title: Viro5p02-95_356_1b

status: Public on Dec 31 2011

type: other

city: San Francisco

first: Joseph

middle: L

last: DeRisi

state: CA

address: Byers Hall, Rm s403c, 1700 4th St.

department: Department of Biochemistry and Biophysics

country: USA

institute: University of California San Francisco

hyb_protocol: Samples were hybridized in 65 degC incubation overnight in standard microarray hybridization chamber.   Hybridization reactions contained labeled sample and probe 70 in 3xSSC, 25 mM HEPES pH7.4, and 0.25pct SDS.  Arrays were washed twice in 0.5x SSC/0.025pct SDS and twice in 0.025x SSC.

scan_protocol: Microarray were scanned with GenePix scanner, software version 6.1

data_processing: Sum-normalized values are Median feature intensity minus median background intensity (Cy3)

molecule: other

organism: Viruses

source_name: Source of nucleic acid is cell-free serum collected during hospitalization for dengue-like illness.

label_protocol: Labeling: Aminoallyl-dUTP was incorporated by PCR.  The aminoallyl moieties were reacted with Cy3-NHS or Cy5-NHS (GE Healthcare); Cy3 for amplified sample, Cy5 for Probe70 (internal reference for GenePix spot finding).  Unreacted dye was removed using a DNA clean & concentrator (Zymo Research) according to the manufacturer's protocol.

extract_protocol: Total nucleic acid extracted from cell-free serum using the Qiagen qiaamp viral RNA mini kit following the manufacturers protocols.  (No DNase treatment.)

tag: tissue

value: serum

tag: disease state

value: dengue like illness but dengue-negative


title: Viro5p02-83_347_1b


title: Viro5p02-94_461_1b


title: Viro5p02-92_296_1c


title: Viro5p02-90_239_1b


title: Viro5p02-87_281_1b


title: Viro5p02-71_193_1b


title: Viro5p02-97_263_1


title: Viro5p02-99_355_1b


title: Viro5p02-73_186_1b


title: Viro5p02-84_325_1b


title: Viro5p02-81_HeLa_control

value: Hela control


title: Viro5p02-195_HeLa_control


title: Viro5p02-186_438_1b


title: Viro5p02-181_383_1b


title: Viro5p02-192_473_1c


title: Viro5p02-191_360_1b


title: Viro5p02-176_414_1c


title: Viro5p02-178_356_1c


title: Viro5p02-93_322_1b


title: Viro5p02-180_378_1c


title: Viro5p02-76_275_1b


title: Viro5p02-72_161_1b


title: Viro5p02-184_448_1b


title: Viro5p02-187_378_1b


title: Viro5p02-183_414_1b


title: Viro5p02-179_441_1b


title: Viro5p02-175_478_1c


title: Viro5p02-168_491_1b


title: Viro5p02-174_390_1b


title: Viro5p02-162_465_1c


title: Viro5p02-158_381_1b


title: Viro5p02-164_377_1b


title: Viro5p02-160_474_1c


title: Viro5p02-172_465_1b


title: Viro5p02-173_401_1b


title: Viro5p02-159_566_1c


title: Viro5p02-157_480_1d


title: Viro5p02-146_367_1b


title: Viro5p02-161_361_1b


title: Viro5p02-169_488_1c


title: Viro5p02-163_373_1b


title: Viro5p02-147_443_1c


title: Viro5p02-143_321_1b


title: Viro5p02-149_401_1c


title: Viro5p02-155_HeLa_control


title: Viro5p02-145_4512_1b


title: Viro5p02-138_297_1b


title: Viro5p02-141_342_1b


title: Viro5p02-135_350_1b


title: Viro5p02-142_274_1b


title: Viro5p02-131_263_1c


title: Viro5p02-133_349_1b


title: Viro5p02-137_264_1


title: Viro5p02-127_329_1b


title: Viro5p02-136_329_1b


title: Viro5p02-126_344_1b


title: Viro5p02-125_271_1b


title: Viro5p02-124_315_1b


title: Viro5p02-122_298_1b


title: Viro5p02-132_354_1b


title: Viro5p02-116_330_1b


title: Viro5p02-066_574


title: Viro5p02-067_575


title: Viro5p02-118_298_1c


title: Viro5p02-120_331_1b


title: Viro5p02-123_280_1b


title: Viro5p02-104_315_1c


title: Viro5p02-059_432


title: Viro5p02-063_505


title: Viro5p02-107_332_1b


title: Viro5p02-106_267_1b


title: Viro5p02-061_459


title: Viro5p02-113_330_1b


title: Viro5p02-121_336_1b


title: Viro5p02-110_282_1b


title: Viro5p02-111_335_1b


title: Viro5p02-057_371


title: Viro5p02-117_270_1c


title: Viro5p02-065_565


title: Viro5p02-062_473


title: Viro5p02-058_399


title: Viro5p02-105_298_1b


title: Viro5p02-064_506


title: Viro5p02-060_450


title: Viro5p02-115_HeLa_control


title: Viro5p02-109_345_1b


title: Viro5p02-102_341_1b


title: Viro5p02-053_283


title: Viro5p02-051_201


title: Viro5p02-047_73


title: Viro5p02-054_323


title: Viro5p02-050_190


title: Viro5p02-052_207


title: Viro5p02-048_160


title: Viro5p01-260_181_1b


title: Viro5p02-049_177


title: Viro5p02-055_363


title: Viro5p02-044_554


title: Viro5p02-056_370


title: Viro5p02-043_544


title: Viro5p01-259_187_1


title: Viro5p02-042_508


title: Viro5p01-258_156_1b


title: Viro5p02-046_586


title: Viro5p02-045_570


title: Viro5p01-239_180_1b


title: Viro5p01-252_157_1b


title: Viro5p01-254_158_1b


title: Viro5p02-041_502


title: Viro5p01-256_175_1b


title: Viro5p01-240_167_1b


title: Viro5p01-253_197_1c


title: Viro5p01-249_179_1c


title: Viro5p01-255_186_1c


title: Viro5p01-251_161_1c


title: Viro5p01-257_183_1b


title: Viro5p01-250_193_1c


title: Viro5p01-238_192_1b


title: Viro5p01-236_168_1b


title: Viro5p01-237_159_1b


title: Viro5p01-235_206_1b


title: Viro5p01-234_131_1b


title: Viro5p01-233_171_1b


title: Viro5p01-194_457


title: Viro5p01-230_88_1b


title: Viro5p01-197_487


title: Viro5p01-192_447


title: Viro5p01-193_451


title: Viro5p01-232_78_1c


title: Viro5p01-188_327


title: Viro5p01-195_475


title: Viro5p01-186_273


title: Viro5p01-196_477


title: Viro5p01-191_387


title: Viro5p01-190_358


title: Viro5p01-187_277


title: Viro5p01-184_243


title: Viro5p01-189_332


title: Viro5p01-183_235


title: Viro5p01-185_245


title: WT at post natal day 21, biological replicate 1

type: RNA

city: Rockville

first: Radu

last: Cojocaru

state: MD

address: 5635 Fishers Lane, Suite 510

institute: Elsevier

description: WT at post natal day 21 flow sorted rod photorecteptor

hyb_protocol: Following fragmentation and labelling, 2.2 ug of cDNA were hybridized at 45C for 18 hours.  GeneChips were washed and scanner in the Affymetrix FS450.

scan_protocol: GeneChips were scanner with an Affymetrix GCS3000 7G

data_processing: We used GCRMA for normalization and background correction with median polish for probeset summarization. The analysis was done using the Gene Spring software from Agilent Technologies (http://www.genomics.agilent.com).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: flow sorted rod photoreceptors

label_protocol: Biotinylated cDNA were prepared for the MOE 430 2.0 arrays using Nugen Ovation RNA Amplification System starting with 40 ng of total RNA.

growth_protocol: Mice were raised using normal growth protocols.

extract_protocol: Total RNA was extracted using RNAqueous-4PCR (Agilent).

treatment_protocol: Retinas were dissociated and processed using FACS to recover rod photoreceptors expressing GFP.

value: Flow sorted Rod Photoreceptor

tag: strain

tag: genotype

value: wild type

tag: age

value: post natal day 21


title: Viro5p01-182_hela


title: WT at post natal day 21, biological replicate 4

description: WT at post natal day 21 flow sorted rod photoreceptor


title: Viro5p01-181_382


title: Viro5p01-179_195


title: WT at post natal day 9, biological replicate 2

description: WT at post natal day 9 flow sorted rod photoreceptor

value: post natal day 9


title: WT at post natal day 9, biological replicate 3


title: WT at post natal day 14, biological replicate 2

description: WT at post natal day 14 flow sorted rod photoreceptor

value: post natal day 14


title: Viro5p01-177_179


title: Viro5p01-176_176


title: WT at post natal day 21, biological replicate 2


title: WT at post natal day 9, biological replicate 4


title: WT at post natal day 14, biological replicate 1

description: WT at post natal day 14 flow sorted rod photorecteptor


title: WT at post natal day 21, biological replicate 3


title: WT at post natal day 14, biological replicate 3


title: Viro5p01-175_170


title: WT at post natal day 9, biological replicate 1

description: WT at post natal day 9 flow sorted rod photorecteptor


title: Viro5p01-178_184


title: WT at post natal day 6, biological replicate 2

description: WT at post natal day 6 flow sorted rod photoreceptor

value: post natal day 6


title: Viro5p01-173_135


title: WT at post natal day 6, biological replicate 4


title: WT at post natal day 6, biological replicate 1

description: WT at post natal day 6 flow sorted rod photorecteptor


title: WT at post natal day 6, biological replicate 3


title: Rds at post natal day 21, biological replicate 3

description: Rds at post natal day 21 flow sorted rod photoreceptor

value: Rds-KO


title: Rds at post natal day 14, biological replicate 3

description: Rds at post natal day 14 flow sorted rod photoreceptor


title: Rds at post natal day 21, biological replicate 2


title: Viro5p01-174_137


title: Rds at post natal day 21, biological replicate 4


title: Rds at post natal day 21, biological replicate 1

description: Rds at post natal day 21 flow sorted rod photorecteptor


title: Viro5p01-172_130


title: Rds at post natal day 14, biological replicate 4


title: Rds at post natal day 9, biological replicate 4

description: Rds at post natal day 9 flow sorted rod photoreceptor


title: Rds at post natal day 14, biological replicate 1

description: Rds at post natal day 14 flow sorted rod photorecteptor


title: Rds at post natal day 9, biological replicate 3


title: Rds at post natal day 14, biological replicate 2


title: Viro5p01-171_118


title: Rds at post natal day 9, biological replicate 2


title: Rds at post natal day 9, biological replicate 1

description: Rds at post natal day 9 flow sorted rod photorecteptor


title: Patient 15 microGIST

type: genomic

city: Taipei

first: Cher-wei

last: Liang

address: 7 Chung-Shan S. Rd.

