array feature

tag: Pool of several individuals.


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B1T2_PBclassic


title: Enzo 2x Tumor Sample 2


title: CIN3 #2


title: CIN3 #3


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B1T1_PBclassic


title: CIN3 #4


title: Total RNA from Human cell line NB4; Sample B1T1


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B3T1


title: Ambion 2X Control Sample 2


title: Ambion 2X Tumor Sample 3


title: Total RNA from Human cell line NB4; Sample B2T2


title: Total RNA from Human cell line NB4; Sample B2T1


title: CIN1 #8

description: cDNA from cervical exfol cells - mild dysplasia


title: Poly(A)+ human placenta tissue RNA pooled from several individuals; Sample B1T3_PBclassic


title: Ambion 2X Tumor Sample 2


title: CIN3 #1


title: Enzo 2x Control Sample 3


title: Ambion 2X Tumor Sample 1


title: Affy 2X Control Sample 2


title: Affy 2X Control Sample 3


title: CIN1 #5


title: CIN1 #7


title: Ambion 2X Control Sample 1


title: Total RNA from Human cell line NB4; Sample B1T2


title: Enzo 2x Tumor Sample 1


title: Ambion 2X Control Sample 3


title: Enzo 2x Tumor Sample 3


title: CIN3 #8


title: Affy 2X Tumor Sample 3


title: CIN1 #6


title: CIN1 #1


title: CIN0 #7

description: cDNA from cervical exfol cells - no abnormalities


title: CIN1 #2


title: Affy 2X Tumor Sample 1


title: Affy 2X Control Sample 1


title: CIN1 #3


title: CIN0 #6


title: Affy 2X Tumor Sample 2


title: CIN0 #5


title: CIN0 #4


title: CIN0 #3


title: CIN0 #1


title: SK-MEL-2 cells treated with Ad-E2F-1 at MOI 2 plus doxorubicin (sample 2)

city: Louisville

first: Hongying

last: Hao

state: KY

address: 505 South Hancock Street

department: Surgery

institute: University of Louisville

description: SK-MEL-2 cells treated with Ad-E2F-1 at an MOI of 2 plus doxorubicin 0.1 uM(sample2)

source_name: SK-MEL-2 cells


title: SK-MEL-2 cells treated with Ad-E2F-1 at MOI 2(sample 2)

description: SK-MEL-2 cells treated with Ad-E2F-1 at an MOI of 2 (sample2)


title: CIN0 #2


title: SK-MEL-2 cells treated with Ad-LacZ at MOI 2 plus doxorubicin (sample 2)

description: SK-MEL-2 cells treated with Ad-LacZ at an MOI of 2 plus doxorubicin 0.1 uM(sample2)


title: Clof 168hr Veh4

status: Public on Jun 02 2005

city: Indianapolis

first: Keith

middle: M

last: Goldstein

state: IN

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly & Co.

description:
Male SD rats were given a single dose of 0.9% saline as a vehicle. Animal was sacrificed 168hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500.
Keywords = Clofibrate, vehicle

organism: Rattus norvegicus

source_name: Liver


title: SK-MEL-2 cells treated with Ad-LacZ at MOI 2 plus doxorubicin (sample 1)

description: SK-MEL-2 cells treated with Ad-LacZ at an MOI of 2 plus doxorubicin 0.1 uM(sample1)


title: Clof 168hr Veh2


title: Clof 168hr Veh5


title: trimethylated K4 histone 3 in HeLa cell, 30 minute - rep3 of 3

description: Genome-wide location analysis of trimethyl-H3K4 binding using RenLab ENCODE PCR tiling array. Array ID is ENC691. Replicate 3 of 3.

source_name: Chromatin immunoprecipitated DNA using trimethyl-H3K4 antibody

source_name: input DNA


title: SK-MEL-2 cells treated with Ad-E2F-1 at MOI 2 plus doxorubicin (sample 1)

description: SK-MEL-2 cells treated with Ad-E2F-1 at an MOI of 2 plus doxorubicin 0.1 uM(sample1)


title: trimethylated K4 histone 3 in HeLa cell, 0 minute - rep3 of 3

description: Genome-wide location analysis of trimethyl-H3K4 binding using RenLab ENCODE PCR tiling array. Array ID is ENC774. Replicate 3 of 3.


