title: Tumor samples from patient No.86 PT86U95C

source_name: PT86, tumor samples from patient No.86


title: Tumor samples from patient No.64 PT64U95B

status: Public on Jan 16 2007

type: RNA

city: Houston

first: Federico

middle: Alberto

last: Monzon

state: TX

address: 6565 Fannin St, MS205

department: Pathology

country: USA

institute: The Methodist Hospital

description: Gene expression data from primary prostate cancer

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95B array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PT64, tumor samples from patient No.64

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

extract_protocol: Total RNA was extracted with Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: Fresh prostate tissues were recovered immediately after surgical removal. Tissues were dissected/trimmed to obtain pure tumor then snap frozen in liquid nitrogen within 30 mintues of excision and stored in -80C untill RNA extraction. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. Only tumor tissues with less than 30% of tromal components were selected.

tag: Tissue

value: primary prostate tumor

tag: Tumor stage

tag: Gleason Grade


title: Tumor samples from patient No.84 PT84U95C

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95C array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: PT84, tumor samples from patient No.84


title: Tumor samples from patient No.62 PT62U95B

source_name: PT62, tumor samples from patient No.62


title: Tumor samples from patient No.90 PT90U95C

source_name: PT90, tumor samples from patient No.90


title: Tumor samples from patient No.67 PT67U95B

source_name: PT67, tumor samples from patient No.67


title: Tumor samples from patient No.69 PT69U95B

source_name: PT69, tumor samples from patient No.69


title: Tumor samples from patient No.68 PT68U95B

source_name: PT68, tumor samples from patient No.68


title: Tumor samples from patient No.74 PT74U95C

source_name: PT74, tumor samples from patient No.74


title: Tumor samples from patient No.65 PT65U95B

source_name: PT65, tumor samples from patient No.65


title: Tumor samples from patient No.66 PT66U95B

source_name: PT66, tumor samples from patient No.66


title: Tumor samples from patient No.73 PT73U95C

source_name: PT73, tumor samples from patient No.73


title: Tumor samples from patient No.70 PT70U95B

source_name: PT70, tumor samples from patient No.70


title: Tumor samples from patient No.57 PT57U95B

source_name: PT57, tumor samples from patient No.57


title: Tumor samples from patient No.55 PT55U95B

source_name: PT55, tumor samples from patient No.55


title: Tumor samples from patient No.68 PT68U95C


title: Tumor samples from patient No.70 PT70U95C


title: Tumor samples from patient No.53 PT53U95B

source_name: PT53, tumor samples from patient No.53


title: Tumor samples from patient No.50 PT50U95B

source_name: PT50, tumor samples from patient No.50

tag: Tissue:primary prostate tumor


title: Tumor samples from patient No.48 PT48U95B

source_name: PT48, tumor samples from patient No.48


title: Tumor samples from patient No.64 PT64U95C

source_name: PT64, tumor samples from patient No.64


title: Tumor samples from patient No.58 PT58U95B

source_name: PT58, tumor samples from patient No.58


title: Tumor samples from patient No.61 PT61U95B

source_name: PT61, tumor samples from patient No.61


title: Tumor samples from patient No.47 PT47U95B

source_name: PT47, tumor samples from patient No.47


title: Tumor samples from patient No.56 PT56U95B

source_name: PT56, tumor samples from patient No.56


title: Tumor samples from patient No.52 PT52U95B

source_name: PT52, tumor samples from patient No.52


title: Tumor samples from patient No.54 PT54U95B

source_name: PT54, tumor samples from patient No.54


title: Tumor samples from patient No.60 PT60U95B

source_name: PT60, tumor samples from patient No.60


title: Tumor samples from patient No.72 PT72U95C

source_name: PT72, tumor samples from patient No.72


title: Tumor samples from patient No.69 PT69U95C

source_name: PT69, tumor samples from patient No.69


title: Tumor samples from patient No.67 PT67U95C

source_name: PT67, tumor samples from patient No.67


title: Tumor samples from patient No.62 PT62U95C

source_name: PT62, tumor samples from patient No.62


title: Tumor samples from patient No.63 PT63U95C

source_name: PT63, tumor samples from patient No.63


title: Tumor samples from patient No.74 PT74U95B

source_name: PT74, tumor samples from patient No.74


title: Tumor samples from patient No.65 PT65U95C

source_name: PT65, tumor samples from patient No.65


title: Tumor samples from patient No.66 PT66U95C

source_name: PT66, tumor samples from patient No.66


title: Tumor samples from patient No.51 PT51U95B

source_name: PT51, tumor samples from patient No.51


title: Tumor samples from patient No.61 PT61U95C


title: Tumor samples from patient No.58 PT58U95C


title: Tumor samples from patient No.46 PT46U95B

source_name: PT46, tumor samples from patient No.46


title: Tumor samples from patient No.60 PT60U95C


title: Tumor samples from patient No.93 PT93U95B

source_name: PT93, tumor samples from patient No.93


title: Tumor samples from patient No.55 PT55U95C

source_name: PT55, tumor samples from patient No.55


title: Tumor samples from patient No.54 PT54U95C


title: Tumor samples from patient No.57 PT57U95C

source_name: PT57, tumor samples from patient No.57


title: Tumor samples from patient No.51 PT51U95C


title: Tumor samples from patient No.52 PT52U95C


title: Tumor samples from patient No.44 PT44U95B

source_name: PT44, tumor samples from patient No.44


title: Tumor samples from patient No.43 PT43U95B

source_name: PT43, tumor samples from patient No.43


title: Tumor samples from patient No.56 PT56U95C

source_name: PT56, tumor samples from patient No.56


title: Tumor samples from patient No.45 PT45U95B

source_name: PT45, tumor samples from patient No.45


title: Tumor samples from patient No.53 PT53U95C

source_name: PT53, tumor samples from patient No.53


title: Tumor samples from patient No.36 PT36U95B

source_name: PT36, tumor samples from patient No.36


title: Tumor samples from patient No.48 PT48U95C

source_name: PT48, tumor samples from patient No.48


title: Tumor samples from patient No.50 PT50U95C

source_name: PT50, tumor samples from patient No.50


title: Tumor samples from patient No.47 PT47U95C

source_name: PT47, tumor samples from patient No.47


title: Tumor samples from patient No.38 PT38U95B

source_name: PT38, tumor samples from patient No.38


title: Tumor samples from patient No.40 PT40U95B

source_name: PT40, tumor samples from patient No.40


title: Tumor samples from patient No.39 PT39U95B

source_name: PT39, tumor samples from patient No.39


title: Tumor samples from patient No.34 PT34U95B

source_name: PT34, tumor samples from patient No.34


title: Tumor samples from patient No.35 PT35U95B

source_name: PT35, tumor samples from patient No.35


title: Tumor samples from patient No.41 PT41U95B

source_name: PT41, tumor samples from patient No.41


title: Tumor samples from patient No.42 PT42U95B

source_name: PT42, tumor samples from patient No.42


title: Tumor samples from patient No.46 PT46U95C

source_name: PT46, tumor samples from patient No.46


title: Metastatic prostate tumor samples in liver from patient FB561 FB561_5BU95B

description: Gene expression data from metastatic prostate cancer

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

source_name: FB561_5B, metastatic prostate tumor samples in liver from patient FB561

treatment_protocol: Specimens were received directly from the operating room. Samples (>500 mg) were excised and snap frozen in liquid nitrogen within 30 min of excision and stored at -80°C until extraction of RNA. Metastatic tumor samples were obtained from a warm autopsy program and processed similarly to primary tumors. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. Dissection of the frozen tissue block was performed with the guidance of a marked H & E slide to minimize the presence of host tissue in the metastatic samples. All samples used in the study contained >80% tumor. Metastatic tumor samples were minced and divided into two equal portions to be extracted with the sample protocol used for each set of primary tumors.

value: prostate tumor metastases in liver


title: Tumor samples from patient No.45 PT45U95C


title: Tumor samples from patient No.39 PT39U95C


title: Metastatic prostate tumor samples in para aortic lymph node from patient FB561 FB561_1CU95B

source_name: FB561_1C, metastatic prostate tumor samples in para aortic lymph node from patient FB561

value: prostate tumor metastases in para aortic lymph node


title: Metastatic prostate tumor samples in para aortic lymph node from patient FB561 FB561_1BU95B

source_name: FB561_1B, metastatic prostate tumor samples in para aortic lymph node from patient FB561


title: Tumor samples from patient No.40 PT40U95C


title: Tumor samples from patient No.44 PT44U95C

source_name: PT44, tumor samples from patient No.44


title: Tumor samples from patient No.42 PT42U95C


title: Metastatic prostate tumor samples in retroperitoneal lymph node from patient FB561 FB561_2GU95B

source_name: FB561_2G, metastatic prostate tumor samples in retroperitoneal lymph node from patient FB561

value: prostate tumor metastases in retroperitoneal lymph node


title: Tumor samples from patient No.43 PT43U95C

source_name: PT43, tumor samples from patient No.43


title: Tumor samples from patient No.38 PT38U95C


title: Metastatic prostate tumor samples in retroperitoneal lymph node from patient FB561 FB561_2FU95B

source_name: FB561_2F, metastatic prostate tumor samples in retroperitoneal lymph node from patient FB561


title: Metastatic prostate tumor samples in para tracheal lymph node from patient FB561 FB561_3BU95B

source_name: FB561_3B, metastatic prostate tumor samples in para tracheal lymph node from patient FB561

value: prostate tumor metastases in paratracheal lymph node


title: Tumor samples from patient No.34 PT34U95C


title: Metastatic prostate tumor samples in para aortic lymph node from patient EB669 EB669_4AU95B

source_name: EB669_4A, metastatic prostate tumor samples in para aortic lymph node from patient EB669


title: Metastatic prostate tumor samples in para tracheal lymph node from patient FB561 FB561_6CU95B

source_name: FB561_6C, metastatic prostate tumor samples in para tracheal lymph node from patient FB561

value: prostate tumor metastases in para tracheal lymph node


title: Tumor samples from patient No.36 PT36U95C

source_name: PT36, tumor samples from patient No.36


title: Tumor samples from patient No.35 PT35U95C


title: Metastatic prostate tumor samples in para tracheal lymph node from patient EB667 EB667_7CU95B

source_name: EB667_7C, metastatic prostate tumor samples in para tracheal lymph node from patient EB667


title: Metastatic prostate tumor samples in liver from patient EB669 EB669_7B+7DU95B

source_name: EB669_7B+7D, metastatic prostate tumor samples in liver from patient EB669


title: Metastatic prostate tumor samples in para tracheal lymph node from patient EB667 EB667_7EU95B

source_name: EB667_7E, metastatic prostate tumor samples in para tracheal lymph node from patient EB667