department: Pathology

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: Agilent Oligo aCGH Hybridization Kit (p/n 5188-5220) and Agilent Oligo aCGH Wash Buffers (p/n 5188-5226) were used according to manufacturer protocols.

scan_protocol: Agilent G2565BA Scanner was used according to manufacturer protocol. Data extraction has been performed with Agilent G2567AA Feature Extraction Software v10.5.1.1.

data_processing: Feature extraction data was obtained using Agilent G2567AA  Feature Extraction Software (v10.5.1.1), normalized using LOcally-WEighted  regression Scatterplot Smoother

molecule: genomic DNA

organism: Homo sapiens

source_name: microGIST FFPE tumor genomic DNA

label_protocol: Genomic DNA ULS Labeling Kit (Agilent Technologies) was used to differentially label the test DNA with Cy3-labeled nucleotides and the reference DNA - with Cy5. See for detailes: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis - ULS Labeling for Blood, Cells, Tissues or FFPE (with a High Throughput option) Protocol; Version 3.1, August 2009; Manual Part Number G4410-90020

extract_protocol: QIAamp® DNA FFPE Tissue Kit (Qiagen, Valencia, CA, USA) for manual microdissection samples and PicoPure® DNA Extraction Kit (Arcturus Bioscience, Mountain View, CA, USA) for laser microdissection samples, respectively, in accordance with the manufacturer's protocol.

tag: cell type

value: Gastrointestinal stroml tumor cells

source_name: FFPE normal tissue DNA from the same patient

value: Lymph node


title: Patient 16 microGIST

value: Thyroid


title: Patient 13 microGIST

value: GI tract mixed cells (not microdissected)


title: Patient 9 GIST

source_name: GIST FFPE tumor genomic DNA


title: Rds at post natal day 6, biological replicate 4

description: Rds at post natal day 6 flow sorted rod photoreceptor


title: Rds at post natal day 6, biological replicate 2


title: Patient 14 microGIST


title: Patient 11 microGIST


title: Patient 9 microGIST


title: Rds at post natal day 6, biological replicate 1

description: Rds at post natal day 6 flow sorted rod photorecteptor


title: Patient 15 GIST


title: Patient 12 microGIST

source_name: male DNA

value: male DNA G147A (Promega, Madison, WI)


title: EA10001_102621 notch2 mutant biological rep 2

hyb_protocol: The cRNA target was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc).  The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix).  The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm.  GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.

scan_protocol: Fluorescent images were detected in an GeneChip® Scanner 3000

data_processing: Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). Data was normalized using RMA and further analyzed using Genespring

source_name: EA10001_102621  notch2 mutant

label_protocol: Total RNA (100 ng) was converted into cDNA by incubation at 42ºC for 2 hrs with Reverse Transcriptase and a modified oligo(dT)24 primer that contains T7 promoter sequences.   After first strand synthesis, a double-stranded cDNA molecule was generated by incubation at 16ºC for 1 hr using DNA Polymerase I and DNA Ligase. The second strand synthesis was terminated by incubation at 65ºC for 10 min, then specimens were placed on ice.  The cDNA products were incubated at 40ºC for 4 hrs with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix).

growth_protocol: Pregnant mice were housed in clean animal facilities in accordance with the NIH guidelines. Pregnant mother was sacrificed on 19.5 days gestation day to obtain embryos at  stage E19.5.

extract_protocol: Embryonic lenses were dissected carefully to get rid of any sorrounding tissues from attaching to the lens. Lenses were immediately snap frozen in dry ice. Total RNA was isolated using Trizol reagent (Invitrogen).Before target production, the quality and quantity of each RNA sample was assessed using a 2100 BioAnalyzer (Agilent).

treatment_protocol: Three littermate of controls and Notch2 mutants, total of 6 embryos were used to . No additional treatment was performed.

value: ocular lens

value: notch2 mutant

tag: genetic background

value: mixed C57BL/6 & FVB/N


title: EA10001_102625 notch2 mutant biological rep 3

source_name: EA10001_102625  notch2 mutant


title: Patient 12 normal

source_name: FFPE normal tissue DNA

value: male DNA G148A (Promega, Madison, WI)


title: Patient 10 microGIST


title: EA10001_102624 wild type control biological rep 3

source_name: EA10001_102624 wild type control


title: EA10001_102619 notch2 mutant biological rep 1

source_name: EA10001_102619  notch2 mutant


title: Rds at post natal day 6, biological replicate 3


title: EA10001_102623 wild type control biological rep 2

source_name: EA10001_102623 wild type control


title: EA10001_102622 wild type control biological rep 1

source_name: EA10001_102622 wild type control


title: Patient 8 GIST

value: GI tract epithelial layer


title: Patient 6 microGIST

value: GI tract smooth muscle cells


title: mutant RQ

city: Frederick

first: Suhwan

last: Chang

address: PO Box B, NCI-Frederick

institute: National Cancer Institute

description:
gene expression data from mouse embroid body with R1669Q mutation of human BRCA1
Chang_RQ_022908.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2. 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 Partek Genomic Suite using default RMA method.

source_name: embroid body with RQ mutation in BRCA1 gene

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

growth_protocol: To generate embryoid bodies, ES cells were trypsinized and the feeder cells were removed by incubating the cells on gelatinized plate for one hour. The ES cells in supernatant were counted and diluted to 5X104 cells/ml. The cell suspension was culture in Petri dish, in DMEM-10 media. The media was changed on day 3 and later it was changed every other day.

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

treatment_protocol: Embroid bodies were collected on day 7.

value: embryoid body

value: 129S7/SvEv Brd-Hprt b-m2


title: Patient 4 microGIST


title: LingualL_5

first: Andrew

last: Jheon

address: 513 Parnassus Ave HSE1501

institute: UCSF

description: Biological replicate 5 of 5. miRNA expression in lingual cervical loop.

hyb_protocol: Equal amounts of Cy3 labeled target were hybridized to Agilent v3.1 multi-species 8x15k miRNA arrays. Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent)

data_processing:
raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent).
Agilent Feature Extraction Software (v10.3) was used for background subtraction and LOWESS normalization.

source_name: LingualL

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent).

growth_protocol: K14-eGFP mice at 6 weeks were harvested

extract_protocol: miRNA extracted using the miRNeasy Micro Kit (Qiagen)

treatment_protocol: the labial cervical loop, lingual cervical loop, and ameloblasts were from the incisors were microdissected

tag: Sex

value: Male

value: 6-week old

tag: genotype/variation


title: LingualL_4

description: Biological replicate 4 of 5. miRNA expression in  lingual cervical loop.


title: Patient 8 microGIST


title: Viro5p01-180_229

value: serum

value: dengue like illness but dengue-negative


title: Patient 7 microGIST

value: Gastrointestinal stroml tumor cells


title: LingualL_2

description: Biological replicate 2 of 5. miRNA expression in  lingual cervical loop.


title: Patient 5 microGIST


title: Patient 2 microGIST


title: Patient 1 normal


title: mutant MI

description:
gene expression data from mouse embroid body with M1652I mutation of human BRCA1
Chang_MI_022908.CEL

source_name: embroid body with MI mutation in BRCA1 gene


title: Heart_4wk_WT_mouse_2

city: Sydney

first: Michael

middle: Li-Hsuan

last: Huang

state: NSW

address: Level 5 Blackburn Building D06, University of Sydney

country: Australia

institute: University of Sydney

description: Gene expression data from a 4-week-old WT mouse, tag #359

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol, GeneChip Scanner 3000

data_processing: GeneChip Scanner 3000, GCOS v1.3. The algorithm used was RMA.

source_name: Heart of 4-week-old WT mouse #359

label_protocol: Standard Affymetrix protocol

extract_protocol: Standard TRIzol RNA extraction protocol

tag: gender

value: female

value: heart

value: frataxin WT


title: LingualL_3

description: Biological replicate 3 of 5. miRNA expression in  lingual cervical loop.


title: Patient 3 microGIST


title: LingualL_1

description: Biological replicate 1 of 5. miRNA expression in lingual cervical loop.


title: WT

description:
gene expression data from mouse embroid body with wild type human BRCA1
Chang_WT_022908.CEL

source_name: embroid body with wild type BRCA1 gene


title: LabialL_1

description: Biological replicate 1 of 5. miRNA expression in labial cervical loop.

source_name: LabialL


title: Heart_4wk_WT_mouse_1

description: Gene expression data from a 4-week-old WT mouse, tag #357

source_name: Heart of 4-week-old WT mouse #357


title: LabialL_4

description: Biological replicate 4 of 5. miRNA expression in  labial cervical loop.


title: AmeloblastR_3

description: Biological replicate 3 of 5. miRNA expression in ameloblasts.

source_name: AmeloblastR


title: Heart_4wk_KO_mouse_2

description: Gene expression data from a 4-week-old KO mouse, tag #358

source_name: Heart of 4-week-old KO mouse #358

value: frataxin KO


title: AmeloblastR_2

description: Biological replicate 2 of 5. miRNA expression in ameloblasts.


title: LabialL_3

description: Biological replicate 3 of 5. miRNA expression in  labial cervical loop.