title: SK-MEL-2 cells treated with Ad-E2F-1 at MOI 2(sample 1)

description: SK-MEL-2 cells treated with Ad-E2F-1 at an MOI of 2 (sample1)


title: Clof 168hr Veh1


title: DEHP 168hr treated2

description:
Male SD rats were given a single dose of 20g/kg DEHP in distilled water as vehicle. Animal was sacrificed 168hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Diethylhexyl phthalate, Phthalic acid bis(2-ethylhexyl ester)


title: Clof 168hr Veh3


title: DEHP 168hr treated5


title: trimethylated K4 histone 3 in HeLa cell, 30 minute - rep1 of 3

description: Genome-wide location analysis of trimethyl-H3K4 binding using RenLab ENCODE PCR tiling array. Array ID is ENC473. Replicate 1 of 3.


title: DEHP 168hr treated3


title: DEHP 168hr treated4


title: trimethylated K4 histone 3 in HeLa cell, 30 minute - rep2 of 3

description: Genome-wide location analysis of trimethyl-H3K4 binding using RenLab ENCODE PCR tiling array. Array ID is ENC857. Replicate 2 of 3.


title: DEHP 168hr treated1


title: Clof 24hr treated POOLED

description:
Male SD rats were given a single dose of 1000mg/kg clofibrate using 0.9% saline as vehicle. Animal was sacrificed 24hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 3.3ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500.
Keywords = Clofibrate, pooled


title: DEHP 168hr treated POOLED

description:
Male SD rats were given a single dose of 20g/kg DEHP in distilled water as vehicle. Animal was sacrificed 168hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 2ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Diethylhexyl phthalate, Phthalic acid bis(2-ethylhexyl ester), pooled


title: trimethylated K4 histone 3 in HeLa cell, 0 minute - rep1 of 3

description: Genome-wide location analysis of trimethyl-H3K4 binding using RenLab ENCODE PCR tiling array. Array ID is ENC472. Replicate 1 of 3.


title: trimethylated K4 histone 3 in HeLa cell, 0 minute - rep2 of 3

description: Genome-wide location analysis of trimethyl-H3K4 binding using RenLab ENCODE PCR tiling array. Array ID is ENC762. Replicate 2 of 3.


title: Clof 168hr Veh POOLED

description:
Male SD rats were given a single dose of 0.9% saline as a vehicle. Animal was sacrificed 168hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 2ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500.
Keywords = Clofibrate, vehicle, pooled


title: CIN1 #4

description: cDNA from cervical exfol cells - mild dysplasia


title: Clof 24hr treated3

description:
Male SD rats were given a single dose of 1000mg/kg clofibrate using 0.9% saline as vehicle. Animal was sacrificed 24hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500.
Keywords = Clofibrate


title: Clof 4hr treated POOLED

description:
Male SD rats were given a single dose of 1000mg/kg clofibrate using 0.9% saline as vehicle. Animal was sacrificed 4hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 3.3ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500.
Keywords = Clofibrate, pooled


title: Clof 24hr treated1


title: Clof 4hr treated2

description:
Male SD rats were given a single dose of 1000mg/kg clofibrate using 0.9% saline as vehicle. Animal was sacrificed 4hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500.
Keywords = Clofibrate


title: VPA 24hr treated2

description:
Male SD rats were given a single dose of 2000mg/kg sodium valproate (VPA) using distilled water as vehicle. Animal was sacrificed 24hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Sodium Valproate, Valproic Acid, VPA


title: VPA 4hr treated POOLED

description:
Male SD rats were given a single dose of 2000mg/kg sodium valproate (VPA) using distilled water as vehicle. Animal was sacrificed 4hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 3.3ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Sodium Valproate, Valproic Acid, VPA, pooled


title: VPA 24hr treated3


title: VPA 24hr treated1


title: DEHP 24hr treated1

description:
Male SD rats were given a single dose of 20g/kg DEHP in distilled water as vehicle. Animal was sacrificed 24hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Diethylhexyl phthalate, Phthalic acid bis(2-ethylhexyl ester)


title: DEHP 24hr treated3


title: Clof 4hr treated3


title: DEHP 4hr treated POOLED

description:
Male SD rats were given a single dose of 20g/kg DEHP in distilled water as vehicle. Animal was sacrificed 4hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 3.3ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Diethylhexyl phthalate, Phthalic acid bis(2-ethylhexyl ester), pooled


title: Clof 4hr treated1


title: DEHP 4hr treated3

description:
Male SD rats were given a single dose of 20g/kg DEHP in distilled water as vehicle. Animal was sacrificed 4hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Diethylhexyl phthalate, Phthalic acid bis(2-ethylhexyl ester)


