title: HeLa Cell Line, unknown: VV-ADAR/E3L, 6 HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VV-ATV, 2 HPI

status: Public on Apr 23 2008

type: RNA

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

country: USA

institute: Translational Genomics

description: vaccinia virus infected

molecule: total RNA

organism: Homo sapiens

source_name: HeLa Cell Line, unknown


title: HeLa Cell Line, unknown: VVdel37N, 2 HPI

description: vaccinia virus infected


title: Placenta e17.0, biological rep3

city: Stanford

first: Kirstin

last: Knox

state: CA

address: 300 Pasteur Dr.

department: Genetics

institute: Stanford Univeristy

description: Gene expression data from fetal placenta at e17.0

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the Affymetrix Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: In order to control for differences in overall strength of hybridization, all arrays were normalized to the same median intensity using the dCHIP invariant set method.  Modeling was performed using the dCHIP Perfect Match (PM) modeling algorithm.

label: biotin

organism: Mus musculus

source_name: Mouse placental tissue at embryonic day 17.0, biological replicate 3

label_protocol: For each sample, labeled cRNA was prepared from 10 ug of starting RNA according to Affymetrix  protocols. Briefly, RNA was reverse transcribed and the resulting double stranded cDNA was purified by phenol-chloroform extraction followed by ethanol precipitation.  The cDNA was used as a template for a biotin labeling in vitro transcription.  The resulting cRNA was purified using an Rneasy column, quantified, then fragmented using KOAc RNA fragmentation buffer.

growth_protocol: A minimum of two to three timed pregnant female Swiss Webster mice were sacrificed at each timepoint used in our analysis, generating two to three biological replicates at each stage.  For each pregnancy, the entire litter of fetuses and placentas was dissected.  Fetal tissues were used to confirm staging of the embryos using Theiler’s morphological criteria.

extract_protocol: Each sample was homogenized in Trizol with a rotor homogenizer.  RNA was isolated by chloroform extraction from the Trizol sample, purified using a Qiagen Rneasy column, then ethanol precipitated.  Due to limited tissue availability, two e8.5 placenta samples (Placenta_e8.5-1 and Placenta_e8.5-2) were homogenized in Ambion lysis buffer rather than Trizol.  For these samples, RNA was isolated using the Ambion Rnaqueous Micro kit prior to ethanol precipitation.

treatment_protocol: Placentas were manually dissected into fetal placenta and decidual (maternal) portions, using fine forceps to separate the decidua from the spongiotrophoblast and trophoblast giant cells.  Fetally derived placenta samples and maternally derived placenta samples were pooled separately for each litter, then flash frozen in liquid nitrogen and stored at –80° C until RNA isolation.  Tissues from two to ten placentas from a single litter were combined for each sample except for two of the e8 samples, which were pooled from multiple litters after staging.

tag: Strain

value: Swiss Webster

tag: Tissue

value: placenta (fetal origin)


title: Placenta e15.0, biological rep3

description: Gene expression data from fetal placenta at e15.0

source_name: Mouse placental tissue at embryonic day 15.0, biological replicate 3


title: Placenta e15.0, biological rep1

source_name: Mouse placental tissue at embryonic day 15.0, biological replicate 1


title: Placenta e15.0, biological rep2

source_name: Mouse placental tissue at embryonic day 15.0, biological replicate 2


title: HeLa Cell Line, unknown: VVE3L Y48F, 9 HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VV-ATV, 9 HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VVE3L Y48A, 2 HPI

description: vaccinia virus infected


title: Placenta e13.5, biological rep2

description: Gene expression data from fetal placenta at e13.5

source_name: Mouse placental tissue at embryonic day 13.5, biological replicate 2


title: Placenta e13.5, biological rep1

source_name: Mouse placental tissue at embryonic day 13.5, biological replicate 1


title: Placenta e12.0, biological rep3

description: Gene expression data from fetal placenta at e12.0

source_name: Mouse placental tissue at embryonic day 12.0, biological replicate 3


title: HeLa Cell Line, unknown: VVE3Ldel7C, 6 HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VVE3Ldel7C, 9 HPI

description: vaccinia virus infected


title: Placenta e12.0, biological rep2

source_name: Mouse placental tissue at embryonic day 12.0, biological replicate 2


title: HeLa Cell Line, unknown: VVE3L Y48A, 6 HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VVE3Ldel7C, 2 HPI

description: vaccinia virus infected


title: Placenta e12.0, biological rep1

source_name: Mouse placental tissue at embryonic day 12.0, biological replicate 1


title: HeLa Cell Line, unknown: VVE3L Y48A, 9 HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VVE3Ldel26C, 6 HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VVE3Ldel26C, 2 HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VVE3Ldel83N, 9 HPI

description: vaccinia virus infected


title: Placenta e10.5, biological rep1

description: Gene expression data from fetal placenta at e10.5

source_name: Mouse placental tissue at embryonic day 10.5, biological replicate 1


title: Placenta e10.5, biological rep2

source_name: Mouse placental tissue at embryonic day 10.5, biological replicate 2


title: HeLa Cell Line, unknown: VVE3Ldel26C, 9 HPI

description: vaccinia virus infected


title: Placenta e9.0, biological rep3

description: Gene expression data from fetal placenta at e9.0

source_name: Mouse placental tissue at embryonic day 9.0, biological replicate 3


title: Placenta e8.5, biological rep3

description: Gene expression data from fetal placenta at e8.5

source_name: Mouse placental tissue at embryonic day 8.5, biological replicate 3


title: Placenta e9.0, biological rep2

source_name: Mouse placental tissue at embryonic day 9.0, biological replicate 2


title: HeLa Cell Line, unknown: VVE3Ldel83N, 2 HPI

description: vaccinia virus infected


title: Placenta e10.5, biological rep3

source_name: Mouse placental tissue at embryonic day 10.5, biological replicate 3


title: HeLa Cell Line, unknown: VVdelE3L, 9 HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VVdelE3L, 2 HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VVdelE3L, 6 HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: wtVV, 9HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VVE3Ldel83N, 6 HPI

description: vaccinia virus infected


title: Placenta e9.0, biological rep1

source_name: Mouse placental tissue at embryonic day 9.0, biological replicate 1


title: Placenta e8.5, biological rep2, technical rep2

source_name: Mouse placental tissue at embryonic day 8.5, biological replicate 2, technical replicate 2


title: HeLa Cell Line, unknown: wtVV, 2 HPI

description: vaccinia virus infected

source_name: HeLa Cell Line, unknown


title: HeLa Cell Line, unknown: wtVV, 6 HPI

description: vaccinia virus infected


title: Placenta e8.5, biological rep1, technical rep2

source_name: Mouse placental tissue at embryonic day 8.5, biological replicate 1, technical replicate 2


title: Placenta e8.5, biological rep1, technical rep1

source_name: Mouse placental tissue at embryonic day 8.5, biological replicate 1, technical replicate 1


title: 2951_Urothelium

status: Public on Apr 22 2008

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9434

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 10ug

scan_protocol: Affymetrix standard protocol

data_processing: Analysis method: Affymetrix GCOS and Gene Spring and Avadis programs GCOS Tgt value: 1500

label: Biotin

source_name: bladder urothelium

extract_protocol: Qiagen: RNeasy

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: Tissue layer isolated and dissected using laser capture microscopy for dissection.
Bladders were isolated from newborn SMGA/EGFP transgenic mice, embedded in OCT, frozen and sectioned (8 microns).  Detrusor, stroma and urothelium were isolated using laser capture microscopy.   The caps were frozen on dry ice and stored at -80 ºC until RNA was extracted for gene expression analysis.

tag: gene reported

value: SMGA/EGFP transgenic /  PMID:14713859

tag: strain

value: FVB/N

tag: sex

value: unknown

tag: developmental stage

value: postnatal day 1

tag: theiler stage

tag: somite count

value: ND

tag: developmental landmark:


title: 2295_Stroma

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9438

source_name: bladder stroma

value: postnatal day 2


title: 2291_Urothelium

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9435


title: 2833_Stroma

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9436


title: 2299_Urothelium

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9433


title: 2865_Stroma

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9437


title: 2715_Detrusor

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9432

source_name: bladder detrusor


title: 1848_Detrusor

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9431


title: 2801_Detrusor

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9430


title: Placenta e8.5, biological rep2, technical rep1

source_name: Mouse placental tissue at embryonic day 8.5, biological replicate 2, technical replicate 1


title: blastocyst calcium-magnesium free medium replicate 3

city: Philadelphia

first: Francesca

middle: Elizabeth

last: Duncan

state: PA

address: 433 South University Avenue/ 205 Lynch Laboratories

department: Biology

institute: University of Pennsylvania

description: Blastocysts dervied from 8-cell embryos that were incubated in calcium-magnesium free medium; replicate 3

hyb_protocol: Penn Microarray Facility

scan_protocol: Penn Microarray Facility

data_processing: The GC-RMA algorithm was used to quantify and normalize microarray signals using Stratagene Array Assist Lite, Version 3.4

source_name: blastocyst CMF replicate 3

label_protocol: Enzo BioArray High Yield RNA Transcript Labeling Kit

extract_protocol: RNA isolation using the Arcturus PicoPure RNA Isolation Kit followed by linear 2-round amplification following the Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II protocol.

