title: KJ_Pup#121_PND35_Testis_Oil-DBP

description: KJ_Pup#121_PND35_Testis_Oil-DBP_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

tag: Sample Preservation


title: KJ_Pup#114_PND35_Testis_Oil-Oil

status: Public on Nov 24 2008

type: RNA

city: RTP

first: Longlong

last: Yang

state: NC

address: 6 Davis Dr.

country: USA

institute: CIIT Centers for Health Research

description: KJ_Pup#114_PND35_Testis_Oil-Oil_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.0

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: testis exposed to oil-oil

label_protocol: standard Affymetrix protocol

extract_protocol: Extraction Method: RNAlater follwed by Qiagen AllPrep DNA/RNA Mini Kit

treatment_protocol: in vivo Treatment: Daily Corn Oil from GD12-20 via dam and single corn oil gavage at PND35, Treatment Duration: GD12-20 and PND35, Treatment Time: sacrificed 6 hr after last exposure, Vehicle for Chemical: Corn Oil, Route of Exposure: Oral Gavage of Dam during Gestation and Oral Gavage at PND35

tag: Sample Type

value: Tissue, Tissue:none, Tissue Harvest Methods:Tissue was excised from animal, detunicated, and snap frozen prior to RNA isolation.

tag: Array Type

tag: Ratio

tag: RNA Integrity Number

tag: Bioanalyzer Results

value: good

value: Snap Frozen

tag: Strain or Line

value: Fisher 344

tag: NCBI Taxonomy ID

tag: Developmental State

value: Peripubertal

tag: Sacrifice Method

value: carbon dioxide

tag: Sex

value: male

tag: Age

tag: Units of Age

value: Postnatal Day

tag: Genetic Modifications

tag: Disease State


title: KJ_Pup#105_PND35_Testis_Oil-DBP

description: KJ_Pup#105_PND35_Testis_Oil-DBP_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

source_name: testis exposed to oil-DBP

treatment_protocol: in vivo Treatment: Daily corn oil from GD12-20 via dam and single 500 mg/kg dibutyl phthalate exposure at PND35, Treatment Duration: GD12-20 and PND35, Treatment Time: sacrificed 6 hr after last exposure, Vehicle for Chemical: Corn Oil, Route of Exposure: Oral Gavage of Dam during Gestation and Oral Gavage at PND35, Dose or Concentration: 500 , Units of Dose or Concentration: mg/kg


title: KJ_Dam5_GD20_Testis_Oil

description: KJ_Dam5_GD20_Testis_Oil_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

source_name: testis exposed to oil

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen Micro Rneasy Kit

treatment_protocol: in vivo Treatment: corn oil, Treatment Repeat: Daily, Treatment Duration: GD12-20, Route of Exposure: Oral Gavage of Dam

value: Gestational Day 20

value: Gestation Day


title: KJ_Dam3_GD20_Testis_Oil

description: KJ_Dam3_GD20_Testis_Oil_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

treatment_protocol:
in vivo Treatment: corn oil, Treatment Duration: GD12-20, Route of Exposure: Oral Gavage of Dam
Treatment_2: in vivo Treatment: corn oil, Treatment Repeat: Daily, Treatment Duration: GD12-20, Route of Exposure: Oral Gavage of Dam


title: KJ_Dam16_GD20_Testis_DBP

description: KJ_Dam16_GD20_Testis_DBP_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

source_name: testis exposed to DBP

treatment_protocol: in vivo Treatment: Dibutyl Phthalate, Treatment Repeat: Daily, Treatment Duration: GD12-20, Treatment Time: Dam was sacrificed 6 hr after last DBP dosing, Vehicle for Chemical: Corn Oil, Route of Exposure: Oral Gavage of Dam, Dose or Concentration: 50, Units of Dose or Concentration: mg/kg


title: KJ_Dam18_GD20_Testis_DBP

description: KJ_Dam18_GD20_Testis_DBP_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).


title: KJ_Dam21_GD20_Testis_DBP

description: KJ_Dam21_GD20_Testis_DBP_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).


title: KJ_Pup#127_PND35_Testis_DBP-Oil

description: KJ_Pup#127_PND35_Testis_DBP-Oil_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

source_name: testis exposed to DBP-oil

treatment_protocol: in vivo Treatment: Daily dibutyl phthalate from GD12-20 via dam and single corn oil exposure at PND35, Treatment Duration: GD12-20 and PND35, Treatment Time: sacrificed 6 hr after last exposure, Vehicle for Chemical: Corn Oil, Route of Exposure: Oral Gavage of Dam during Gestation and Oral Gavage at PND35, Dose or Concentration: 50, Units of Dose or Concentration: mg/kg


title: KJ_Pup#111_PND35_Testis_Oil-DBP

description: KJ_Pup#111_PND35_Testis_Oil-DBP_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).


title: KJ_Pup#104_PND35_Testis_Oil-Oil

description: KJ_Pup#104_PND35_Testis_Oil-Oil_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen Clean up


title: KJ_Dam4_GD20_Testis_Oil

description: KJ_Dam4_GD20_Testis_Oil_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).


title: KJ_Pup#110_PND35_Testis_Oil-Oil

description: KJ_Pup#110_PND35_Testis_Oil-Oil_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).


title: KJ_Dam19_GD20_Testis_DBP

description: KJ_Dam19_GD20_Testis_DBP_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).


title: KJ_Dam2_GD20_Testis_Oil

description: KJ_Dam2_GD20_Testis_Oil_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

tag: Pooled from Multiple Samples

value: Yes


title: Case 45.1, Normal, Grade 2, Gene Expression experiment

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

hyb_protocol: See label protocol

scan_protocol: Agilent scanner

data_processing: Loess-normalized log2 ratio

organism: Homo sapiens

label_protocol: Due to the antisense orientation of the amplified RNA samples, a labelling protocol based on a method published by Schlingemann et al.  was used to generate fluorescent labelled antisense cDNA for hybridisation to sense-oriented oligonucleotide microarrays. Briefly, 1 microgram of amplified RNA was reverse transcribed using random primers (pdN6, Amersham Biosciences) followed by RNase H digestion. cDNA labelling by Klenow fragment and amino-allyl incorporation was performed using the Bioprime Kit with a modified protocol (see Supplementary Methods for detailed description of labelling protocol). The appropriate NHS ester Cy dye (Cy3 or Cy5, Amersham Biosciences) was then coupled to the test and reference samples.

extract_protocol:
DCIS foci were isolated from 10 micrometer serial frozen tissue sections by laser capture microdissection (PALM Microlaser Technologies AG, Bernried, Germany), guided by interval sections stained with haematoxylin and eosin. In addition, LCIS and co-existing areas of atypical ductal hyperplasia (ADH), proliferative disease without atypia (PDWA) and benign epithelium were sampled from a proportion of cases. For in situ lesions care was taken to capture pure intraduct cell populations. Benign epithelium samples were lobular tissue collected with intralobular stroma.

RNA was extracted from microdissected tissue using the Absolutely RNA MicroPrep Kit (Stratagene, CA, USA) and quantitated using the RiboGreen Quantitation Reagent (Molecular Probes, OR, USA) both according to the manufacturers instructions. RNA quality was assessed by running RNA isolated from each tissue on the Agilent 2100 Bioanalyser (Agilent Technologies, Victoria, Australia). This showed a degree of RNA degradation in all samples but 18S and 28S ribosomal bands were clearly distinguished in 39/46 (84.8%) of cases. RNA was subject to two rounds of amplification using the RiboAmp RNA amplification kit (Acturus, CA, USA) according to the manufacturer’s instructions. For samples with sufficient RNA available, 100ng was used in the initial amplification reaction. Lesser initial quantities (50ng or 20ng) were used from smaller samples.