title: Clof 24hr treated2


title: DEHP 24hr treated2


title: VPA 24hr treated POOLED

description:
Male SD rats were given a single dose of 2000mg/kg sodium valproate (VPA) using distilled water as vehicle. Animal was sacrificed 24hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 3.3ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Sodium Valproate, Valproic Acid, VPA, pooled


title: VPA 4hr treated3

description:
Male SD rats were given a single dose of 2000mg/kg sodium valproate (VPA) using distilled water as vehicle. Animal was sacrificed 4hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Sodium Valproate, Valproic Acid, VPA


title: DEHP 4hr treated2


title: VPA 4hr treated1


title: VPA 48hr treated3

description:
Male SD rats were given a single dose of 2000mg/kg sodium valproate (VPA) using distilled water as vehicle. Animal was sacrificed 48hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Sodium Valproate, Valproic Acid, VPA


title: DEHP 4hr treated1


title: DEHP 24hr treated POOLED

description:
Male SD rats were given a single dose of 20g/kg DEHP in distilled water as vehicle. Animal was sacrificed 24hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 3.3ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Diethylhexyl phthalate, Phthalic acid bis(2-ethylhexyl ester), pooled


title: VPA 48hr treated2


title: VPA 48hr treated1


title: VPA 4hr treated2


title: VPA 48hr treated4


title: VPA 48hr treated POOLED

description:
Male SD rats were given a single dose of 2000mg/kg sodium valproate (VPA) using distilled water as vehicle. Animal was sacrificed 48hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc.Approximately 2.5ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Sodium Valproate, Valproic Acid, VPA, pooled


title: VPA 168hr treated4

description:
Male SD rats were given a single dose of 2000mg/kg sodium valproate (VPA) using distilled water as vehicle. Animal was sacrificed 168hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Sodium Valproate, Valproic Acid, VPA


title: VPA 168hr treated POOLED

description:
Male SD rats were given a single dose of 2000mg/kg sodium valproate (VPA) using distilled water as vehicle. Animal was sacrificed 168hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 2.5ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Sodium Valproate, Valproic Acid, VPA, pooled


title: VPA 168hr treated1


title: VPA 168hr treated3


title: Clof 48hr treated POOLED

description:
Male SD rats were given a single dose of 1000mg/kg clofibrate using 0.9% saline as vehicle. Animal was sacrificed 48hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. . Approximately 2ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500.
Keywords = Clofibrate, pooled


title: Clof 48hr Veh1

description:
Male SD rats were given a single dose of 0.9% saline as a vehicle. Animal was sacrificed 48hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500.
Keywords = Clofibrate, vehicle


title: Clof 48hr Veh2


title: DEHP 48hr treated POOLED

description:
Male SD rats were given a single dose of 20g/kg DEHP in distilled water as vehicle. Animal was sacrificed 48hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 2ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Diethylhexyl phthalate, Phthalic acid bis(2-ethylhexyl ester), pooled


title: Clof 48hr treated5

description:
Male SD rats were given a single dose of 1000mg/kg clofibrate using 0.9% saline as vehicle. Animal was sacrificed 48hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500.
Keywords = Clofibrate


title: Clof 48hr Veh5


title: Clof 48hr Veh3


title: Clof 48hr Veh POOLED

description:
Male SD rats were given a single dose of 0.9% saline as a vehicle. Animal was sacrificed 48hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 2ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500.
Keywords = Clofibrate, vehicle, pooled


title: Clof 48hr treated1


title: VPA 48hr Veh POOLED

description:
Male SD rats were given a single dose of distilled water as a vehicle. Animal was sacrificed 48hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 2ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Sodium Valproate, Valproic Acid, VPA, vehicle, pooled


title: Clof 48hr treated4


title: DEHP 48hr treated1

description:
Male SD rats were given a single dose of 20g/kg DEHP in distilled water as vehicle. Animal was sacrificed 48hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Diethylhexyl phthalate, Phthalic acid bis(2-ethylhexyl ester)


title: DEHP 48hr treated2


title: Clof 48hr treated3


title: VPA 48hr Veh5

description:
Male SD rats were given a single dose of distilled water as a vehicle. Animal was sacrificed 48hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Sodium Valproate, Valproic Acid, VPA, vehicle


title: DEHP 48hr treated3


title: DEHP 48hr treated4


title: DEHP 48hr treated5


title: Clof 48hr treated2


title: VPA 48hr Veh2


title: VPA 168hr treated2


title: VPA 48hr Veh3


title: VPA 48hr Veh4


title: VPA 48hr Veh1


title: VPA 168hr Veh5

description:
Male SD rats were given a single dose of distilled water as a vehicle. Animal was sacrificed 168hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Sodium Valproate, Valproic Acid, VPA, vehicle