title: Metastatic prostate tumor samples in liver from patient FB561 FB561_5BU95C


title: Metastatic prostate tumor samples in para aortic lymph node from patient FB561 FB561_1CU95C


title: Metastatic prostate tumor samples in para tracheal lymph node from patient FB561 FB561_6BU95B

source_name: FB561_6B, metastatic prostate tumor samples in para tracheal lymph node from patient FB561


title: Metastatic prostate tumor samples in para tracheal lymph node from patient EB667 EB667_7FU95B

source_name: EB667_7F, metastatic prostate tumor samples in para tracheal lymph node from patient EB667


title: Metastatic prostate tumor samples in retroperitoneal lymph node from patient FB561 FB561_2GU95C


title: Metastatic prostate tumor samples in para tracheal lymph node from patient EB667 EB667_7B+7DU95B

source_name: EB667_7B+7D, metastatic prostate tumor samples in para tracheal lymph node from patient EB667


title: Tumor samples from patient No.71 PT71U95C

source_name: PT71, tumor samples from patient No.71


title: Metastatic prostate tumor samples in para aortic lymph node from patient FB561 FB561_1BU95C


title: Metastatic prostate tumor samples in paratracheal lymph node from patient EB667 EB667_7AU95B

source_name: EB667_7A, metastatic prostate tumor samples in paratracheal lymph node from patient EB667


title: Metastatic prostate tumor samples in retroperitoneal lymph node from patient FB561 FB561_2FU95C


title: Metastatic prostate tumor samples in para tracheal lymph node from patient FB561 FB561_3BU95C


title: Metastatic prostate tumor samples in left inguinal lymph node from patient EB667 EB667_5A+5BU95B

source_name: EB667_5A+5B, metastatic prostate tumor samples in left inguinal lymph node from patient EB667

value: prostate tumor metastases in left inguinal lymph node


title: Metastatic prostate tumor samples in para tracheal lymph node from patient FB561 FB561_6CU95C


title: Metastatic prostate tumor samples in retroperitoneal lymph node from patient EB667 EB667_6AU95B

source_name: EB667_6A, metastatic prostate tumor samples in retroperitoneal lymph node from patient EB667


title: Metastatic prostate tumor samples in lung from patient FB561 FB561_7BU95B

source_name: FB561_7B, metastatic prostate tumor samples in lung from patient FB561

value: prostate tumor metastases in lung


title: Metastatic prostate tumor samples in para tracheal lymph node from patient FB561 FB561_6BU95C


title: Metastatic prostate tumor samples in liver from patient EB669 EB669_7A+7CU95C

source_name: EB669_7A+7C, metastatic prostate tumor samples in liver from patient EB669


title: Metastatic prostate tumor samples in liver from patient EB669 EB669_7B+7DU95C


title: Metastatic prostate tumor samples in kidney from patient EB667 EB667_2A+2B+2CU95B

source_name: EB667_2A+2B+2C, metastatic prostate tumor samples in kidney from patient EB667

value: prostate tumor metastases in kidney


title: Serum treated MEF, total RNA, biological rep4

city: Bern

first: Marc

last: Kenzelmann

address: Friedbuhlstrasse 51

department: Molecular Genome Analysis

country: Switzerland

institute: Institute of Medical Microbiology, University of Bern

description: Gene expression data from primary serum treated MEF cells grown to near confluency.

hyb_protocol: Following fragmentation, 10µg of cRNA were hybridized to MU74Av2 GeneChip (Affymetrix) according to manufacturer's instructions.

scan_protocol: GeneChips were scanned using the GeneChip' Scanner 3000 7G System (Affymetrix).

data_processing: The data were analyzed with the SAS MicroArray Solution 1.0, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (10% FBS) and labelling (s4U) considered to be constant and the chip-ID as random.

organism: Mus musculus

source_name: 48h serum starved primary mouse embryonic fibroblasts (MEF)

label_protocol: RNA was reverse-transcribed, linearly amplified as described previously (Kenzelmann M. et al. (2004), Genomics 83, 550-558.), and biotin-labelled via a T7-based strategy according to manufacturer's instructions (Affymetrix).

growth_protocol: Cells were grown using high glucose-DMEM (Invitrogen) with 1% Penicillin/Streptomycin (Invitrogen) and 10% dialyzed FBS (cutoff 10,000Da, Sigma) to near confluency. Cells were serum-starved for 48h with 1% dialyzed FBS, and then incubated for 2h with media containing 200µM 4-thiouridine (s4U, Sigma), 10% FBS and 1µCi 3H-cytidine (20Ci/mmol, Biotrend).

extract_protocol: RNA was isolated according to the Qiagen RNeasy Midi protocol. RNA quality and yield were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies)

treatment_protocol: Primary mouse embryonic fibroblasts were isolated as described previously (Todaro G.J. and Green H. (1963), J. Cell Biol., 17, 299-313; Brusselbach S.U. et al. (1995), Oncogene, 10, 79-86.).

tag: Genotype

value: C57/BLACK6, ATF1 -/+

tag: Age


title: Serum starved MEF, total RNA, biological rep4

description: Gene expression data from primary serum starved MEF cells grown to near confluency.

growth_protocol: Cells were grown using high glucose-DMEM (Invitrogen) with 1% Penicillin/Streptomycin (Invitrogen) and 10% dialyzed FBS (cutoff 10,000Da, Sigma) to near confluency. Cells were serum-starved for 48h with 1% dialyzed FBS, and then incubated for 2h with media containing 200µM 4-thiouridine (s4U, Sigma), 1% FBS and 1µCi 3H-cytidine (20Ci/mmol, Biotrend).


title: Serum treated MEF, total RNA, biological rep3


title: Metastatic prostate tumor samples in adrenal gland from patient EB669 EB669_8BU95B

source_name: EB669_8B, metastatic prostate tumor samples in adrenal gland from patient EB669

value: prostate tumor metastases in adrenal gland


title: Metastatic prostate tumor samples in para tracheal lymph node from patient EB667 EB667_7FU95C


title: Tumor samples from patient No.41 PT41U95C

source_name: PT41, tumor samples from patient No.41


title: Metastatic prostate tumor samples in para tracheal lymph node from patient EB667 EB667_7EU95C


title: Metastatic prostate tumor samples in lung from patient FB561 FB561_7BU95C


title: Metastatic prostate tumor samples in adrenal gland from patient EB669 EB669_8CU95B

source_name: EB669_8C, metastatic prostate tumor samples in adrenal gland from patient EB669


title: Metastatic prostate tumor samples in liver from patient EB666 EB666_1G+1HU95B

source_name: EB666_1G+1H, metastatic prostate tumor samples in liver from patient EB666


title: Metastatic prostate tumor samples in para tracheal lymph node from patient EB667 EB667_7B+7DU95C


title: Serum starved MEF, total RNA, biological rep3


title: Metastatic prostate tumor samples in para aortic lymph node from patient EB669 EB669_4AU95C

source_name: EB669_4A, metastatic prostate tumor samples in para aortic lymph node from patient EB669


title: Metastatic prostate tumor samples in retroperitoneal lymph node from patient EB667 EB667_6AU95C


title: Metastatic prostate tumor samples in adrenal gland from patient EB669 EB669_8CU95C


title: Serum treated MEF, total RNA, biological rep2


title: Serum starved MEF, total RNA, biological rep2


title: Metastatic prostate tumor samples in adrenal gland from patient EB669 EB669_8BU95C


title: Metastatic prostate tumor samples in paratracheal lymph node from patient EB667 EB667_7AU95C


title: Metastatic prostate tumor samples recurrent in prostate from patient FB561 FB561_4HU95B

source_name: FB561_4H, metastatic prostate tumor samples recurrent in prostate from patient FB561

value: metastases recurrent in prostate


title: Serum treated MEF, total RNA, biological rep1


title: Metastatic prostate tumor samples in left inguinal lymph node from patient EB667 EB667_5A+5BU95C


title: Metastatic prostate tumor samples in liver from patient FB561 FB561_5FU95B

source_name: FB561_5F, metastatic prostate tumor samples in liver from patient FB561


title: Serum starved MEF, total RNA, biological rep1


title: Normal prostate tissue free of any pathological alteration from organ donor PD019 PD019U95B

description: Gene expression data from normal prostate tissues free of any pathological alteration

source_name: PD019, normal prostate tissue free of any pathological alteration from organ donor PD019

treatment_protocol: Donor prostate tissues were obtained at the time of organ donation in brain-dead men. Samples were collected from peripheral zone of the prostate gland with at least 60% glandular components and free of any pathological alteration.

tag: Tissue:normal prostate tissue free of any pathological alteration from brain-dead organ donor

tag: Race

value: Caucasian


title: Metastatic prostate tumor samples in kidney from patient EB667 EB667_2A+2B+2CU95C


title: Metastatic prostate tumor samples recurrent in prostate from patient FB561 FB561_4HU95C


title: Metastatic prostate tumor samples in liver from patient EB666 EB666_1G+1HU95C


title: Metastatic prostate tumor samples in liver from patient EB669 EB669_7A+7CU95B


title: Normal prostate tissue free of any pathological alteration from organ donor PD014 PD014U95B

source_name: PD014, normal prostate tissue free of any pathological alteration from organ donor PD014


title: Normal prostate tissue free of any pathological alteration from organ donor PD015 PD015U95B

source_name: PD015, normal prostate tissue free of any pathological alteration from organ donor PD015


title: Normal prostate tissue free of any pathological alteration from organ donor PD016 PD016U95B

source_name: PD016, normal prostate tissue free of any pathological alteration from organ donor PD016


title: Normal prostate tissue free of any pathological alteration from organ donor PD015 PD015U95C


title: Serum treated MEF, newly transcribed RNA, biological rep4

extract_protocol: RNA was isolated according to the Qiagen RNeasy Midi protocol. RNA quality and yield were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies). 100µg of RNA were diluted in binding buffer and loaded onto ~150µl packaged volume of the equilibrated organomercurial matrix (Squarix Biotechnology Germany) loaded to a Small Spin Column (Qiagen). After 4h incubation under constant gentle rotation and light protection at 4°C, non-bound RNA was eliminated by sequential washing steps. Bound (thiolated) RNA was eluted using binding buffer supplemented with 20mM 2-mercaptoethanol and ethanol precipitated. Specific activity of eluted RNA was calculated via 3H-cytidine measurement on a Beckman Coulter LS6500.