tag: Sample Type:Normal;Grade:2

source_name: Stratagene Universal Human Reference RNA


title: Case 50, DCIS, Grade 2, Gene Expression experiment

tag: Sample Type:DCIS;Grade:2

tag: Stratagene Universal Human Reference RNA


title: Case 48, DCIS, Grade 2, Gene Expression experiment


title: Case 46, LCIS, Grade 3, Gene Expression experiment

tag: Sample Type:LCIS;Grade:3


title: Case 39, DCIS, Grade 3, Gene Expression experiment

tag: Sample Type:DCIS;Grade:3


title: Case 37.1, LG DCIS, Grade 1, Gene Expression experiment

tag: Sample Type:LG DCIS;Grade:1


title: Case 45, DCIS, Grade 2, Gene Expression experiment


title: Case 42, DCIS, Grade 3, Gene Expression experiment


title: Case 41, DCIS, Grade 2, Gene Expression experiment


title: Case 38, DCIS, Grade NA, Gene Expression experiment

tag: Sample Type:DCIS;Grade:NA


title: Case 28, DCIS, Grade 2, Gene Expression experiment


title: Case 32, DCIS, Grade 1, Gene Expression experiment

tag: Sample Type:DCIS;Grade:1


title: Case 30, DCIS, Grade 3, Gene Expression experiment


title: Case 43, DCIS, Grade 1, Gene Expression experiment


title: Case 40, DCIS, Grade 2, Gene Expression experiment


title: Case 35, DCIS, Grade 2, Gene Expression experiment


title: Case 29, DCIS, Grade 3, Gene Expression experiment


title: Case 26, DCIS, Grade 2, Gene Expression experiment


title: Case 25, DCIS, Grade 1, Gene Expression experiment


title: Case 27, DCIS, Grade 1, Gene Expression experiment


title: Case 29.1, Normal, Grade 3, Gene Expression experiment

tag: Sample Type:Normal;Grade:3


title: Case 44, DCIS, Grade 2, Gene Expression experiment


title: Case 24, DCIS, Grade 1, Gene Expression experiment


title: Case 37, IG DCIS, Grade 1, Gene Expression experiment

tag: Sample Type:IG DCIS;Grade:1


title: Case 31, DCIS, Grade 3, Gene Expression experiment


title: Case 34, DCIS, Grade 1, Gene Expression experiment


title: Case 21, DCIS, Grade 3, Gene Expression experiment


title: Case 28.1, ADH, Grade 2, Gene Expression experiment

tag: Sample Type:ADH;Grade:2


title: Case 22, DCIS, Grade 1, Gene Expression experiment


title: Case 23, DCIS, Grade 2, Gene Expression experiment


title: Case 20, DCIS, Grade 2, Gene Expression experiment


title: Case 20.1, Normal, Grade 2, Gene Expression experiment


title: Case 16, DCIS, Grade 1, Gene Expression experiment


title: Case 19, DCIS, Grade 2, Gene Expression experiment


title: Case 13, DCIS, Grade 2, Gene Expression experiment


title: Case 17, DCIS, Grade 2, Gene Expression experiment


title: Case 15, DCIS, Grade 2, Gene Expression experiment


title: Case 18, DCIS, Grade 2, Gene Expression experiment


title: Case 10.1, ADH, Grade 1, Gene Expression experiment

tag: Sample Type:ADH;Grade:1


title: Case 18.1, ADH, Grade 2, Gene Expression experiment


title: Case 11, DCIS, Grade NA, Gene Expression experiment


title: Case 12, DCIS, Grade 1, Gene Expression experiment


title: Case 7, DCIS, Grade 3, Gene Expression experiment


title: Case 10, DCIS, Grade 1, Gene Expression experiment


title: Case 6, DCIS, Grade 1, Gene Expression experiment


title: Case 14, DCIS, Grade 2, Gene Expression experiment


title: Case 9, DCIS, Grade 3, Gene Expression experiment


title: Case 9.2, PDWA, Grade 3, Gene Expression experiment

tag: Sample Type:PDWA;Grade:3


title: Case 5.1, Normal, Grade 2, Gene Expression experiment


title: Case 2.2, ADH, Grade 1, Gene Expression experiment


title: Case 8.1, Normal, Grade 2, Gene Expression experiment


title: Case 8, DCIS, Grade 2, Gene Expression experiment


title: Case 3.1, Normal, Grade NA, Gene Expression experiment

tag: Sample Type:Normal;Grade:NA


title: Case 5, DCIS, Grade 2, Gene Expression experiment


title: Case 2.1, LCIS, Grade 1, Gene Expression experiment

tag: Sample Type:LCIS;Grade:1


title: Case 2, DCIS, Grade 1, Gene Expression experiment


title: Case 4, DCIS, Grade 1, Gene Expression experiment


title: Case 9.1, Normal, Grade 3, Gene Expression experiment


title: Case 3, DCIS, Grade NA, Gene Expression experiment


title: Case 1, HG DCIS, Grade 3, Gene Expression experiment

tag: Sample Type:HG DCIS;Grade:3


title: Case 1.1, IG DCIS, Grade 3, Gene Expression experiment

tag: Sample Type:IG DCIS;Grade:3


title: Case 48, DCIS, Grade 2, CGH experiment

type: genomic

description: Case 48, DCIS, Grade 2, CGH experiment

data_processing: Median-centered Log2 ratio

molecule: genomic DNA

source_name: Case 48, DCIS, Grade 2, CGH experiment

label_protocol: DNA was labelled with the Bioprime Kit (Invitrogen) using a modified protocol. Briefly, 3 micrograms of amplified test and reference DNA were directly labelled with either Cy3-dUTP or Cy5-dUTP (see Supplementary Methods for detailed description of labelling protocol). Samples were hybridised to the same oligonucleotide microarrays used for gene expression profiling.

extract_protocol:
DCIS foci were isolated from 10 micrometer serial frozen tissue sections by laser capture microdissection (PALM Microlaser Technologies AG, Bernried, Germany), guided by interval sections stained with haematoxylin and eosin. In addition, LCIS and co-existing areas of atypical ductal hyperplasia (ADH), proliferative disease without atypia (PDWA) and benign epithelium were sampled from a proportion of cases. For in situ lesions care was taken to capture pure intraduct cell populations. Benign epithelium samples were lobular tissue collected with intralobular stroma.

DNA was extracted from laser microdissected material using the QIAamp DNA Micro Kit (Qiagen Inc., Valencia, CA, USA) and quantitated using the PicoGreen dsDNA Quantitation Reagent (Molecular Probes) both according to the manufacturers instructions. Ten nanograms of DNA was amplified using the GenomiPhi DNA Amplification Kit (Amersham Biosciences, Piscataway, NJ, NY) according to the manufacturer’s instructions.