title: VPA 168hr POOLED Veh

description:
Male SD rats were given a single dose of distilled water as a vehicle. Animal was sacrificed 168hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 2ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Sodium Valproate, Valproic Acid, VPA, vehicle, pooled


title: VPA 168hr Veh4


title: VPA 168hr Veh2


title: VPA 168hr Veh3


title: DEHP 48hr Veh1

description:
Male SD rats were given a single dose of distilled water as a vehicle. Animal was sacrificed 48hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Diethylhexyl phthalate, Phthalic acid bis(2-ethylhexyl ester), vehicle


title: DEHP 48hr Veh2


title: DEHP 48hr Veh POOLED

description:
Male SD rats were given a single dose of distilled water as a vehicle. Animal was sacrificed 48hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 2ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Diethylhexyl phthalate, Phthalic acid bis(2-ethylhexyl ester), vehicle, pooled


title: DEHP 48hr Veh5


title: Clof 168hr treated2

description:
Male SD rats were given a single dose of 1000mg/kg clofibrate using 0.9% saline as vehicle. Animal was sacrificed 168hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500.
Keywords = Clofibrate


title: DEHP 48hr Veh4


title: DEHP 168hr Veh POOLED

description:
Male SD rats were given a single dose of distilled water as a vehicle. Animal was sacrificed 168hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 2ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Diethylhexyl phthalate, Phthalic acid bis(2-ethylhexyl ester), vehicle, pooled


title: Clof 168hr treated3


title: DEHP 168hr Veh2

description:
Male SD rats were given a single dose of distilled water as a vehicle. Animal was sacrificed 168hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500
Keywords = Diethylhexyl phthalate, Phthalic acid bis(2-ethylhexyl ester), vehicle


title: VPA 168hr Veh1


title: Clof 168hr treated5


title: DEHP 168hr Veh1


title: DEHP 168hr Veh5


title: Clof 168hr treated4


title: Clof 168hr treated1


title: Clof 168hr treated POOLED

description:
Male SD rats were given a single dose of 1000mg/kg clofibrate using 0.9% saline as vehicle. Animal was sacrificed 168hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 2ug of RNA from each sample was pooled (10ug total) and labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500.
Keywords = Clofibrate, pooled


title: DEHP 168hr Veh3


title: DEHP 168hr Veh4


title: S026BHW

status: Public on Jun 01 2005

city: Portland

first: Siming

last: Shou

state: OR

address: 3181 Sam Jackson Park Road

department: Medical Genetics

institute: Oregon Health & Science University

description: Wild type mouse E12.5 hindlimb autopod. MOE430 B GeneChip, MAS5.0 signal.

source_name: mouse hindlimb autopod


title: PF05 EpPnT2N1G1

city: Bordeaux

first: Richard

last: Iggo

address: 229 cours de l'Argonne

department: Bergonie Cancer Institute

country: France

institute: University of Bordeaux

description: EORTC 10994

source_name: Biopsy


title: S025BFW

description: Wild type mouse E12.5 forelimb autopod. MOE430 B GeneChip, MAS5.0 signal.

source_name: mouse forelimb autopod


title: PF35 EpPpT2N1G3

description: EORTC 10994


title: S014BHW

description: Wild type mouse E12.5 Hindlimb autopod. MOE430 B GeneChip, MAS5.0 signal.


title: S012BHWB


title: DEHP 48hr Veh3


title: S013BFW


title: S011BFW

description:
Wild type mouse E12.5 autopod.
Affymetrix MOE430 B GeneChip. MAS5.0 signal.


title: rpb1-11 vs wt expression profiling

status: Public on May 01 2005

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description:
Two independent RNA preparations were used to hybridise to two microarrays one on
which wildtype was labelled with Cy5 and rpb-11 with Cy3 and the other on which dyes
were swapped.
The data were normalized using 'Lowess' (per chip per spot normalizations and checked
against luciferase spiking controls).
Using a 1.5 fold cutoff value for changes in expression levels 33 genes showed
reproducible up or down regulation, none of which are known to be involved in RNAidependent
transcriptional gene silencing.
The methodology and arrays were as previously described by Xue et al (2004).
Lot batch = F010D slide #3

organism: Schizosaccharomyces pombe

source_name: wt


title: S014HW

description: Wild type mouse E12.5 autopod. MOE430 A GeneChip. MAS5.0 Signal.