title: Normal prostate tissue free of any pathological alteration from organ donor PD016 PD016U95C


title: Normal prostate tissue free of any pathological alteration from organ donor PD013 PD013U95B

source_name: PD013, normal prostate tissue free of any pathological alteration from organ donor PD013


title: Normal prostate tissue free of any pathological alteration from organ donor PD019 PD019U95C


title: Normal prostate tissue free of any pathological alteration from organ donor PD013 PD013U95C


title: Serum treated MEF, newly transcribed RNA, biological rep3


title: Normal prostate tissue free of any pathological alteration from organ donor PD012 PD012U95C

source_name: PD012, normal prostate tissue free of any pathological alteration from organ donor PD012


title: Metastatic prostate tumor samples in liver from patient FB561 FB561_5FU95C


title: Normal prostate tissue free of any pathological alteration from organ donor PD012 PD012U95B


title: Serum starved MEF, newly transcribed RNA, biological rep4


title: Metastatic prostate tumor samples in para tracheal lymph node from patient EB667 EB667_7CU95C

source_name: EB667_7C, metastatic prostate tumor samples in para tracheal lymph node from patient EB667


title: Serum starved MEF, newly transcribed RNA, biological rep3


title: Serum starved MEF, newly transcribed RNA, biological rep2


title: Serum treated MEF, newly transcribed RNA, biological rep2


title: Normal prostate tissue free of any pathological alteration from organ donor PD011 PD011U95C

source_name: PD011, normal prostate tissue free of any pathological alteration from organ donor PD011


title: Normal prostate tissue free of any pathological alteration from organ donor PD011 PD011U95B


title: Contralateral (not clamped) untreated mouse kidney, total RNA, biological rep2

description: Gene expression data from contralateral (untreated) kidneys of Ischemia-Reperfusion-Injury mice (IRI-mice).

hyb_protocol: Following fragmentation, 10µg of cRNA were hybridized to MOE430A GeneChip (Affymetrix) according to manufacturer's instructions.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G System (Affymetrix).

data_processing: The data were analyzed with the SAS MicroArray Solution 1.0, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (IRI-treatment) and labelling (s4U) considered to be constant and the chip-ID as random.

growth_protocol: Mice were grown under standard conditions with free access to nutrition.

treatment_protocol: Mice were anesthesized with diethylether. After flank incision, the renal artery and vein of the left kidney were occluded by a vascular clamp for 45 min. The clamp was removed, and the organ was allowed to reperfuse (time 0). Animals were allowed to recover with free access to nutrition. At time 0+1h, 200µM s4U (bi-distilled water as control) together with 34µCi 3H-cytidine (20Ci/mmol; ARC) were injected ip in a total volume of 1ml of 0.9% NaCl solution. At time 0+2h, injection was repeated. At time 0+3h, mice were sacrificed and contralateral (untreated) kidneys removed for histopathologic examination and RNA isolation.

value: C57/BLACK6, males

value: 7 weeks, body weight appr. 20g


title: Normal prostate tissue free of any pathological alteration from organ donor PD010 PD010U95C

source_name: PD010, normal prostate tissue free of any pathological alteration from organ donor PD010


title: Normal prostate tissue free of any pathological alteration from organ donor PD009 PD009U95C

source_name: PD009, normal prostate tissue free of any pathological alteration from organ donor PD009


title: Normal prostate tissue free of any pathological alteration from organ donor PD014 PD014U95C


title: Normal prostate tissue free of any pathological alteration from organ donor PD010 PD010U95B


title: Normal prostate tissue free of any pathological alteration from organ donor PD008 PD008U95C

source_name: PD008, normal prostate tissue free of any pathological alteration from organ donor PD008

value: African American


title: Serum treated MEF, newly transcribed RNA, biological rep1

source_name: 48h serum starved primary mouse embryonic fibroblasts (MEF)


title: Serum starved MEF, newly transcribed RNA, biological rep1


title: Normal prostate tissue free of any pathological alteration from organ donor PD009 PD009U95B


title: Serum treated MEF, amplified total RNA, biological rep4


title: Normal untreated mouse kidney, total RNA, biological rep2

description: Gene expression data from normal mouse kidneys.

source_name: Normal untreated mouse kidney

treatment_protocol: Untreated normal mice were injected ip with 200µM s4U (bi-distilled water as control) together with 34µCi 3H-cytidine (20Ci/mmol; ARC) in a total volume of 1ml of 0.9% NaCl solution. At time 0+1h, injection was repeated. At time 0+2h, mice were sacrificed and kidneys removed for histopathologic examination and RNA isolation.


title: Normal prostate tissue free of any pathological alteration from organ donor PD008 PD008U95B


title: Normal prostate tissue free of any pathological alteration from organ donor PD007 PD007U95B

source_name: PD007, normal prostate tissue free of any pathological alteration from organ donor PD007


title: Normal untreated mouse kidney, total RNA, biological rep1


title: Normal prostate tissue free of any pathological alteration from organ donor PD004 PD006U95C

source_name: PD004, normal prostate tissue free of any pathological alteration from organ donor PD004


title: Serum treated MEF, amplified total RNA, biological rep2


title: Normal prostate tissue free of any pathological alteration from organ donor PD004 PD006U95B


title: Contralateral (not clamped) untreated mouse kidney, total RNA, biological rep1


title: Normal prostate tissue free of any pathological alteration from organ donor PD005 PD004U95C

source_name: PD005, normal prostate tissue free of any pathological alteration from organ donor PD005


title: Normal prostate tissue free of any pathological alteration from organ donor PD006 PD005U95B

source_name: PD006, normal prostate tissue free of any pathological alteration from organ donor PD006


title: Normal prostate tissue free of any pathological alteration from organ donor PD006 PD005U95C


title: Contralateral (not clamped) untreated mouse kidney, amplified total RNA, biological rep2


title: Normal prostate tissue free of any pathological alteration from organ donor PD007 PD007U95C


title: Serum starved MEF, amplified total RNA, biological rep3


title: Normal prostate tissue free of any pathological alteration from organ donor PD005 PD004U95B


title: Serum starved MEF, amplified total RNA, biological rep2


title: Normal prostate tissue free of any pathological alteration from organ donor PD002 PD002U95C

source_name: PD002, normal prostate tissue free of any pathological alteration from organ donor PD002


title: Serum treated MEF, amplified total RNA, biological rep1


title: Normal prostate tissue free of any pathological alteration from organ donor PD003 PD003U95B

source_name: PD003, normal prostate tissue free of any pathological alteration from organ donor PD003


title: Normal untreated mouse kidney, newly transcribed RNA, biological rep1


title: Normal untreated mouse kidney, amplified total RNA, biological rep2


title: Serum treated MEF, amplified total RNA, biological rep3


title: Contralateral (not clamped) untreated mouse kidney, newly transcribed RNA, biological rep1


title: Contralateral (not clamped) untreated mouse kidney, amplified total RNA, biological rep1


title: Normal prostate tissue free of any pathological alteration from organ donor PD003 PD003U95C


title: Normal prostate tissue free of any pathological alteration from organ donor PD002 PD002U95B


title: Normal prostate tissue free of any pathological alteration from organ donor PD001 PD001U95B

source_name: PD001, normal prostate tissue free of any pathological alteration from organ donor PD001


title: Normal untreated mouse kidney, amplified total RNA, biological rep1


title: Serum starved MEF, amplified total RNA, biological rep1


title: ES cells tertiary clone no 13-42

status: Public on Jan 13 2007

type: genomic

city: Montreal

first: Guy

last: Sauvageau

state: Quebec

address: Marcelle-Coutu Building 2900 Boul. Edouard Montpetit Quai 20

department: Université de Montréal

country: Canada

institute: IRIC

description: no additional information

hyb_protocol: Prior to hybridization, the test and reference probes were combined with 100 ug mouse fluorimetric Cot-1 (Invitrogen) and ethanol precipitated.  Following centrifugation, the probes were resuspended in 110ul SlideHyb Buffer #3 (Ambion) containing 5ul of 100μg/ul Yeast tRNA (Invitrogen), heated to 95ºC for 5 minutes and incubated for 30 minutes at 37ºC to block repetitive elements on the probe.  Hybridization was performed for 16 hours at 55ºC using a GeneMachine hybridization station (Genomic Solutions, Inc.) as described (Cowell, J. K. and N. J. Nowak. 2003. High-resolution analysis of genetic events in cancer cells using bacterial artificial chromosome arrays and comparative genome hybridization. Adv Cancer Res 90:91-125).  After hybridization, the slides were automatically washed in the GeneMachines station with reducing concentrations of SSC and SDS.   The final wash was 30 seconds in 0.1X SSC, followed by a two second 100 % ethanol dip.  The slides were spun dry and scanned immediately at 5µm resolution using a GenePix 4200A laser scanner (Axon Inc.)

scan_protocol: Slides were scanned on a GenePix 4200A laser Scanner (Axon Inc.) using GenePix Pro V5.0. Both lasers were set to 100% and the PMT was set to 500 for cy3 and 450 for cy5.

data_processing: Images were analyzed using Imagene 6.0 (BioDiscovery Inc.). The output of Image analysis was further processed by in-house developed programs. The log2 ratios of the test/control (values are not background subtracted) were normalized using a subgrid loess, with all flagged spots and clones on the sex chromosome are given a weight of zero. The mean of the replicate measures was taken and the final normalized log2 ratio was plotted against its genomic location.

molecule: genomic DNA

source_name: ES cells_tertiary clone_no 13-42

label_protocol: 1μg of test sample genomic DNA was fluorescently labeled using the BioArray CGH Labeling System (Enzo Life Sciences).  Initially, the DNA was denatured in the presence of the random primer at 99ºC for 10 minutes in a thermalcycler, and then quickly cooled to 4ºC.  The tubes were transferred to ice and labeling occurred with the addition of dNTP-cyanine 5 mix and Klenow.  Incubation took place overnight at 37ºC in a thermalcycler.  The unincorporated nucleotides were removed using a QIAquick PCR purification column (Qiagen) and the labeled probe was eluted with 2 x 25 ul washes.

growth_protocol: Prior to DNA extraction, ES cells were grown on gelatin coated dishes, in a media (DMEM high glucose with L-glutamine and pyruvate (Invitrogen), 15% fetal calf serum (Invitrogen),1.5 x 10-4 M alpha-monothioglycerol (Sigma) and 1x10-4 M non-essential amino acids (Invitrogen)) supplemented with 1000 U ml-1 of ESGRO (Chemicon) or leukemia inhibitory factor (LIF, conditioned media from transfected COS cells).

extract_protocol: Genomic DNA was isolated using DNAzol according to the manufacturer instructions (Invitrogen).