source_name: Promega Normal male genomic DNA

tag: Promega Normal male DNA


title: Case 35, DCIS, Grade 2, CGH experiment

description: Case 35, DCIS, Grade 2, CGH experiment

source_name: Case 35, DCIS, Grade 2, CGH experiment

tag: Sample Type:DCIS;Grade:2


title: Case 42, DCIS, Grade 3, CGH experiment

description: Case 42, DCIS, Grade 3, CGH experiment

source_name: Case 42, DCIS, Grade 3, CGH experiment


title: Case 43, DCIS, Grade 1, CGH experiment

description: Case 43, DCIS, Grade 1, CGH experiment

source_name: Case 43, DCIS, Grade 1, CGH experiment


title: Case 46, LCIS, Grade 3, CGH experiment

description: Case 46, LCIS, Grade 3, CGH experiment

source_name: Case 46, LCIS, Grade 3, CGH experiment


title: Case 44, DCIS, Grade 2, CGH experiment

description: Case 44, DCIS, Grade 2, CGH experiment

source_name: Case 44, DCIS, Grade 2, CGH experiment


title: Case 40, DCIS, Grade 2, CGH experiment

description: Case 40, DCIS, Grade 2, CGH experiment

source_name: Case 40, DCIS, Grade 2, CGH experiment


title: Case 37, IG DCIS, Grade 1, CGH experiment


title: Case 39, DCIS, Grade 3, CGH experiment

description: Case 39, DCIS, Grade 3, CGH experiment

source_name: Case 39, DCIS, Grade 3, CGH experiment


title: Case 38, DCIS, Grade NA, CGH experiment

description: Case 38, DCIS, Grade NA, CGH experiment

source_name: Case 38, DCIS, Grade NA, CGH experiment


title: Case 41, DCIS, Grade 2, CGH experiment

description: Case 41, DCIS, Grade 2, CGH experiment

source_name: Case 41, DCIS, Grade 2, CGH experiment


title: Case 45, DCIS, Grade 2, CGH experiment

description: Case 45, DCIS, Grade 2, CGH experiment

source_name: Case 45, DCIS, Grade 2, CGH experiment


title: Case 50, DCIS, Grade 2, CGH experiment

description: Case 50, DCIS, Grade 2, CGH experiment

source_name: Case 50, DCIS, Grade 2, CGH experiment


title: Case 37.1, LG DCIS, Grade 1, CGH experiment


title: Case 34, DCIS, Grade 1, CGH experiment

description: Case 34, DCIS, Grade 1, CGH experiment

source_name: Case 34, DCIS, Grade 1, CGH experiment


title: Case 30, DCIS, Grade 3, CGH experiment

description: Case 30, DCIS, Grade 3, CGH experiment

source_name: Case 30, DCIS, Grade 3, CGH experiment


title: Case 32, DCIS, Grade 1, CGH experiment

description: Case 32, DCIS, Grade 1, CGH experiment

source_name: Case 32, DCIS, Grade 1, CGH experiment


title: Case 31, DCIS, Grade 3, CGH experiment

description: Case 31, DCIS, Grade 3, CGH experiment

source_name: Case 31, DCIS, Grade 3, CGH experiment


title: Case 29, DCIS, Grade 3, CGH experiment

description: Case 29, DCIS, Grade 3, CGH experiment

source_name: Case 29, DCIS, Grade 3, CGH experiment


title: Case 28, DCIS, Grade 2, CGH experiment

description: Case 28, DCIS, Grade 2, CGH experiment

source_name: Case 28, DCIS, Grade 2, CGH experiment

source_name: Promega Normal male genomic DNA


title: Case 27, DCIS, Grade 1, CGH experiment

description: Case 27, DCIS, Grade 1, CGH experiment

source_name: Case 27, DCIS, Grade 1, CGH experiment


title: Case 24, DCIS, Grade 1, CGH experiment

description: Case 24, DCIS, Grade 1, CGH experiment

source_name: Case 24, DCIS, Grade 1, CGH experiment


title: Case 28.1, ADH, Grade 2, CGH experiment

description: Case 28.1, ADH, Grade 2, CGH experiment

source_name: Case 28.1, ADH, Grade 2, CGH experiment


title: Case 25, DCIS, Grade 1, CGH experiment

description: Case 25, DCIS, Grade 1, CGH experiment

source_name: Case 25, DCIS, Grade 1, CGH experiment


title: Case 26, DCIS, Grade 2, CGH experiment

description: Case 26, DCIS, Grade 2, CGH experiment

source_name: Case 26, DCIS, Grade 2, CGH experiment


title: Case 22, DCIS, Grade 1, CGH experiment

description: Case 22, DCIS, Grade 1, CGH experiment

source_name: Case 22, DCIS, Grade 1, CGH experiment


title: MEFB H3K4me3 MS9

city: Vienna

first: Florian

middle: M

last: Pauler

state: Vienna

address: Dr Bohrgasse 9/4

country: Austria

institute: CeMM

description: Chip-chip MEF cells H3K4me3

hyb_protocol: samples were hybridized by Nimblegen Iceland

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: TUKEY NORMALISED log2 (ChIP/Input DNA) ratio

organism: Mus musculus

source_name: H3K4me3 ChIP DNA from MEFB cells

label_protocol: Samples were T7 amplified as published (Regha et al., 2007 PMID: 17679087) and labeled and hybridized by Nimblegen Iceland (http://www.nimblegen.com).

growth_protocol: MEF cell lines were cultured according to standard protocols

extract_protocol: Native ChIP was performed as published (Regha et al., 2007 PMID: 17679087).

treatment_protocol: MEFF and MEFB1 are spontaneously immortalized 12.5dpc mouse embryo fibroblast cells. The 93Mb long Chr.17 sequence in the two cell lines is identical with the exception of reciprocal Thp deletions on the paternal and maternal chromosome. The Thp deletion spans at least 4,6Mbp spanning the region between the genes T and Sod2 (8,6Mbp-13,2Mbp Mouse July 2007 mm9) and contains the 400kb Igf2r imprinted gene cluster (Regha et al., 2007).

tag: Genotype

value: +/Thp

tag: Age

value: cell line

tag: Tissue

value: embryo

tag: Strain

value: FVBN

tag: Antibody

tag: Type

value: Native ChIP

source_name: Input DNA from +/Thp MEF cells

label_protocol: Samples were T7 amplified as published (Regha et al., 2007 PMID: 17679087) and labeled by Nimblegen Iceland (http://www.nimblegen.com).

extract_protocol: see chanel 1

value: Input


title: Case 23, DCIS, Grade 2, CGH experiment

description: Case 23, DCIS, Grade 2, CGH experiment

source_name: Case 23, DCIS, Grade 2, CGH experiment


title: MEFB polyA RNA MS57

type: mixed

description: RNA-chip MEF cells polyA RNA

molecule: polyA RNA

source_name: polyA RNA from MEFB cells

label_protocol: Samples were labeled and hybridized by Nimblegen Iceland (http://www.nimblegen.com).

extract_protocol: total RNA was extracted, DNase1 treated and enriched for polyA RNA according to standard protocols. Double stranded cDNA (ds cDNA) was prepared according to standard protocols (Regha et al., 2007 PMID: 17679087).

value: ds cDNA from polyA RNA

value: sonicated genomic DNA


title: MEFF H3K4me3 MS43

description: Chip-chip MEF cells H3K4me3

source_name: H3K4me3 ChIP DNA from MEFF cells

value: Thp/+

source_name: Input DNA from Thp/+ MEF cells


title: MEFF polyA RNA MS58

description: RNA-chip MEF cells polyA RNA

source_name: polyA RNA from MEFF cells


title: MEFF polyA RNA MS59

description: RNA-chip MEF cells polyA RNA


title: MEFF total RNA MS63

description: RNA-chip MEF cells total RNA

source_name: total RNA from MEFF cells

extract_protocol: total RNA was extracted and DNase1 trated according to standard protocols. Double stranded cDNA (ds cDNA) was prepared according to standard protocols (Regha et al., 2007 PMID: 17679087).