title: AmeloblastR_5

description: Biological replicate 5 of 5. miRNA expression in ameloblasts.


title: Heart_4wk_KO_mouse_1

description: Gene expression data from a 4-week-old KO mouse, tag #356

source_name: Heart of 4-week-old KO mouse #356


title: LabialL_2

description: Biological replicate 2 of 5. miRNA expression in  labial cervical loop.


title: Heart_10wk_WT_mouse_2

description: Gene expression data from a 10-week-old WT mouse, tag #104

source_name: Heart of 10-week-old WT mouse #104


title: Heart_10wk_KO_mouse_2

description: Gene expression data from a 10-week-old KO mouse, tag #105

source_name: Heart of 10-week-old KO mouse #105


title: Heart_10wk_WT_mouse_1

description: Gene expression data from a 10-week-old WT mouse, tag #103

source_name: Heart of 10-week-old WT mouse #103


title: AmeloblastR_1

description: Biological replicate 1 of 5. miRNA expression in ameloblasts.


title: Patient 1 microGIST

source_name: microGIST FFPE tumor genomic DNA

source_name: male DNA

value: male DNA G147A (Promega, Madison, WI)


title: AmeloblastR_4

description: Biological replicate 4 of 5. miRNA expression in ameloblasts.


title: Hindlimb E13.5 5

city: Livermore

first: Gabriela

last: Loots

address: 7000 East Avenue

department: BBTD

institute: Lawrence Livermore National Laboratory

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit was used according to the manufacturer's instructions.

scan_protocol: Arrays were scanned using a Gene Chip Scanner3000 scanner enabled for high-resolution scanning according to the manufacturer's instructions.

data_processing: Gene expression data was processed using Robust Multi-Chip Average (RMA), as implemented in the R statistical package provided by Bioconductor.  RMA data processing includes background correction, quantile normalization, and expression summarization.  Genes were filtered in order to eliminate those with cross-sample variation, using a variation filter estimated on 14 HeLa cell lines and 5 Strategene samples.

source_name: Mus musculus hind-limb bud, E13.5

label_protocol: Total RNA samples were labeled using Affymetrix GeneChip Two-Cycle Target Labeling and Control Reagent Kit (biotin labeling) according to the manufacturer's instructions.

growth_protocol: Embryos were collected at scheduled time points where E0.5 was considered noon on the day a copulatory plug was discovered.

extract_protocol: Total RNA was extracted with Qiagen RNEASy mini columns, with a proteinase K digestion step before loading onto the columns, and DnaseI digestion on the column, according to the manufacturer's instructions.

treatment_protocol: Embryos were dissected into ice-cold PBS, followed by limb dissection (for limb samples, whole embryo samples were left intact) and immediate placement into Qiagen RLT buffer for RNA extraction.

tag: developmental stage

value: hind-limb

value: FVB


title: Forelimb E13.5 5

source_name: Mus musculus fore-limb bud, E13.5

value: fore-limb


title: Forelimb E13.5 3


title: Hindlimb E13.5 4


title: HC445 25°G2-20°G3 rep1

city: Cambridge

first: Daniel

last: Schott

state: MA

address: 16 Divinity Avenue

department: Molecular and Cellular Biology

institute: Harvard University

hyb_protocol: Agilent one-color hybridization protocol.  To minimize post-amplification biases, we randomized the position and order of hybridizations.

scan_protocol: Scanned at 10% laser power to avoid signal saturation

data_processing: Agilent Feature Extraction software (GE1-v5_95_Feb07) used to calculate fluorescence values which were then log2-transformed and quantile-normalized across 120 hybridizations (see Bolstad et al 2003).

organism: Caenorhabditis elegans

label_protocol: 10 µg aRNA labeled with Cy3 using the Ambion MessageAmpII kit and 1.65µg labeled aRNA used to hybridize with each array

growth_protocol: We used standard methods to culture and handle C. elegans (Brenner, 1974), except we used the sporulation-defective Bacillus subtilis strain RL1275 (spoIIAC::erm in a PY79 background, kind gift from Richard Losick) as worm food, in order to see temperature effects independently of pathogen response.  B. subtilis is substantially less pathogenic to C. elegans than the standard C. elegans food E. coli OP50 at 25°C (Garsin et al., 2003).

extract_protocol: We collected embryos and purified RNA as described (Baugh et al., 2003), except we increased the number of embryos per sample to 50.  In brief, we picked young adults into water, chopped them in half, treated them with alkaline bleach to destroy any RNA and protein not protected by the eggshell, stopped the bleach reaction with bovine serum albumin, collected and washed early embryos in DEPC-treated water using a glass mouth pipette, flash-froze the embryos in liquid nitrogen in low-adhesion 600 μl microcentrifuge tubes, and transferred the tubes to a -80° freezer for storage.  For the microarray experiment, the total time from picking of the first worm to bleaching was not allowed to exceed 15 min.  For all subsequent experiments, the time was not allowed to exceed 8 min.  We added Trizol (phenol/guanidine isothiocyanate, Invitrogen), with added linear polyacrylamide and yeast tRNA as carriers, to the frozen embryos for RNA extraction and isopropanol precipitation.  We used the RNA pellet directly for RT (reverse transcription), starting from a T7-oligo-dT RT primer.  To obtain sufficient RNA for microarray analysis, RNA was amplified by two rounds of in vitro transcription (IVT) using the MessageAmpII kit (Ambion) with the following modifications designed to increase the average lengths of the aRNA populations (Baugh et al. 2001): First-round cDNA construction from total RNA was carried out at 1/5 of the recommended quantities and total volume, while IVT was carried out at 1/2 of the recommended volume.  100ng aRNA from the first round was used as input for the second round of amplification following the manufacturers protocol for amino-allyl modified nucleotides.

treatment_protocol: Before each of the experiments, we cultured the worms for at least three generations at 20°C without allowing the worms to deplete their food.  Other than the 25°C treatments, done in a 25±0.5° incubator, all incubations and procedures involving live worms were done in a temperature controlled room at 20±0.3°C.  To minimize temperature variation during handling, we used large (10 cm diameter) plates, wore insulated gloves while handling plates, and used an external light source for the dissecting microscope.  For the microarray experiment, we used a platinum wire loop to transfer several hundred embryos to fresh plates for each generation.  For the multigenerational follow-up experiments (not included in this accession because they were analyzed by RT-QPCR only), we used a platinum wire pick to transfer 60 L4 larvae to fresh plates for each generation.  The purpose of transferring L4s instead of embryos in the multigenerational experiment was to eliminate males from the cultures, thereby eliminating variation in the frequency of sex-specific imprinting (most C. elegans individuals are hermaphrodites, with a low rate of spontaneous males that increases with temperature).  For the same set of experiments, we used HOBO miniature temperature loggers (Onset) to continuously monitor culture temperatures.  For post-25° steps of all experiments, we interleaved the constant 20° (control) plates with post-25° treatment plates in common stacks whenever possible, so that treatment and control plates experience the same microenvironment on average.  In practice, the treatment plates were slightly staggered in time relative to the corresponding control plates of the same generation, because of time constraints and because development time from zygote to adult is ~17 hours faster at 25° than at 20°.  For each combination of condition and generation in the microarray experiment, we collected 3 replicates (50 embryos each replicate) of the standard C. elegans laboratory strain N2 and three replicates (50 embryos each replicate) of the strain HC445 (sid-1(qt9) in an N2 background).

value: sid-1(qt9); suspected haf-6(-)

value: 4-cell embryo

tag: grandparent growth temperature

tag: parental growth temperature

tag: generation


title: Heart_10wk_KO_mouse_1

description: Gene expression data from a 10-week-old KO mouse, tag #101

source_name: Heart of 10-week-old KO mouse #101


title: Forelimb E13.5 2


title: Hindlimb E13.5 1


title: Hindlimb E13.5 3


title: Hindlimb E13.5 2


title: HC445 25°G2-20°G3 rep3

description:
H2c
10x spike-in concentration relative to most hybridizations in series


title: Forelimb E13.5 4


title: HC445 25°G2-20°G3 rep2


title: Hindlimb E12.5 5

source_name: Mus musculus hind-limb bud, E12.5


title: HC445 20°G2-20°G3 rep2


title: Hindlimb E12.5 4


title: N2 25°G2-20°G3 rep3

description:
G2c
10x spike-in concentration relative to most hybridizations in series

value: wild type (standard lab strain)


title: HC445 20°G2-20°G3 rep3


title: HC445 20°G2-20°G3 rep1


title: N2 20°G2-20°G3 rep3


title: N2 25°G2-20°G3 rep1


title: N2 25°G2-20°G3 rep2


title: Forelimb E12.5 5


title: Hindlimb E12.5 1


title: Hindlimb E12.5 2


title: Forelimb E12.5 4

source_name: Mus musculus fore-limb bud, E12.5


title: Forelimb E13.5 1


title: N2 20°G2-20°G3 rep2


title: Hindlimb E12.5 3


title: N2 20°G2-20°G3 rep1


title: HC445 20°G2 rep2


title: Forelimb E12.5 3


title: HC445 25°G2 rep1


title: N2 25°G2 rep3

description:
E2c
10x spike-in concentration relative to most hybridizations in series


title: N2 25°G2 rep2


title: Hindlimb E11.5 1

source_name: Mus musculus hind-limb bud, E11.5


title: HC445 20°G2 rep1

description:
F1a
10x spike-in suspected


title: N2 25°G2 rep1

description:
E2a
10x spike-in concentration relative to most hybridizations in series


title: HC445 25°G2 rep2


title: Forelimb E12.5 2


title: N2 20°G2 rep3


title: Hindlimb E11.5 4


title: Hindlimb E11.5 3


title: Hindlimb E10.5 3

source_name: Mus musculus hind-limb bud, E10.5


title: Hindlimb E11.5 5


title: HC445 20°G2 rep3


title: Forelimb E11.5 1

source_name: Mus musculus fore-limb bud, E11.5


title: HC445 25°G2 rep3

description:
F2c
10x spike-in concentration relative to most hybridizations in series


title: Forelimb E11.5 3


title: Hindlimb E11.5 2


title: Hindlimb E10.5 1


title: N2 20°G2 rep1


title: Forelimb E11.5 4


title: Forelimb E12.5 1


title: N2 20°G2 rep2


title: Forelimb E11.5 2


title: Hindlimb E10.5 2


title: LabialL_5

description: Biological replicate 5 of 5. miRNA expression in  labial cervical loop.