treatment_protocol:
Infection of target cells.  ES cells were infected with the anchor retrovirus A1 for 24h using 4ug ml-1 of polybren (Sigma). Fresh media was added the next day and puromycin (1.5 ug ml-1) selection started 48h after infection. 7-9 days later, colonies were isolated in 96 wells plates and expanded (primary clone). 10 millions ES cells were infected with the saturation retrovirus S1.  24h infections were carried out using 4ug ml-1 of polybren (Sigma). Fresh media were added the next day and hygromycin (150 ug ml-1) selection started 48h after infection.  7 days later, a polyclonal population of secondary clones was obtained.  Retroviruses were produced by the GP+E-86 ecotropic packaging cell line.  Viral titers were kept low to ensure low infection rate and to minimize chances of multiple integrations.
Cre-induced recombination in ES cells.  10 millions ES cells were transfected with a cre plasmid.  Cells were resuspended in 800 ul of ES cell media and electroporated with 25 ug of supercoiled pCX-cre or pOG231, using 225 V and 950 uF or 230 V and 500 uF parameters, respectively.  After an incubation of 20 minutes at room temperature, cells were distributed on 3 dishes (100 mm) covered with irradiated MEFs.  48h after electroporation, G418 selection started at 300 ug ml-1.  7-9 days later, colonies were isolated in 96 wells plates and expanded in presence of G418.  Fractions of these clones were put aside on gelatin coated plates and used to extract DNA.

tag: Strain

tag: Gender

value: male

tag: Passage

tag: Neomycin resistant, puromycin sensitive, hygromycin sensitive

source_name: normal mouse

label_protocol: 1μg of reference genomic DNA was fluorescently labeled using the BioArray CGH Labeling System (Enzo Life Sciences).  Initially, the DNA was denatured in the presence of the random primer at 99ºC for 10 minutes in a thermalcycler, and then quickly cooled to 4ºC.  The tubes were transferred to ice and labeling occurred with the addition of dNTP-cyanine 3 mix and Klenow.  Incubation took place overnight at 37ºC in a thermalcycler.  The unincorporated nucleotides were removed using a QIAquick PCR purification column (Qiagen) and the labeled probe was eluted with 2 x 25 ul washes.

extract_protocol: DNA was extracted using the Quiagen FlexiGene DNA kit, according to the manufacturer instructions.

treatment_protocol: no treatment

value: female


title: ES cells unmodified R1

description: no additional information

source_name: ES cells_unmodified_R1


title: ES cells tertiary clone no 10-21

description: no additional information

source_name: ES cells_tertiary clone_no 10-21


title: ES cells primary clone no 10

description: no additional information

source_name: ES cells_primary clone_no 10

treatment_protocol: Infection of target cells.  ES cells (passage 18) were infected with the anchor retrovirus A1 produced by the GP+E-86 ecotropic packaging cell line.  Viral titers were kept low to ensure low infection rate and to minimize chances of multiple integrations.  24h infections were carried out using 4ug ml-1 of polybren (Sigma). Fresh media was added the next day and puromycin (1.5 ug ml-1) selection started 48h after infection. 7-9 days later, colonies were isolated in 96 wells plates and expanded in presence of puromycin (primary clone).  Fractions of these clones were put aside on gelatin coated plates and used to extract DNA.

tag: Puromycin resistant


title: ES cells tertiary clone no 9-37

description: no additional information

source_name: ES cells_tertiary clone_no 9-37


title: ES cells tertiary clone no 9-62

description: no additional information

source_name: ES cells_tertiary clone_no 9-62


title: ES cells tertiary clone no 10-18

description: no additional information

source_name: ES cells_tertiary clone_no 10-18


title: ES cells tertiary clone no 9-35

description: no additional information

source_name: ES cells_tertiary clone_no 9-35


title: ES cells tertiary clone no 9-90

description: no additional information

source_name: ES cells_tertiary clone_no 9-90


title: ES cells primary clone no 9

description: no additional information

source_name: ES cells_primary clone_no 9


title: ES cells tertiary clone no 13-34

description: no additional information

source_name: ES cells_tertiary clone_no 13-34


title: ES cells tertiary clone no 9-18

description: no additional information

source_name: ES cells_tertiary clone_no 9-18


title: ES cells tertiary clone no 14-39

description: no additional information

source_name: ES cells_tertiary clone_no 14-39

tag: Neomycin resistant, puromycin sensitive, hygromycin resistant


title: ES cells tertiary clone no 7-30

description: no additional information

source_name: ES cells_tertiary clone_no 7-30


title: ES cells primary clone no 13

description: no additional information

source_name: ES cells_primary clone_no 13


title: ES cells primary clone no 4

description: no additional information

source_name: ES cells_primary clone_no 4


title: ES cells primary clone no 7

description: no additional information

source_name: ES cells_primary clone_no 7


title: ES cells tertiary clone no 4-39

description: no additional information

source_name: ES cells_tertiary clone_no 4-39

source_name: Normal mouse


title: ES cells tertiary clone no 6-36

description: no additional information

source_name: ES cells_tertiary clone_no 6-36

source_name: normal mouse


title: ES cells tertiary clone no 14-32

description: no additional information

source_name: ES cells_tertiary clone_no 14-32


title: ES cells primary clone no 6

description: no additional information

source_name: ES cells_primary clone_no 6


title: ES cells primary clone no 14

description: no additional information

source_name: ES cells_primary clone_no 14


title: TGFb1, 3hr, Smad4 antibody, set2, replicate 2

city: Columbus

first: Sandya

last: Liyanarachchi

state: OH

address: Rm 830, 460, W 12th Avenue

department: Human Genetics

institute: OSU

description: Chromatin immunoprecipitated DNA (Cy5) was co-hybridized with total genomic DNA (Cy3). The ratio between Cy5 and Cy3 signal was calculated for all high quality features.

hyb_protocol: After dye coupling, about 200pmol of each Cy dye were hybridized onto the microarray for 20 hr at 40C. Microarray were washed 1 time with wash buffer I (6x SSPE, 0.005% sacrosine) and 1 time with wash buffer II (0.06x SSPE) and finally dip into acetonitrile.

scan_protocol: microarrays were scanned using the Axon GenePix 4000A Scanner

data_processing: The acquired microarray image was analyzed with GenePix Pro 6.0 software. After excluding the spots flagged for bad quality, signal ratios were log2 transformed and normalized using intensity-dependent normalization.

source_name: IOSE cells immunoprecipitated

label_protocol: DNA were amino-allyl labelled using randomly-primed, Klenow-based extension protocol. Cy5 dye was then incorporated into the DNA using in-direct labeling by incubating the dye with DNA for 3hrs.

extract_protocol: genomic DNA were extracted using standard pheno/chloroform extraction

tag: IOSE cells, anti-Smad4 immunoprecipitated DNA

source_name: IOSE cells_input

label_protocol: DNA were amino-allyl labelled using randomly-primed, Klenow-based extension protocol. Cy3 dye was then incorporated into the DNA using in-direct labeling by incubating the dye with DNA for 3hrs.

tag: IOSE cells, total input DNA


title: ES cells tertiary clone no 14-16

description: no additional information

source_name: ES cells_tertiary clone_no 14-16


title: TGFb1, 3hr, Smad4 antibody, set2, replicate 1


title: ES cells tertiary clone no 2-22

description: no additional information

source_name: ES cells_tertiary clone_no 2-22


title: ES cells primary clone no 2

description: no additional information

source_name: ES cells_primary clone_no 2


title: ES cells tertiary clone no 2-41

description: no additional information

source_name: ES cells_tertiary clone_no 2-41


title: ES cells primary clone no 1

description: no additional information

source_name: ES cells_primary clone_no 1

treatment_protocol:
Primary clone
Infection of target cells.  ES cells (passage 18) were infected with the anchor retrovirus A1 produced by the GP+E-86 ecotropic packaging cell line.  Viral titers were kept low to ensure low infection rate and to minimize chances of multiple integrations.  24h infections were carried out using 4ug ml-1 of polybren (Sigma). Fresh media was added the next day and puromycin (1.5 ug ml-1) selection started 48h after infection. 7-9 days later, colonies were isolated in 96 wells plates and expanded in presence of puromycin (primary clone).  Fractions of these clones were put aside on gelatin coated plates and used to extract DNA.


title: ES cells tertiary clone no 1-24

description: no additional information

source_name: ES cells_tertiary clone_no 1-24


title: ES cells tertiary clone no 1-13

description: no additional information

source_name: ES cells_tertiary clone_no 1-13


title: TGFb1, 0hr, Smad4 antibody, set1, replicate 2


title: TGFb1, 3hr, Smad4 antibody, set1, replicate 1


title: Patient W, lesional skin

status: Public on Jan 12 2007

city: Berlin

first: Rainer

last: Ternes

address: Mullerstrasse

country: Germany

institute: Bayer Schering Pharma

description: Human skin biposy (lesional) from male patient, 47 years old, 27 years of psoriasis, moderate erythema, moderate induration, moderate scaling.

hyb_protocol: Following fragmentation, 12 microg of cRNA were hybridized to the Affymetrix HG-U133A chip according to the protocols provided by the manufacturer.

data_processing: The data were condensed with MAS 5.0 using the Refiner software from Genedata, Basel,	Switzerland using default settings. The normalization target was set to 500.

source_name: Human skin biopsy from psoriatic patient (lesional skin)

label_protocol: Biotinylated cRNA were prepared from 2 microg total RNA using the BioArray-High-Yield-RNA-Transcript-Labeling-Kit (Enzo, Farmingdale, NY).

extract_protocol:
Full thickness skin 4 millimeter punch biopsy of lesional skin
RNA was extracted using the Invisorb RNA Kit II (Invitek, Berlin, Germany) according to the manufacturer's instructions.  As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

tag: Patient identifyier

value: W

tag: Sex

tag: Age of patient

value: 47 years

tag: Duration of psoriasis

value: 27 years

tag: Body surface area

value: 6 percent

tag: Overall erythema

value: moderate

tag: Induration

value: moderate (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

tag: Scaling


title: TGFb1, 0hr, Smad4 antibody, set2, replicate 2


title: Patient R, lesional skin

description: Human skin biposy (lesional) from male patient, 56 years old, 16 years of psoriasis, moderate erythema, moderate induration, mild scaling.

value: R

value: 56 years

value: 16 years

value: 30 percent

value: mild (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)


title: Patient P, lesional skin

description: Human skin biposy (lesional) from male patient, 76 years old, 56 years of psoriasis, mild erythema, mild induration, minimal scaling.

value: P

value: 76 years

value: 15 percent

value: mild

value: minimal (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)


title: TGFb1, 0hr, Smad4 antibody, set1, replicate 1


title: Patient N, uninvolved skin

description: Human skin biposy (uninvolved) from male patient, 40 years old, 20 years of psoriasis, clear erythema, clear induration, clear scaling.