value: ds cDNA from total RNA


title: MEFB H4Ac MS19

description: Chip-chip MEF cells H4Ac

source_name: H4Ac ChIP DNA from MEFB cells


title: MEFF total RNA MS62

description: RNA-chip MEF cells total RNA


title: MEFF H3K9Ac MS38

description: Chip-chip MEF cells H3K9Ac

source_name: H3K9Ac ChIP DNA from MEFF cells


title: Case 16, DCIS, Grade 1, CGH experiment

description: Case 16, DCIS, Grade 1, CGH experiment

source_name: Case 16, DCIS, Grade 1, CGH experiment

tag: Sample Type:DCIS;Grade:1

source_name: Promega Normal male genomic DNA


title: Case 18, DCIS, Grade 2, CGH experiment

description: Case 18, DCIS, Grade 2, CGH experiment

source_name: Case 18, DCIS, Grade 2, CGH experiment


title: Case 20, DCIS, Grade 2, CGH experiment

description: Case 20, DCIS, Grade 2, CGH experiment

source_name: Case 20, DCIS, Grade 2, CGH experiment


title: Case 18.1, ADH, Grade 2, CGH experiment

description: Case 18.1, ADH, Grade 2, CGH experiment

source_name: Case 18.1, ADH, Grade 2, CGH experiment


title: MEFF H4Ac MS20

description: Chip-chip MEF cells H4Ac

source_name: H4Ac ChIP DNA from MEFF cells


title: Case 19, DCIS, Grade 2, CGH experiment

description: Case 19, DCIS, Grade 2, CGH experiment

source_name: Case 19, DCIS, Grade 2, CGH experiment


title: Case 21, DCIS, Grade 3, CGH experiment

description: Case 21, DCIS, Grade 3, CGH experiment

source_name: Case 21, DCIS, Grade 3, CGH experiment

tag: Sample Type:DCIS;Grade:3


title: MEFB H3K9Ac MS37

description: Chip-chip MEF cells H3K9Ac

source_name: H3K9Ac ChIP DNA from MEFB cells

source_name: Input DNA from +/Thp MEF cells


title: MEFB H3K9Ac MS33

description: Chip-chip MEF cells H3K9Ac


title: MEFF H3K9Ac MS34

description: Chip-chip MEF cells H3K9Ac


title: MEFF H3Ac MS22

description: Chip-chip MEF cells H3Ac

source_name: H3Ac ChIP DNA from MEFF cells


title: Case 15, DCIS, Grade 2, CGH experiment

description: Case 15, DCIS, Grade 2, CGH experiment

source_name: Case 15, DCIS, Grade 2, CGH experiment


title: MEFB H3K9me3 MS8C

description: Chip-chip MEF cells H3K9me3

source_name: H3K9me3 ChIP DNA from MEFB cells


title: Case 17, DCIS, Grade 2, CGH experiment

description: Case 17, DCIS, Grade 2, CGH experiment

source_name: Case 17, DCIS, Grade 2, CGH experiment


title: MEFF H3K9me3 MS26

description: Chip-chip MEF cells H3K9me3

source_name: H3K9me3 ChIP DNA from MEFF cells

source_name: Input DNA from Thp/+ MEF cells


title: MEFF H3K9me3 MS25

description: Chip-chip MEF cells H3K9me3


title: MEFB H3K9me3 MS10

description: Chip-chip MEF cells H3K9me3


title: Case 11, DCIS, Grade NA, CGH experiment

description: Case 11, DCIS, Grade NA, CGH experiment

source_name: Case 11, DCIS, Grade NA, CGH experiment

tag: Sample Type:DCIS;Grade:NA


title: MEFB H4Ac MS23

description: Chip-chip MEF cells H4Ac

source_name: H4Ac ChIP DNA from MEFB cells


title: Case 14, DCIS, Grade 2, CGH experiment

description: Case 14, DCIS, Grade 2, CGH experiment

source_name: Case 14, DCIS, Grade 2, CGH experiment

source_name: Promega Normal male genomic DNA


title: Case 10, DCIS, Grade 1, CGH experiment

description: Case 10, DCIS, Grade 1, CGH experiment

source_name: Case 10, DCIS, Grade 1, CGH experiment


title: Case 7, DCIS, Grade 3, CGH experiment

description: Case 7, DCIS, Grade 3, CGH experiment

source_name: Case 7, DCIS, Grade 3, CGH experiment


title: Case 3, DCIS, Grade NA, CGH experiment

description: Case 3, DCIS, Grade NA, CGH experiment

source_name: Case 3, DCIS, Grade NA, CGH experiment


title: Case 10.1, ADH, Grade 1, CGH experiment

description: Case 10.1, ADH, Grade 1, CGH experiment

source_name: Case 10.1, ADH, Grade 1, CGH experiment

tag: Sample Type:ADH;Grade:1


title: Case 1.1, IG DCIS, Grade 3, CGH experiment


title: Case 8, DCIS, Grade 2, CGH experiment

description: Case 8, DCIS, Grade 2, CGH experiment

source_name: Case 8, DCIS, Grade 2, CGH experiment


title: Case 9, DCIS, Grade 3, CGH experiment

description: Case 9, DCIS, Grade 3, CGH experiment

source_name: Case 9, DCIS, Grade 3, CGH experiment


title: MEFB H3Ac MS17

description: Chip-chip MEF cells H3Ac

source_name: H3Ac ChIP DNA from MEFB cells

source_name: Input DNA from +/Thp MEF cells


title: Case 6, DCIS, Grade 1, CGH experiment

description: Case 6, DCIS, Grade 1, CGH experiment

source_name: Case 6, DCIS, Grade 1, CGH experiment


title: Case 12, DCIS, Grade 1, CGH experiment

description: Case 12, DCIS, Grade 1, CGH experiment

source_name: Case 12, DCIS, Grade 1, CGH experiment


title: Case 4, DCIS, Grade 1, CGH experiment

description: Case 4, DCIS, Grade 1, CGH experiment

source_name: Case 4, DCIS, Grade 1, CGH experiment


title: Case 13, DCIS, Grade 2, CGH experiment

description: Case 13, DCIS, Grade 2, CGH experiment

source_name: Case 13, DCIS, Grade 2, CGH experiment


title: MEFF H4Ac MS24

description: Chip-chip MEF cells H4Ac

source_name: H4Ac ChIP DNA from MEFF cells

source_name: Input DNA from Thp/+ MEF cells


title: Case 1, HG DCIS, Grade 3, CGH experiment


title: Case 5, DCIS, Grade 2, CGH experiment

description: Case 5, DCIS, Grade 2, CGH experiment

source_name: Case 5, DCIS, Grade 2, CGH experiment


title: MEFF H4K20me1 MS16

description: Chip-chip MEF cells H4K20me1

source_name: H4K20me1 ChIP DNA from MEFF cells


title: MEFF H4K20me1 MS15

description: Chip-chip MEF cells H4K20me1


title: MEFB H4K20me1 MS14

description: Chip-chip MEF cells H4K20me1

source_name: H4K20me1 ChIP DNA from MEFB cells


title: MEFB H4K20me1 MS13

description: Chip-chip MEF cells H4K20me1


title: MEFB H3Ac MS21

description: Chip-chip MEF cells H3Ac


title: Trial2 Subject ID G03 Day 7

status: Public on Nov 23 2008

city: Atlanta

first: Troy

middle: D

last: Querec

state: GA

address: 954 Gatewood Rd

department: Emory Vaccine Rearch Center

institute: Emory University

description: Gene expression from YF-17D Vaccinee

hyb_protocol: After hybridization on Human U133 Plus 2.0 Arrays for 16 hours at 45 C and 60 rpm in a Hybridization Oven 640, slides were washed and stained with a Fluidics Station 450.

scan_protocol: Scanning was performed on a 7th generation GeneChip Scanner 3000, and the Affymetrix GCOS software was used to perform image analysis and generate raw intensity data.

data_processing: For this analysis, we used Affymetrix Human Genome U133 Plus 2.0 Array, but instead of using Affymetrix’s sequence clusters to define genes, gene sequence clusters were RMA pre-processed and normalized with the UniGene (Build 199, January 16, 2007) Custom CDF Version 9 available from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp to yield a list of 20,077 genes. Log2 fold changes versus day 0 (unvaccinated) of RMA pre-processed gene intensities for each subject are linked to the submission as a supplementary file.

label: Biotin

label_protocol: Total RNA sample quality was evaluated by spectrophotometer to determine quantity, protein contamination and organic solvent contamination, and an Agilent 2100 Bioanalyzer was used to check for RNA degradation.  Two-round IVT amplification and labeling was performed starting with 50 ng intact, uncontaminated total RNA per sample, following the Affymetrix protocol (http://www.affymetrix.com/Auth/support/downloads/manuals/expression_print_manual.zip) (Affymetrix, CA).

extract_protocol: Following PMBC isolation from CPT, 2 x 106 cells were lysed in 1 ml of TRIzol and stored at -80C (Cat# 15596-026; Invitrogen Life Technologies).  After all time points were collected for a subject, the samples were thawed, and the RNA isolation proceeded according to the manufacturer’s protocol.

tag: PBMC

tag: T Cell Activation

tag: Neuralizing Antibody Titer

tag: Time

tag: Trial


title: Trial2 Subject ID G01 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID G01 Day 0

description: Gene expression from YF-17D Vaccinee


title: rice grain_mature_rep3

city: Saint Louis

first: Sara

middle: Elizabeth

last: Heisel

state: MO

address: 800 North Lindbergh

department: Biotechnology

institute: Monsanto

description:
total endogenous small RNAs isolated from mature rice grain using gel purification and adaptor-mediated ligation.
library_strategy: EST
library_source: non-genomic
library_selection: PCR

data_processing: Small RNA inserts in the raw sequences were parsed by locating the 5’ and 3’ adaptors to obtain strand and position information by Perl scripts.

organism: Oryza sativa

source_name: mature rice grain

growth_protocol: Plant materials and RNA isolation. Oryza sativa spp. japonica cv. Nipponbare was used for small RNA library construction.  Plant material for RNA isolation was obtained from dehulled mature grain and 23 day old seedlings planted from the same seed lot and grown in a greenhouse under non-stress conditions. Total RNA was isolated from plant tissues using TRIzol reagent (Invitrogen).

extract_protocol: Sixteen- to 26-nt siRNAs from 500 µg of total RNA were gel extracted from a 17% denaturing acrylimide gel (0.5X TBE, 0.42 g/ml urea, 17% 19:1 acrylimide:bisacrylimide). After elution from the gel (twice incubated at 4°C in 0.3 M NaCl for several hours), siRNAs were precipitated. A 5' adapter was ligated to the siRNA (20 uM adapter, 15% DMSO, 50 mM Tris•HCl, pH 7.6, 10 mM MgCl2, 10 mM 2-ME, 0.2 mM ATP, 0.1 mg/ml BSA, 1 unit/µl T4 RNA ligase, 1 unit/µl RNase inhibitor) before gel extraction (30- to 50-nt fragments) and elution as above. After precipitation, a 3' adapter was ligated in the same manner, gel extracted (50-70 nt), and precipitated. Adapter-ligated siRNA was subjected to reverse transcription using standard protocols. RT was stopped by addition of 150 mM KOH, 20 mM Tris-base and neutralized with HCl (final volume approximately 180 µL). 50 µL of this was used as template for PCR. Purified amplicons were sent to 454 Life Sciences for sequencing.

tag: japonica Nipponbare, mature grain


title: Trial2 Subject ID G03 Day 0

description: Gene expression from YF-17D Vaccinee


title: 4552/4554/4556/4558

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
This sample consists of four replicate RNA extractions performed of each genotype using independent pools of plants.
hmgb1#1 (Cy5) vs. Col-0#1 (Cy3)
Col-0#2 (Cy5) vs. hmgb1#2 (Cy3) dye-swap
hmgb1#3 (Cy5) vs. Col-0#3 (Cy3)
Col-0#5 (Cy5) vs. hmgb1#4 (Cy3) dye-swap
The data were normalized over all 4 hybridizations to obtain one, single log-ratio(Sample/Reference).

hyb_protocol: For each color 10 pmol incorporated dye was fragmented and resuspended in 500 ml hybridization solution (Agilent).The arrays were hybridized in microarray hybridization chambers (Agilent) overnight at 60ºC.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent) using the `extended dynamic range' (scanner control software v7 update) and images were processed with the Feature Extraction Software version 9.5 (Agilent).

data_processing: Empty, control spots, and spots with signals below the background in all arrays and in both channels (according to gIsPosAndSignif and rIsPosAndSignif features obtained from the Agilent Feature Extraction software v9.5.1.1) were removed prior to the analysis.  The Agilent processed signal values (i.e., feature gProcessedSignal for the Cy3 signal and rProcessedSignal for the Cy5 signal from Agilent Feature Extraction v9.5.1.1) were used for the data analysis.  Using Limma (Bioconductor package http://bioconductor.org/packages/2.1/bioc/html/limma.html), a linear model was fitted and based on the resulting coefficients, contrasts Sail versus Col-0 were fitted.