source_name: LabialL


title: Hindlimb E10.5 4


title: Forelimb E10.5 2

source_name: Mus musculus fore-limb bud, E10.5


title: Forelimb E10.5 4


title: Forelimb E9.5 3

source_name: Mus musculus fore-limb bud, E9.5


title: Forelimb E10.5 5


title: Whole Embryo E13.5 1

source_name: Mus musculus whole embryo, E13.5

value: whole embryo


title: Forelimb E9.5 1


title: Forelimb E9.5 2


title: lca milk presence intestinal juice 8h rep2

city: Huhhot

first: Heping

last: Zhang

address: 306 Zhaowuda Road

country: China

institute: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University

description: gene expression pattern of L. casei Zhang in the presence of fermented milk in simulated intestinal juice at 8h

hyb_protocol: Microarray hybridizations were carried out on labelled cRNAs with specificity greater than 8 using the Gene Expression Hybridization Kit (Agilent Technologies). Arrays were incubated at 65 °C for 17 h in Agilent's microarray hybridization chambers and subsequently washed using Gene Expression Wash Buffer Kit.

scan_protocol: Arrays were scanned Agilent G2565BA MicroArrayScanner System.

data_processing: Feature extraction and data normalization were conducted with Agilent Feature Extraction software (Agilent Technologies, Palo Alto, CA). Array normalization was performed using the quantile normalization method. The average of the normalized expression values of the 2 biological replicates for each probe was regarded as the expression value of a predicted gene. To identify the expression pattern of each gene across different treatments, n-fold change ratios were calculated for every gene in pure L. casei Zhang versus L. casei Zhang in fermented milk.

organism: Lacticaseibacillus casei str. Zhang

source_name: L. casei Zhang, milk presence, in simulated intestinal juice, 8h

label_protocol: 2 μg of total RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo Alto, CA). Synthesized cDNA was transcribed into cRNA and labelled with either cyanine 3 or cyanine 5-labelled nucleotide (Perkin Elmer, Wellesley, MA). Labelled cRNA was purified with QIAGEN RNeasy Mini kit (QIAGEN).

growth_protocol: L. casei Zhang was grown in MRS broth at 37°C for 18 h

extract_protocol: Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) and purified using the Rneasy Mini kit (QIAGEN, Valencia, CA). The concentration and purity of RNA samples were determined by electrophoresis on agarose gels and standard spectrophotometer measurements.

treatment_protocol: The bacterial cells collected from MRS broth by centrifugation at 2,500 g at 4°C for 10 min were suspended in sterile saline and inoculated into simulated gastric juice (pH 2.5). After 3 h incubation in simulated gastric juice, the solution was divided into two samples. One sample was centrifuged at 30,000g. The bacterial cells were collected and frozen in liquid nitrogen for RNA isolation. Another sample was centrifuged and 1 mL of the cell suspension was taken and added to 9 mL of simulated intestinal juice (pH 8.0) and incubated at 37℃. The bacterial cells were collected at 4 h and 8 h by centrifugation and frozen in liquid nitrogen for RNA isolation. Another sample of bacterial cells collected from MRS broth by centrifugation were inoculated into 11% skim milk (supplemented with 1.5% glucose) to ferment at 37℃. The fermented milk was cooled immediately in ice water when the sample achieved a pH of 4.5. Subsequently, the fermented milk (1 mL) was mixed with simulated gastric juice (9 mL) and incubated at 37℃ for 3 h, and then divided into two samples. One sample was centrifuged at 30,000g. The bacterial cells were collected and frozen in liquid nitrogen for RNA isolation. Another sample was centrifuged and the supernatant was removed, the suspension was mixed into 10 mL of simulated intestinal juice and incubated at 37℃. The bacterial cells were collected at 4 h and 8 h respectively by centrifugation and frozen in liquid nitrogen for RNA isolation.

value: L. casei Zhang

tag: sample type

value: in simulated intestinal juice, 8h

tag: media

value: intestinal juice + fermented milk

tag: time


title: Whole Embryo E12.5 1

source_name: Mus musculus whole embryo, E12.5

tag: tissue


title: Whole Embryo E9.5 2

source_name: Mus musculus whole embryo, E9.5


title: Whole Embryo E13.5 2


title: Whole Embryo E10.5 2

source_name: Mus musculus whole embryo, E10.5


title: Forelimb E10.5 1


title: lca milk presence intestinal juice 8h rep1


title: lca milk presence intestinal juice 4h rep2

description: gene expression pattern of L. casei Zhang in the presence of fermented milk in simulated intestinal juice at 4h

source_name: L. casei Zhang, milk presence, in simulated intestinal juice, 4h

value: in simulated intestinal juice, 4h


title: Whole Embryo E12.5 2

description: Bubble in the scan.  This .CEL file was generated using R package Harshlight.


title: Whole Embryo E10.5 1


title: Whole Embryo E11.5 2

source_name: Mus musculus whole embryo, E11.5


title: T. gondii (RH strain)-infected BMdM, biological rep3

city: Irvine

first: Melissa

last: Lodoen

address: 3238 McGaugh Hall

institute: UC Irvine

description: Gene expression data from macrophages that were infected with T. gondii (RH strain)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˙C on Affymetrix Mouse 430 2.0 Microarrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with the Robust Multichip Average algorithm implemented in Agilent GeneSpring GX v11.0 for background adjustment, quantile normalization, and summarization.

source_name: Bone marrow-derived macrophages - T. gondii-infected (6 hpi) sample

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 3 ug of total RNA.

growth_protocol: Bone marrow was harvested from the femurs of C57BL/6 mice, red blood cells were lysed, and white blood cells were cultured in medium supplemented with M-CSF for 7 days.

treatment_protocol: BMdM cultures (day 7) containing 2x10^6 cells per well of a 6-well plate were infected with 4x10^6 T. gondii (Type I, RH strain) for an MOI of 2.  Infections were performed in biological triplicates.

value: bone marrow-derived macrophages

tag: infection

value: T. gondii (Type I, RH strain)


title: Forelimb E10.5 3

tag: strain


title: T. gondii (RH strain)-infected BMdM, biological rep1

value: female


title: mock-treated BMdM, biological rep3

description: Gene expression data from macrophages that were mock-treated

source_name: Bone marrow-derived macrophages - mock-treated sample

value: mock


title: Whole Embryo E11.5 1


title: lca milk presence intestinal juice 4h rep1


title: lca milk absence intestinal juice 8h rep2

description: gene expression pattern of L. casei Zhang in the absence of fermented milk in simulated intestinal juice at 8h

source_name: L. casei Zhang, milk absence, in simulated intestinal juice, 8h

value: intestinal juice


title: lca milk presence gastric juice 3h rep2

description: gene expression pattern of L. casei Zhang in the presence of fermented milk in simulated gastric juice at 3h

source_name: L. casei Zhang, milk presence, in simulated gastric juice, 3h

value: in simulated gastric juice, 3h

value: gastric juice +  fermented milk


title: lca milk absence intestinal juice 4h rep2

description: gene expression pattern of L. casei Zhang in the absence of fermented milk in simulated intestinal juice at 4h

source_name: L. casei Zhang, milk absence, in simulated intestinal juice, 4h


title: lca milk absence intestinal juice 8h rep1


title: lca milk absence intestinal juice 4h rep1


title: lca milk presence gastric juice 3h rep1


title: Whole Embryo E9.5 1

value: FVB


title: lca milk absence gastric juice 3h rep2

description: gene expression pattern of L. casei Zhang in the absence of fermented milk in simulated gastric juice at 3h

source_name: L. casei Zhang, milk absence, in simulated gastric juice, 3h

value: gastric juice


title: T. gondii (RH strain)-infected BMdM, biological rep2


title: defective processing CLL_34

city: ULM

first: Danilo

last: Allegra

address: Albert-Einstein-Allee 23

country: Germany

institute: University Hospital of Ulm

description: sample ID : 34

hyb_protocol: according to producer's instructions (Agilent microRNA Labeling & Hybridization Kit)

data_processing: miRNAs detected in at least 12 /23 samples were analyzed. Values for each miRNA were normalized to the average of six housekeeping RNAs represented in the array (U1, U2, U4, U5, U6 and MRP)

source_name: CLL - defective processing

label_protocol: Cy3 labeling by ligation of Cy3-pCp (Agilent microRNA Labeling & Hybridization Kit)

extract_protocol: TRizol (invitrogen)

tag: cancer type

value: Chronic Lymphocytic Leukemia

tag: karyotype

tag: IGVH status

value: unmutated


title: AS

city: Sendai

first: Masaharu

last: Nakayama

address: 1-1 Seiryo-machi, Aoba-ku

country: Japan

institute: Tohoku University School of Medicine

description: Gene expression data from LV at 1w after control.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS).

source_name: LV at 1w after control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

value: Balb/c

value: Left ventricle


title: lca_milkgrowth_18h_1_rep2

description: Gene expression pattern when grown to stationary phase.

hyb_protocol: Microarray hybridizations were carried out on labelled cRNAs with specificity greater than 8 using the Gene Expression Hybridization Kit (Agilent Technologies). Arrays were incubated at 65°C for 17 h in Agilent's microarray hybridization chambers and subsequently washed using the Gene Expression Wash Buffer Kit.

scan_protocol: Arrays were scanned using the Agilent G2565BA MicroArrayScanner System.

data_processing: Signal intensity was normalized by quantile. Systematic differences between the biological duplicates were confirmed by comparing the error between replicates to the within array error between duplicate spots. To identify genes responded during growth, spot data points with feature of absent or marginal were masked and the remaining data were averaged for each biological duplicates. Subsequently, biological replicates were treated as duplicate measurements, and their averages were compared between stationary phase and exponential phase.