tag: Sex

value: Female

tag: Blastocysts

tag: calcium-magnesium free medium


title: blastocyst acid replicate 3

description: Blastocysts dervied from 8-cell embryos that were subjected to acid Tyrode's treatment; replicate 3

source_name: blastocyst A replicate 3

tag: Acid


title: blastocyst acid replicate 2

description: Blastocysts dervied from 8-cell embryos that were subjected to acid Tyrode's treatment; replicate 2

source_name: blastocyst A replicate 2


title: blastocyst calcium-magnesium free medium + acid replicate 5

description: Blastocysts derived from 8-cell embryos that were incubated in calcium-magnesium free medium and subjected to acid Tyrode's treatment; replicate 5

source_name: blastocyst CMF + A replicate 5

tag: calcium-magnesium free medium + Acid


title: blastocyst untreated replicate 5

description: Blastocysts derived from 8-cell embryos that were not treated; replicate 5

source_name: blastocyst UT replicate 5

tag: Untreated


title: blastocyst calcium-magnesium free medium replicate 5

description: Blastocysts derived from 8-cell embryos that were incubated in calcium-magnesium free medium; replicate 5

source_name: blastocyst CMF replicate 5


title: blastocyst calcium-magnesium free medium + acid replicate 2

description: Blastocysts derived from 8-cell embryos that were incubated in calcium-magnesium free medium and subjected to acid Tyrode's treatment; replicate 2

source_name: blastocyst CMF + A replicate 2


title: blastocyst acid replicate 5

description: Blastocysts derived from 8-cell embryos that were subjected to acid Tyrode's treatment; replicate 5

source_name: blastocyst A replicate 5


title: peripheral ganglion, unknown: nicotine 24 hr

status: Public on Apr 19 2008

description:
Total RNA extracted from SH-SY5Y treated with 1mM nicotine for 24 hour.
Treatment, type=time_course, measurement=24.0 h

source_name: peripheral ganglion, unknown


title: peripheral ganglion, unknown: nicotine 24 hr_2


title: peripheral ganglion, unknown: control 24 hr _3

description:
The untreated control sample for SH-SY5Y treated with 1mM nicotine for 24 hour.
Treatment, type=time_course, measurement=24.0 h


title: blastocyst embryo biopsy replicate 5

description: Blastocysts derived from 8-cell embryos that were subjected to embryo biopsy; replicate 5

source_name: blastocyst PGD replicate 5

tag: Embryo Biopsy


title: blastocyst untreated replicate 2

description: Blastocysts derived from 8-cell embryos that were not treated; replicate 2

source_name: blastocyst UT replicate 2


title: Placenta e17.0, biological rep1

description: Gene expression data from fetal placenta at e17.0

source_name: Mouse placental tissue at embryonic day 17.0, biological replicate 1


title: peripheral ganglion, unknown: nicotine 24 hr_3


title: blastocyst calcium-magnesium free medium + acid replicate 4

description: Blastocysts derived from 8-cell embryos that were incubated in calcium-magnesium free medium and subjected to acid Tyrode's treatment; replicate 4

source_name: blastocyst CMF + A replicate 4


title: blastocyst untreated replicate 4

description: Blastocysts derived from 8-cell embryos that were not treated; replicate 4

source_name: blastocyst UT replicate 4


title: blastocyst embryo biopsy replicate 2

description: Blastocyst that underwent embryo biopsy procedure; replicate 2

source_name: blastocyst PGD replicate 2

tag: Embryo biopsy


title: peripheral ganglion, unknown: control 24 hr_2


title: blastocyst calcium-magnesium free medium replicate 2

description: Blastocysts dervied from 8-cell embryos that were incubated in calcium-magnesium free medium; replicate 2

source_name: blastocyst CMF replicate 2

tag: Strain

tag: Sex:

tag: Female


title: blastocyst embryo biopsy replicate 3

description: Blastocysts derived from 8-cell embryos that were subjected to embryo biopsy; replicate 3

source_name: blastocyst PGD replicate 3


title: blastocyst embryo biopsy replicate 4

description: Blastocysts derived from 8-cell embryos that were subjected to embryo biopsy; replicate 4

source_name: blastocyst PGD replicate 4


title: blastocyst untreated replicate 3

description: Blastocysts derived from 8-cell embryos that were not treated; replicate 3

source_name: blastocyst UT replicate 3


title: blastocyst calcium-magnesium free medium + acid replicate 3

description: Blastocysts derived from 8-cell embryos that were incubated in calcium-magnesium free medium and subjected to acid Tyrode's treatment; replicate 3

source_name: blastocyst CMF + A replicate 3


title: blastocyst calcium-magnesium free medium replicate 4

description: Blastocysts derived from 8-cell embryos that were incubated in calcium-magnesium free medium; replicate 4

source_name: blastocyst CMF replicate 4


title: peripheral ganglion, unknown: nicotine 1hr_3

description:
Total RNA extracted from SH-SY5Y treated with 1mM nicotine for 1 hour.
Treatment, type=time_course, measurement=1.0 h


title: peripheral ganglion, unknown: nicotine 1hr


title: peripheral ganglion, unknown: control 24 hr


title: blastocyst acid replicate 4

description: Blastocysts derived from 8-cell embryos that were subjected to acid Tyrode's treatment; replicate 4

source_name: blastocyst A replicate 4


title: peripheral ganglion, unknown: control 1 hr

description:
Untreated 1 hour control sample.
Treatment, type=time_course, measurement=1.0 h


title: peripheral ganglion, unknown: control 1 hr_2


title: Embryonic Stem Cells, Cell line: H9 hES cells pool#3_e1_le1

description: A pool of hES cells from H9p26, H9p28, H9p29 pool#3

source_name: Embryonic Stem Cells, Cell line


title: Embryonic Stem Cells, Cell line: H9 hES cell derived d10 primitive neural epithelial treated with bFGF pool #3_e1_le1

description:
H9 hES cell derived d10 neural epithelial treated with 20 ug/ml bFGF pool #3 from d6-d10
Treatment, type=pharmacogenomic_treatment


title: Embryonic Stem Cells, Cell line: H9 derived d10 neural epithelial cells pool #3_e1_le1

description: RNA from day 10 neural epithelial cells pool #3


title: Embryonic Stem Cells, Cell line: H9 derived d6 EBs pool#2_e1_le1

description: day  6 EBs generated from h9p27, H9p28, H9p31 hES cells


title: Embryonic Stem Cells, Cell line: H9 hES cell derived d17 definitive neural epithelial treated with FGF2 pool #2_e1_le1

description: H9 hES cell derived d17 definitive neural epithelial pool #2 treated with 20 ng/ml bFGF from day6-day17


title: Embryonic Stem Cells, Cell line: H9 hES cell RNA pool#2_e1_le1

description: A pool of hES cells from H9p24, H9p25, H9p26


title: Embryonic Stem Cells, Cell line: H9 hES cell derived d10 neural epithelial treated with 20 ug/ml bFGF pool #2_e1_le1

description:
H9 hES cell derived d10 neural epithelial treated with 20 ug/ml bFGF pool #1 from d6-d10
Treatment, type=pharmacogenomic_treatment


title: Embryonic Stem Cells, Cell line: H9 hES cell derived d17 definitive neural epithelial pool #3_e1_le1


title: Embryonic Stem Cells, Cell line: H9 hES cell derived d17 definitive neural epithelial treated with bFGF pool #1_e1_le1

description: H9 hES cell derived d17 definitive neural epithelial pool #1 treated with 20 ng/ml bFGF from day6-day17


title: Embryonic Stem Cells, Cell line: H9 hES cell derived d17 definitive neural epithelial treated with bFGF pool #3_e1_le1

description: H9 hES cell derived d17 definitive neural epithelial pool #3 treated with 20 ng/ml bFGF from day6-day17


title: Embryonic Stem Cells, Cell line: H9 hES cell derived d10 primitive neural epithelial pool#2_e1_le1

description: A pool of RNA from day 10 neural epithelial cells


title: Embryonic Stem Cells, Cell line: H9 derived d6 EBs pool #1_e1_le1


title: Embryonic Stem Cells, Cell line: H9 hES cell derived d17 definitive neural epithelial pool #2_e1_le1


title: Embryonic Stem Cells, Cell line: H9 hES cell derived d10 primitive neural epithelial treated with bFGF pool #1_e1_le1


title: HeLa Cell Line, unknown: VVE3L Y48F, 2 HPI

description: vaccinia virus infected

source_name: HeLa Cell Line, unknown


title: Embryonic Stem Cells, Cell line: H9 hES cell derived d10 primitive neural epithelial pool #1_e1_le1


title: nerve, dorsal root ganglion: sample 4 L3-S2

description:
total RNA extracted from 20 DiI retrograde labeled medium to small diameter neurons
Treatment, type=purify

source_name: nerve, dorsal root ganglion


title: nerve, dorsal root ganglion: sample 2 L3-B2

description:
total RNA extracted from 50 control medium to small diameter neurons
Treatment, type=purify


title: Embryonic Stem Cells, Cell line: Trizol with RNeasy_le1

description: A pool of hES cells from H9p27, H9p28, H9p31


title: nerve, dorsal root ganglion: sample 3 L3-S

description:
total RNA from 20 DiI retrograde labeled big diameter neurons
Treatment, type=purify


title: nerve, dorsal root ganglion: sample 1 L3-B

description:
total RNA from 50 control big diameter DRG neurons
Treatment, type=purify, description=follow picopure RNA isolation kit to purify total RNA


title: nerve, dorsal root ganglion: sample 5 L6-R


title: embryonic liver sample at 145, biological rep1

status: Public on Apr 18 2008

city: Boston

first: Hasan

middle: Huseyin

last: Otu

state: MA

address: 4 Blackfan Circle Rm. 238

department: Medicine

institute: Harvard Medical School

description: Gene expression data from 14.5 dpc mouse embryonic (minus liver) sample.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with dChip using smoothing spline invariant set method with the model based expression algorithm following the perfect match (PM)-mismatch (MM) difference model. In the dChip analysis, array outliers are not treated as missing expression values and no truncation on signal values is applied.

source_name: Sample from mouse embryo minus liver at 14.5 days post conception (dpc)

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

growth_protocol: All experiments used CD-1 mice obtained from Charles River Laboratories (Wilmington, MA) or our own breeding colony. Animals were maintained in a pathogenfree facility administered by Harvard Medical School in accordance with the institutional guidelines of Harvard Medical School and Beth Israel Deaconess Medical Center. A maximum of five minutes was allowed to elapse between sacrifice and liver harvest to prevent RNA degradation and transcriptional changes.

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

treatment_protocol: Pregnant CD-1 females were sacrificed with carbon dioxide asphyxiation followed by cervical dislocation. The abdomen was opened and the uterus removed. After removal of the uterine musculature, embryos were removed from the yolk sacs and livers microdissected, taking care to remove all extraneous tissue including the retrohepatic vena cava.

tag: Genotype

value: CD-1 mouse embryo

tag: Age


title: embryonic liver sample at 125, biological rep1

description: Gene expression data from 12.5 dpc mouse embryonic (minus liver) sample.

source_name: Sample from mouse embryo minus liver at 12.5 days post conception (dpc)


title: embryonic liver sample at 105, biological rep1

description: Gene expression data from 10.5 dpc mouse embryonic (minus liver) sample.

source_name: Sample from mouse embryo minus liver at 10.5 days post conception (dpc)


title: nerve, dorsal root ganglion: sample 6 L6-R2


title: embryonic liver sample at 115, biological rep1

description: Gene expression data from 11.5 dpc mouse embryonic (minus liver) sample.

source_name: Sample from mouse embryo minus liver at 11.5 days post conception (dpc)


title: postnatal day 2 bladder cells EGFP positive, EYFP positive, rep 2

status: Public on Apr 17 2008

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9427

hyb_protocol: Affymetrix standard protcol Amount labeled  target hybridization to array: 10µg

scan_protocol: Affymetrix standard protcol

source_name: postnatal day 2 bladder cells EGFP positive, EYFP positive (detrusor muscle of bladder)

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: Bladder microdissected based on SMGA/EGFP and SMAA/EYFP expression and digested using lysis enzymes.
SMAA/EYFP mice were time mated to SMGA/EGFP transgenic mice. Postnatal mice were euthanized by decapitation and tissues were micro-dissected and digested with Blendzymes 1 & 4 and subjected to FACS sorting.  The separated cell populations were rapidly stored at -80ºC until RNA was extracted for gene expression analysis.