source_name: Human skin biopsy from psoriatic patient (uninvolved skin)

extract_protocol:
Full thickness skin 5 millimeter punch biopsy of uninvolved skin
RNA was extracted using the Invisorb RNA Kit II (Invitek, Berlin, Germany) according to the manufacturer's instructions.  As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

value: N

value: male

value: 40 years

value: 20 years

value: 25 percent

value: clear

value: clear (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)


title: Patient L, uninvolved skin

description: Human skin biposy (uninvolved) from male patient, 34 years old, 22 years of psoriasis, clear erythema, clear induration, clear scaling.

value: L

value: 34 years

value: 22 years

value: 10 percent


title: Patient Z, uninvolved skin

description: Human skin biposy (uninvolved) from female patient, 42 years old, 36 years of psoriasis, clear erythema, clear induration, clear scaling.

value: Z

value: female

value: 42 years

value: 36 years

value: 5 percent


title: Patient N, lesional skin

description: Human skin biposy (lesional) from male patient, 40 years old, 20 years of psoriasis, moderate erythema, moderate induration, mild scaling.

value: moderate

value: moderate (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

value: mild (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)


title: Patient R, uninvolved skin

description: Human skin biposy (uninvolved) from male patient, 56 years old, 16 years of psoriasis, clear erythema, clear induration, clear scaling.

value: R

value: male

value: 56 years

value: 16 years

value: 30 percent


title: Patient P, uninvolved skin

description: Human skin biposy (uninvolved) from male patient, 76 years old, 56 years of psoriasis, clear erythema, clear induration, clear scaling.

value: P

value: 76 years

value: 15 percent

value: clear

value: clear (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)


title: TGFb1, 3hr, Smad4 antibody, set1, replicate 2


title: Patient Z, lesional skin

description: Human skin biposy (lesional) from female patient, 42 years old, 36 years of psoriasis, mild erythema, minimal induration, mild scaling.

value: Z

value: female

value: mild

value: minimal (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)


title: Patient L, lesional skin

description: Human skin biposy (lesional) from male patient, 34 years old, 22 years of psoriasis, moderate erythema, mild induration, moderate scaling.

value: L

value: 34 years

value: 22 years

value: 10 percent

value: moderate


title: TGFb1, 0hr, Smad4 antibody, set2, replicate 1


title: Patient J, uninvolved skin

description: Human skin biposy (uninvolved) from female patient, 54 years old, 48 years of psoriasis, clear erythema, clear induration, clear scaling.

value: J

value: 54 years

value: 48 years

value: 9 percent


title: Patient G, uninvolved skin

description: Human skin biposy (uninvolved) from male patient, 40 years old, 19 years of psoriasis, clear erythema, clear induration, clear scaling.

value: G

value: male

value: 40 years

value: 19 years

value: 12 percent


title: Patient J, lesional skin

description: Human skin biposy (lesional) from female patient, 54 years old, 48 years of psoriasis, mild erythema, mild induration, mild scaling.

value: female

value: mild (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)


title: ES cells tertiary clone no 1-03

description: no additional information

source_name: ES cells_tertiary clone_no 1-03


title: Patient G, lesional skin

description: Human skin biposy (lesional) from male patient, 40 years old, 19 years of psoriasis, moderate erythema, moderate induration, moderate scaling.

value: moderate (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)


title: angiogenesis HET PFD 14

city: Stony Brook

first: Michael

last: Hadjiargyrou

state: NY

address: Psy A, Room 338

department: Biomedical Engineering

institute: Stony Brook University

hyb_protocol: The manufacturer’s protocol for hybridization, washing, blocking and ECL detection were followed.

scan_protocol: Signals were captured by exposure to film (BioMax MR, Kodak) for 30 seconds.  Films were digitally scanned (HP ScanJet 5370C) at a resolution of 800 DPI and saved as TIF files.  The resultant images were analyzed using the GEArray Expression Analysis Suite software package (SuperArray).  After uploading, cropping and rotating the images, the software’s autogrid function used to align the grid with the image.  The spot group function was then used to manually position the 4 circles corresponding to each tetra-spot group over the image spots.  In addition, tetra-spots with no signal that bordered bleeding spots (as identified by software) were moved away from the bleeding spots to eliminate erroneous readings.   Upon completion of the spot alignment for all of the images, they were analyzed subject to the following dataset parameters: Background correction, Minimum Value; Summation Type, Average Density; Normalization, Selected Genes (B-Actin); Clover Mode, Off.

data_processing: Background subtracted (minimum value) normalized (B-actin) signal intensities

source_name: fracture callus

label_protocol: Equivalent amounts of RNA from 3 animals were pooled.  Three ug of pooled RNA was labeled and amplified utilizing the AmpoLabeling-LPR kit (SuperArray), according to the manufacture’s instructions.

growth_protocol: normal

extract_protocol: Samples crushed in liquid nitrogen, RNA isolation with TriZOL (Invitrogen) according to manufacturer’s protocol.  Samples then treated with DNase (Qiagen) according to on-column digestion and clean up protocol.  Concentration determined with RiboGreen (Molecular Probes) assay following supplied protocol.

treatment_protocol: fixed closed femoral fracture

tag: HIF-1alpha +/- mouse

tag: post fracture day 14


title: Patient F, uninvolved skin

description: Human skin biposy (uninvolved) from male patient, 47 years old, 28 years of psoriasis, clear erythema, clear induration, clear scaling.

value: F

value: 47 years

value: 28 years

value: 15 percent

value: clear

value: clear (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)


title: hypoxia HET PFD 7

tag: post fracture day 7


title: angiogenesis WT PFD 14

tag: wild type mouse


title: angiogenesis HET PFD 7


title: hypoxia HET PFD 14


title: hypoxia HET PFD 10

tag: post fracture day 10


title: angiogenesis HET PFD 10


title: hypoxia WT PFD 10


title: hypoxia WT PFD 14


title: angiogenesis WT PFD 10


title: Patient F, lesional skin

description: Human skin biposy (lesional) from male patient, 47 years old, 28 years of psoriasis, moderate erythema, mild induration, moderate scaling.

value: moderate


title: hypoxia WT PFD 7

tag: wild type mice


title: angiogenesis WT PFD 7


title: Patient B, uninvolved skin

description: Human skin biposy (uninvolved) from male patient, 34 years old, 15 years of psoriasis, clear erythema, clear induration, clear scaling.

value: B

value: 34 years

value: 15 years

value: 6 percent


title: Patient D, lesional skin

description: Human skin biposy (lesional) from male patient, 61 years old, 21 years of psoriasis, mild erythema, moderate induration, mild scaling.

value: D

value: male

value: 61 years

value: 21 years

value: mild


title: Patient D, uninvolved skin

description: Human skin biposy (uninvolved) from male patient, 61 years old, 21 years of psoriasis, clear erythema, clear induration, clear scaling.

value: 12 percent


title: Patient E, lesional skin

description: Human skin biposy (lesional) from male patient, 51 years old, 24 years of psoriasis, mild erythema, mild induration, mild scaling.

value: E

value: 51 years

value: 24 years

value: 8 percent

value: mild (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)


title: Patient C, lesional skin

description: Human skin biposy (lesional) from male patient, 32 years old, 17 years of psoriasis, moderate erythema, severe induration, moderate scaling.

value: C

value: 32 years

value: 17 years

value: severe (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

value: moderate (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)


title: Patient C, uninvolved skin

description: Human skin biposy (uninvolved) from male patient, 32 years old, 17 years of psoriasis, clear erythema, clear induration, clear scaling.

value: clear

value: clear (classified by the investigators according to the following six grades:clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)


title: Patient E, uninvolved skin

description: Human skin biposy (uninvolved) from male patient, 51 years old, 24 years of psoriasis, clear erythema, clear induration, clear scaling.

value: male


title: Normal prostate tissue free of any pathological alteration from organ donor PD001 PD001U95C

description: Gene expression data from normal prostate tissues free of any pathological alteration

source_name: PD001, normal prostate tissue free of any pathological alteration from organ donor PD001

tag: Tissue:normal prostate tissue free of any pathological alteration from brain-dead organ donor

tag: Age

tag: Race

value: Caucasian


title: Patient W, uninvolved skin

description: Human skin biposy (uninvolved) from male patient, 47 years old, 27 years of psoriasis, clear erythema, clear induration, clear scaling.

tag: Patient identifyier

value: W

value: 47 years

value: 27 years

value: 6 percent


title: 120min ischemia+reperfusion, 1st prep dup 1

status: Public on Jan 11 2007

city: Westminster

first: Kelly

last: Pitts

state: CO

department: Molecular Pharmacology

institute: Gilead Sciences

description: gene expression data from isolated NRVMs subjected to coverslip hypoxia.

hyb_protocol: 10ug purified biotinylated cRNAs were hybridized to Affymetrix Rat Genome 230 2.0 arrays for 16hrs at 45C.  Arrays were washed and stained on an Affymetrix FS450 fluidic station.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip 3000 scanner.

data_processing: CEL files were imported into a Rosetta Resolver database and analyzed with Rosetta Resolver BioSoftware versions 4.0.1.0.7 and 5.0.0.0.

organism: Rattus norvegicus

source_name: Isolated neonatal rat ventricular myocytes subjected with 120 minutes of ischemia+reperfusion

label_protocol: Biotinylated cRNA was prepared using a modified Eberwine protocol

extract_protocol: RNeasy spin column extraction performed according to manufacturer's instructions

tag: Isolated NRVMs 2 days post isolation


title: Patient B, lesional skin

description: Human skin biposy (lesional) from male patient, 34 years old, 15 years of psoriasis, severe erythema, moderate induration, mild scaling.