title: S026HW


title: NOD S2

status: Public on Apr 14 2005

first: Zheng

last: Liu

description: using NOD spleen T cells to extract mRNA as experimental group with cy5(F635), B6 spleen T cells as control group with cy3(F535)

source_name: NOD spleen T cells

source_name: B6 spleen T cells


title: S012HBW


title: S011FW

description: Wild type,dissected mouse developing E12.5 limb autopod.

source_name: E12.5 mouse autopod


title: expression profiling rpb1-11 vs wt

description:
Two independent RNA preparations were used to hybridise to two microarrays one on
which wildtype was labelled with Cy5 and rpb-11 with Cy3 and the other on which dyes
were swapped.
The data were normalized using 'Lowess' (per chip per spot normalizations and checked
against luciferase spiking controls).
Using a 1.5 fold cutoff value for changes in expression levels 33 genes showed
reproducible up or down regulation, none of which are known to be involved in RNAidependent
transcriptional gene silencing.
The methodology and arrays were as previously described by Xue et al (2004).
Lot batch = F010D slide#4


title: NODtoB6 S2

status: Public on Apr 20 2005

description: bone marrow transffered mice NODtoB6 (donor: NOD, recepient: B6)

source_name: spleen T cells from bone marrow transferred mice NODtoB6

source_name: spleen T cells of B6 mice


title: B6.NODIdd1,5 kidney S1

description: using B6.NODIdd1,5 kidney cells to extract mRNA as experimental group with cy5(F635), B6 kidney cells as control group with cy3(F532)

source_name: Kidney cells from B6.NODIdd1,5

source_name: Kidney cells from B6


title: B6toNOD S1

description: bone marrow transferred mice B6toNOD (donor: B6, recipient:NOD)

source_name: spleen T cells of bone marrow transferred mice B6toNOD


title: NOD S1

description: using NOD spleen T cells to extract mRNA as experimental group with cy5(F635), B6 spleen T cells to extract mRNA as control groups with cy3(F532)


title: B6toNOD S2

source_name: spleen T cells from bone marrow transferred mice B6toNOD

source_name: spleen T cells from B6 mice


title: RH_RRE2_14028_cheY versus cheY suppressor on plate at 3.0h_5D_2

status: Public on Mar 30 2005

city: Austin

first: Rasika

last: Harshey

state: TX

department: Section of Molecular Genetics and Microbiology

institute: Institute of Cellular and Molecular Biology

description:
Typhimurium 14028 cheY and cheY suppressor transcripts after 3.0h growth on swarming paltes
User - TWang
Date_of_Scan = 2004/11/19 13:31:10

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 4-4(cheY suppressor) on swarming plate at 3.0h

source_name: Typhimurium 14028 cheY on swarming palte at 3.0h


title: NOD.H2h4 S2

description: using NOD.H2h4 spleen T cells to extract mRNA as experimental group with cy5(F635), B6 spleen T cells as control group with cy3(F532)

source_name: spleen T cells of NOD.H2h4

source_name: spleen T cells of B6


title: RH_RRE2_14028_cheY versus cheY suppressor on plate at 3.0h_5D_1


title: RH_RRE2_14028_cheY versus cheY suppressor on plate at 3.0h_5D_3


title: NOD.H2h4 S1

source_name: spleen T cells from NOD.H2h4

source_name: spleen T cells from B6


title: RH_RRE2_14028_4-4(cheY suppressor) versus cheY on plate at 3.0h_5D_3

description:
Typhimurium 14028 cheY suppressor and cheY transcripts after 3.0h growth on swarming plates
User - TWang
Date_of_Scan = 2004/08/27 10:49:51

source_name: Typhimurium 14028 4-4 (cheY suppressor) on swarming plate at 3.0h

source_name: Typhimurium 14028 cheY on swarming plate at 3.0h


title: B6.NODIdd1,5 S1

description: using B6.NODIdd1,5 spleen T cells to extract mRNA as experimental group with cy5(F635), B6 spleen T cells as control group with cy3(F532)

source_name: spleen T cells from B6.NODIdd1,5


title: S025FW

description:
Wild type mouse E12.5 autopod.
MEO430 A GeneChip, MAS5.0 signal.