tag: gene reported

value: SMAA/EYFP SMGA/EGFP transgenic / PMID:14713859

tag: strain

tag: sex

value: male

tag: developmental stage

tag: developmental landmark

value: EGFP positive, EYFP positive


title: postnatal day 2 bladder cells EGFP positive, EYFP negative, rep 3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9428

source_name: postnatal day 2 bladder cells EGFP positive, EYFP negative (detrusor muscle of bladder)

tag: theiler stage

tag: somite count

value: EGFP positive, EYFP negative


title: postnatal day 2 bladder cells EGFP positive, EYFP negative, rep 2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9426


title: postnatal day 2 bladder cells EGFP positive, EYFP negative, rep 1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9424


title: postnatal day 2 bladder cells EGFP positive, EYFP positive, rep 3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9429


title: PBMC-1-RR-Pat.7 [wf20071123u133v2_U_17_LP21_Lc1_M_56yr_No_151]

city: Basel

first: Edward

middle: James

last: Oakeley

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Pre-interferon blood sample

hyb_protocol: Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA is stained with streptavidin phycoerythrin and arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

scan_protocol: GeneChips were scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

data_processing: GCRMA-calculated Signal intensity

source_name: Pre-interferon blood sample

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

tag: treatment status

value: Pre-interferon


title: PBMC-2-RR-Pat.8 [wf20071123u133v2_U_20_CH22_Lc2_M_38yr_alpha_151]

description: Post-interferon blood sample

source_name: Post-interferon blood sample

value: Post-interferon


title: PBMC-1-RR-Pat.9 [wf20071123u133v2_U_15_HT20_Lc1_F_50yr_No_151]

description: Pre-interferon blood sample


title: PBMC-2-RR-Pat.9 [wf20071123u133v2_U_16_HT20_Lc2_F_50yr_alpha_151]

description: Post-interferon blood sample


title: PBMC-1-Non-RR-Pat.13 [wf20071123u133v2_U_21_BJ23_Lc1_M_49yr_No_151]

description: Pre-interferon blood sample


title: PBMC-2-Non-RR-Pat.13 [wf20071123u133v2_U_22_BJ23_Lc2_M_49yr_alpha_151]

description: Post-interferon blood sample


title: peripheral ganglion, unknown: nicotine 1hr_2

description:
Total RNA extracted from SH-SY5Y treated with 1mM nicotine for 1 hour.
Treatment, type=time_course, measurement=1.0 h

source_name: peripheral ganglion, unknown


title: PBMC-1-RR-Pat.8 [wf20071123u133v2_U_19_CH22_Lc1_M_38yr_No_151]

description: Pre-interferon blood sample


title: PBMC-2-RR-Pat.7 [wf20071123u133v2_U_18_LP21_Lc2_M_56yr_alpha_151]

description: Post-interferon blood sample


title: B2-Non-RR-Pat.13 [wf20071123u133v2_U_12_BJ23_B2_M_49yr_alpha_151]

description: Post-interferon liver biopsy

source_name: Post-interferon liver biopsy


title: not used-treatment interrupted [wf20071123u133v2_U_13_SZ13_Lc1_M_46yr_No_151]

description: Pre-interferon blood sample


title: not used-treatment interrupted [wf20071123u133v2_U_14_SZ13_Lc2_M_46yr_alpha_151]

description: Post-interferon blood sample


title: B1-RR-Pat.8 [wf20071123u133v2_U_09_CH22_B1_M_38yr_No_151]

description: Pre-interferon liver biopsy

source_name: Pre-interferon liver biopsy


title: B2-RR-Pat.9 [wf20071123u133v2_U_06_HT20_B2_F_50yr_alpha_151]

description: Post-interferon liver biopsy


title: B1-Non-RR-Pat.14 [wf20070510u133v2_U_05_SK15_M_B1_None_107_1]

description: Pre-interferon liver biopsy


title: not used-treatment interrupted [wf20071123u133v2_U_04_SZ13_B2_M_46yr_alpha_151]

description: Post-interferon liver biopsy


title: PBMC-2-Non-RR-Pat.14 [wf20070510u133v2_U_08_SK15_M_LC2_IFNa_107_1]

description: Post-interferon blood sample


title: B2-RR-Pat.7 [wf20071123u133v2_U_08_LP21_B2_M_56yr_alpha_151]

description: Post-interferon liver biopsy


title: B2-Non-RR-Pat.14 [wf20070510u133v2_U_06_SK15_M_B2_IFNa_107_1]

description: Post-interferon liver biopsy


title: B1-RR-Pat.9 [wf20071123u133v2_U_05_HT20_B1_F_50yr_No_151]

description: Pre-interferon liver biopsy


title: not used- treatment interrupted [wf20071123u133v2_U_03_SZ13_B1_M_46yr_No_151]

description: Pre-interferon liver biopsy


title: B1-RR-Pat.6 [wf20070510u133v2_U_01_BC14_F_B1_None_107_1]

description: Pre-interferon liver biopsy


title: PBMC-2-Non-RR-Pat.12 [wf20070302u133v2_U_14_HW_LC2_73]

description: Post-interferon blood sample


title: PBMC-2-RR-Pat.6 [wf20070510u133v2_U_04_BC14_F_LC2_IFNa_107_1]

description: Post-interferon blood sample


title: PBMC-1-Non-RR-Pat.14 [wf20070510u133v2_U_07_SK15_M_LC1_None_107_1]

description: Pre-interferon blood sample


title: PBMC-1-Non-RR-Pat.12 [wf20070302u133v2_U_13_HW_LC1_73]

description: Pre-interferon blood sample


title: postnatal day 2 bladder cells EGFP positive, EYFP positive, rep 1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9425


title: B2-Non-RR-12 [wf20070302u133v2_U_12_HW_B2_73]

description: Post-interferon liver biopsy


title: B2-RR-Pat.6 [wf20070510u133v2_U_02_BC14_F_B2_IFNa_107_1]

description: Post-interferon liver biopsy


title: PBMC-1-RR-Pat.6 [wf20070510u133v2_U_03_BC14_F_LC1_None_107_1]

description: Pre-interferon blood sample


title: B1-RR-Pat.5 [wf20070302u133v2_U_05_GP_B1_73]

description: Pre-interferon liver biopsy


title: Liver biopsy-Control-B1 [wf20070302u133v2_U_10_OR_B1_73]

description: Pre-interferon liver biopsy


title: PBMC-1-RR-Pat.5 [wf20070302u133v2_U_07_GP_LC1_73]

description: Pre-interferon blood sample


title: B1-RR-Pat.7 [wf20071123u133v2_U_07_LP21_B1_M_56yr_No_151]

description: Pre-interferon liver biopsy


title: B2-RR-Pat.5 [wf20070302u133v2_U_06_GP_B2_73]

description: Post-interferon liver biopsy


title: B1-Non-RR-12 [wf20070302u133v2_U_11_HW_B1_73]

description: Pre-interferon liver biopsy


title: Liver biopsy-Control-B1 [wf20070302u133v2_U_09_TT_B1_73]

description: Pre-interferon liver biopsy


title: PBMC-2-RR-Pat.5 [wf20070302u133v2_U_08_GP_LC2_73]

description: Post-interferon blood sample


title: Embryonic Stem Cells, Cell line: H9 derived d6 EBs pool #3_e1_le1

description: day  6 EBs generated from H9p26, H9p28, H9p29 hES cells pool#3


title: PBMC-2-RR-Pat.4 [wf20070302u133v2_U_04_SC_LC2_73]

description: Post-interferon blood sample


title: B2-RR-Pat.4 [wf20070302u133v2_U_02_SC_B2_73]

description: Post-interferon liver biopsy


title: PBMC-1-RR-Pat.3 [wf20070130u133v2_U_19-Lc1-Pat.9-WV]

description: Pre-interferon blood sample


title: B1-RR-Pat.4 [wf20070302u133v2_U_01_SC_B1_73]

description: Pre-interferon liver biopsy


title: PBMC-2-RR-Pat.3 [wf20070130u133v2_U_20-Lc2-Pat.9-WV]

description: Post-interferon blood sample


title: B2-Non-RR-11 [wf20070130u133v2_U_14-B2-Pat.8-WE]

description: Post-interferon liver biopsy


title: PBMC-1-RR-Pat.4 [wf20070302u133v2_U_03_SC_LC1_73]

description: Pre-interferon blood sample


title: B2-RR-Pat.3 [wf20070130u133v2_U_18-B2-Pat.9-WV]

description: Post-interferon liver biopsy


title: B1-RR-Pat.3 [wf20070130u133v2_U_17-B1-Pat.9-WV]

description: Pre-interferon liver biopsy


title: PBMC-2-Non-RR-Pat.11 [wf20070130u133v2_U_16-Lc2-Pat.8-WE]

description: Post-interferon blood sample


title: PBMC-1-Non-RR-Pat.11 [wf20070130u133v2_U_15-Lc1-Pat.8-WE]

description: Pre-interferon blood sample


title: B1-RR-Pat.10 [wf20070130u133v2_U_09-B1-Pat.7-RS]

description: Pre-interferon liver biopsy


title: B2-RR-Pat.10 [wf20070130u133v2_U_10-B2-Pat.7-RS]

description: Post-interferon liver biopsy


title: B1-Non-RR-11 [wf20070130u133v2_U_13-B1-Pat.8-WE]

description: Pre-interferon liver biopsy


title: PBMC-1-RR-Pat.10 [wf20070130u133v2_U_11-Lc1-Pat.7-RS]

description: Pre-interferon blood sample


title: PBMC-2-RR-Pat.10 [wf20070130u133v2_U_12-Lc2-Pat.7-RS]

description: Post-interferon blood sample


title: PBMC-2-RR-Pat.2 [wf20070130u133v2_U_08-Lc2-Pat.6-PS]

description: Post-interferon blood sample


title: PBMC-1-RR-Pat.2 [wf20070130u133v2_U_07-Lc1-Pat.6-PS]

description: Pre-interferon blood sample


title: B1-Non-RR-2 [wf20070130u133v2_U_05-B1-Pat.6-PS]

description: Pre-interferon liver biopsy


title: B2-Non-RR-2 [wf20070130u133v2_U_06-B2-Pat.6-PS]

description: Post-interferon liver biopsy


title: B2-Non-RR-16 [wf20070130u133v2_U_02-B2-Pat.5-CE]

description: Post-interferon liver biopsy


title: PBMC-1-Non-RR-Pat.16 [wf20070130u133v2_U_03-Lc1-Pat.5-CE]