value: B

tag: Sex

tag: Age of patient

value: 34 years

value: 15 years

value: severe


title: 120min ischemia+reperfusion, 2nd prep dup 1


title: 120min ischemia+reperfusion, 1st prep dup 2


title: 60min ischemia+reperfusion, 2nd prep dup 2

source_name: Isolated neonatal rat ventricular myocytes subjected with 60 minutes of ischemia+reperfusion


title: 60min ischemia+reperfusion, 1st prep dup 2


title: 30min ischemia+reperfusion, 1st prep dup 2

source_name: Isolated neonatal rat ventricular myocytes subjected with 30 minutes of ischemia+reperfusion


title: 30min ischemia+reperfusion, 1st prep dup 1


title: 120min ischemia+reperfusion, 2nd prep dup 2


title: 30min ischemia+reperfusion, 2nd prep dup 1


title: 60min ischemia+reperfusion, 1st prep dup 1


title: 120min ischemia, 2nd prep dup 1

source_name: Isolated neonatal rat ventricular myocytes subjected with 120 minutes of ischemia


title: 0min ischemia+reperfusion, 1st prep dup 2

source_name: Isolated neonatal rat ventricular myocytes subjected with ischemia+reperfusion


title: 10min ischemia+reperfusion, 1st prep dup 2

source_name: Isolated neonatal rat ventricular myocytes subjected with 10 minutes of ischemia+reperfusion


title: 10min ischemia+reperfusion, 1st prep dup 1


title: 0min ischemia+reperfusion, 2nd prep dup 2


title: 10min ischemia+reperfusion, 2nd prep dup 2


title: 120min ischemia, 1st prep dup 1


title: 120min ischemia, 2nd prep dup 2


title: 10min ischemia, 1st prep dup 2

source_name: Isolated neonatal rat ventricular myocytes subjected with 10 minutes of ischemia


title: 10min ischemia, 2nd prep dup 1


title: 10min ischemia+reperfusion, 2nd prep dup 1


title: 10min ischemia, 2nd prep dup 2


title: 60min ischemia+reperfusion, 2nd prep dup 1


title: 60min ischemia, 2nd prep dup 1

source_name: Isolated neonatal rat ventricular myocytes subjected with 60 minutes of ischemia


title: 0min ischemia+reperfusion, 2nd prep dup 1


title: 0min ischemia+reperfusion, 1st prep dup 1


title: 0min ischemia, 2nd prep dup 2

source_name: Isolated neonatal rat ventricular myocytes subjected with ischemia


title: 60min ischemia, 2nd prep dup 2


title: 120min ischemia, 1st prep dup 2


title: 60min ischemia, 1st prep dup 1


title: 30min ischemia, 1st prep dup 1

source_name: Isolated neonatal rat ventricular myocytes subjected with 30 minutes of ischemia


title: 30min ischemia, 2nd prep dup 2


title: 30min ischemia, 1st prep dup 2


title: 30min ischemia+reperfusion, 2nd prep dup 2


title: 0min ischemia, 1st prep dup 2


title: 40 week placenta basal plate B

city: SAN FRANCISCO

first: Susan

last: Fisher

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

description: 40 week placenta basal plate

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: placental basal plate

label_protocol: Approximately 2 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Clin Chem. 2006 Jan;52(1):159-60. Modification of the Standard Trizol-Based Technique Improves the Integrity of RNA Isolated from RNase-Rich Placental Tissue. Haimov-Kochman R, Fisher SJ, Winn VD.)

tag: Placenta, basal plate


title: 39 week placenta basal plate 5 B

description: 39 week placenta basal plate


title: 60min ischemia, 1st prep dup 2


title: 0min ischemia, 2nd prep dup 1


title: 30min ischemia, 2nd prep dup 1


title: 0min ischemia, 1st prep dup 1


title: 39 week placenta basal plate 5 A

description: 39 week placenta basal plate


title: 39 week placenta basal plate 3 A

description: 39 week placenta basal plate


title: 40 week placenta basal plate A

description: 40 week placenta basal plate


title: 39 week placenta basal plate 3 B

description: 39 week placenta basal plate


title: 39 week placenta basal plate 4 B

description: 39 week placenta basal plate


title: 39 week placenta basal plate 2 B

description: 39 week placenta basal plate


title: 39 week placenta basal plate 4 A

description: 39 week placenta basal plate


title: 39 week placenta basal plate 1 B

description: 39 week placenta basal plate


title: 37 week placenta basal plate 2 B

description: 37 week placenta basal plate


title: 39 week placenta basal plate 2 A

description: 39 week placenta basal plate


title: 38 week placenta basal plate 1 B

description: 38 week placenta basal plate


title: 37 week placenta basal plate 1 B

description: 37 week placenta basal plate


title: 23 week placenta basal plate 3 B

description: 23 week placenta basal plate


title: 38 week placenta basal plate 1 A

description: 38 week placenta basal plate


title: 24 week placenta basal plate 1 B

description: 24 week placenta basal plate


title: 24 week placenta basal plate 2 A

description: 24 week placenta basal plate


title: 24 week placenta basal plate 2 B

description: 24 week placenta basal plate


title: 37 week placenta basal plate 2 A

description: 37 week placenta basal plate


title: 23 week placenta basal plate 3 A

description: 23 week placenta basal plate


title: 23 week placenta basal plate 2 B

description: 23 week placenta basal plate


title: 39 week placenta basal plate 1 A

description: 39 week placenta basal plate


title: 22 week placenta basal plate 1 B

description: 22 week placenta basal plate


title: 23 week placenta basal plate 1 A

description: 23 week placenta basal plate


title: 21 week placenta basal plate 6 B

description: 21 week placenta basal plate


title: 23 week placenta basal plate 1 B

description: 23 week placenta basal plate


title: 22 week placenta basal plate 1 A

description: 22 week placenta basal plate


title: 24 week placenta basal plate 1 A

description: 24 week placenta basal plate


title: 21 week placenta basal plate 5 A

description: 21 week placenta basal plate


title: 21 week placenta basal plate 6 A

description: 21 week placenta basal plate


title: 23 week placenta basal plate 2 A

description: 23 week placenta basal plate


title: 10min ischemia, 1st prep dup 1


title: 21 week placenta basal plate 3 B

description: 21 week placenta basal plate


title: 21 week placenta basal plate 4 B

description: 21 week placenta basal plate


title: 21 week placenta basal plate 4 A

description: 21 week placenta basal plate


title: 21 week placenta basal plate 1 A

description: 21 week placenta basal plate


title: 21 week placenta basal plate 2 B

description: 21 week placenta basal plate


title: 21 week placenta basal plate 5 B

description: 21 week placenta basal plate


title: 18 week placenta basal plate 6 A

description: 18 week placenta basal plate


title: 18 week placenta basal plate 6 B

description: 18 week placenta basal plate


title: 19 week placenta basal plate 3 B

description: 19 week placenta basal plate


title: 19 week placenta basal plate 2 B

description: 19 week placenta basal plate


title: 21 week placenta basal plate 2 A

description: 21 week placenta basal plate


title: 21 week placenta basal plate 3 A

description: 21 week placenta basal plate


title: 19 week placenta basal plate 3 A

description: 19 week placenta basal plate


title: 18 week placenta basal plate 5 A

description: 18 week placenta basal plate


title: 21 week placenta basal plate 1 B

description: 21 week placenta basal plate


title: 18 week placenta basal plate 4 A

description: 18 week placenta basal plate


title: 19 week placenta basal plate 1 B

description: 19 week placenta basal plate


title: 19 week placenta basal plate 2 A

description: 19 week placenta basal plate


title: 18 week placenta basal plate 3 A

description: 18 week placenta basal plate


title: 18 week placenta basal plate 4 B

description: 18 week placenta basal plate


title: 19 week placenta basal plate 1 A

description: 19 week placenta basal plate


title: 18 week placenta basal plate 5 B

description: 18 week placenta basal plate


title: 18 week placenta basal plate 1 A

description: 18 week placenta basal plate


title: 18 week placenta basal plate 3 B

description: 18 week placenta basal plate


title: 18 week placenta basal plate 2 A

description: 18 week placenta basal plate


title: 16 week placenta basal plate 4 A

description: 16 week placenta basal plate


title: 18 week placenta basal plate 1 B

description: 18 week placenta basal plate


title: 16 week placenta basal plate 4 B

description: 16 week placenta basal plate


title: 18 week placenta basal plate 2 B

description: 18 week placenta basal plate


title: 16 week placenta basal plate 3 A

description: 16 week placenta basal plate


title: 16 week placenta basal plate 3 B

description: 16 week placenta basal plate


title: 16 week placenta basal plate 2 A

description: 16 week placenta basal plate


title: 16 week placenta basal plate 2 B

description: 16 week placenta basal plate


title: 14 week placenta basal plate 2 B

description: 14 week placenta basal plate


title: 16 week placenta basal plate 1 A

description: 16 week placenta basal plate


title: 16 week placenta basal plate 1 B

description: 16 week placenta basal plate


title: 14 week placenta basal plate 1 B

description: 14 week placenta basal plate


title: 14 week placenta basal plate 2 A

description: 14 week placenta basal plate


title: 14 week placenta basal plate 1 A

description: 14 week placenta basal plate


title: SEKH0751_EM

status: Public on Jan 09 2007

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description: Peripheral blood mononuclear cells (PBMCs) from healthy adult individuals were isolated by Ficoll-HyPaque (Pharmacia) density gradient. We first enriched for CD4+ T cells using negative immunomagnetic beads selection (Automacs, Myltenii), cells were then labeled with anti-CD4-APCcy7, anti-CD45RA-ECD, anti-CD27-FITC and anti-CCR7-PEcy7 and sorted into Naïve cells described as CD4+, CD45RA+, CD27+ and CCR7+, Central Memory cells (TCM) described as CD4+, CD45RA-, CD27+ and CCR7+ cells and Effector Memory cells (TEM) described as CD4+, CD45RA-, CD27- and CCR7- cells. Sorting was performed using a BDAria (BD Pharmingen).  Purity of the TCM and TEM sub-populations was ranging from 96 to 99%. All procedures were done at 4C to avoid any changes in cell phenotype or gene expression.

hyb_protocol: similar to direct labelling protocol lists at UHN Microarray facility web site.

scan_protocol: Scanned at 16 bits using the ScanArray Express Scanner (Packard Bioscience) at 10micro-meter resolution at 635 nm (Cy5) and 532 nm (Cy3) using Genepix Pro 6.0 analysis software (Molecular Divices Corporation)

data_processing: Each quantified output file was run though the following pre-processing steps using R (URL: www.r-project.org)and the Limma package. For Minimum Intensity filtering, R and G values were treated with a surrogate replacement policy for estimating sub-threshold values. For normalization within Arrays, the raw merged R and G channels were lowess-normalized (grouped by print-tip) and transformed to log2 ratios (70).

source_name: Universal RNA

tag: Tissue:Universal RNA

source_name: PBMC from healthy donors

extract_protocol: Total RNA was isolated from beads purified CD4+T cell populations using an RNA extraction kit (Quiagen) then amplified using the MessageAmp RNA kit (Ambion) as per the manufacturer's instructions.


title: SEKH0750_CM


title: SEKH0088_EM


title: SEKH0068_CM


title: SEKH0067_EM


title: SEKH0021_CM


title: SEKH0013_CM


title: SEKH0719_CM


title: SEKH0740_EM


title: SEKH0728_CM


title: SEKH0739_CM


title: SEKH0720_EM


title: SEKH0729_EM


title: SEKH0621_EM


title: SEKH0561_EM


title: SEKH0709_EM


title: SEKH0568_CM


title: SEKH0606_EM


title: SEKH0549_EM


title: SEKH0560_CM


title: SEKH0569_EM


title: SEKH0548_CM


title: SEKH0014_EM


title: SEKH0579_EM


title: SEKH0634_EM


title: SEKH0605_CM


title: SEKH0633_CM


title: SEKH0627_EM


title: SEKH0708_CM


title: SEKH0626_CM


title: SEKH0087_CM


title: SEKH0553_EM


title: CM093_TranscriptionalProfiling_rep4

city: San Francisco

first: Cheryl

last: Chun

institute: UC San Francisco

hyb_protocol: Microarrays were post-proccessed and hybridized as previously described (Derisi JL, Iyer VR, Brown PO, 1997)

scan_protocol: Arrays were scanned on an Axon 4000B Scanner using GenePix software

data_processing: Data was bulk-normalized using NOMAD software (available from http://ucsf-nomad.sourceforge.net).  Ratios were converted into log scale (base 2).