organism: Arabidopsis thaliana

label_protocol: Probes were prepared from 1 µg total RNA using the Low RNA input Fluorescent Linear Amplification Kit-plus for dual color (Agilent). Probes were verified for amplification yield and incorporation efficiency by measuring the DNA concentration at 280 nm, Cy5 incorporation at 650 nm using a Nanodrop.

extract_protocol: RNA was extracted from 10-day old Col-0 and hmgb1 seedlings using the RNeasy Plant Mini Kit (Qiagen).

tag: Arabidopsis thaliana (ecotype Col-0) homozygous for a T-DNA insertion in the HMGB1 gene,  confirmed by PCR and Southern blot. RNA was isolated from 10d seedlings.

label_protocol: Probes were prepared from 1 µg total RNA using the Low RNA input Fluorescent Linear Amplification Kit-plus for dual color (Agilent). Probes were verified for amplification yield and incorporation efficiency by measuring the DNA concentration at 280 nm, Cy3 incorporation at 550 nm.

tag: Arabidopsis thaliana (ecotype Col-0) - reference for the T-DNA insertion mutant. RNA was isolated from 10d seedlings.


title: rice grain_mature_rep2


title: Trial2 Subject ID E09 Day 3

description: Gene expression from YF-17D Vaccinee


title: rice seedling_23 day old_rep1

description:
total endogenous small RNAs isolated from 23 day old rice seedling, germinated from seed source used for mature rice grain libraries.  Small RNAs isolated using gel purification and adaptor-mediated ligation.
library_strategy: EST
library_source: non-genomic
library_selection: PCR

source_name: 23 day old rice seedling

tag: japonica Nipponbare, 23 day old seedling


title: rice grain_mature_rep1


title: MEFF H4K20me3 MS32

description: Chip-chip MEF cells H4K20me3

source_name: H4K20me3 ChIP DNA from MEFF cells

tag: Genotype

tag: Age

tag: Tissue


title: Trial2 Subject ID E09 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID E09 Day 7

description: Gene expression from YF-17D Vaccinee


title: MEFB H4K20me3 MS12

description: Chip-chip MEF cells H4K20me3

source_name: H4K20me3 ChIP DNA from MEFB cells

tag: Strain

tag: Antibody

tag: Type


title: Trial2 Subject ID G03 Day 3

description: Gene expression from YF-17D Vaccinee


title: MEFB H3K27me3 MS35

description: Chip-chip MEF cells H3K27me3

source_name: H3K27me3 ChIP DNA from MEFB cells


title: Trial2 Subject ID E08 Day 3

description: Gene expression from YF-17D Vaccinee


title: MEFF H3K27me3 MS40

description: Chip-chip MEF cells H3K27me3

source_name: H3K27me3 ChIP DNA from MEFF cells


title: Trial2 Subject ID E08 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID E08 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID D03 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID D03 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID E04 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID G01 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID D03 Day 7

description: Gene expression from YF-17D Vaccinee


title: MEFF H3Ac MS18

description: Chip-chip MEF cells H3Ac

source_name: H3Ac ChIP DNA from MEFF cells


title: Trial2 Subject ID B08 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID B09 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID B09 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID B09 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID B08 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID E04 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID E04 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID B08 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID B02 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID B03 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID B03 Day 0

description: Gene expression from YF-17D Vaccinee


title: MEFF H3K27me3 MS39

description: Chip-chip MEF cells H3K27me3


title: MEFF H3K4me3 MS6

description: Chip-chip MEF cells H3K4me3

source_name: H3K4me3 ChIP DNA from MEFF cells


title: Trial2 Subject ID B02 Day 0

description: Gene expression from YF-17D Vaccinee


title: MEFB H3K9me3 MS8

description: Chip-chip MEF cells H3K9me3

source_name: H3K9me3 ChIP DNA from MEFB cells

source_name: Input DNA from +/Thp MEF cells


title: MEFB H3K4me2 MS2

description: Chip-chip MEF cells H3K4me2

source_name: H3K4me2 ChIP DNA from MEFB cells


title: MEFF H3K4me2 MS3

description: Chip-chip MEF cells H3K4me2

source_name: H3K4me2 ChIP DNA from MEFF cells


title: Trial1 Subject ID 1915 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1916 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1912 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1913 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1916 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1914 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1916 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1915 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1912 Day 21

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1914 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1912 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1912 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1911 Day 21

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1913 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1913 Day 21

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1914 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1913 Day 3

description: Gene expression from YF-17D Vaccinee


title: MEFF H3K4me2 MS4

description: Chip-chip MEF cells H3K4me2


title: Trial1 Subject ID 1912 Day 1

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID B02 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1915 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1911 Day 1

description: Gene expression from YF-17D Vaccinee


title: MEFB H3K4me2 MS1

description: Chip-chip MEF cells H3K4me2


title: Trial1 Subject ID 1911 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1911 Day 3

description: Gene expression from YF-17D Vaccinee


title: MEFB H3K4me3 MS7

description: Chip-chip MEF cells H3K4me3

source_name: H3K4me3 ChIP DNA from MEFB cells


title: Trial1 Subject ID 1911 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1910 Day 1

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1910 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1910 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1909 Day 1

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1910 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1908 Day 21

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1909 Day 21

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1908 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1906 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1907 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1907 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1909 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1908 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1906 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1904 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1910 Day 21

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1909 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1913 Day 1

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1906 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1908 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1904 Day 3

description: Gene expression from YF-17D Vaccinee


title: Trial2 Subject ID B03 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1907 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1909 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1908 Day 1

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1903 Day 7

description: Gene expression from YF-17D Vaccinee


title: Subject ID 126 time 12hr YF-17D stimulation

description: Gene expression from YF-17D Vaccinee

hyb_protocol: After hybridization on Human Genome U133 A 2.0 Arrays for 16 hours at 45 C and 60 rpm in a Hybridization Oven 640, slides were washed and stained with a Fluidics Station 450.

data_processing: For this analysis, we used Affymetrix Human Genome U133 A 2.0 Array, but instead of using Affymetrix’s sequence clusters to define genes, gene sequence clusters were RMA pre-processed and normalized with the UniGene (Build 199, January 16, 2007) Custom CDF Version 9 available from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp to yield a list of 11,639 genes.

growth_protocol: PBMCs from 2 healthy unvaccinated donors were isolated and plated at 1 x 106 cells per well in 48-well plates with 1 ml RPMI with 10% FBS and penicillin/streptomycin.  The cells were cultured in the presence or absence of YF-17D at a MOI of 1.  After 3 and 12 hours, RNA was isolated from the cells and processed for microarray analysis.

extract_protocol: Following culture, RNA was isolated with 1 ml of TRIzol following the manufacturer's protocol (Cat# 15596-026; Invitrogen Life Technologies).

tag: Stimulation


title: Subject ID 126 time 12hr no stimulation

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1904 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1903 Day 3

description: Gene expression from YF-17D Vaccinee


title: Subject ID 138 time 0hr

description: Gene expression from YF-17D Vaccinee

value: no culturing


title: Subject ID 138 time 12hr YF-17D stimulation

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1903 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1902 Day 7

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1902 Day 3

description: Gene expression from YF-17D Vaccinee


title: Subject ID 138 time 12hr no stimulation

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1901 Day 7

description: Gene expression from YF-17D Vaccinee


title: Subject ID 138 time 3hr no stimulation

description: Gene expression from YF-17D Vaccinee


title: Subject ID 138 time 3hr YF-17D stimulation

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1901 Day 3

description: Gene expression from YF-17D Vaccinee


title: Subject ID 126 time 3hr no stimulation

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1901 Day 0

description: Gene expression from YF-17D Vaccinee


title: Trial1 Subject ID 1902 Day 0

description: Gene expression from YF-17D Vaccinee


title: Subject ID 126 time 3hr YF-17D stimulation

description: Gene expression from YF-17D Vaccinee


title: BALB/c 8B

status: Public on Nov 22 2008

city: Tucson

first: Pawel

middle: R.

last: Kiela

state: AZ

address: 1501 N. Campbell Ave.

department: Pediatrics

institute: University of Arizona

description: Gene expression data from the colon of curcumin-treated mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC to GeneChip® Mouse Genome 430 Array set. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were initially analyzed with Afymetrix GCOS software using Affymetrix default analysis settings and global scaling as normalization method. Subsequently, data were imported to GeneSpring v.7.3.1 (Agilent).

source_name: Curcumin diet, control enema

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: whole colonic tissue was dissected from mice 6-8 weeks of age

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

treatment_protocol: 6-8 week old BALB/c mice were treated with respecive diet two days prior to enema administration (day 0) and sacrificed on day 7. Whole colon was dissected from  mice and their wild-type littermates and total RNA isolated for microarray analysis using Affymetrix murine MOE430 mouse array set. RNA was pooled from 3 mice in each dietary/treatment group.