source_name: L. casei Zhang, grown in milk, 18h

label_protocol: 2 μg of total RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo Alto, CA). Synthesized cDNA was transcribed into cRNA and labelled with either Cyanine 3- or Cyanine 5-labelled nucleotide (Perkin Elmer, Wellesley, MA). Labelled cRNA was purified using the QIAGEN RNeasy Mini kit (QIAGEN).

growth_protocol: Nonfat milk powder was blended with water at 50°C to a total solids content of 11 g/100 g. The hydrated solution was supplemented with 1.5 g/100 g of glucose, and heated at 85°C for 30 min. Subsequently, the samples were cooled to the incubation temperature (37°C), and inoculated with 1 × 10^7 of L. casei Zhang.

extract_protocol: Samples were obtained from 2 biological replicates at late logarithmic phase (14 h, pH=5.2) and stationary phase (18 h, pH=4.5), followed by centrifugation at 200 g for 10 min at 4°C. The supernatant was removed to a fresh tube and centrifugated at 12000 g for 5 min at 4°C. The cell pellets were ground into fine powder in the presence of liquid nitrogen, and then resuspended in 1 mL Trizol by vortexing. After repeated centrifugation at 12000 g for 5 min at 4°C, the supernatant was removed to a fresh tube and incubated for 5 min at room temperature. Next, 0.2 mL chloroform was added, followed by vortexing 15 s and incubation for 3 min. The mixtures were centrifugated at 12000 g for 15 min at 4°C, the upper aqueous phase was transferred into a fresh tube, mixed with 0.5 ml isopropanol, and incubated at room temperature for 10 min, and RNA was precipitated at 12000 g for 10 min at 4 °C. After washing in 75% ethanol, the RNA pellet was dried and dissolved in 20 μL of water. The isolated total RNA was purfied using the RNeasy Mini kit . Quality and concentration of RNA samples were determined by using the Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment.

value: Zhang

tag: growth stage

value: stationary phase

tag: growth time

value: 18 hours

tag: growth medium

value: milk

tag: ph


title: defective processing CLL_28

description: sample ID : 28

scan_protocol: according to producer's instructions (Agilent microRNA Labeling & Hybridization Kit)


title: mock-treated BMdM, biological rep1

tag: Sex

tag: cell type

value: bone marrow-derived macrophages


title: lca milk absence gastric juice 3h rep1

value: L. casei Zhang


title: lca_milkgrowth_14h_1_rep1

description: Gene expression pattern when grown to late logarithmic phase.

source_name: L. casei Zhang, grown in milk, 14h

value: late logarithmic phase

value: 14 hours


title: lca_milkgrowth_14h_1_rep2


title: lca_milkgrowth_18h_1_rep1


title: mock-treated BMdM, biological rep2

value: female

value: mock


title: AI

description: Gene expression data from LV at 1w after ATII.

source_name: LV at 1w after ATII


title: SI1M

description: Gene expression data from LV at 1m after sham operation.

source_name: LV at 1m after sham operation


title: SI1W

description: Gene expression data from LV at 1w after sham operation.

source_name: LV at 1w after sham operation


title: MI1W

description: Gene expression data from LV at 1w after coronary ligation.

source_name: LV at 1w after coronary ligation


title: MI1M

description: Gene expression data from LV at 1m after coronary ligation.

source_name: LV at 1m after coronary ligation


title: SM


title: defective processing CLL_25

description: sample ID : 25

value: normal

value: mutated


title: defective processing CLL_29

description: sample ID : 29


title: BM

description: Gene expression data from LV at 1m after TAC

source_name: LV at 1m after TAC


title: defective processing CLL_68

description: sample ID : 68


title: defective processing CLL_75

description: sample ID : 75


title: defective processing CLL_47

description: sample ID : 47


title: defective processing CLL_53

description: sample ID : 53


title: defective processing CLL_52

description: sample ID : 52


title: defective processing CLL_30

description: sample ID : 30


title: defective processing CLL_71

description: sample ID : 71


title: defective processing CLL_70

description: sample ID : 70


title: normal processing CLL_74

description: sample ID : 74

source_name: CLL - normal processing


title: normal processing CLL_31

description: sample ID : 31


title: normal processing CLL_38

description: sample ID : 38


title: normal processing CLL_79

description: sample ID : 79


title: normal processing CLL_32*

description: sample ID : 32*


title: BW

description: Gene expression data from LV at 1w after TAC.

source_name: LV at 1w after TAC


title: BD

description: Gene expression data from LV at 1d after TAC.

source_name: LV at 1d after TAC


title: normal processing CLL_B4

description: sample ID : B4


title: normal processing CLL_81

description: sample ID : 81


title: blood NOD/ShiLtJ 0hours rep2

city: Durham

first: Nicole

last: Johnson

state: NC

address: 2424 Erwin Rd

institute: Duke University

description: RMA processed expression data can be found on GSE23584.

hyb_protocol: Labeled cDNA was hybridized to the arrays for 16 hours at 45°C following the manufacturer’s instruction. The arrays were then washed and labeled with streptavidinphycoerythrin (strep-PE), and the signal was amplified using biotinylated antistreptavidin followed by another round of staining with strep-PE.

scan_protocol: Labeled gene chips were scanned using an Affymetrix Genechip Scanner 7G (Affymetrix).

data_processing: Preprocessing was conducted using the Robust Multichip Analysis (RMA) (PMID: 12925520) implementation in the Bioconductor “affy” package (http://www.bioconductor.org/), with an additional step to account for differences in probe hybridization resulting from single nucleotide polymorphisms (SNP) between A/J and C57BL/6J mice.  The additional step is referred to as SNP masking (PMID:17762873) and is applied after background correction and quantile-quantile normalization but prior to the determination of probeset expression values.  Genomic locations hybridized by each probe were obtained from the Ensembl database (http://www.ensembl.org/index.html), and these genomic locations were compared to the locations of SNPs for which A/J and C57BL/6J mice have different alleles.  Probes that hybridize to such SNPs within the target transcripts were excluded from the determination of probeset expression values.  Statistically significant differences in expression between A/J and C57BL/6J mice were determined using a standard ANOVA with model terms for batch, strain, and time post-infection, with uninfected mice coded as 0 hours post-infection.

label: Biotin

source_name: blood NOD/ShiLtJ mouse strain NOT infected with S. aureus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Affymetrix).

growth_protocol: S. aureus strain Sanger 476 was used in this study. For preparation of S. aureus for injection, an overnight bacterial culture of S. aureus was diluted with fresh tryptic soy broth (TSB) and incubated (37°C) with aeration to log-phase growth (optical density at wavelength 600 nm (O.D.600) of ~1.0) (Rice 2003). S. aureus was harvested by centrifugation, rinsed, and resuspended in saline.

extract_protocol: Total RNA was prepared using the Mouse RiboPure Blood RNA isolation kit (Ambion) following the manufacturer’s instruction. Globin mRNA was removed from whole blood RNA samples using the Globinclear kit (Ambion).

treatment_protocol: To mimic the natural course of S. aureus infection in humans, which typically arises from a primary focus of infection and disseminates to other sites, we employed an intraperitoneal (i.p.) route of infection in our animal model. For experiments involving RNA analysis, blood was collected by intracardiac puncture and stored in RNAlater at -20oC.

value: NOD/ShiLtJ

tag: time point


title: normal processing CLL_72

description: sample ID : 72

value: Chronic Lymphocytic Leukemia


title: blood NOD/ShiLtJ 2hours rep2

source_name: blood NOD/ShiLtJ mouse strain blood taken 2 hours after infection with S. aureus

value: S. aureus strain Sanger 476

value: 2 hours


title: blood C3H/HeJ 2hours rep3

source_name: blood C3H/HeJ  mouse strain blood taken 2 hours after infection with S. aureus


title: normal processing CLL_69

description: sample ID : 69

value: unmutated


title: blood NOD/ShiLtJ 0hours rep3


title: blood NOD/ShiLtJ 2hours rep3


title: SW

value: Balb/c

value: Left ventricle


title: normal processing CLL_33

description: sample ID : 33


title: blood C3H/HeJ 0hours rep3

source_name: blood C3H/HeJ  mouse strain NOT infected with S. aureus


title: blood C3H/HeJ 0hours rep2


title: normal processing CLL_80

description: sample ID : 80


title: blood BALB/cByJ 2hours rep3

source_name: blood BALB/cByJ mouse strain blood taken 2 hours after infection with S. aureus

value: BALB/cByJ


title: blood C3H/HeJ 2hours rep2


title: blood BALB/cByJ 0hours rep2

source_name: blood BALB/cByJ mouse strain NOT infected with S. aureus


title: blood C57BL/6J 2hours rep2

source_name: blood C57BL/6J mouse strain blood taken 2 hours after infection with S. aureus


title: blood C57BL/6J 2hours rep3


title: blood BALB/cByJ 2hours rep2


title: blood AKR/J 2hours rep2

source_name: blood AKR/J mouse strain blood taken 2 hours after infection with S. aureus

value: AKR/J


title: blood C57BL/6J 0hours rep3

source_name: blood C57BL/6J mouse strain NOT infected with S. aureus


title: blood BALB/cByJ 0hours rep3


title: SD

description: Gene expression data from LV at 1d after sham operation.

source_name: LV at 1d after sham operation


title: blood AKR/J 2hours rep3


title: Vibrio_alginolyticus_EPGS_dPpkA_dPppA_study_PppA_mutant_rep3

city: shanghai

first: Yuanxing

address: 130 meilong road

department: School of Biotechnology

institute: East China University Of Science And Technology

description: This sample is of Vibrio alginolyticus EPGS delta-pppA, a deletion mutant in which phosphatase PppA is truncated . It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Axon Instruments Gene Pix 4000B.Scan parameters were set to wavelength 532, PMT Gain 530, Pixel size 5μm, Lines to average 1 and Focus position 0μm.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Vibrio alginolyticus

source_name: Vibrio alginolyticus EPGS delta-pppA strain

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: V. alginolyticus EPGS was cultured in Luria-Bertani (LB) medium at 30°C for 7h. V. alginolyticus EPGS delta-PppA and delta-PpkA were cultured in Luria-Bertani (LB) medium at 30°C for 7h.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with the Agilent 2100 Bioanalyzer.