description: Pre-interferon blood sample


title: PBMC-2-RR-Pat.1 [wf20061103u133v2_U_10-Lc2-Pat-4-SA]

description: Post-interferon blood sample


title: PBMC-1-Non-RR-Pat.15 [wf20061103u133v2_U_07-Lc1-Pat-3-HC]

description: Pre-interferon blood sample


title: PBMC-2-Non-RR-Pat.16 [wf20070130u133v2_U_04-Lc2-Pat.5-CE]

description: Post-interferon blood sample


title: PBMC-1-RR-Pat.1 [wf20061103u133v2_U_09-Lc1-Pat-4-SA]

description: Pre-interferon blood sample


title: B1-Non-RR-Pat.13 [wf20071123u133v2_U_11_BJ23_B1_M_49yr_No_151]

description: Pre-interferon liver biopsy


title: test experiment not for use [wf20061103u133v2_U_05-Lc1-Pat-2-EM]

description: Pre-interferon blood sample


title: test experiment not for use [wf20061103u133v2_U_04-Lc2-Pat-1-GD]

description: Post-interferon blood sample


title: PBMC-2-Non-RR-Pat.15 [wf20061103u133v2_U_08-Lc2-Pat-3-HC]

description: Post-interferon blood sample


title: B1-Non-RR-16 [wf20070130u133v2_U_01-B1-Pat.5-CE]

description: Pre-interferon liver biopsy


title: B1-RR-Pat.1 [wf20061103u133v2_U_01-B1-Pat-4-SA]

description: Pre-interferon liver biopsy


title: B2-RR-Pat.8 [wf20071123u133v2_U_10_CH22_B2_M_38yr_alpha_151]

description: Post-interferon liver biopsy


title: test experiment not for use [wf20060926u133v2_U_03_B1-Pat.2-EM]

description: Pre-interferon liver biopsy


title: test experiment not for use [wf20061103u133v2_U_06-Lc2-Pat-2-EM]

description: Post-interferon blood sample


title: B1-Non-RR-Pat.15 [wf20060926u133v2_U_05_B1-Pat.3-HC]

description: Pre-interferon liver biopsy


title: test experiment not for use [wf20060926u133v2_U_04_B2-Pat.2-EM-alpha]

description: Post-interferon liver biopsy


title: B2-Non-RR-Pat.15 [wf20060926u133v2_U_06_B2-Pat.3-HC-alpha]

description: Post-interferon liver biopsy


title: test experiment not for use [wf20060926u133v2_U_02_B2-Pat.1-GD-alpha]

description: Post-interferon liver biopsy


title: B2-RR-Pat.1 [wf20061103u133v2_U_02-B2-Pat-4-SA]

description: Post-interferon liver biopsy


title: test experiment not for use [wf20060926u133v2_U_01_B1-Pat.1-GD]

description: Pre-interferon liver biopsy


title: test experiment not for use [wf20061103u133v2_U_03-Lc1-Pat-1-GD]

description: Pre-interferon blood sample


title: KT0977_6_D_test3

status: Public on Apr 16 2008

first: Li

last: Li

address: 300 pastuer dr.,

department: Pediatric

institute: Stanford University

hyb_protocol: 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays. 2. Equilibrate probe array to room temperature immediately before use. 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block. 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa. 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation. 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes. 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture. 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2). 9. Place probe array into the hybridization oven, set to 45°C. 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm. 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.

scan_protocol: 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run. 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list. 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required. 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner. 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam. • Pixel value = 3 μm • Wavelength = 570 nm If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed. 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode. 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.

data_processing: Dchip MBEI processing, quantile-quantile normalization

source_name: kidney allograft biopsy, 6 months, deceased donor, test set3

label_protocol: NuGen FL-Ovation cDNA Biotin Module V2

extract_protocol: For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).

tag: 6 months, deceased donor, test set3


title: KT0477_3_L_test3

source_name: kidney allograft biopsy, 3 months, living donor, test set3

tag: 3 months, living donor, test set3


title: KT0780_3_L_paired

source_name: kidney allograft biopsy, 3 months, living donor, paired set

tag: 3 months, living donor, paired set


title: KT1084_6_L_test3

source_name: kidney allograft biopsy, 6 months, living donor, test set3

tag: 6 months, living donor, test set3


title: KT0877_6_L_test3


title: KT0627_3_L_test3


title: KT0704_6_L_test3


title: KT0691_3_L_paired_test3

source_name: kidney allograft biopsy, 3 months, living donor, paired set and test set3


title: KT0975_6_D_test3


title: KT0763_3_L_test3


title: KT0889_6_L_test3


title: KT0921_12_L_paired_test3

source_name: kidney allograft biopsy, 12 months, living donor, paired set and test set3


title: KT0430_3_D_test2_test3

source_name: kidney allograft biopsy, 3 months, deceased donor, test set2 and test set3


title: KT0702_6_L_test3


title: KT0785_3_L_paired


title: KT0878_6_L_test3


title: KT0663_3_L_test3


title: KT0880_6_L_paired

source_name: kidney allograft biopsy, 6 months, living donor, paired set

tag: 6 months, living donor, paired set


title: KT0876_12_L_paired

source_name: kidney allograft biopsy, 12 months, living donor, paired set

tag: 12 months, living donor, paired set


title: KT0381_3_L_test3


title: KT0322_6_L_test3


title: KT0548_12_L_paired


title: KT0440_6_L_test3


title: KT0723_3_L_test3


title: KT0497_3_L_test3


title: KT0545_6_L_test3


title: KT0519_6_L_test3

source_name: kidney allograft biopsy, 6 months. living donor, test set3

tag: 6 months. living donor, test set3


title: KT0325_6_L_test3


title: KT0998_12_L_test3

source_name: kidney allograft biopsy, 12 months, living donor, test set3

tag: 12 months, living donor, test set3


title: KT0626_12_D_test2_test3

source_name: kidney allograft biopsy, 12 months, deceased donor, test set2 and test set3


title: KT0555_24_D_test2_test3

source_name: kidney allograft biopsy, 24 months, deceased donor, test set2 and test set3


title: KT0481_12_D_test2

source_name: kidney allograft biopsy, 12 months, deceased donor, test set2

tag: 12 months, deceased donor, test set2


title: KT0588_3_D_test2_test3

tag: 3 months, deceased donor, test set2 and test set3


title: KT0947_6_D_test2_test3

source_name: kidney allograft biopsy, 6 months, deceased donor, test set2 and test set3


title: KT1122_12_D_test2_test3

tag: 12 months, deceased donor, test set2 and test set3


title: KT0602_3_D_test2_test3


title: KT0563_24_L_test2_test3

source_name: kidney allograft biopsy, 24 months, living donor, test set2 and test set3


title: KT0474_12_L_test2

source_name: kidney allograft biopsy, 12 months, living donor, test set2

tag: 12 months, living donor, test set2


title: KT0955_12_L_test3


title: KT1111_12_L_test3


title: KT0296_12_L_test3


title: KT0646_12_L_test3


title: KT1131_12_D_test2_test3


title: KT0581_24_L_test2_test3

tag: 24 months, living donor, test set2 and test set3


title: KT0367_3_L_test2_test3

source_name: kidney allograft biopsy, 3 months, living donor, test set2 and test set 3


title: KT1125_24_L_test3

source_name: kidney allograft biopsy, 24 months, living donor, test set3

tag: 24 months, living donor, test set3


title: KT0652_3_L_test2_test3

source_name: kidney allograft biopsy, 3 months, living donor, test set2 and test set3


title: KT0664_12_L_test3


title: KT0833_0_D_test1

source_name: kidney allograft biopsy, baseline, deceased donor, test set1

tag: baseline, deceased donor, testset1


title: KT0331_12_L_test3


title: KT0452_12_L_test3


title: KT0614_12_L_test3


title: KT0525_6_L_test2_test3

source_name: kidney allograft biopsy, 6 months, living donor, test set2 and test set3


title: KT0819_0_D_test1


title: KT0596_12_L_test2_test3

source_name: kidney allograft biopsy, 12 months, living donor, test set2 and test set3


title: KT1046_12_L_test2_test3

tag: 12 months, living donor, test set2 and test set3


title: KT0799_0_D_test1


title: KT0567_3_L_test2_test3

tag: 3 months, living donor,test set2 and test set3


title: KT0832_0_D_test1

source_name: kidney allograft biopsy, baseline, deceased donor,  test set1

tag: baseline, deceased donor,  test set1


title: KT0352_24_L_test3


title: KT0816_0_L_test1

source_name: kidney allograft biopsy, baseline, living donor, test set1

tag: baseline, living donor, testset1


title: KT0387_24_L_test3


title: KT0616_0_L_test1


title: KT0516_24_L_test3


title: KT0801_0_L_test1


title: KT0575_0_D_test1


title: KT0752_0_L_test1

tag: baseline, living donor, test set1


title: KT0986_0_D_training

source_name: kidney allograft biopsy, baseline, deceased donor, training set

tag: baseline, deceased donor, training set


title: KT0818_0_D_training

tag: baseline, deceased, training set


title: KT0922_0_D_training


title: KT0738_0_L_test1


title: KT0600_24_L_test3


title: KT0781_0_D_training


title: KT0814_0_D_training


title: KT0727_24_L_test3


title: KT0607_24_D_test3

source_name: kidney allograft biopsy, 24 months, deceased donor, test set3

tag: 24 months, deceased donor, test set3


title: KT1007_24_L_test3


title: KT0796_0_D_training


title: KT0597_24_L_test3


title: KT0812_0_D_training

source_name: kidney allograft biopsy, baseline, deceased donor, training

tag: baseline, deceased donor, training


title: KT0730_0_L_training

source_name: kidney allograft biopsy, baseline, living donor, training set

tag: baseline, living donor, trainingset


title: KT0760_24_L_test3

source_name: kidney allograft biopsy, 24 months, living donor, test set 3

tag: 24 months, living donor, test set 3


title: KT0817_0_D_training


title: KT0776_0_D_training


title: KT0703_24_L_test3


title: KT0736_0_L_training

tag: baseline, living donor, training set


title: KT0422_24_L_test3


title: KT0755_0_L_training


title: KT0690_0_L_training


title: KT0650_0_L_training


title: KT0636_0_L_training


title: KT0412_0_L_training


title: KT1041_3_L_test3

source_name: kidney allograft biopsy, 3 months, living donor, test set3

tag: 3 months, living donor, test set3


title: KT0613_0_L_training


title: Resistant, replicate 1 (286_1)

city: Baltimore

first: Aik Choon

last: Tan

state: MD

address: 1650 Orleans Street, RM 1M86

department: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins

institute: Johns Hopkins University

description: training

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Tumor

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

tag: Human pancreatic tumor was xenografted in six-week-old female athymic nude mice


title: Resistant, replicate 1 (163_1)