source_name: mouse forelimb autopod


title: S013FW


title: RH_RRE2_14028_4-4(cheY suppressor) versus cheY on plate at 3.0h_5D_2


title: B6.NODIdd1,5 kideny S2

source_name: kidney cells from B6.NODIdd1,5 kidney

source_name: kidney cells from B6 kidney


title: B6.NODIdd1,5 S2


title: NODtoB6 S1

source_name: spleen T cells from bone marrow transferred mice-NODtoB6


title: RH_RRE2_14028_WT versus 4-4(cheY suppressor) on plate at 3.0h_5D_3

description:
Typhimurium 14028 WT versus cheY suppressor transcripts after 3.0h growth on swarming plates
User - TWang
Date_of_Scan = 2004/08/20 11:45:28

source_name: Typhimurium 14028 Wild type RNA from swarming plate at 3.0h

source_name: Typhimurium 14028 4-4(cheY suppressor) RNA from swarming plate at 3.0h


title: GAP_Carbon_2B

status: Public on Jan 01 2005

city: Lynchburg

first: Michael

middle: S

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

description:
RNA was isolated from lyophilized cultures of Aspergillus parasiticus (SUI) using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using a protocol modified from Chhabra, et al., 2003. J Biol Chem 278:7540. Sucrose supports aflatoxin (AF) production, whereas lactose supresses AF production.
Keywords = aspergillus
Keywords = aflatoxin
Keywords = secondary metabolism

organism:
Aspergillus flavus
Aspergillus parasiticus

source_name: Aspergillus parasiticus (Lactose carbon source)

source_name: Aspergillus parasiticus (Sucrose carbon source)


title: RH_RRE2_14028_4-4(cheY suppressor) versus cheY on plate at 3.0h_5D_1


title: GAP_Nitrogen_1A

description:
RNA was isolated from lyophilized cultures of Aspergillus parasiticus (SUI)using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using the 3DNA detection system from Genisphere (Hatfield, PA) as recommended by the manufacturer. The NH4 nitrogen source supports aflatoxin (AF) production, whereas the NO3 nitrogen source supresses AF production.
Keywords = aspergillus
Keywords = aflatoxin
Keywords = secondary metabolism

source_name: Aspergillus parasiticus (NH4 nitrogen source)

source_name: Aspergillus parasiticus (NO3 nitrogen source)


title: GAP_Nitrogen_1B

description:
RNA was isolated from lyophilized cultures of Aspergillus parasiticus (SUI)using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using the 3DNA detection system from Genisphere (Hatfield, PA) as recommended by the manufacturer. The NH4 nitrogen source supports aflatoxin (AF) production, whereas the NO3 nitrogen source supresses AF production.
If Value=undefined then Value was set to 0 and FLAG was set to 1.
Keywords = aspergillus
Keywords = aflatoxin
Keywords = secondary metabolism


title: GAP_Carbon_2A


title: RH_RRE2_14028 WT_Plate versus cheYflgM_P_5D_2

description:
Typhimurium 14028 WT versus cheYflgM transcripts after 3.0h growth on swarming plate
User - TWang
Date_of_Scan = 2005/01/13 13:15:49

source_name: Typhimurium 14028 WT on Plate 3.0h

source_name: Typhimurium 14028 QW136 (cheYflgM) on Plate 3.0h


title: MDS patient MDS11 (Repl. 1)

status: Public on Jan 10 2005

city: Oxford

first: Andrea

last: Pellagatti

address: John Radcliffe Hospital

department: NDCLS, RDM

country: United Kingdom

institute: University of Oxford

description: The patient RNA was compared to the normal RNA pool using a T7-based amplification method: 1 microgram of total RNA was reverse-transcribed using a T7-oligodT primer and then labelled aRNAs produced via in vitro transcription in the presence of either Cy3-UTP or Cy5-UTP. The labelled aRNAs were then purified and hybridized competitively to the microarray.

source_name: Neutrophils from 7 healthy controls (RNA pooled)<->Neutrophils from MDS patient


title: GAP_Carbon_1B


title: RH_RRE2_14028 WT_Plate versus cheYflgM_P_5D_3


title: RH_RRE2_14028 WT_Plate versus cheYflgM_P_5D_1


title: GAP_pH_2B

description:
RNA was isolated from lyophilized cultures of Aspergillus parasiticus (SUI) using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using a protocol modified from Chhabra, et al., 2003. J Biol Chem 278:7540. pH4.5 growth supports aflatoxin (AF) production, whereas pH8.0 growth supresses AF production.
Keywords = aspergillus
Keywords = aflatoxin
Keywords = secondary metabolism

source_name: Aspergillus parasiticus (pH8.0 growth)

source_name: Aspergillus parasiticus (pH4.5 growth)


title: GAP_Carbon_1A


title: GAP_pH_2A

description:
RNA was isolated from lyophilized cultures of Aspergillus parasiticus (SUI) using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using a protocol modified from Chhabra, et al., 2003. J Biol Chem 278:7540. pH4.5 growth supports aflatoxin (AF) production, whereas pH8.0 growth supresses AF production.  If Value=undefined then Value was set to 0 and FLAG was set to 1.
Keywords = aspergillus
Keywords = aflatoxin
Keywords = secondary metabolism