value: EPGS

tag: genotype

value: delta-pppA


title: Vibrio_alginolyticus_EPGS_dPpkA_dPppA_study_PppA_mutant_rep1

description: This sample is of Vibrio alginolyticus EPGS delta-pppA, a deletion mutant in which Ser-Thr kinase PpkA is truncated . It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures.


title: Vibrio_alginolyticus_EPGS_dPpkA_dPppA_study_PppA_mutant_rep2

description: This sample is of Vibrio alginolyticus EPGS delta-pppA, a deletion mutant in which phosphatase PppA is truncated . It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: blood C57BL/6J 0hours rep2


title: Vibrio_alginolyticus_EPGS_dPpkA_dPppA_study_PpkA_mutant_rep2

description: This sample is of Vibrio alginolyticus EPGS delta-ppkA, a deletion mutant in which Ser-Thr kinase PpkA is truncated . It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures.

source_name: Vibrio alginolyticus EPGS delta-ppkA strain

value: delta-ppkA


title: Vibrio_alginolyticus_EPGS_dPpkA_dPppA_study_wild-type_rep2

description: This sample is of wild-type Vibrio alginolyticus EPGS. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Vibrio alginolyticus EPGS wild-type

value: Wild-type


title: blood AKR/J 0hours rep3

source_name: blood AKR/J mouse strain NOT infected with S. aureus


title: Vibrio_alginolyticus_EPGS_dPpkA_dPppA_study_wild-type_rep1

description: This sample is of wild-type Vibrio alginolyticus EPGS. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Vibrio_alginolyticus_EPGS_dPpkA_dPppA_study_PpkA_mutant_rep1

description: This sample is of Vibrio alginolyticus EPGS delta-ppkA, a deletion mutant in which Ser-Thr kinase PpkA is truncated . It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures.


title: blood AKR/J 0hours rep2


title: Vibrio_alginolyticus_EPGS_dPpkA_dPppA_study_wild-type_rep3

description: This sample is of wild-type Vibrio alginolyticus EPGS. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: blood A/J 2hours rep3

source_name: blood A/J mouse strain blood taken 2 hours after infection with S. aureus

value: A/J


title: blood A/J 2hours rep2


title: blood NOD/ShiLtJ 2hours rep1


title: blood A/J 0hours rep2

source_name: blood A/J mouse strain NOT infected with S. aureus


title: blood A/J 0hours rep3


title: blood NOD/ShiLtJ 0hours rep1


title: transgenic CCRI 12-45 day-rep 3

city: Shanghai

first: Fan

last: Sun

address: 220 Handan Road

institute: Fudan University

description: constitutively overexpressing the second RRM domain of Brassica napus FCA

hyb_protocol: see manufacturer's web site at http://www.agilent.com/

scan_protocol: Agilent Technologies Scanner G2505C US10113787 was used.

data_processing: Signal intensities were extracted by Feature Extraction software (version 10.5.1.1, Agilent Technologies) at the default settings. Data were quantile normalized across all samples with the Bioconductor.

organism: Gossypium hirsutum

source_name: leaf

extract_protocol: QIAGEN RNeasy® Mini Kit

value: leaf

value: transgenic

tag: age

value: 45 days


title: transgenic CCRI 12-45 day-rep 2

label_protocol: see manufacturer's web site at http://www.agilent.com/


title: blood C3H/HeJ 2hours rep1


title: transgenic CCRI 12-45 day-rep 1


title: blood BALB/cByJ 2hours rep1


title: transgenic CCRI 12-25 day-rep 2

value: 25 days


title: blood BALB/cByJ 0hours rep1


title: blood C3H/HeJ 0hours rep1


title: transgenic CCRI 12-25 day-rep 1


title: Control CCRI 12-45 day-rep 3

value: wild type


title: blood AKR/J 0hours rep1


title: transgenic CCRI 12-25 day-rep 3


title: blood C57BL/6J 2hours rep1

value: S. aureus strain Sanger 476


title: Control CCRI 12-45 day-rep 2


title: blood AKR/J 2hours rep1

value: 2 hours


title: blood C57BL/6J 0hours rep1


title: Control CCRI 12-25 day-rep 3


title: 24 hr shikonin-1

first: Ning-Sun

last: Yang

state: Taiwan

address: No.128 Sec.2, Academia Rd.

department: Agricultural Biotechnology Research Center

institute: Academia Sinica

description: febits biochip Geniom R Biochip MPEA mus musculus was used. The probes are designed as the reverse complements of all major mature miRNAs and the mature  sequences as published in the current Sanger miRBase release

hyb_protocol: For each array, the RNA was suspended in Febit's proprietary microRNA hybridization buffer (25 μl per array). Hybridization was done automatically for 16 h at 42oC using the Geniom RT-Analyzer

scan_protocol: For maximum sensitivity, febit used biotin and its detection with streptavidin-phycoerythrin (SAPE), in combination with febit's consecutive Signal Enhancement (CSE) procedure. The feature recognition (using Cy3  lter set) and signal calculation were done automati-cally within milliseconds using the Geniom RTr-Analyzer.

data_processing: The raw intensity was normalized by the value of VSN (variance stabilizing normalization) and transformed to log2 scale. The whole data set (710 microRNAs) of microRNAs was systematically analyzed without any filtering on fold change of their expression level. Changes in expression levels were also revealed as averages of log2 (shikonin treatment)/(acetone treatment).

source_name: 24 hr shikonin

label_protocol: Febit applied the microfluidic-based primer extension assay (MPEA). This assay utilizes the bound miRNAs as a primer for an enzymatic elongation with labeled nucleotides. The elongation was done with Klenow Fragment and biotinylated nucleotides at 37 C for 15 minutes. Finally, the Biochip was washed automatically

growth_protocol: Solutions containing 10 μg/μl shikonin or 100 μnM phorbol 12-myristate 13-acetate (TPA) in acetone were prepared immediately before use. A volume of 100 μl of the test chemicals was pipetted onto the abdominal skin area of mice and allowed to completely air dry. The skin treated with solvent (acetone) alone was used as negative control.

extract_protocol: RNA extraction by Trizol agent. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).

value: abdominal skin

tag: stimulation

value: shikonin

tag: time period

value: 24 hr


title: 24 hr acetone-2

source_name: 24 hr acetone

tag: tissue

value: acetone


title: 24 hr acetone-1


title: blood A/J 2hours rep1

tag: infection


title: blood A/J 0hours rep1

tag: strain


title: 24 hr shikonin-2


title: Control CCRI 12-25 day-rep 2


title: Day19 b febit

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

institute: University Hospital Aachen

description: mouse ES cells (D3, ATCC CRL 1934) transfected with the alpha-MHC-Pac-IRES-EGFP vector

hyb_protocol: Hybridization for 16 hours at 42°C has been carried out overnight according to manufacturs instructions. Then, the biochip was washed automatically and a program for signal enhancement was processed with the Geniom Real Time Analyzer

scan_protocol: The resulting detection pictures were evaluated using the Geniom Wizard Software.

data_processing: Data was quantile normalized (Bioconductor, stats package).

source_name: cardiomyocyte-specific differentiated murine ES cell

label_protocol: Sample labeling with biotin has been carried out by microfluidic-based enzymatic on-chip labeling of miRNAs (MPEA).

growth_protocol: aPIG 44 cells were cultured on mouse embroynic fibroblasts in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with nonessential amino acids (0.1 mM), L-glutamine (2 mM), beta-mercaptoethanol (0.1 mM), LIF (ESGR) (500 U/ml), neomycin (6 µg/mL), and batch-tested fetal calf serum (FCS) (15% v/v) (all Invitrogen, Karlsruhe, Germany).

extract_protocol: Total RNAs were extracted by using PeqGold RNApure (Peqlab Biotechnology, Erlangen, Germany) according to the manufacturer's instructions.

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and -mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 7 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish and cultured for 6h before extracting RNA.

tag: cell line

value: ES-D3 murine pluripotent cells

tag: atcc catalog#

tag: time

value: day 19


title: Day26 a febit

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and beta-mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 21 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish and cultured for 6h before extracting RNA.

value: day 26


title: Control CCRI 12-45 day-rep 1


title: Day19 a febit

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and beta-mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 14 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish and cultured for 6h before extracting RNA.


title: Day26 b febit


title: Control CCRI 12-25 day-rep 1


title: Day0 b febit

source_name: undifferentiated murine embryonic stem cell

treatment_protocol: ES cells were trypsinized at d-2, seeded onto a gelatin-coated 6cm TC dish (Becton Dickinson, Heidelberg, Germany), and cultured for 48h in DMEM 15% FCS.  The timing of this last passage was in parallel with the ES cell passage used to initiate differentiation.

value: day 0


title: Day12 b febit

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and -mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 7 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish as described above, and cultured for 6h before extracting RNA.

value: day 12


title: Day12 a febit


title: osteocytes_postlactation_rep3

city: KANSAS CITY

first: Lynda

middle: F

last: Bonewald

state: MO

address: 650 E 25th Street

department: Department of Oral Biology

institute: School of dentistry University of Missouri-Kansas City

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G with autoloader.

data_processing: The data were analyzed with Genepattern using RMA analysis with quantile normalization and background correct. After preprocess, the data were statistical analyzed with bioconductor software package using ANOVA analysis.

source_name: purifed tibiae osteocytes from virgin by enzyme digestions

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA  reversely transcribed to cDNA, subjected to T7 mediated invitro-transcription amplification and labeling

growth_protocol: All mice were housed in standard conditions of temperature 23 ± 2°C and light-controlled environment 12-h light/12-h dark cycle, and had free access to water and pelleted food UAR rodent diet No.R03-25; UAR, Epinay/Orge.  All animal experiments were approved by the University of Missouri at Kansas City IACUC committee in accordance with regulations and guidelines.