description: training


title: Resistant, replicate 2 (163_2)

description: training


title: Resistant, replicate 1 (159_1)

description: validation


title: Resistant, replicate 2 (140_2)

description: training


title: Resistant, replicate 2 (287_2)

description: training


title: Resistant, replicate 2 (159_2)

description: validation


title: Resistant, replicate 1 (265_1)

description: training


title: Resistant, replicate 2 (286_2)

description: training


title: Resistant, replicate 2 (354_2)

description: validation


title: Sensitive, replicate 1 (219_1)

description: validation


title: Resistant, replicate 1 (287_1)

description: training


title: Resistant, replicate 2 (253_2)

description: training


title: Resistant, replicate 1 (140_1)

description: training


title: Resistant, replicate 1 (420_1)

description: validation


title: Resistant, replicate 1 (354_1)

description: validation


title: Resistant, replicate 2 (194_2)

description: training


title: Resistant, replicate 2 (420_2)

description: validation


title: Resistant, replicate 2 (215_2)

description: training


title: KT0624_0_L_training


title: Resistant, replicate 2 (265_2)

description: training


title: Resistant, replicate 1 (185_1)

description: validation


title: Resistant, replicate 1 (253_1)

description: training


title: Resistant, replicate 2 (247_2)

description: validation


title: Sensitive, replicate 2 (219_2)

description: validation


title: Resistant, replicate 2 (185_2)

description: validation


title: Resistant, replicate 2 (294_2)

description: validation


title: Resistant, replicate 1 (194_1)

description: training


title: Resistant, replicate 1 (247_1)

description: validation


title: GATA6 KO #3

status: Public on Apr 15 2008

last: Morrisey

address: 941 Curie Blvd.

department: Medicine and Cell and Developmental Biology

description: Comparison of GATA6 null mouse tissue and wild type controls to determine the role GATA6 plays in lung development and regeneration.

hyb_protocol: The cRNA products were fragments to 200 bp or less, heated for 5 min (100-C) and hybridized for 16 hours at 45-C.  Arrays washed at low and hi strigency and stained with streptavidin coupled with fuorscent marker.

scan_protocol: Confocal scanner used to collect fuorescence signal.  The average signal from 2 sequential scans wa scalculated for each microarray feature.

data_processing: Affy cel files were processed using GC-RMA in Stratagene ArrayAssist Lite version 3.4, MAS5 flags were calculated simultaneously and both the gc-rma expession value and the MAS5 detection flag were included in the .chp files. Default paramters were used.

source_name: GATA6 KO lung E18.5 mouse

label_protocol: Standard Affymetrix protocol using 5 micorgrams total RNA, Superscript II RT.  Second strand synthesis and in vitro amplification and incorporation with biotynalted CTP and UTP.

growth_protocol: mouse embryonic lungs were isolated at E18.5 of development

extract_protocol: Trizol

tag: GATA6 KO lung E18.5 mixed strain


title: GATA6 KO #1

description: Comparison of GATA6 null tissue and wild type controls to determine the role GATA6 plays in lung development and regeneration.


title: wild-type #2

source_name: wild-type E18.5 mouse

tag: wild-type E18.5


title: Resistant, replicate 1 (281_1)

description: validation


title: Sensitive, replicate 2 (410_2)

description: training


title: Resistant, replicate 1 (294_1)

description: validation


title: Sensitive, replicate 1 (410_1)

description: training


title: Sensitive, replicate 2 (198_2)

description: training


title: Resistant, replicate 2 (281_2)

description: validation


title: wild-type #1


title: mouse progenitors_WT_LSK sorted_rep1

city: New York

first: Iannis

last: Aifantis

state: NY

address: 550 First Ave

department: Pathology

institute: NYU Sch of Medicine

description: no additional information

hyb_protocol: 15 mcg of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring 7.2 program. No further adjustments were made to the data in the table.

source_name: Lin-ckit+Sca1+ (LSK) sorted from total bone marrow

label_protocol: 20 ng total RNA converted to cRNA using Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

extract_protocol: Rneasy (QIAGEN) according to manufacturer's protocol.

treatment_protocol: Animals were injected intra-peritoneally with 20 ug/g polyI:C 3 times on alternate days.  Two weeks post-treatment, total bone marrow was harvested and LSK and MP cells were sorted by FACS.

tag: C57BL/6x129 mice

tag: mixed male and female

tag: 2 weeks post polyI:C treatment

tag: Fbw7 flox/flox, Mx1Cre-


title: mouse progenitors_WT_MP sorted_rep1

description: no additional information

source_name: Lin-ckit+Sca1- myeloid progenitors (MP) sorted from total bone marrow


title: GATA6 KO #2


title: mouse progenitors_Fbw7 deficient_LSK sorted_rep1

description: no additional information

tag: Fbw7 flox/flox, Mx1Cre+


title: whole embryo, patUPD18, 430

status: Public on Apr 14 2008

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

institute: King's College London

description: Comparison of gene expression levels between matUPD18 and patUPD18 samples. Identification of highly differentially expressed transcripts. See UPD18 series record.

hyb_protocol: 15µg of labeled probe was hybridised to the array, washed and stained on the Affymetrix fluidics station 450. Standard protocol.

scan_protocol: The Affymetrix Scanner 3000 system was used. Standard protocol.

data_processing: MAS5/GCOS: TGT=500, otherwise default values.

source_name: 8.5 dpc whole embryo, patUPD18

label_protocol: Biotin-labelled with an Enzo labelling kit. The biotinylated cRNA target was purified using cRNA Cleanup spin columns (Affymetrix), fragmented with 5x fragmentation buffer (Affymetrix), and quantified prior to hybridization on an Agilent Bioanalyser.

extract_protocol: Qiagen kit according to manufacturers protocol. The RNA was amplified using the RiboAmp RNA amplification kit (Arcturus).

treatment_protocol: Tissues were snap frozen in liquid nitrogen, permanently stored at -80C, and put on dry ice during transport.

tag: Strain

value: offspring with a paternally-derived uniparental disomy of whole Chr 18

tag: Age

value: 8.5 dpc

tag: Tissue

value: whole embryo


title: wild-type #3


title: whole embryo, matUPD18, 430

source_name: 8.5 dpc whole embryo, matUPD18

value: offspring with a maternally-derived uniparental disomy of whole Chr 18


title: Sensitive, replicate 1 (198_1)

description: training


title: Resistant, replicate 1 (215_1)

description: training


title: Mouse Anatomy Ontology: 5 DR-P_e1_le1

status: Public on Apr 12 2008

description: RNA extracted from postnatal mouse

source_name: Mouse Anatomy Ontology


title: Mouse Anatomy Ontology: 1DR-E_le1

description: RNA from embryonal brains, downregulation of polytopic protease


title: Mouse Anatomy Ontology: 3DR-P_le1

description: RNA from post-natal brains of mice with downregulation of polytopic protease


title: brain, hippocampus: (-) control 1_le1

description:
Isolated DGCs from control mouse #2
Treatment, type=preservation

source_name: brain, hippocampus


title: embryo_Dnmt3l-/+_8.5dpc_rep1

hyb_protocol: The biotinylated target cRNA was purified using a cRNA Cleanup spin column (Affymetrix), fragmented with 5x fragmentation buffer (Affymetrix), and quantified again with the Bioanalyser prior to hybridization. 15 µg of labeled and fragmented target cRNA was used per array. Hybridization, washing and staining were all performed on an Affymetrix Fluidics station 450.

scan_protocol: An Affymetrix Scanner 3000 was used to generate the raw array image data.

data_processing: The raw array image was transformed into CEL files and analyzed at the probe level using the Affymetrix GCOS (MAS5). The array was normalized to a target (TGT) value of 500.

source_name: whole embryo, Dnmt3l-/+ 8.5dpc maternal methylation-deficient mutant

label_protocol: Total RNA was quantified on an Agilent Bioanalyzer and 3µg was used to prepare biotin-labeled target cRNA as detailed in the Affymetrix expression manual (http://www.affymetrix.com/Auth/support/downloads/manuals/expression_ever_manual.zip).

extract_protocol: Trizol (Invitrogen)

tag: gender

value: mixed (eight pooled litter mates)

tag: age

tag: tissue

tag: genotype

value: Dnmt3l-/+ (offspring of a Dnmt3l-/- dam and a wildtype sire) on a C57Bl/6J background


title: Mouse Anatomy Ontology: 4WT-P_le1

description: RNA from post-natal brains, wild type phenotype


title: brain, hippocampus: Tg re-LCM block_le1

description:
Isolated DGCs from trangenic mouse #2
Treatment, type=preservation


title: brain, hippocampus: control re-LCM_le1

description:
Isolated DGCs from control mouse #1
Treatment, type=preservation


title: Mouse Anatomy Ontology: 6 WT-P_e1_le1

description: RNA from postnatal mouse


title: brain, hippocampus: Tg_le1


title: blood, Blood: 24h-nicotine-3_e1_le1

description:
10uM nicotine treatment for 24 hours
Treatment, type=incubate

source_name: blood, Blood


title: brain, hippocampus: (-) control 2_le1


title: embryo_Dnmt3l-/+_8.5dpc_rep2

value: mixed (six pooled litter mates)


title: brain, hippocampus: Tg re-LCM_le1

description:
Isolated DGCs from trangenic mouse #1
Treatment, type=preservation


title: embryo_normal_8.5dpc_control

source_name: whole embryo, normal (non-methylation mutant) 8.5dpc control

tag: strain


title: brain, Hippocampus - Dentate Gyrus: 1215-7_e1_le1

description: Bitransgenic

source_name: brain, Hippocampus - Dentate Gyrus


title: brain, Hippocampus - Dentate Gyrus: 1217-5_e1_le1

description: Bitransgenic


title: blood, Blood: 24h-nicotine-2_e1_le1


title: brain, Hippocampus - Dentate Gyrus: 1217-3_e1_le1

description: Monotransgenic


title: brain, Hippocampus - Dentate Gyrus: 1215-2_e1_le1

description: Monotransgenic


title: Mouse Anatomy Ontology: 2WT-E_le1

description: RNA from embryonal brains,  wt  phenotype control


title: blood, Blood: 24h-control-3_e1_le1

description:
no nicotine treatment
Treatment, type=incubate


title: brain, Hippocampus - Dentate Gyrus: Sample # 5 (Exp. 2) Bitransgenic_le1

description: Bitransgenic treated with water (never exposed to doxycycline)


title: brain, Hippocampus - Dentate Gyrus: 1220-1_e1_le1

description: Bitransgenic


title: blood, Blood: 24h-nicotine-1_e1_le1


title: brain, Hippocampus - Dentate Gyrus: 1221-5_e1_le1

description: Monotransgenic


title: blood, Blood: 1mM nic - 3_e1_le1

description:
1mM nicotine treatment for 1 hour
Treatment, type=incubate


title: blood, Blood: 24h-control-2_e1_le1


title: brain, Hippocampus - Dentate Gyrus: Sample # 4 (Exp. 2) Bitransgenic_le1


title: brain, Hippocampus - Dentate Gyrus: Sample # 7 (Exp. 2) Bitransgenic_le1

description: Bitransgenic treated with water (never expoed to doxycycline)


title: blood, Blood: 10uM nic - 3_e1_le1

description:
10uM nicotine treatment for 1 hour
Treatment, type=incubate


title: blood, Blood: 10nM nic - 3_e1_le1

description:
10nM nicotine treatment for 1 hour
Treatment, type=incubate


title: brain, Hippocampus - Dentate Gyrus: Sample #8 (Exp. 2)  Monotransgenic

description: Monotransgenic treated with water


title: brain, Hippocampus - Dentate Gyrus: Sample #1 (Exp. 2)  Monotransgenic _le1

description: Monotransgenic treated with water


title: brain, Hippocampus - Dentate Gyrus: sample #8 NgR

description:
Monotransgenic treated with water
Treatment, type=add, description=Doxycycline removed to prevent NgR transgene expression. Monotransgenic lacks tTA.