tag: colon

tag: Treatment

value: control

tag: Diet

value: 2% curcumin


title: Subject ID 126 time 0hr

description: Gene expression from YF-17D Vaccinee

tag: PBMC


title: BALB/c 6B

description: Gene expression data from the colon of TNBS-treated mice

source_name: Standard diet, TNBS enema

value: TNBS

value: standard


title: BALB/c 11B

description: Gene expression data from the colon of curcumin/TNBS-treated mice

source_name: Curcumin diet, TNBS enema


title: BALB/c 10B


title: BALB/c 2B

description: Gene expression data from the colon of control mice

source_name: Standard diet, control enema


title: BALB/c 3B


title: BALB/c 12B


title: BALB/c 9B


title: BALB/c 11A


title: BALB/c 5B


title: BALB/c 1B


title: BALB/c 12A


title: BALB/c 10A


title: BALB/c 8A


title: BALB/c 4B


title: BALB/c 1A


title: BALB/c 7B


title: BALB/c 5A


title: BALB/c 3A


title: BALB/c 4A


title: BALB/c 7A


title: BALB/c 9A


title: Oral_normal_brushing_rep68

type: SAGE

anchor: NlaIII

city: Vancouver

first: Greg

last: Vatcher

address: 675 West 10th Ave.

country: Canada

institute: BC Cancer Research Centre

description: Tissue was collected by brushing the surface of the tongue with a 3mm teflon brush.

data_processing: The raw sequence data was converted to SAGE tags and counts using in-house Perl scripts and the Bio-SAGE-DataProcessing-1.20 Perl module from CPAN (http://search.cpan.org/~scottzed/Bio-SAGE-DataProcessing-1.20).

source_name: Normal oral brushing

extract_protocol: RNA was isolated from cell lysate by guanidium isothiocyanate and phenol/chloroform extraction.

tag: Gender

value: female

tag: Tisue

value: normal oral

tag: Collection

value: brushing


title: Oral_normal_biopsy_rep65

description: Tissue was collected from a biopsy of the oral gingiva.

source_name: Normal oral biopsy

value: male

value: biopsy


title: BALB/c 2A


title: BALB/c 6A


title: Oral_normal_brushing_rep52


title: 60min_with xylose_rep3

status: Public on Nov 21 2008

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

state: MA

address: 31 Ames Street, 68-530

department: Biology

institute: MIT

description:
Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD.
A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.

organism: Bacillus subtilis

source_name: 60min with xylose

tag: Grown in the presence of 0.5% xylose for 60min to induce single dsDNA break.

tag: Strain LAS210.

source_name: Pooled RNA

label_protocol: pooled RNA

extract_protocol: pooled RNA

tag: Pooled reference RNA.


title: 60min_with xylose_no cut site_rep1

hyb_protocol: Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.

source_name: 60min with xylose, strain with no cut site

tag: Strain without an SceI cut site grown in the presence of xylose for 60 min.

tag: Strain LAS195.


title: Oral_normal_biopsy_rep57

description: Tissue was collected from a biopsy of the right buccal mucosa.

tag: Age


title: Oral_normal_brushing_rep43

tag: Tissue

value: tongue


title: Patient H451

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

country: Germany

institute: Saarland University

description: Patient H451

hyb_protocol: As per Codelink instructions: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection

scan_protocol: The arrays were scanned with ScanArray Lite Scanner (Perkin Elmer, Inc.) and analyzed with CodeLink Expression Analysis software.

data_processing: Measured raw expression values were background subtracted and not correctly measured expression values (about 0.3% of all expression values) were excluded from further considerations. In a last pre-processing step, each microarray was median normalized and the logarithm of expression values was computed.

source_name: meningioma

label_protocol: As per Codelink instructions: CodeLink Gene Expression System: Manual Labelled cRNA Target Preparation

extract_protocol: Total RNA was isolated from samples using Trizol Reagent (Invitrogen, Germany) according to manufacturer’s instructions and subsequently purified using RNeasy-Kit (Qiagen, Hilden, Germany).

tag: SEX

value: Female

tag: AGE

tag: HIST

value: fibroblastic and syncytial areas


title: Patient H108

description: Patient H108

value: syncytial


title: 60min_with xylose_no cut site_rep3

scan_protocol: Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.


title: Oral_normal_biopsy_rep64


title: Patient Dura1

description: Patient Dura1

source_name: dura mater

tag: normal

value: Male


title: Patient H588

description: Patient H588


title: Patient H767

description: Patient H767

value: fibroblastic


title: Patient H444

description: Patient H444

value: unknown


title: Patient H386

description: Patient H386


title: 60min_with xylose_rep2

data_processing:
Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD.
A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.


title: 60min_with xylose_rep1

label_protocol:
Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD.
A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.


title: Patient H429

description: Patient H429


title: 60min_with xylose_no cut site_rep2

extract_protocol:
Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD.
A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.


title: Patient H469

description: Patient H469


title: Patient H1239

description: Patient H1239


title: Patient H1179

description: Patient H1179


title: 60min_no xylose_rep3

source_name: 60min untreated

tag: Exponentially growing cells.

tag: Control.


title: Patient Dura2

description: Patient Dura2


title: Patient H149

description: Patient H149


title: 60min_no xylose_rep2


title: 60min_no xylose_rep1


title: Patient H1334

description: Patient H1334


title: Patient H362

description: Patient H362

value: meningothelial


title: Patient H103

description: Patient H103


title: Patient H365

description: Patient H365


title: Patient H1242

description: Patient H1242


title: Patient H526

description: Patient H526


title: Patient H78

description: Patient H78


title: IPF (IPF37) Non-contractile Total RNA

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description: Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3000.

data_processing: The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732.

label_protocol: Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA

growth_protocol: Lung tissue explants were cultivated in 35 mm tissue culture dishes in explant medium (DMEM + 20% FBS + antibiotics and antimycotics) at 37°C in 95% air, 5% CO2. Outgrowth was evident in 5 to 7 days, and cells filled the dish in 2 to 3 weeks.  Cells from each 35 mm dish were released with trypsin-EDTA and placed in 100 mm tissue culture dishes after trypsin was neutralized with fresh explant medium. These cells, designated passage 1, were cultivated in growth medium (DMEM + 10% FBS + antibiotics) at 37°C in 95% air, 5%CO2.  Medium was replaced twice weekly, and cells were subcultivated weekly at a 1:4 split ratio. Cells designated myofibroblasts in both IPF and control samples had typical spindle morphology, were vimentin- and alpha smooth muscle actin-positive; and factor VIII- and surfactant C-negative. Cells used in this study were between passage 4 and 9.

extract_protocol: Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis.

treatment_protocol: Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts.

tag: Lung myofibroblasts

tag: IPF

tag: Non-contractile


title: Patient H90

description: Patient H90


title: IPF (IPF37) Non-contractile Heavy polyribosomal RNA

type: other

molecule: other

tag: Non-contractile Heavy polyribosomal RNA


title: IPF (IPF13) Non-contractile Total RNA


title: SLE-7 #4 @12wks, asymptomatic (-2069619621)

first: Padmalatha

last: Reddy

address: 35 Cambridgepark Drive

institute: WYETH

description: Cohort ID = 7:2000023040

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: Affymetrix MAS 5.0 algorithm

label_protocol: Affymetrix in-vitro labeling protocol

extract_protocol: RNA was extracted from mouse kidney

tag: Strain:NZB/W F1


title: IPF (IPF75) Non-contractile Total RNA


title: IPF (IPF14) Non-contractile Total RNA


title: IPF (IPF14) Non-contractile Heavy polyribosomal RNA


title: Patient H82

description: Patient H82


title: Patient H392

description: Patient H392


title: SLE-7 #1 @36wks, diseased/symptomatic (-2101152309)

description: Cohort ID = 2:2000023004


title: IPF (IPF75) Non-contractile Heavy polyribosomal RNA


title: Patient H72

description: Patient H72


title: IPF (IPF129) Non-contractile Total RNA


title: SLE-7 #1 @42wks, diseased/symptomatic (-2101152273)

description: Cohort ID = 4:2000023010


title: SLE-7 #2 @36wks, asymptomatic on treatment with sirolimus (-2099597721)

description: Cohort ID = 3:2000023008

tag: Disease_status:asymptomatic on treatment with sirolimus


title: SLE-7 #3 @36wks, diseased/symptomatic (-2101152297)

description: Cohort ID = 2:2000023006


title: Patient H28

description: Patient H28


title: IPF (IPF12) Non-contractile Total RNA


title: Control (Control57) Non-contractile Total RNA

tag: Control


title: IPF (IPF129) Non-contractile Heavy polyribosomal RNA


title: IPF (IPF13) Non-contractile Heavy polyribosomal RNA


title: Control (Control78) Non-contractile Total RNA


title: Control (Control54) Non-contractile Total RNA


title: SLE-7 #3 @42wks, diseased/symptomatic (-2099597707)

description: Cohort ID = 4:2000023012


title: SLE-7 #1 @42wks, asymptomatic on treatment with sirolimus (-2099597697)

description: Cohort ID = 5:2000023013


title: SLE-7 #1 @36wks, asymptomatic on treatment with sirolimus (-2099597727)

description: Cohort ID = 3:2000023007


title: Control (Control89) Non-contractile Heavy polyribosomal RNA


title: SLE-7 #3 @36wks, asymptomatic on treatment with sirolimus (-2101152279)

description: Cohort ID = 3:2000023009


title: Patient H375

description: Patient H375


title: SLE-7 #2 @12wks, asymptomatic (-2069738429)

description: Cohort ID = 7:2000023038


title: IPF (IPF12) Non-contractile Heavy polyribosomal RNA


title: Control (Control89) Non-contractile Total RNA


title: Control (Control128) Non-contractile Heavy polyribosomal RNA


title: SLE-7 #3 @12wks, asymptomatic (-2069737912)

description: Cohort ID = 7:2000023039


title: Control (Control54) Non-contractile Heavy polyribosomal RNA


title: Control (Control106) Non-contractile Total RNA


title: HRV-infected, asthmatic S4 (HG-Focus array)

city: Madison

first: Yury

middle: A

last: Bochkov

state: WI

address: 600 Highland Ave, K4/945 CSC

institute: University Of Wisconsin-Madison

description: Gene expression data from HRV-infected PBE cells from asthmatic individual