extract_protocol: Tibiae from CD1 mice in Virgin, Lactation and Post lactation groups were processed immediately after sacrifice. Osteocyte RNA was extracted from tibia diaphyses with all surface cells such as osteoclasts and osteoblasts removed by sequential digestion. The digestion procedure generally followed the published procedure. Namely, soft tissue and periosteum were removed from the femurs. Epiphyses were cut off and bone marrows were removed by centrifuging. Diaphyses were incubated at 37°C with 0.2% type 1 collagenase Sigma/ 0.05% trypsin Sigma for 30 minutes for 3 times, and then washed with PBS. Remaining diaphyses were digested in 0.53 mM EDTA/ 0.05 % trypsin Cellgro, Mediatech,Inc, Manassas, VA at 37°C for 30 min, and then were rinsed with PBS and digested with 0.2 % collagenase/ 0.05% trypsin solution at 37°C for 30 min. Finally the remaining diaphyses are rinsed with PBS and pulverized in liquid nitrogen, and bone powder was added to Trizol reagent Invitrogen, Carlsbad, CA. Total RNA was isolated as per the Trizol manufacturer’s instructions.

treatment_protocol: Twelve-week-old, CD1 mice purchased from Charles River Laboratories Wilmington, MA were allowed to become pregnant, deliver and lactate. Litter size was adjusted to 8–13 pups to equalize suckling intensity between dams. Pups were removed on the 12th day of lactation to induce the weaning response. Age-matched, virgin CD1 mice were used as controls. Mice were sacrificed on the 12th day of lactation or the 7th day after forced weaning. Age-matched, virgin CD1 mice were used as controls.

value: tibiae bone

value: CD1 wild type


title: osteocytes_postlactation_rep1


title: Day0 a febit


title: osteocytes_lactation_rep2

source_name: purifed tibiae osteocytes from lactation mice by enzyme digestions


title: osteocytes_postlactation_rep2


title: osteocytes_lactation_rep3


title: Day0 b Febit VSN

data_processing: Data was normalized with VSN (Bioconductor, vsn package).


title: osteocytes_virgin_rep2


title: Day0 a Febit VSN


title: osteocytes_lactation_rep1


title: osteocytes_virgin_rep3


title: Day26 a Febit VSN

hyb_protocol: Hybridization for 16 hours at 42°C has been carried out overnight according to manufacturs instructions. Then, the biochip was washed automatically and a program for signal enhancement was processed with the Geniom Real Time Analyzer.

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and beta-mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 21 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish as described above, and cultured for 6h before extracting RNA.


title: osteocytes_virgin_rep1


title: Day19 a Febit VSN

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and beta-mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 14 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish as described above, and cultured for 6h before extracting RNA.


title: Day12 b Febit VSN

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and beta-mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 7 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish as described above, and cultured for 6h before extracting RNA.


title: Day19 b Febit VSN


title: Day12 a Febit VSN


title: Day26 b Febit VSN


title: Gene expression in CD8a- SPDCs sample1

city: Suita

first: Satoshi

last: Uematsu

state: Osaka

address: 3-1 Yamada-oka

department: Department of Host Defense

institute: Research Institute for Microbial Diseases, Osaka University

description: Gene expression data from CD8a- SPDCs

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila 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: CD8a- SPDCs

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

value: CD8a- SPDCs


title: Met31 10min

city: singapore

first: Xiaowei

last: XUE

address: 60 Biopolis Street, #02-01, Genome

department: systems biology 1

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: Afer fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45ºC on GeneChip Yeast Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. The protocol used for infividual module array stain is EuKGE_WS2v4_450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000.

organism: Saccharomyces cerevisiae

source_name: BY4741 MET31 deletion

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

growth_protocol: Yeast strain was precultured in SC medium at 28ºC overnight and transferred into fresh SC medium to dilute to 1.4 liter (6  time points) or 1.6 liter (8 time points).

extract_protocol: Extraction of total RNA was performed as manufacture's instractions

treatment_protocol: 200ml cells were collected and harvested when cells grew in SC medium to reach OD600nm=0.5 as time point 0. 3-aminotriazol was added to a final concentration of 100mM to induce amino acid starvation. 200ml cells were taken and pelleted at each time point after 3AT treatment.

value: MET31 deletion

tag: collection time after 3at treatment

tag: genetic background


title: Met31 45min


title: Met31 60min


title: Gene expression in CD8a- SPDCs sample2

description: Gene expression data from CD8a- SPDCs

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


title: Met31 20min


title: Gat1Leu3 60min_3AT_1

source_name: BY4741 GAT1LEU3 double deletion

value: GAT1LEU3 double deletion

tag: treatment


title: Met31 0min

value: baseline


title: Gat1Leu3 45min_3AT_3


title: Gat1Leu3 60min_3AT_2


title: Gene expression in CD8α+ SPDCs sample2

description: Gene expression data from CD8a+ SPDCs

source_name: CD8a+ SPDCs

value: CD8a+ SPDCs


title: Gat1Leu3 60min_3AT_3


title: Gat1Leu3 45min_3AT_2


title: Gene expression in CD8α+ SPDCs sample1

description: Gene expression data from CD8a+ SPDCs

source_name: CD8α+ DCs from spleen


title: Met31 30min


title: Gat1Leu3 20min_3AT_3


title: Gat1Leu3 30min_3AT_1


title: Gat1Leu3 30min_3AT_2


title: Gat1Leu3 20min_3AT_2


title: Gat1Leu3 20min_3AT_1


title: Gat1Leu3 30min_3AT_3


title: 9QSA_anaerobic_yhcR_log_cy3_WT_cy5_482_MDS.mev.refIsIB.out

city: Rockville

first: Chun-Hua

last: Wan

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

hyb_protocol: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min. The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry. Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate. Resuspended probes were heated to 95 C degree prior to hybridization. The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.  Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).

organism: Staphylococcus aureus subsp. aureus str. Newman

source_name: Newman yhcR knockout (query) total RNA extracted at log phase under anaerobic growth condition

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

growth_protocol: Cells were grown in TSA media overnight. Overnight cultures were diluted to an OD600 of 0.1. Cells were grown to log phase under anaerobic conditions.

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manusfacturer.

value: Newman yhcR knockout

tag: phase

value: log

tag: growth condition

value: anaerobic

source_name: Newman (reference) total RNA extracted at log phase under anaerobic growth condition

value: Newman


title: A5212010 Butanol 2% Challenge Time Point 3 (135 min)

city: College Station

first: James

last: Winkler

state: TX

address: 3122 TAMU

institute: Texas A&M University

hyb_protocol: Agilent's two-color prokaryotic microarray protocol was followed for the array hybridization procedure.

scan_protocol: A Genepix 4200A personal scanner was used to image the arrays (resolution: 5 um). Block ID in raw data file: 3.

data_processing: Arrays were LOWESS normalized individually with MIDAS. Log2 values were computed from the averaged normalized signals of all probes corresponding to a particular gene (VALUE column). Gene annotations were obtained from GenBank on 4/2010.

organism: Levilactobacillus brevis

source_name: Lactobacillus 2% Butanol Challenged Sample (135 min)

label_protocol: Fairplay Kit III Labeling protocol (Agilent)

extract_protocol: Fungal/Bacterial Total RNA Extraction Kit (Zymo Research Corp)

treatment_protocol: Cultures were grown in MRS media at 30 C (100 rpm). Butanol was added to 2% v/v; cultures were then harvested at 15, 75, and 135 min. Samples were preserved in RNALater.

value: L. brevis ATCC 367

tag: temp

tag: rotation

value: 100 rpm

tag: media

value: MRS

value: 2% Butanol

value: 135 min

source_name: Reference

treatment_protocol: Cultures were grown in MRS media at 30 C (100 rpm). Samples were preserved in RNALater.

value: control

value: Reference


title: 9QSA_anaerobic_yhcR_staionary_cy3_WT_stationary_cy5_487_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus subsp.aureus strain Newman yhcR knockout

growth_protocol: Cells were grown in TSA media overnight. Overnight cultures were diluted to an OD600 of 0.1. Cells were grown to stationary phase under anaerobic conditions.

value: stationary


title: lca_soymilkgrowth_9h_1_rep2

description: gene expression pattern when grown to late logarithmic phase

data_processing: Signal intensity was normalized by quantile. Systematic differences between the biological duplicates were confirmed by comparing the error between replicates to the within array error between duplicate spots. To identify genes responded during growth, spot data points with feature of absent or marginal were masked and the remaining data were averaged for each biological duplicates. Subsequently, biological replicates were treated as duplicate measurements, and their averages were compared between different growth phases next to each other (exponential phase versus lag phase, stationary phase versus exponential phase).

source_name: L. casei Zhang, growth in soymilk, 9h

growth_protocol: Nonfat soymilk powder was blended with water at 50 °C to a total solids content of 6.0 g/100 g. The hydrated solutions was supplemented with 1.5 g/100 g of glucose, and heated at 85 °C for 30 min. Subsequently, the samples were cooled to the incubation temperature (37 °C), inoculated with 1 × 107 of L. casei Zhang.