title: brain, Hippocampus - Dentate Gyrus: sample #3 NgR


title: brain, Hippocampus - Dentate Gyrus: sample#16 pTRE/NgR

description:
Bitransgenic treated with doxycycline to inhibit (over)expression of NgR.
Treatment, type=add, description=Doxycycline continuously present in the diet to prevent expression of the transgene


title: blood, Blood: 10 nm nic - 2_e1_le1


title: blood, Blood: control-3_e1_le1


title: blood, Blood: control-2_e1_le1


title: blood, Blood: 10uM nic - 2_e1_le1


title: blood, Blood: 10 nM nicotine_le1


title: brain, Hippocampus - Dentate Gyrus: sample#22 pTRE/NgR


title: blood, Blood: 1mM nic - 2_e1_le1


title: brain, Hippocampus - Dentate Gyrus: sample #13 pTRE/NgR


title: blood, Blood: 1mM nicotine treatment_le1


title: blood, Blood: 10uM nicotine treatment_le1


title: brain, Hippocampus - Dentate Gyrus: Sample #25 pTRE/NgR

description:
Bitransgenic treated with water
Treatment, type=add, description=Doxycycline removed to induce NgR overexpression


title: mouse progenitors_Fbw7 deficient_MP sorted_rep1

description: no additional information


title: brain, Hippocampus - Dentate Gyrus: Sample #12 pTRE/NgR


title: brain, Hippocampus - Dentate Gyrus: Sample #2 NgR


title: brain, Hippocampus - Dentate Gyrus: Sample #9 pTRE/NgR


title: blood, Blood: control-1_e1_le1


title: Df(16)A/+_HPC, biological replicate 10

status: Public on Apr 10 2008

first: Joseph

last: Gogos

department: Physiology

institute: Columbia University

description: Gene expression data from Df(16)A/+ mouse hippocampus

hyb_protocol: According to Affymetrix Standard Protocols

data_processing: The CEL files were analyzed with ArrayAssist (version 5.0, Stratagene Inc). The raw intensity data of all PFC samples or HPC samples were first GCRMA normalized and log2 transformed. T-test with FDR correction were then conducted for differential expression analysis.

source_name: hippocampus

growth_protocol: 8 weeks old male littemate mice

extract_protocol: Trizol extraction of total RNA were performed according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen).

tag: C57BL/6, Gender

value: male, Age:8 weeks,


title: wt_HPC, biological replicate 10

description: Gene expression data from wt  mouse hippocampus

scan_protocol: According to Affymetrix Standard Protocols


title: MIA_4_MOE430_2

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: E18.5 FVB/N mouse embryos, SP-C/MIA overexpressor

hyb_protocol: The cRNA was then hybridized to the murine genome MOE430 (consists of ≈ 45000 gene entries) chips (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.

scan_protocol: Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings.

data_processing: raw data processed by Affymetrix Microarray Suite 5.0 is provided

source_name: MIA_DS: MIA, double transgenic

label_protocol: based on Affymetrix protocols

extract_protocol: GITC


title: Df(16)A/+_HPC, biological replicate 7

label_protocol: According to Affymetrix Standard Protocols


title: wt_HPC, biological replicate 8


title: wt_HPC, biological replicate 4


title: Df(16)A/+_HPC, biological replicate 8


title: wt_HPC, biological replicate 7


title: wt_HPC, biological replicate 9


title: MIA_6_MOE430_2

tag: E18.5 FVB/N mouse embryos, SP-C/MIA overexpressor


title: wt_HPC, biological replicate 3


title: wt_HPC, biological replicate 1


title: Df(16)A/+_HPC, biological replicate 6


title: Df(16)A/+_HPC, biological replicate 9


title: MIA_1_MOE430_2

description: E18.5 FVB/N mouse embryos, SP-C/MIA control

source_name: MIA_SS: MIA, single transgenic


title: Df(16)A/+_HPC, biological replicate 4


title: MIA_3_MOE430_2

tag: E18.5 FVB/N mouse embryos, SP-C/MIA control


title: wt_HPC, biological replicate 5


title: Df(16)A/+_HPC, biological replicate 5


title: wt_HPC, biological replicate 2


title: wt_HPC, biological replicate 6


title: Df(16)A/+_HPC, biological replicate 3


title: Df(16)A/+_PFC, biological replicate 9

description: Gene expression data from Df(16)A/+ mouse prefrontal cortex

source_name: prefrontal cortex


title: Df(16)A/+_PFC, biological replicate 10


title: Df(16)A/+_HPC, biological replicate 2


title: wt_PFC, biological replicate 10

description: Gene expression data from wt  mouse prefrontal cortex


title: brain, Hippocampus - Dentate Gyrus: Sample # 2 (Exp. 2) Monotransgenic_le1

description: Monotransgenic treated with water


title: wt_PFC, biological replicate 7


title: Df(16)A/+_PFC, biological replicate 6


title: Df(16)A/+_PFC, biological replicate 7


title: wt_PFC, biological replicate 5


title: Df(16)A/+_HPC, biological replicate 1


title: Df(16)A/+_PFC, biological replicate 5


title: Df(16)A/+_PFC, biological replicate 2


title: Df(16)A/+_PFC, biological replicate 8


title: wt_PFC, biological replicate 2


title: Df(16)A/+_PFC, biological replicate 4


title: wt_PFC, biological replicate 3


title: wt_PFC, biological replicate 6


title: Df(16)A/+_PFC, biological replicate 3


title: wt_PFC, biological replicate 8


title: wt_PFC, biological replicate 4


title: Endometrium tissue

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

hyb_protocol: Biotinylated cRNA was hybridized with a probe array for 16h at 45C, and the hybridized biotinylated cRNA was stained with streptavidin-PE.

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

source_name: total RNA

label_protocol: cDNA was subjected to in vitro transcription in the presence of biotinylated nucleoside triphosphates using the Enzo BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences), according to the manufacturer's protocol (One-Cycle Target Labeling and Control Reagent package).

extract_protocol: Total cellular RNA was isolated with the RNeasy Mini Kit (Qiagen), according to manufacture's instructions.). Genomic DNA was eliminated by DNase I (TAKARA BIO INC.) treatments.

tag: Endometrium, tissue  (UtE1104 tissue)


title: Df(16)A/+_PFC, biological replicate 1


title: wt_PFC, biological replicate 9


title: Umbilical cord (2), P0

tag: Umbilical cord (2), primary (hUC)


title: wt_PFC, biological replicate 1


title: Umbilical cord (1), P0

tag: Umbilical cord (1), primary (UC712-1)


title: Hepatocyte, P0

tag: Hepatocyte, primary  (Human primary hepatocyte)


title: Amniotic epithelium, P4

tag: Amniotic epithelium, passage 4 (AM910EP P4)


title: Periostium, P1

tag: Periostium, passage 1 (Yub673P,P1PD2)


title: Cortical bone, P3

tag: Cortical bone, passage 3 (Yub650BL P3PD5)


title: Sclera, P1

tag: Sclera, passage 1 (EY1401Sc,P1PD3)


title: Dermis, P2

tag: Dermis, passage 2 (Yub667DE,P2PD5)


title: Normal, biol rep 4 (430 2.0)

status: Public on Apr 09 2008

city: San Francisco

first: Holger

last: Willenbring

address: 35 Medical Center Way

institute: UCSF

description: Global gene expression in adult mouse liver sample.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 18 hours at 45 degree Celsius on MG 430A 2.0 or MG 430 2.0 GeneChip arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed in the Affymetrix GCOS version 1.4.0.036 software using the Microarray Suite version 5.0 (MAS 5.0) algorithm, and global scaling was used as the normalization method. The mean target intensity of each array was set to 350 and alpha1 and alpha2 were set to 0.05 and 0.065, respectively.

source_name: liver, Fah, p21 knockout mouse on NTBC

label_protocol: Standard one cycle cDNA synthesis followed by in vitro transcription (Affymetrix) to produce biotinylated cRNA.

growth_protocol: Adult mice 10 weeks of age were used for this study.

extract_protocol: RNA isolation with RNeasy (Qiagen) from 10 mg of liver tissue stabilized with RNAlater.

treatment_protocol: Mice were either kept on NTBC or treated with water 14 days before liver analysis.

tag: Fah, p21 knockout, male, 10 weeks old, 129 strain


title: Elastic cartilage, P1

tag: Elastic cartilage, passage 1 (Mim1501E,P1PD3)


title: Double knockout, biol rep 3 (430 2.0)

source_name: liver, Fah, p21 knockout mouse off NTBC


title: Double knockout, biol rep 4 (430 2.0)


title: 5 MUD GVHD

city: Tampa

first: Matthew

last: Buzzeo

state: FL

address: 12901 Bruce B. Downs Blvd

institute: University of South Florida College of Medicine

description: engraftment

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45degC onto HG U133 Plus 2.0 GeneChips. Gene Chips 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 analyzed with  GeneChip Operating Software Version 1.2, using Affymetrix default analysis settings, a target value of 500 and a normalization value of 1.

source_name: peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RBC lysis with ammonium chloride Buffer EL, followed by RNA column purification

tag: no additional information


title: 6 MUD GVHD

description: engraftment


title: 7 related GVHD

description: engraftment


title: E13.5 External Carotid Arteries

first: David

middle: D

last: Ginty

address: 725 N. Wolf ST

department: Neuroscience

institute: HHMI/Johns Hopkins Univ

description: Standered Protocol was applied by JHMI Microarray Core Facility.