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human HG-Focus Focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the HP GeneArray Scanner (Hewlett-Packard).

data_processing: Fluorescent signal intensities were extracted from scanned images by Affymetrix Microarray Suite 5.0 software using their statistical expression algorithm. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. Log2 transformed expression values across all the chips were obtained using the Robust Multichip Average (RMA) method with median scaling as normalization.

source_name: HRV-infected PBE cells, asthmatic S04, 16 h p.i.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).

growth_protocol: Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).

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

treatment_protocol: One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.

tag: Human primary bronchial epithelial cells from patients with mild asthma, cultured in monolayers, passage 3


title: HRV-infected, asthmatic S6 (HG-Focus array)

source_name: HRV-infected PBE cells, asthmatic S06, 16 h p.i.


title: IPF (IPF75) Contractile Total RNA

tag: Contractile


title: SLE-7 #2 @36wks, diseased/symptomatic (-2101152303)

description: Cohort ID = 2:2000023005


title: SLE-7 #3 @42wks, asymptomatic on treatment with sirolimus (-2101152243)

description: Cohort ID = 5:2000023015


title: Control (Control128) Non-contractile Total RNA


title: IPF (IPF37) Contractile Total RNA


title: IPF (IPF37) Contractile Heavy polyribosomal RNA

tag: Contractile Heavy polyribosomal RNA


title: HRV-infected, normal S2 (HG-Focus array)

description: Gene expression data from HRV-infected PBE cells from normal (control) individual

source_name: HRV-infected PBE cells, normal S02, 16 h p.i.

tag: Human primary bronchial epithelial cells from normal (control) individuals, cultured in monolayers, passage 3


title: SLE-7 #2 @42wks, diseased/symptomatic (-2101152267)

description: Cohort ID = 4:2000023011


title: HRV-infected, normal S1 (HG-Focus array)

source_name: HRV-infected PBE cells, normal S01, 16 h p.i.


title: IPF (IPF14) Contractile Heavy polyribosomal RNA


title: HRV-infected, asthmatic S5 (HG-Focus array)

source_name: HRV-infected PBE cells, asthmatic S05, 16 h p.i.


title: mock-infected, asthmatic S6 (HG-Focus array)

description: Gene expression data from mock-infected PBE cells from asthmatic individual

source_name: mock-infected PBE cells, asthmatic S06, 16 h p.i.


title: IPF (IPF13) Contractile Total RNA


title: SLE-7 #2 @42wks, asymptomatic on treatment with sirolimus (-2101152249)

description: Cohort ID = 5:2000023014


title: Control (Control106) Non-contractile Heavy polyribosomal RNA


title: mock-infected, asthmatic S4 (HG-Focus array)

source_name: mock-infected PBE cells, asthmatic S04, 16 h p.i.


title: HRV-infected, normal S3 (HG-Focus array)

source_name: HRV-infected PBE cells, normal S03, 16 h p.i.


title: IPF (IPF75) Contractile Heavy polyribosomal RNA


title: SLE-7 #1 @12wks, asymptomatic (-2069738435)

description: Cohort ID = 7:2000023037


title: mock-infected, asthmatic S5 (HG-Focus array)

source_name: mock-infected PBE cells, asthmatic S05, 16 h p.i.


title: mock-infected, normal S3 (HG-Focus array)

description: Gene expression data from mock-infected PBE cells from normal (control) individual

source_name: mock-infected PBE cells, normal S03, 16 h p.i.


title: IPF (IPF129) Contractile Heavy polyribosomal RNA


title: Cardiac cells_24hrHypoxia_rep3

city: Dublin

first: Christine

middle: Marie

last: Costello

address: University College Dublin

country: Ireland

institute: Conway Institute

description: All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).

hyb_protocol: Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm.  Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).

scan_protocol: Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).

data_processing: Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median.  Genes that were absent in a majority of chips were eliminated from further analyses.

source_name: Cardiac Microvascular endothelial cells,hypoxia,24hr

label_protocol: Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).

growth_protocol: Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).

extract_protocol: At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK).  Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.

treatment_protocol: At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs.  Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.

tag: Primary cells


title: Cardiac cells_3hrHypoxia_rep3

source_name: Cardiac Microvascular endothelial cells,hypoxia,3hr


title: Control (Control89) Contractile Heavy polyribosomal RNA


title: IPF (IPF129) Contractile Total RNA


title: IPF (IPF14) Contractile Total RNA


title: Cardiac cells_48hrHypoxia_rep3

source_name: Cardiac Microvascular endothelial cells,hypoxia,48hr


title: IPF (IPF13) Contractile Heavy polyribosomal RNA


title: IPF (IPF12) Contractile Heavy polyribosomal RNA


title: Control (Control89) Contractile Total RNA


title: IPF (IPF12) Contractile Total RNA


title: Control (Control57) Contractile Total RNA


title: Cardiac cells_48hrHypoxia_rep2


title: Control (Control78) Contractile Total RNA


title: mock-infected, normal S1 (HG-Focus array)

source_name: mock-infected PBE cells, normal S01, 16 h p.i.


title: Cardiac cells_Normoxia_rep2

source_name: Cardiac Microvascular endothelial cells,normoxia,0hrControl


title: mock-infected, normal S2 (HG-Focus array)

source_name: mock-infected PBE cells, normal S02, 16 h p.i.


title: Control (Control54) Contractile Total RNA


title: Cardiac cells_48hrHypoxia_rep1


title: Cardiac cells_Normoxia_rep3


title: Control (Control57) Contractile Heavy polyribosomal RNA


title: Control (Control57) Non-contractile Heavy polyribosomal RNA


title: Cardiac cells_24hrHypoxia_rep1


title: Control (Control54) Contractile Heavy polyribosomal RNA


title: Cardiac cells_3hrHypoxia_rep2


title: Cardiac cells_Normoxia_rep1


title: Cardiac cells_24hrHypoxia_rep2


title: Control (Control128) Contractile Total RNA


title: Control (Control128) Contractile Heavy polyribosomal RNA


title: Lung cells_48hrHypoxia_rep3

source_name: Lung Microvascular endothelial cells,hypoxia,48hr


title: Control (Control106) Contractile Heavy polyribosomal RNA


title: Control (Control78) Contractile Heavy polyribosomal RNA


title: Technical Analysis of Fundulus heteroclitus 384 cDNA microarray-10X

city: Miami

first: Cinda

middle: P

last: Scott

state: FL

address: 4600 Rickenbacker Cswy

department: Marine Biology and Fisheries

institute: University of Miami

hyb_protocol: Hybridization buffer consisted of 5X SSPE, 1% SDS, 50% formamide, 1mg/ml polyA, 1mg/ml sheared herring sperm carrier DNA, and 1mg/ml BSA.  Slides were washed in sodium borohydride solution in order to reduce autofluorescence.  Following rinsing, slides were boiled for 2 minutes and spin-dried in a centrifuge at 800 rpm for 3 minutes.  Samples (15ul) were heated to 90ºC for 2 minutes, quick cooled to 42ºC, applied to the slide (hybridization zone area was 350mm2), and covered with a cover slip.  Slides were placed in an airtight chamber humidified with paper soaked in 5X SSPE and incubated 24-48 hours at 42ºC.

scan_protocol: The microarray slides were scanned using ScanArray Express.  The raw TIFF-image data was quantified using Imagene (v5).  Genes with a fluorescence signal greater than 60,000 or less than the Ctenophore negative controls were eliminated from the analysis.

data_processing: To adjust for systematic variation, gene expression values were first sum normalized and then loess normalized using Microarray Data Analysis System Software (MIDAS).  For every gene, eight fluorescence values were captured; four for Cy3 and four for Cy5.