organism: Cryptococcus neoformans

source_name: CM093, normoxia

label_protocol: cDNA reverse transcribed from total RNA with aminoallyl-dUTP was coupled to Cy3-dye per manufacturer (Amersham Biosciences) instructions.

extract_protocol: Culture was collected by centrifugation, lyophilized, then total RNA was extracted using TRIzol Reagent (Invitrogen). Total RNA was treated for 1 hr with DNase I, followed by two chloroform extractions and resuspension in DEPC treated water. ~150 ug of total RNA was reverse-transcribed with oligo dT to prime and using a (1:1) mix of aminallyl-dUTP to dTTP in a dNTP mix.

tag: strain CM093

source_name: H99, normoxia

label_protocol: cDNA reverse transcribed from total RNA with aminoallyl-dUTP was coupled to Cy5-dye per manufacturer (Amersham Biosciences) instructions.

tag: strain H99


title: SEKH0578_CM


title: SEKH0022_EM


title: SEKH0552_CM


title: CM093_TranscriptionalProfiling_rep2

treatment_protocol: Culture was collected by centrifugation, lyophilized, then total RNA was extracted using TRIzol Reagent (Invitrogen). Total RNA was treated for 1 hr with DNase I, followed by two chloroform extractions and resuspension in DEPC treated water. ~150 ug of total RNA was reverse-transcribed with oligo dT to prime and using a (1:1) mix of aminallyl-dUTP to dTTP in a dNTP mix.


title: CM093_TranscriptionalProfiling_rep3


title: CM093_TranscriptionalProfiling_rep1


title: CM098_HypoxiaResponse_rep2

source_name: CM098, normoxia

tag: strain CM098

source_name: CM098, hypoxia


title: SEKH0839_CM

description: Peripheral blood mononuclear cells (PBMCs) from healthy adult individuals were isolated by Ficoll-HyPaque (Pharmacia) density gradient. We first enriched for CD4+ T cells using negative immunomagnetic beads selection (Automacs, Myltenii), cells were then labeled with anti-CD4-APCcy7, anti-CD45RA-ECD, anti-CD27-FITC and anti-CCR7-PEcy7 and sorted into Na�ve cells described as CD4+, CD45RA+, CD27+ and CCR7+, Central Memory cells (TCM) described as CD4+, CD45RA-, CD27+ and CCR7+ cells and Effector Memory cells (TEM) described as CD4+, CD45RA-, CD27- and CCR7- cells. Sorting was performed using a BDAria (BD Pharmingen).  Purity of the TCM and TEM sub-populations was ranging from 96 to 99%. All procedures were done at 4C to avoid any changes in cell phenotype or gene expression.


title: CM098_HypoxiaResponse_rep4


title: CM092_HypoxiaResponse_rep3

source_name: CM092, normoxia

tag: strain CM092

source_name: CM092, hypoxia


title: CM098_HypoxiaResponse_rep3


title: CM092_HypoxiaResponse_rep2


title: SEKH0620_CM


title: CM092_HypoxiaResponse_rep4


title: H99_HypoxiaResponse_rep2

extract_protocol: Culture was collected by centrifugation, lyophilized, then total RNA was extracted using TRIzol Reagent (Invitrogen).  Total RNA was treated for 1 hr with DNase I, followed by two chloroform extractions and resuspension in DEPC treated water.  ~150 ug of total RNA was reverse-transcribed with oligo dT to prime and using a (1:1) mix of aminallyl-dUTP to dTTP in a dNTP mix.

source_name: H99, hypoxia


title: CM098_HypoxiaResponse_rep1


title: CM092_HypoxiaResponse_rep1


title: H99_HypoxiaResponse_rep1


title: Whole Genome array hippocampus_cocaine3

city: Baltimore

first: Svetlana

middle: I

last: Novikova

state: MD

address: 666 W. Baltimore st

department: Biomedical Sciences

institute: University of Maryland

description:
These data were used as preliminary results for paper:
Maternal Cocaine Administration Alters DNA Methylation in Hippocampal Neurons of Neonatal and Prepubertal Mice
Svetlana I. Novikova, Fang He, Jie Bai, Nicholas J. Curtufello, Ashiwel S. Undie and Michael S. Lidow

hyb_protocol: Hybridizations and washing were carried out as required by “3DNA Array 350: Alexa Fluor 546, Alexa Fluor 647” (Genisphere Inc.) kit protocol “Hybridization of Agilent Oligo Array” with using 2x Agilent Hybridization Buffer. The cDNAs containing the capture sequences are first hybridized to the array overnight (16 hours) in Agilent Hybridization Buffer at 60°C. On the following morning the arrays were washed for 10 minutes with 6X SSC, 0.005% Triton, then for 5 minutes in chilled (+4°C) 0.1X SSC, 0.005% Triton at room temperature and 1 minute in chilled (+4°C) 0.1X SSC. The arrays were dried and incubated at 65°C in dry incubator for 5 minutes to prewarm the array. The 3DNA capture reagents hybridization mixture was added to each array and hybridized complementary to cDNA capture sequence for 3 hours at 65°C. The arrays were washed for 10 minutes with 2X SSC, 0.005% Triton at room temperature and 10 minutes in 0.2X SSC at room temperature. The slides were dried and ready to scan.

scan_protocol: Processed slides were scanned at a GenePix 4100A personal microarray scanner (Axon Instruments) with the lasers excitation to 635 nm (emission filter 670DF40, PMT voltage 695) for Alexa 647   and 532 nm (emission filter 575DF35, PMT voltage 550) for Alexa 546 according manufacturer’s protocol. The scan resolution was 10 microns. The intensity of each spot and ratios of Alexa 647/Alexa 546 were analyzed and finally the differentially expressed genes were selected by GenePix Pro 4.1 software (Axon Instruments). Background was subtracted using “Local background correction” method in GenePix Pro 4.1 software. For quality control we utilized house-keeping genes and special Agilent’s “QC-spots” on array.

data_processing: Data of each slide were further normalized in Acuity 3.1 (Axon Instruments) software by way of locally weighted scatterplot smoothing (LOWESS) method. Normalized data were analyzed via the significant analyses for microarray (SAM) algorithm. Two-class unpaired analysis was applied to compare cocaine samples to the control. SAM calculates a false discovery rate (FDR), which is the median percentage of genes from a list that are likely to be mistakenly identified as differentially expressed. According to the SAM algorithm, genes are identified as differentially expressed based on the difference in expression among the sample groups and the consistency of this expression difference.

label: Alexa 647

source_name: P3 hippocampus, cocaine

label_protocol: For each assay 2 mkg of RNA from control tissue and 2 mg from experimental tissue were reverse transcribed using SuperScript™ II Reverse Transcriptase (Invitrogen) and 3DNA Array Detection Array 350™ Kit (Genisphere) with primers containing different ‘capture’ sequences for control and experimental samples. The obtained cDNA were  hybridized to microarray slides overnight at 60C in hybridization buffer (Agilent Technologie). For fluorescent labeling of microarray-bound cDNA, the slides will be further incubated for 3 h at 65C with Capture Reagent Hybridization Mixture from a 3DNA Array Detection Array 900™ Kit (Genisphere). In this mixture, Alexa 546 fluorochrome-incorporating dendrimers will contain single-stranded arms complimentary to the ‘capture’ sequence used in the reverse transcription of RNA from the control tissue, while Alexa 647 fluorochrome-incorporating dendrimers will contain single-stranded arms complimentary to the ‘capture’ sequence used in the reverse transcription of RNA from experimental tissue.

growth_protocol:
Laser microdissection.
Upon collection, the brains were cut into left and right hemispheres, which were subjected to freezing for 5 min on aluminium foil placed on top of dry ice. The frozen tissue was transferred to -80oC freezer for storage not exceeding 2 months after collection. For each brain hemisphere selected for the study, the initial serial coronal 12-µm-thick sections were generated on a Zeiss Cryostat (Carl Zeiss, Thornwood, NY). All sections containing hippocampus were mounted on sterile PEN foil-covered slides (Leica Microsystems, Wetzlar, Germany). Slides with sections were boxed without taking out of the cryostat. The boxed slides were transferred to -80oC freezer until use within 2 weeks from sectioning. No more than 20 slides were processed for staining and microdissection at a time. The staining was conducted in RNAs-free environment in laminar flow hood. It included the following 30-sec-long steps: 57% ethanol - distilled water - Histo-Gene stain (Arcturus, Mountain View, CA) - distilled water - 75%,  - 95%, and - 100% ethanol. After that, the sections were air-dried for 0.5-1.0 h. The laser microdissection was performed on an AS LMD Microscope System (Leica Microsystems, Wetzlar, Germany). All dissections were executed by a single investigator without knowledge of the group assignment of the samples. On every section, the pyramidal layer, encompassing the C1, C2 and C3 hippocampal regions was carefully cut out. The pieces of tissue cut out from the left hemisphere of the brains from the two 3-day-old males taken from each litter were combined and used for investigating CGI methylation. The tissue cut out from the right hemisphere of one of these brains was used for analyzing gene expression. The tissue cut out from every 5th section from the right hemisphere of the second brain was used for measuring the total DNA content, while the remaining cut out tissue was used for evaluating the global DNA methylation.

extract_protocol: Total RNA was extracted from the designated tissue by RNeasy Micro kit (Qiagen, Valencia CA). The quantity and quality of the obtained RNA was determined by NANOChip on an 2100 Bioanalyzer (Agilent, Palo Alto, CA). All samples showed the 28S to 18S ratio >1.5 and the absence of low molecular weight smears indicating the appropriateness of the RNA.