hyb_protocol: 16hrs at 45 C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

source_name: Microdissected vascular segment from mouse embryos

label_protocol: Two round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

extract_protocol: GTC extraction followed by RNaeasy purification

tag: Strain

value: ICR

tag: age

tag: External Carotid Arteries


title: 4 related Ctrl

description: engraftment


title: 3 related Ctrl

description: engraftment


title: 2 MUD Ctrl

description: engraftment


title: CLC5 ko rep 3

status: Public on Apr 03 2008

first: Jerry

middle: M.

last: Wright

address: 725 N. Wolfe St

institute: Johns Hopkins Medical Institutions

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 1.

source_name: Clcn5 knockout in proximal tubules of mouse kidney

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

tag: Clcn5 knockout


title: 8 related GVHD

description: engraftment


title: Wild type rep 3

source_name: wild type proximal tubules of mouse kidney

tag: Wild type


title: Wild type rep 2


title: Wild type rep 1


title: 1 MUD Ctrl

description: engraftment


title: CLC5 ko rep 1


title: CLC5 ko rep 2


title: E13.5 Internal Carotid Arteries

tag: Internal Carotid Arteries


title: Mammary Gland_CBA_Lactation day 9_rep5

city: Camperdown

first: Peter

last: Williamson

state: NSW

address: RMC Gunn Building, B19

department: Faculty of Veterinary Science

country: Australia

institute: University of Sydney

description: 3 replicates from each strain were hybridised to MOE 430 v2 Genechip (45,101 probesets) while another 2 replicates from each strain were hybridised to MOE 430 A v2 Genechip(22,690 probesets). So normalisation was done using the data from 22,690 probesets common to both chip types using "matchprobes" package available from http://www.bioconductor.org in R

hyb_protocol: Samples that pass QC were then prepared for hybridisation to the Mouse 430 version 2.0 GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300ul was prepared for each sample and 200ul loaded into a Mouse 430 version 2.0 GeneChip.  The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm.  After hybridisation the chip was washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.

scan_protocol: Upon completion of the washing, the chips are then scanned using the Affymetrix GeneChip Scanner 3000.  The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which will then be used for generating subsequent CEL and CHP files for analysis.

data_processing: Quantile normalisation and calculation of probe-set intensity was performed using the robust-multi array average (RMA) function available from the “affy” package in R (Gautier et al., 2004). Data filtering removed low intensity probesets close to background noise by selecting probesets having an un-logged intensity of over 20 in at least one of the conditions. Differential expression was assessed by ranked penalised t-statistics on the logged data using lm.series and e-bayes function in the “limma” package in R (Smyth, 2004).

source_name: Mammary gland excised from lactating day 9 CBA strain of mice

label_protocol: A total of 7ug was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millenium Sciences cat no. 900431).  The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371).  Upon cleaning of the cDNA the next step was to incorporate biotin into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449).  After the IVT process the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. The quantity of product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.

extract_protocol: Total RNA was extracted from 20 mg of mammary tissue by using Qiagen RNeasy Minipreps according to the manufacturer’s instructions.Mouse total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.

treatment_protocol: Mammary glands were immediately snap frozen in Liquid Nitrogen and stored at -80 degree C.

tag: Strain-CBA/CaH; Female; RNA isolated from inguinal mammary glands collected from Day 9 lactating mice


title: Mammary Gland_QSi5_Lactation day 9_rep4

source_name: Mammary gland excised from lactating day 9 QSi5 strain of mice

tag: Strain-QSi5; Female; RNA isolated from inguinal mammary glands collected from Day 9 lactating mice


title: Mammary Gland_QSi5_Lactation day 9_rep5


title: Mammary Gland_CBA_Lactation day 9_rep4


title: Mammary Gland_CBA_Lactation day 9_rep1


title: Mammary Gland_QSi5_Lactation day 9_rep3


title: AND T cells-short dox, FGK-rep2

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

description: AND CD4+ T cells, transient antigen expression, with DC activation. jos3194

data_processing: RMA

source_name: lymph node AND T cells, short dox, FGK

label_protocol: BioArray High Yield RNA Transcript Labeling T7 Kit (Enzo Life Sciences)

extract_protocol: RNA isolated with Trizol reagent and amplified twice with the MessageAmp aRNA Kit (Ambion)

treatment_protocol: dox from d-1 to d0, FGK ip on d-1, AND cells iv on d0

tag: Genetic background

tag: Transgene donor cells

value: AND T cell receptor genes,

tag: Transgenes recipients

value: Ii-rTA+, TIM+,

tag: Age

value: 6-8 weeks,

tag: Tissue

value: subcutaneous lymph nodes,

tag: Isolation

value: FACS on CD4+CD90.1+ cells


title: AND T cells-short dox, PBS-rep2

description: AND CD4+ T cells, transient antigen expression, no DC activation. jos3193

source_name: lymph node AND T cells, short dox, PBS

treatment_protocol: dox from d-1 to d0, PBS ip on d-1, AND cells iv on d0


title: AND T cells-long dox, FGK-rep1

description: AND CD4+ T cells, persistent antigen expression, with DC activation. jos3049

source_name: lymph node AND T cells, long dox, FGK

treatment_protocol: dox from d-1 to d3, FGK ip on d-1, AND cells iv on d0


title: AND T cells-short dox, PBS-rep3

description: AND CD4+ T cells, transient antigen expression, no DC activation. jos3059


title: AND T cells-no dox, FGK-rep1

description: AND CD4+ T cells, no antigen expression, with DC activation. jos3045

source_name: lymph node AND T cells, no dox, FGK

value: Ii-rTA-, TIM+,


title: AND T cells-long dox, PBS-rep2

description: AND CD4+ T cells, persistent antigen expression, no DC activation. jos3195

source_name: lymph node AND T cells, long dox, PBS

treatment_protocol: dox from d-1 to d3, PBS ip on d-1, AND cells iv on d0


title: AND T cells-no dox, PBS-rep2

description: AND CD4+ T cells, no antigen expression, no DC activation. jos3091

source_name: lymph node AND T cells, no dox, PBS


title: AND T cells-long dox, FGK-rep2

description: AND CD4+ T cells, persistent antigen expression, with DC activation. jos3196


title: AND T cells-long dox, FGK-rep3

description: AND CD4+ T cells, persistent antigen expression, with DC activation. jos3061


title: AND T cells-no dox, PBS-rep3

description: AND CD4+ T cells, no antigen expression, no DC activation. jos3058

treatment_protocol: dox from d-1 to d3, PBS ip at d-1, AND cells iv at d0


title: AND T cells-long dox, PBS-rep3

description: AND CD4+ T cells, persistent antigen expression, no DC activation. jos3060


title: AND T cells-short dox, FGK-rep1

description: AND CD4+ T cells, transient antigen expression, with DC activation. jos3047


title: HeLa, PIK3CB-6340 mock

status: Public on Apr 02 2008

first: Dimos

last: Gaidatzis

institute: Friedrich Miescher Institute

description: Array was analyzed for sense and antisense strand enrichment of "seed"-complementary sequences. For details please see: Chen PY, Weinmann L, Gaidatzis D, Pei Y, Zavolan M, Tuschl T, Meister G. RNA (2008) 14(2):263-74.

hyb_protocol: According to manufacturer (Affymetrix)

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: All arrays were condensed together using gcRMA with quantile normalization using bioconductor in R.

source_name: HeLa cells, PIK3CB-6340 mock

label_protocol: According to manufacturer (Affymetrix)

extract_protocol: Trizol; according to manufacturer (Invitrogen)

treatment_protocol: Transfected with 50nM siRNA with RNAiMAX according to manufacturer (Invitrogen)

tag: HeLa cells, PIK3CB-6340 mock


title: HeLa, s/meT-as

source_name: HeLa cells, s/meT-as

tag: HeLa cells, s/meT-as


title: AND T cells-no dox, FGK-rep2

description: AND CD4+ T cells, no antigen expression, with DC activation. jos3092


title: AND T cells-no dox, PBS-rep1

description: AND CD4+ T cells, no antigen expression, no DC activation. jos3044

value: AND T cell receptor genes

value: Ii-rTA-, TIM+

value: 6-8 weeks

tag: Tissue subcutaneous lymph nodes


title: HeLa, s/as

source_name: HeLa cells, s/as

tag: HeLa cells, s/as


title: AND T cells-short dox, PBS-rep1

description: AND CD4+ T cells, transient antigen expression, no DC activation. jos3046


title: AND T cells-long dox, PBS-rep1

description: AND CD4+ T cells, persistent antigen expression, no DC activation. jos3048


title: HeLa, PIK3CB-6340

source_name: HeLa cells, PIK3CB-6340

tag: HeLa cells, PIK3CB-6340


title: HeLa, meT-a/meT-as

source_name: HeLa cells, meT-a/meT-as

tag: HeLa cells, meT-a/meT-as


title: HeLa, meT-s/as

source_name: HeLa cells, meT-s/as

tag: HeLa cells, meT-s/as


title: HeLa, s/as mock

source_name: HeLa cells, s/as mock

tag: HeLa cells, s/as mock


title: D20_A

status: Public on Apr 01 2008

city: Valencia

first: Manolo

last: Mata

address: Avda. Blasco Ibanez, 17

department: UCIM

country: Spain

institute: university of valencia

description: Gene expression data from cell line knocked-down for SDHB gene

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The TGT intensity of each array was arbitrarily set to 500.

source_name: hepatocellular carcinoma cell line Hep3B cells, plasmid siSDHB, clone D20

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

growth_protocol: cell lines were grown in MEM medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM L-Glutamine, 1mM non-essential aminoacids, 1 mM sodium pyruvate and 400 µg/ml G418. Cell cultures were propagated at 37 ºC in a humidified 5% CO2, 95% air atmosphere.

extract_protocol: total RNA was extracted from pelleted cells using the RNeasy minikit from Qiagen.

treatment_protocol: cell lines were grown until nearly confluent, washed in PBS, and scraped off in PBS using a cell scraper. Cells were collected by centrifugation before RNA extraction.

tag: Hep3B cells stably transfected with short hairpin vectors containing an siRNA directed to SDHB

tag: Hep3B cells stably transfected with plasmid siSDHB, clone D20, replicate 1


title: D20_C

tag: Hep3B cells stably transfected with plasmid siSDHB, clone D20, replicate 3


title: pU62_B

description: Gene expression data from control cell line

source_name: hepatocellular carcinoma cell line Hep3B cells, plasmid pU6, clone 2

tag: Hep3B cells stably transfected with short hairpin vectors (plasmid pU6 is the host vector)

tag: Hep3B cells stably transfected with plasmid pU6, clone 2, replicate 2


title: D20_B

tag: Hep3B cells stably transfected with plasmid siSDHB, clone D20, replicate 2


title: pU62_C

tag: Hep3B cells stably transfected with plasmid pU6, clone 2, replicate 3


title: pU62_A

tag: Hep3B cells stably transfected with plasmid pU6, clone 2, replicate 1


title: HCT116_1

city: Sakyo-ku

first: Yoshinao

last: Ruike

state: Kyoto

address: 46-29 Yoshida-Shimo-Adachi-cho

department: Pharmaceutical Sciences

institute: Kyoto University

description: Genome-wide mRNA expression profiles of sixteen human cell lines were obtained by microarray analysis with the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array as manufacture’s instructions.