title: RH_RRE2_14028_WT versus 4-4(cheY suppressor) on plate at 3.0h_5D_2


title: RH_RRE2_14028_WT versus 4-4(cheY suppressor) on plate at 3.0h_5D_1


title: Clof 48hr Veh4

description:
Male SD rats were given a single dose of 0.9% saline as a vehicle. Animal was sacrificed 48hrs post-dosing. Total RNA was extracted using the RNA STAT-60 kit from Tel-Test inc. Approximately 10ug of RNA was labeled according to the standard Affymetrix protocol. Signal values were calculated using the MAS 5.0 algorithm, with global scaling to 1500.
Keywords = Clofibrate, vehicle

source_name: Liver


title: GAP_Temperature_2B

description:
RNA was isolated from lyophilized cultures of Aspergillus parasiticus (SUI) using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using a protocol modified from Chhabra, et al., 2003. J Biol Chem 278:7540. 28C growth supports aflatoxin (AF) production, whereas 37C growth supresses AF production.
Keywords = aspergillus
Keywords = aflatoxin
Keywords = secondary metabolism

source_name: Aspergillus parasiticus (37C growth temperature)

source_name: Aspergillus parasiticus (28C growth temperature)


title: Rasagiline_2_protein

status: Public on Dec 01 2004

type: protein

city: Haifa

first: Yotam

last: Sagi

address: 2 Efron st.

department: Department of Pharmacology , Faculty of Medicine

institute: Technion - Israel institute of Technology

description:
10 mice (22-24gr) received Rasagiline Mesylate (0.1mg/kg in 0.1ml water) for 14 days orally, killed by cervical translocation. Midbrains were punched under dissecting microscope, pooled and total protein was produced and analyzed using Poerblot service.
Keywords = powerblot
Keywords = mAb

molecule: protein

source_name: C57/Bl Mouse Midbrain


title: MPTP_1_protein

description:
10 mice (22-24gr) received water for 14 days oraly followed by MPTP (24mg/kg/day i.p for 4 days). 4 days after last MPTP dose mice were killed by cervical translocation. Midbrains were punched under dissecting microscope, pooled and total protein was produced and analyzed by the Powerblot service.
Keywords = powerblot
Keywords = mAb


title: Rasagiline_1_protein


title: Rasagiline_3_protein


title: P2 Slide2

status: Public on Mar 01 2004

city: Memphis

first: Donald

middle: B.

last: Thomason

address: 894 Union Ave

department: Physiology

institute: The University of Tennessee Health Science Center

description:
Slide2 P2 Cy5/Cy3 remission/presentation
Lot batch = Lot 2090032

source_name: remission

source_name: presentation


title: Control_2_protein

description:
10 mice (22-24gr) received water for 14 days orally, killed by cervical translocation. Midbrains were punched under dissecting microscope, pooled and total protein was produced and analyzed using Poerblot service.
Keywords = powerblot
Keywords = mAb


title: GAP_Temperature_1A


title: GAP_pH_1A


title: MPTP_3_protein


title: GAP_Nitrogen_2B

description:
RNA was isolated from lyophilized cultures of Aspergillus parasiticus (SUI) using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using a protocol modified from Chhabra, et al., 2003. J Biol Chem 278:7540. The NH4 nitrogen source supports aflatoxin (AF) production, whereas the NO3 nitrogen source supresses AF production.
Keywords = aspergillus
Keywords = aflatoxin
Keywords = secondary metabolism


title: Control_1_protein


title: MPTP_2_protein


title: P2 Slide1

description:
Slide 1 P2 Cy5/Cy3 presentation/remission
Lot batch = Lot 2090032


title: GAP_pH_1B


title: GAP_Temperature_2A


title: GAP_Temperature_1B


title: GAP_Nitrogen_2A


title: RNA_DNA CRG_1

status: Public on Feb 21 2005

type: mixed

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Simple annotation: Absolute transcript levels, RNA/DNA hybridizations
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-12/22925.gif

source_name: Cy3 - Normal female genomic DNA

source_name: Cy5 - Common reference, CRG


title: P1 Cy5/Cy3 post/pre

description:
Muscle P1 Cy5/Cy3 remission/presentation
Lot batch = Lot 2090032-53


title: P1 slide1

description:
P1 Slide 1 labelled Cy5/Cy3 presentation/remission
Lot batch = Lot 2090032-52