treatment_protocol: Timed pregnant CD1 dams were maintained in individual cages in a climate-controlled room on a 12/12-h light/dark cycle. They were divided into two groups. The first (COC-injected) group received subcutaneous (at the dorsum of the neck) injections of 20 mg/kg cocaine hydrochloride (Research Technology Branch, National Institute of Drug Abuse, Rockville, MD) dissolved in 200 µl of 0.9% saline, twice a day (at 8:00 AM and 8:00 PM) from 8th through 19th day of pregnancy (E8 – E19). The second (saline-control) group was subjected to the same schedule of 0.9% saline only injections. The selected period of treatment started prior to hippocampal neurogenesis and ended after all hippocampal pyramidal neurons should have been generated and began to assemble into pyramidal layer. Throughout the treatment, all mice were weighed daily, and from E8, the control and experimental animals were pair-fed, with the daily amount of food (Mouse Chow; Ralston Purina Co. Saint Louis, MO) provided to each control dam being matched to that consumed by the paired experimental dam. Water was available ad libitum. We found that this feeding regiment resulted in similar weight gains from E8 to E19 in both experimental and control animal groups. The animals were allowed to deliver at term (~gestational day 20; P0). From the time of birth, all the litters were fostered by inhalation-procedure-naive surrogate dams that had given birth within the preceding 24-72 h. Ten litters from each group were used in this study. On P3, two male pups from every litter were identified based on the anogenital distance. The selected pups were deeply anesthetized with halothane and their brains were collected. In addition, pieces of liver were dissected out to verify the sex of the animals by TaqMan Gene Expression Mm01339632-s1 Assay Kit for Sry gene-sex determining region of Y chromosome (Applied Biosystems, Foster City, CA). The assay confirmed that all the sacrificed pups were males. The anesthetized pups were used for brain collection. All experiments conducted in this study were approved by the University of Maryland Animal Care and Use Committee.

tag: P3, hippocampus, male, from cocaine-treated mother

label: Alexa 546

source_name: P3 hippocampus, saline

extract_protocol: same as channel 1

tag: P3, hippocampus, male, from saline-control mother


title: Whole Genome array hippocampus_cocaine4

description:
These data were used as preliminary results for paper:
Maternal Cocaine Administration Alters DNA Methylation in Hippocampal Neurons of Neonatal and Prepubertal Mice
Svetlana I. Novikova, Fang He, Jie Bai, Nicholas J. Cutrufello, Ashiwel S. Undie and Michael S. Lidow


title: E9_Embryo_Heterozygous_3

city: Tel Aviv

first: Illana

last: Gozes

address: Einstein

country: Israel

institute: Tel Aviv University

description: Embryo dissections: All procedures involving animals have been approved previously by the Animal Care and Use Committee Tel Aviv University. ADNP heterozygous mice were housed in a 12-h light and 12-h dark cycle facility and free access to rodent chow and water was available. Mice were checked for plug every three hours. Plug day was assigned as day 0 (E0). A definitive determination of the developmental stage of each embryo at the time of harvesting was also based on anatomical analysis. E9 whole embryos were separated from the extra embryonic tissue (yolk sac and amnion), immersed in ice-cold magnesium- and calcium-free phosphate-buffered saline, snap-frozen in liquid nitrogen, and stored at -80°C until analysis. The extra embryonic tissue was stored separately and used for genotyping. Genotyping: Genomic DNA was extracted from embryonic yolk sacs. Lysis buffer (100 mM Tris HCl pH 8.5, 5mM EDTA, 0.2% SDS, 200 mM NaCl, proteinase K 0.35 mg/ml) was added to each sample (0.5ml) followed by a 16hr incubation period at 37°C with gentle shaking. Isopropanol (0.5 ml) was then added and samples were mixed. Precipitated DNA was then transferred to a new tube containing 1ml ethanol, subjected to centrifugation at 20,000g and the resulting DNA pellet was air-dried and dissolved in 50 microLl 10 mM Tris-HCl, pH 8, 1 mM EDTA (TE) buffer. The resulting DNA was then subjected to polymerase chain reaction (PCR) amplification to check for the existence of ADNP and/or neomycin resistance gene in the embryonic genome. The PCR mixtures contained 0.5μg genomic DNA, 0.25 μM of each primer (sense and antisense), 1.5 mM MgCl2 and 3 units Taq polymerase in a final volume of 50 μl. (Buffers and enzyme were obtained from Life Technology Gibco BRL, Paisley, Scotland). PCR was performed using the following cycle parameters: 94 °C for 4 min, followed by 30 cycles, each including 94 °C for 30 s, specific annealing temperature for 40 s and elongation at 72 °C for 40 s. Reactions were terminated at 72 °C for 10 min. Control reactions containing water instead of DNA template for each primer used (PCR-) were included. RNA extraction: Two embryos from the same genotype and gestational time were pooled and RNA was isolated using Qiagene RNeasy mini kit (Quiagene, Hilden, Germany). Because of the small amounts of RNA extracted from one embryo at age E9 (~1.5μg) a two embryo pool comprised of littermates possessing the same genotype was used. For comparative experiments all embryos were at approximately the same age. Gene array: All experiments were performed using Affymetrix MOE430A oligonucleotide arrays, as described at http://www.affymetrix.com/products/arrays/specific/mouse430a_2.affx. Total RNA from each sample was used to prepare biotinylated target RNA, with minor modifications from the manufacturer's recommendations (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Briefly, 3-5 µg of mRNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Diagnostics), resulting in approximately 100-fold amplification of RNA. A complete description of procedures is available at: http://bioinf.picr.man.ac.uk/mbcf/downloads/GeneChip_Target_Prep_Protocol_CRUK_v_2.pdf. The target cDNA generated from each sample was processed according to manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Briefly, spike controls were added to 10 µg fragmented cDNA before overnight hybridization. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix Gene Chip scanner. A complete description of these procedures is available at http://bioinf.picr.man.ac.uk/mbcf/downloads/GeneChip_Hyb_Wash_Scan_Protocol_v_2_web.pdf Additionally, quality and amount of starting RNA was confirmed using an agarose gel. After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface. 3'/5' ratios for GAPDH and beta-actin were confirmed to be within acceptable limits (0.8-0.88), and BioB spike controls were found to be present on all the arrays, with BioC, BioD and CreX also present in increasing intensity.

data_processing: When scaled to a target intensity of 100 (using Affymetrix MAS 5.0 array analysis software), scaling factors for all arrays were within acceptable limits (0.607-0.982), as were background, Q values and mean intensities.

label: Biotin

source_name: Whole body

tag: Strain

value: C57BL/6, ADNP+/- Gender:mixed Age:E9 Tissue:whole embryonic body

tag: Please refer to

value: Activity-dependent neuroprotective protein:a novel gene essential for brain formation.

tag: Brain Res Dev Brain Res. 2003 Aug 12;144(1):83-90.

tag: PMID

value: 12888219 [PubMed - indexed for MEDLINE]


title: Whole Genome array hippocampus_cocaine5


title: E9_Embryo_Heterozygous_2


title: H99_HypoxiaResponse_rep4

tag: Strain H99


title: SEKH0784_CM


title: E9_Embryo_KO_1

value: C57BL/6, Genotype:ADNP gene knockout Gender:mixed Age:E9 Tissue:whole embryonic body


title: E9_Embryo_Wild Type_1

description:
Embryo dissections:
All procedures involving animals have been approved previously by the Animal Care and Use Committee Tel Aviv University. ADNP heterozygous mice were housed in a 12-h light and 12-h dark cycle facility and free access to rodent chow and water was available. Mice were checked for plug every three hours. Plug day was assigned as day 0 (E0). A definitive determination of the developmental stage of each embryo at the time of harvesting was also based on anatomical analysis. E9 whole embryos were separated from the extra embryonic tissue (yolk sac and amnion), immersed in ice-cold magnesium- and calcium-free phosphate-buffered saline, snap-frozen in liquid nitrogen, and stored at -80°C until analysis. The extra embryonic tissue was stored separately and used for genotyping.
Genotyping:

Genomic DNA was extracted from embryonic yolk sacs. Lysis buffer (100 mM Tris HCl pH 8.5, 5mM EDTA, 0.2% SDS, 200 mM NaCl, proteinase K 0.35 mg/ml) was added to each sample (0.5ml) followed by a 16hr incubation period at 37°C with gentle shaking. Isopropanol (0.5 ml) was then added and samples were mixed. Precipitated DNA was then transferred to a new tube containing 1ml ethanol, subjected to centrifugation at 20,000g and the resulting DNA pellet was air-dried and dissolved in 50 microLl 10 mM Tris-HCl, pH 8, 1 mM EDTA (TE) buffer. The resulting DNA was then subjected to polymerase chain reaction (PCR) amplification to check for the existence of ADNP and/or neomycin resistance gene in the embryonic genome. The PCR mixtures contained 0.5μg genomic DNA, 0.25 μM of each primer (sense and antisense), 1.5 mM MgCl2 and 3 units Taq polymerase in a final volume of 50 μl. (Buffers and enzyme were obtained from Life Technology Gibco BRL, Paisley, Scotland). PCR was performed using the following cycle parameters: 94 °C for 4 min, followed by 30 cycles, each including 94 °C for 30 s, specific annealing temperature for 40 s and elongation at 72 °C for 40 s. Reactions were terminated at 72 °C for 10 min. Control reactions containing water instead of DNA template for each primer used (PCR-) were included.

 RNA extraction:
Two embryos from the same genotype and gestational time were pooled and RNA was isolated using Qiagene RNeasy mini kit (Quiagene, Hilden, Germany). Because of the small amounts of RNA extracted from one embryo at age E9 (~1.5μg) a two embryo pool comprised of littermates possessing the same genotype was used. For comparative experiments all embryos were at approximately the same age.

Gene array:

All experiments were performed using Affymetrix MOE430A oligonucleotide arrays, as described at http://www.affymetrix.com/products/arrays/specific/mouse430a_2.affx. Total RNA from each sample was used to prepare biotinylated target RNA, with minor modifications from the manufacturer's recommendations (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
 Briefly, 3-5 µg of mRNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Diagnostics), resulting in approximately 100-fold amplification of RNA. A complete description of procedures is available at: http://bioinf.picr.man.ac.uk/mbcf/downloads/GeneChip_Target_Prep_Protocol_CRUK_v_2.pdf.
The target cDNA generated from each sample was processed according to manufacturer's recommendation using an Affymetrix GeneChip Instrument System
(http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Briefly, spike controls were added to 10 µg fragmented cDNA before overnight hybridization. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix Gene Chip scanner. A complete description of these procedures is available at
http://bioinf.picr.man.ac.uk/mbcf/downloads/GeneChip_Hyb_Wash_Scan_Protocol_v_2_web.pdf Additionally, quality and amount of starting RNA was confirmed using an agarose gel. After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface. 3'/5' ratios for GAPDH and beta-actin were confirmed to be within acceptable limits (0.8-0.88), and BioB spike controls were found to be present on all the arrays, with BioC, BioD and CreX also present in increasing intensity.

tag: Gender

value: mixed

tag: Tissue

value: whole embryonic body


title: E9_Embryo_KO_2


title: H99_HypoxiaResponse_rep3


title: Whole Genome array hippocampus_cocaine2