organism: Fundulus heteroclitus

source_name: Fundulus heteroclitus cardiac tissue

label_protocol: During the in vitro transcription of aRNA amino allyl UTP (aaUTP) is incorporated into the elongating strand.  aaUTP incorporation allows for the coupling of Cy3 (or Cy5) dyes (GE biosciences) onto aRNA for microarray hybridization.  Dye labeled aRNA aliquots for each hybridization (30 pmol each of Cy3 and Cy5) were vacuum dried together and resuspended in 15ul hybridization buffer (final concentration of each labeled sample = 2 pmol/ul).

extract_protocol: Total RNA was isolated from using 4.5M guanidinium thiocyanate, 2% N-lauroylsarcosine, 50mM EDTA, 25mM Tris-HCl, 0.1M beta-Mercaptoethanol and .2% Antifoam A.  The extracted RNA was further purified using a Qiagen RNeasy Mini kit in accordance with the manufacturer’s protocols.  The quantity and quality of the RNA was determined using a spectrophotometer (Nanodrop, ND-1000 V3.2.1) and a bioanalyzer (Agilent 2100).  RNA was then converted into amino allyl labeled RNA (aRNA) using the Ambion Amino Allyl MessageAmp II aRNA Amplification kit.  This method converts poly-A RNA into cDNA with a T7 RNA polymerase binding site and T7 is used to synthesize many new strands of RNA (in vitro transcription) (Eberwine, 1996).

tag: Tissue

value: F. heteroclitus cardiac tissue.  Fish were acclimated to laboratory conditions for approximately 6 months.


title: Technical Analysis of Fundulus heteroclitus 384 cDNA microarray-5X


title: Lung cells_24hrHypoxia_rep3

source_name: Lung Microvascular endothelial cells,hypoxia,24hr


title: Control (Control106) Contractile Total RNA


title: Cardiac cells_3hrHypoxia_rep1


title: SLE-7 #1 @12wks, asymptomatic (-2077090535)

description: Cohort ID = 7:2000023037


title: Technical Analysis of Fundulus heteroclitus 384 cDNA microarray-.1X


title: Lung cells_3hrHypoxia_rep3

source_name: Lung Microvascular endothelial cells,hypoxia,3hr


title: Technical Analysis of Fundulus heteroclitus 384 cDNA microarray-1X


title: SLE-7 #2 @36wks, asymptomatic on treatment with sirolimus (-2101365652)

description: Cohort ID = 3:2000023008


title: SLE-7 #2 @12wks, asymptomatic (-2077090529)

description: Cohort ID = 7:2000023038


title: SLE-7 #3 @36wks, asymptomatic on treatment with sirolimus (-2101365196)

description: Cohort ID = 3:2000023009


title: Technical Analysis of Fundulus heteroclitus 384 cDNA microarray-50X


title: Lung cells_48hrHypoxia_rep2


title: SLE-7 #3 @36wks, diseased/symptomatic (-2102085829)

description: Cohort ID = 2:2000023006


title: SLE-7 #1 @42wks, asymptomatic on treatment with sirolimus (-2101365170)

description: Cohort ID = 5:2000023013


title: SLE-7 #2 @42wks, asymptomatic on treatment with sirolimus (-2102085846)

description: Cohort ID = 5:2000023014


title: SLE-7 #1 @42wks, diseased/symptomatic (-2101365185)

description: Cohort ID = 4:2000023010


title: Control (Control78) Non-contractile Heavy polyribosomal RNA


title: Lung cells_Normoxia_rep3

source_name: Lung Microvascular endothelial cells,normoxia,0hrControl


title: B. thetaiotaomicron complemented 5xECF mutant strain in vivo, simple sugar diet 3 of 3

city: Ann Arbor

first: Eric

middle: Charles

last: Martens

state: MI

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

institute: University of Michigan Medical School

description: B. thetaiotaomicron tdk mutant strain with 5 ECF-sigma factors deleted and complemented back into the genome at NBU2 attachment site, grown in vivo in the cecum of NMRI inbred mouse fed a glucose (35%) / sucrose (35%) 'simple sugar' diet. Extracted 10d after colonization. Replicate 3 of 3.

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Signals normalized to 500 using Affymetrix MAS5 software

organism: Bacteroides thetaiotaomicron

source_name: bacterial

label_protocol: Enzo Biochemicals Bioarray terminal labeling kit

extract_protocol: Qiagen RNAeasy column and Ambion DNAfree DNAseI treatment

tag: strain VPI-5482


title: SLE-7 #2 @36wks, diseased/symptomatic (-2101366115)

description: Cohort ID = 2:2000023005


title: SLE-7 #1 @36wks, diseased/symptomatic (-2101366147)

description: Cohort ID = 2:2000023004


title: SLE-7 #3 @12wks, asymptomatic (-2077090523)

description: Cohort ID = 7:2000023039


title: B. thetaiotaomicron complemented 5xECF mutant strain in vivo, simple sugar diet 1 of 3

description: B. thetaiotaomicron tdk mutant strain with 5 ECF-sigma factors deleted and complemented back into the genome at NBU2 attachment site, grown in vivo in the cecum of NMRI inbred mouse fed a glucose (35%) / sucrose (35%) 'simple sugar' diet. Extracted 10d after colonization. Replicate 1 of 3.


title: B. thetaiotaomicron complemented 5xECF mutant strain in vivo, simple sugar diet 2 of 3

description: B. thetaiotaomicron tdk mutant strain with 5 ECF-sigma factors deleted and complemented back into the genome at NBU2 attachment site, grown in vivo in the cecum of NMRI inbred mouse fed a glucose (35%) / sucrose (35%) 'simple sugar' diet. Extracted 10d after colonization. Replicate 2 of 3.


title: Lung cells_24hrHypoxia_rep2


title: B. thetaiotaomicron 5xECF mutant strain in vivo, simple sugar diet 2 of 3

description: B. thetaiotaomicron tdk mutant strain with 5 ECF-sigma factors deleted from genome, grown in vivo in the cecum of NMRI inbred mouse fed a glucose (35%) / sucrose (35%) 'simple sugar' diet. Extracted 10d after colonization. Replicate 2 of 3.


title: B. thetaiotaomicron 5xECF mutant strain in vivo, simple sugar diet 3 of 3

description: B. thetaiotaomicron tdk mutant strain with 5 ECF-sigma factors deleted from genome, grown in vivo in the cecum of NMRI inbred mouse fed a glucose (35%) / sucrose (35%) 'simple sugar' diet. Extracted 10d after colonization. Replicate 3 of 3.


title: Lung cells_3hrHypoxia_rep2


title: Lung cells_24hrHypoxia_rep1


title: SLE-7 #3 @42wks, diseased/symptomatic (-2101365176)

description: Cohort ID = 4:2000023012


title: Lung cells_Normoxia_rep2


title: SLE-7 #4 @12wks, asymptomatic (-2077090517)

description: Cohort ID = 7:2000023040


title: Lung cells_48hrHypoxia_rep1


title: B. thetaiotaomicron 5xECF mutant strain in vivo, simple sugar diet 1 of 3

description: B. thetaiotaomicron tdk mutant strain with 5 ECF-sigma factors deleted from genome, grown in vivo in the cecum of NMRI inbred mouse fed a glucose (35%) / sucrose (35%) 'simple sugar' diet. Extracted 10d after colonization. Replicate 1 of 3.


title: SLE-7 #2 @42wks, diseased/symptomatic (-2102085823)

description: Cohort ID = 4:2000023011


title: SLE-7 #3 @42wks, asymptomatic on treatment with sirolimus (-2101365164)

description: Cohort ID = 5:2000023015


title: B. thetaiotaomicron tdk strain in vivo, simple sugar diet 3 of 3

description: B. thetaiotaomicron tdk mutant strain ('wild-type' parent for gene deletion strains), grown in vivo in the cecum of NMRI inbred mouse fed a glucose (35%) / sucrose (35%) 'simple sugar' diet. Extracted 10d after colonization. Replicate 3 of 3.


title: Lung cells_Normoxia_rep1


title: B. thetaiotaomicron responses to purified host glycans and components: alpha mannan 2

description: B. thetaiotaomicron grown in minimal medium plus 0.5% alpha-mannan, 5ml culture in an anaerobic tube. Replicate 2 of 2.

data_processing: Data values for B. thetaiotamicron genes normalized to 500 in Affymetrix MAS5 software (excluded other species that were on chip using electronic mask)

extract_protocol: Qiagen RNAeasy mini column and Ambion DNAfree DNAseI digestion


title: Ventral striatum VS-SHR

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

hyb_protocol: 16hrs 45C 60rpm

source_name: brain

label_protocol: Ovation (Nugen)

extract_protocol: Qiagen RNeasy

tag: p55-65 males


title: B. thetaiotaomicron tdk strain in vivo, simple sugar diet 2 of 3

description: B. thetaiotaomicron tdk mutant strain ('wild-type' parent for gene deletion strains), grown in vivo in the cecum of NMRI inbred mouse fed a glucose (35%) / sucrose (35%) 'simple sugar' diet. Extracted 10d after colonization. Replicate 2 of 3.