hyb_protocol: As manufacture’s instructions (Affymetrix).

scan_protocol: Scanned by a Genechip Scanner 3000

data_processing: We used the robust multi-array analysis (RMA) expression measure that represents the log transform of (background corrected and normalized) intensities of the GeneChips. The RMA measures were computed using the R package program (http://www.bioconductor.org).

source_name: HCT116 cell line, no treatment

label_protocol: Double-stranded cDNA was synthesized from total RNA. An in vitro transcription reaction was then carried out to produce biotin-labeled complementary RNA (cRNA) from the cDNA. The cRNA was then fragmented and used for hybridization.

growth_protocol: Cells were cultured in DMEM medium containing 10% FBS and exponentially growing cells were harvested.

extract_protocol: Exponentially growing cells were harvested and total RNA was collected by standard procedures using ISOGEN (Nippon Gene) and chloroform and precipitated with isopropanol.

tag: human cultured cell line derived from colon carcinoma


title: HEK293T_1

source_name: HEK293T cell line, no treatment

tag: human cultured cell line derived from embryonal kidney


title: HeLa_1

source_name: HeLa cell line, no treatment

tag: human cultured cell line derived from cervix carcinoma


title: MCF7_1

source_name: MCF7 cell line, no treatment

tag: human cultured cell line derived from breast adenocarcinoma


title: HT29_1

source_name: HT29 cell line, no treatment

tag: human cultured cell line derived from colon adenocarcinoma


title: K562_1

source_name: K562 cell line, no treatment

growth_protocol: Cells were cultured in RPMI medium containing 10% FBS and exponentially growing cells were harvested.

tag: human cultured cell line derived from chronic myeloid leukemia


title: HT1080_1

source_name: HT1080 cell line

tag: human cultured cell line derived from fibrosarcoma


title: Jurkat_1

source_name: Jurkat cell line, no treatment

tag: human cultured cell line derived from T cell lukemia


title: HepG2_1

source_name: HepG2 cell line, no treatment

tag: human cultured cell line derived from hepatocellular carcinoma


title: HeLaS3_1

source_name: HeLaS3 cell line


title: MDAMB231_1

source_name: MDA-MB-231 cell line, no treatment


title: Huh7_1

source_name: Huh7 cell line

tag: human cultured cell line derived from hapatocellular carcinoma


title: HEK293_1

source_name: HEK293 cell line, no treatment


title: SKNMC_1

source_name: SKNMC cell line, no treatment

tag: human cultured cell line derived from neuroblastoma


title: CACO2_1

source_name: Caco2 cell line, no treatment


title: A549_1

source_name: A549 cell line, no treatment

tag: human cultured cell line derived from lung carcinoma


title: Angiopoietin-1(sparse)-1

city: Osaka

first: NAOKI

last: MOCHIZUKI

address: 5-7-1 Fujishirodai, Suita

department: Structural Analysis

institute: Natl. Cardiovasc. Ctr. Res. Inst

description: Sparse HUVECs were stimulated with COMP-Ang1 after overnight starvation

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix Microarray Suite v5.0 with target intensity=100

molecule: polyA RNA

source_name: human umbilical vein endothelial cells

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: HUMEDIA; sparse growth

extract_protocol: Total RNAs were extracted using RNAzol. 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

treatment_protocol: HUVECs stimulated 100 ng /ml COMP-Angiopoietin-1 after starvation overnight

tag: sparse HUVECs stimulated with Angiopoietin for 1 hour after overnight starvation


title: unstimulated(sparse)-1

description: Sparse HUVECs unstimulated

treatment_protocol: no treatment

tag: unstimulated sparse HUVECs


title: Angiopoietin-1(confluent)-2

description: Confluent HUVECs were stimulated with COMP-Ang1 for 1 hour after starvation overnight

growth_protocol: HUMEDIA; confluent growth

tag: confluent HUVECs stimulated with Angiopoietin for 1 hour


title: unstimulated(sparse)-2

description: Sparse HUVECs were unstimulated


title: Angiopoietin-1(sparse)-2

description: Sparse HUVECs were stimulated with COMP-Ang1 or 1 hour after overnight starvation

treatment_protocol: sparse HUVECs stimulated 100 ng /ml COMP-Angiopoietin-1 after starvation overnight

tag: sparse HUVECs stimulated with Angiopoietin for 1 hour


title: unstimulated(confluent)-1

description: Unstimulated HUVEC under confluent condition

extract_protocol: Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

tag: unstimulated confluent HUVECs


title: Angiopoietin-1(confluent)-1

description: Confluent HUVECs were stimulated with COMP-Ang1 (more potent Angiopoietin-1 than native Angiopoietin-1) for 1 hour after starvation overnight

extract_protocol: Total RNAs were extracted using RNAzol . 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).


title: unstimulated(confluent)-2

description: Confluent HUVECs unstimulated


title: TERT6-217, TERT transfected, Affymetrix

city: Hiroshima

first: Keiko

last: Hiyama

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Research Institute for Radiation Biology and Medicine

institute: Hiroshima University

description: immortal lifespan

hyb_protocol: The synthesized 20 microgram of cRNA, quantified by spectrometry and qualified using an Agilent 2100 Bioanalyzer, was then fragmented and hybridized to each array.

scan_protocol: Each microarray was scanned using an Affymetrix GeneChip Scanner 3000 with Affymetrix GeneChip Operating System (GCOS) 1.2.

data_processing: Using Affymetrix GeneChip Operating System (GCOS) 1.2., scale factor was set as 500.

source_name: human fetal lung fibroblast TIG-1 clone TERT6 transfected with TERT

label_protocol: The first-strand cDNA was generated from 1 microgram of total RNA using reverse transcriptase and a T7 primer using the GeneGhip One-Cycle Target Labeling kit, and then second-strand cDNA was produced using DNA polymerase mix and RNase H. cRNA (complementary RNA) was generated via an in vitro transcription reaction using T7 RNA polymerase and biotinilated ribonucleotide analog.

growth_protocol: Cells were cultured in Dulbecco's modified Eagle's minimal essential medium (DMEM; Sigma-Aldrich Japan, Tokyo, Japan) containing 10% heat-inactivated fetal bovine serum (FBS; BioWhittaker, Verviers, Belgium) in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted from the frozen cultured cell pellets using QIAGEN RNeasy mini kit (QIAGEN, Inc., Valencia, CA), respectively, according to the manufacturer's protocols. The quality of the RNA was checked using Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: TERT expression vector was transfected to TIG-1 and isolated as a G418 resistant clone. Exponentially growing cultured cells were collected using trypsin followed by rinse with PBS, and frozen until use.

tag: human fetal lung fibroblast TIG-1 clone TERT6 at 217 PDL transfected with TERT


title: control participant P330

city: Jena

first: Sandy

last: Mosig

address: Bachstrasse 18

department: Molecular Hemostaseology - Institute of Vascular Medicine

country: Germany

institute: University Hospital Jena

description: Gene expression data from control participant T2

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133A2.0 GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: control participant P330 (human CD3 positive T cells)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

extract_protocol: the RNA was worked up using PLG Tubes and the Qiagen Rneasy Kit

treatment_protocol: T cells were precipitated untouched from 4 ml peripheral blood mononuclear cells, washed in PBS + 2mM EDTA, lysed in TriZol

tag: cell type

value: T cell

tag: disease state

value: control participant


title: control participant P310

description: Gene expression data from control participant LF

source_name: control participant P310 (human CD3 positive T cells)


title: control participant P332wh

description: Gene expression data from control participant T3

source_name: control participant P332wh (human CD3 positive T cells)


title: control participant P312

description: Gene expression data from control participant SH

source_name: control participant P312 (human CD3 positive T cells)


title: TERT5-71, TERT transfected, Affymetrix

description: mortal elongated lifespan

source_name: human fetal lung fibroblast TIG-1 clone TERT5 transfected with TERT

tag: human fetal lung fibroblast TIG-1 clone TERT5 at 71 PDL transfected with TERT


title: control participant P318

description: Gene expression data from control participant TL

source_name: control participant P318 (human CD3 positive T cells)


title: control participant P302

description: Gene expression data from control participant BL

source_name: control participant P302 (human CD3 positive T cells)


title: TERT8-70, TERT transfected, Affymetrix

description: mortal elongated lifespan

source_name: human fetal lung fibroblast TIG-1 clone TERT8 transfected with TERT

tag: human fetal lung fibroblast TIG-1 clone TERT8 at 70 PDL transfected with TERT


title: control participant P328wh

description: Gene expression data from control participant T1

source_name: control participant P328wh (human CD3 positive T cells)


title: TERT6-121, TERT transfected, Affymetrix

description: immortal lifespan

tag: human fetal lung fibroblast TIG-1 clone TERT6 at 121 PDL transfected with TERT


title: heterozygot FH P387

description: Gene expression data from control participant LW

source_name: heterozygot FH P387 (human CD3 positive T cells)

value: heterozygote FH


title: control participant P350

description: Gene expression data from control participant RF

source_name: control participant P350 (human CD3 positive T cells)


title: heterozygot FH P278

description: Gene expression data from the heterozygous FH participant F

source_name: heterozygot FH P278 (human CD3 positive T cells)


title: control participant P316

description: Gene expression data from control participant MO

source_name: control participant P316 (human CD3 positive T cells)


title: TIG-1-45, parent, Affymetrix

description: mortal lifespan

source_name: human fetal lung fibroblast TIG-1

treatment_protocol: Exponentially growing cultured cells were collected using trypsin followed by rinse with PBS, and freezed until use.

tag: normal human fetal lung fibroblast at 45 PDL  before gene transfection


title: control participant P338

description: Gene expression data from control participant T6

source_name: control participant P338 (human CD3 positive T cells)


title: control participant P306wdh

description: Gene expression data from control participant KP

source_name: control participant P306wdh (human CD3 positive T cells)


title: control participant P300

description: Gene expression data from control participant DB

source_name: control participant P300 (human CD3 positive T cells)


title: heterozygot FH P283

description: Gene expression data from the heterozygous FH participant M

source_name: heterozygot FH P283 (human CD3 positive T cells)


title: control participant P336

description: Gene expression data from control participant T5

source_name: control participant P336 (human CD3 positive T cells)


title: heterozygot FH P273

description: Gene expression data from the heterozygous FH participant D

source_name: heterozygot FH P273 (human CD3 positive T cells)