title: Control_3_protein


title: Life cycle stage - sporozoite

status: Public on Dec 23 2002

city: La Jolla

first: Laurence

last: Florens

address: SR-11, 10550 North Torrey Pines Road

department: Department of Cell Biology

institute: The Scripps Research Institute

description:
A proteomic view of the sporozoite stage (infectious form injected by mosquito).
Sporozoites were initially isolated from the salivary glands of Anopheles stephansi mosquitoes, 14 days after infection, by centrifugation in a Renograffin 60 gradient. Four sporozoite samples were used as is. A fifth sample underwent an additional purification step on Dynabeads M-450 Epoxy coupled to NFS1 (an anti-P. falciparum CS protein monoclonal antibody) according to the manufacturer's instructions (Dynal).
Proteome was analyzed by multidimentional protein identification technology (MudPIT), which combines in-line, high-resolution liquid chromatography and tandem mass spectrometry.

organism: Plasmodium falciparum 3D7

source_name: sporozoites


title: Life cycle stage - trophozoite

description:
A proteomic view of the trophozoite stage (form that multiplies in erythrocytes).
Trophozoite-infected erythrocytes from synchronized cultures were purified on 70% Percoll-alanine, and the trophozoites released from the erythrocytes. Of the of 260 parasitized erythrocytes counted by Giemsa-stained thin-blood film, 100% were identified as trophozoites.
Proteome was analyzed by multidimentional protein identification technology (MudPIT), which combines in-line, high-resolution liquid chromatography and tandem mass spectrometry.

source_name: trophozoites


title: RNA_DNA CRG_3

description:
Simple annotation: Absolute transcript levels, RNA/DNA hybridizations
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-12/23453.gif


title: RNA_DNA Kidney FT557 Tissue

description:
Simple annotation: Absolute transcript levels, RNA/DNA hybridizations
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-12/23459.gif

source_name: Cy5 - Kidney FT557 mRNA


title: Life cycle stage - merozoite

description:
A proteomic view of the merozoite (invasive stage of the erythrocytes).
Merozoites were prepared essentially as described by Blackman (1994), using highly synchronized schizonts and purifying the merozoites by passage through membrane filters.
Proteome was analyzed by multidimentional protein identification technology (MudPIT), which combines in-line, high-resolution liquid chromatography and tandem mass spectrometry.

source_name: merozoites


title: RNA_DNA Heart FT24 Tissue

description:
Simple annotation: Absolute transcript levels, RNA/DNA hybridizations
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-12/23457.gif

source_name: Cy5 - Heart FT24 mRNA


title: RNA_DNA CRG_2

description:
Simple annotation: Absolute transcript levels, RNA/DNA hybridizations
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-12/22928.gif


title: RNA_DNA Liver FT560 Tissue

description:
Simple annotation: Absolute transcript levels, RNA/DNA hybridizations
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-12/23455.gif

source_name: Cy5 - Liver FT560 mRNA


title: ES cell line, RNA 68

status: Public on Sep 28 2003

city: Troy

first: Derek

last: Symula

institute: Wadsworth Center Genomics Institute

description:
Abca1 +/- ES cell line was grown on irradiated MEF feeders using standard culture conditions.  Feeders were then depleted and ES cells plated on gelatin for ~2 days.  RNA was isolated using Trizol/RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol.  Data were normalized by AffyMetrix MAS5.0 using defaults.
Keywords = embryonic stem cholesterol transport

source_name: Abca1 +/- ES cell line


title: RNA_DNA Prostate PC23 Tissue

description:
Simple annotation: Absolute transcript levels, RNA/DNA hybridizations
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-12/23462.gif

source_name: Cy5 - Prostate PC23 mRNA


title: RNA_DNA Breast FT162 Tissue

description:
Simple annotation: Absolute transcript levels, RNA/DNA hybridizations
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-12/23465.gif

source_name: Cy5 - Breast FT162 mRNA


title: GSC dpp2

status: Public on Jun 15 2005

city: Baltimore

first: Allan

last: Spradling

state: MD

address: 3520 San Martin Dr

department: Embryology

institute: Carnegie Institution/HHMI

description: RNA from highly purified germline stem cells prepared from ovaries overexpressing Dpp from c587-GAL4 was profiled.  This is replicate 2.  See  Kai et al. (2005). Developmental Biology, in press.

data_processing: MAS 5.0

label: BioArray transcript labeling kit (Enzo)

organism: Drosophila melanogaster

source_name: germ line stem cell

tag: purified germ line stem cells from ovaries overexpressing Dpp from c587-GAL4; replicate 2