extract_protocol: Samples were obtained from 2 biological replicates at lag phase (2 h, pH=6.4), late logarithmic phase (9 h, pH=5.2), and stationary phase (14.5 h, pH=4.5), followed by centrifugation at 200 g for 10 min at 4 °C. The supernatant was removed to a fresh tube and centrifugated at 12000 g for 5 min at 4 °C. The cell pellets were ground into find powder in the presence of liquid nitrogen, and then resuspended in 1 mL Trizol by vortexing. After repeated centrifugation at 12000 g for 5 min at 4 °C, the supernatant was removed to a fresh tube and incubated for 5 min at room temperature. Next, 0.2 mL chloroform was added, followed by vortexing 15 s and incubation for 3 min. The mixtures were centrifugated at 12000 g for 15 min at 4 °C, upper aqueous phase was transferred into a fresh tube, mixed with 0.5 ml isopropanol, and incubated at room temperature for 10 min and RNA was precipitated at 12000 g for 10 min at 4 °C. After washing in 75% ethanol, the RNA pellet was dried and dissolved in 20 μL of water. The isolated total RNA was purfied using the RNeasy Mini kit . Quality and concentration of RNA samples were determined by using Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment

value: Zhang

tag: growth stage

value: late logarithmic phase (9 h, pH=5.2)


title: lca_soymilkgrowth_14.5h_1_rep2

description: gene expression pattern when grown to stationary phase

source_name: L. casei Zhang, growth in soymilk, 14.5h

value: stationary phase (14.5 h, pH=4.5)


title: lca_soymilkgrowth_14.5h_1_rep1


title: lca_soymilkgrowth_2h_1_rep1

description: gene expression pattern when grown to lag phase

source_name: L. casei Zhang, growth in soymilk, 2h

value: lag phase (2 h, pH=6.4)


title: A5212010 Butanol 2% Challenge Time Point 2 (75 min)

scan_protocol: A Genepix 4200A personal scanner was used to image the arrays (resolution: 5 um). Block ID in raw data file: 5.

source_name: Lactobacillus 2% Butanol Challenged Sample (75 min)

value: 75 min


title: A5212010 Butanol 2% Challenge Time Point 1 (15 min)

scan_protocol: A Genepix 4200A personal scanner was used to image the arrays (resolution: 5 um). Block ID in raw data file: 7.

source_name: Lactobacillus 2% Butanol Challenged Sample (15 min)

value: 15 min


title: A5142010 Butanol 2% Challenge Time Point 3 (135 min)

scan_protocol: A Genepix 4200A personal scanner was used to image the arrays (resolution: 5 um). Block ID in the raw data file: 4.


title: A5142010 Butanol 2% Challenge Time Point 2 (75 min)

scan_protocol: A Genepix 4200A personal scanner was used to image the arrays (resolution: 5 um). Block ID in the raw data file: 6.


title: A5142010 Butanol 2% Challenge Time Point 1 (15 min)

scan_protocol: A Genepix 4200A personal scanner was used to image the arrays (resolution: 5 um). Block ID in raw data file: 8.


title: 9QSA_anaerobic_stationary_newman_cy5_yhcR_cy3_14194568_MDS.mev.refIsIB.out

source_name: Newman yhcR knockout (query) total RNA extracted at stationary phase under anaerobic growth condition

source_name: Newman (reference) total RNA extracted at stationary phase under anaerobic growth condition


title: 9QSA_anaerobic_yhcR_staionary_cy3_WT_stationary_cy5_488_MDS.mev.refIsIB.out

value: Newman yhcR knockout

source_name: Staphylococcus aureus subsp.aureus strain Newman


title: lca_soymilkgrowth_9h_1_rep1

scan_protocol: Arrays were scanned Agilent G2565BA MicroArrayScanner System.


title: Gat1Leu3 10min_3AT_3

tag: genotype

value: GAT1LEU3 double deletion


title: 9QSA_anaerobic_midlog_newman_cy5_yhcR_cy3_14194565_MDS.mev.refIsIB.out

source_name: Newman yhcR knockout (query) total RNA extracted at midlog phase under anaerobic growth condition

growth_protocol: Cells were grown in TSA media overnight. Overnight cultures were diluted to an OD600 of 0.1. Cells were grown to midlog phase under anaerobic conditions.

value: midlog

value: anaerobic

source_name: Newman (reference) total RNA extracted at midlog phase under anaerobic growth condition

value: Newman


title: Gat1Leu3 10min_3AT_2

source_name: BY4741 GAT1LEU3 double deletion


title: 9QSA_anaerobic_yhcR_log_cy3_WT_cy5_484_MDS.mev.refIsIB.out

value: log


title: A4232010 Butanol 1% Challenge Time Point 2 (75 min)

hyb_protocol: The hybridization protocol described by Agilent (Two-Color prokaryotic microarray manual) was used.

scan_protocol: A Genepix 4200A personal scanner was utilized to scanning the arrays following 18 hours of hybridization. Resolution: 5 um. Block ID in raw data file: 7.

label: Alexa Fluor 647

source_name: Lactobacillus 1% Butanol Challenged Sample (75 min)

label_protocol: The Agilent Fairplay Kit III labeling protocol was used in this case.

extract_protocol: Total RNA was extracted with the Zymo Research Corp Fungal/Bacterial RNA Extraction kit.

treatment_protocol: Strain ATCC367 in MRS media was challenged with 1% butanol. After 75 min, 30 ml of culture was harvested and placed into RNALater to preserve the transcriptome.

value: L. brevis ATCC 367

value: MRS

value: 100 rpm

value: 1% Butanol

label: Alexa Fluor 555

treatment_protocol: An unchallenged reference culture was harvested and preserved in RNALater for comparison later.


title: Gat1Leu3 0min_3AT_3

value: baseline


title: A4162010 Butanol 1% Challenge Time Point 3 (135 min)

scan_protocol: A Genepix 4200A personal scanner was utilized to scanning the arrays following 18 hours of hybridization. Resolution: 5 um. Block ID in raw data file: 6.

source_name: Lactobacillus 1% Butanol Challenged Sample (135 min)

treatment_protocol: Strain ATCC367 in MRS media was challenged with 1% butanol. After 135 min, 30 ml of culture was harvested and placed into RNALater to preserve the transcriptome.

value: 135 min

value: control

value: Reference


title: A4232010 Butanol 1% Challenge Time Point 1 (15 min)

scan_protocol: A Genepix 4200A personal scanner was utilized to scanning the arrays following 18 hours of hybridization. Resolution: 5 um. Block ID in the raw data file: 6.

source_name: Lactobacillus 1% Butanol Challenged Sample (15 min)

treatment_protocol: Strain ATCC367 in MRS media was challenged with 1% butanol. After 15 min, 30 ml of culture was harvested and placed into RNALater to preserve the transcriptome.


title: A4162010 Butanol 1% Challenge Time Point 2 (75 min)

scan_protocol: A Genepix 4200A personal scanner was utilized to scanning the arrays following 18 hours of hybridization. Resolution: 5 um. Block ID in the raw data file: Block 2.


title: A4232010 Butanol 1% Challenge Time Point 3 (135 min)

scan_protocol: A Genepix 4200A personal scanner was utilized to scanning the arrays following 18 hours of hybridization. Resolution: 5 um. Block ID in raw data file: 3.


title: 9QSA_anaerobic_WT_staionary_cy3_yhcR_stationary_cy5_827_MDS.mev.refIsIA.out

value: stationary

source_name: Newman yhcR knockout(query) total RNA extracted at stationary phase under anaerobic growth condition


title: 9QSA_anaerobic_WT_staionary_cy3_yhcR_stationary_cy5_490_MDS.mev.refIsIA.out


title: A4162010 Butanol 1% Challenge Time Point 1 (15 min)

scan_protocol: A Genepix 4200A personal scanner was utilized to scanning the arrays following 18 hours of hybridization. Resolution: 5 um. Block ID in the raw data file: Block 3.

source_name: Reference


title: A492010 Butanol 1% Challenge Time Point 1 (15 min)

scan_protocol: A Genepix 4200A personal scanner was utilized to scanning the arrays following 18 hours of hybridization. Resolution: 5 um. Block ID in the supplementary data file is Block 6.


title: Gat1Leu3 0min_3AT_1

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000.


title: 14190397_Srrb-_30m_Cy3_M_30m_Cy5_MDS.mev.refIsIB.out

first: Fatma

last: Onmus-Leone

address: 9704 Medical Center Dr.

institute: JCVI

hyb_protocol: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95 C degree  prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus subsp.aureus strain Newman srrb knockout(query)

growth_protocol: Cells were grown in TSA media overnight.  Overnight cultures were diluted to an OD600 of 0.1.  Cells were grown to  early log (30 min).

value: Staphylococcus aureus subsp. aureus strain Newman srrb knockout

tag: growth phase

value: early log (30 min).

source_name: Staphylococcus aureus subsp.aureus strain Newman (reference)


title: Gat1Leu3 10min_3AT_1


title: A4232010 FA Array Time Point 1 (15 min) (Dye Swap)

hyb_protocol: Microarray hybridization was carried out as prescribed by the Agilent Fairplay Kit III protocol.

scan_protocol: An Axon GenePix 4200A was used to scan the slides.

source_name: Lactobacillus Ferulic Acid Challenged Sample (FA 24 mM, 15 min)

label_protocol: Indirect labeling via amino-allyl coupling with cyanine dyes (Agilent Fairplay Kit III).

extract_protocol: The total Bacterial/Fungal RNA extraction kit from Zymo was used to extract total RNA from harvested samples stored in RNALater (Ambion).

treatment_protocol: Induced with 24 mM Ferulic acid; sample harvested at 15 min following induction.

tag: agent

value: ferulic acid

value: 15 min

treatment_protocol: A pooled reference was created from three L. brevis cultures, harvested, and stored in RNALater for downstream RNA extraction.

tag: sample type

value: reference


title: 14190394_Srrb-_60m_Cy3_M_60m_Cy5_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus subsp.aureus strain Newman srrb knockout

growth_protocol: Cells were grown in TSA media overnight.  Overnight cultures were diluted to an OD600 of 0.1.  Cells were grown to mid log (60 min).

tag: strain

value: Mid log.


title: A492010 Butanol 1% Challenge Time Point 3 (135 min)

scan_protocol: A Genepix 4200A personal scanner was utilized to scanning the arrays following 18 hours of hybridization. Resolution: 5 um. The ID of the raw data in the supplementary GPR file is block 3.


title: Gcn4Leu3 60min_3AT_3

source_name: BY4741 GCN4LEU3 double deletion

value: GCN4LEU3 double deletion


title: A492010 Butanol 1% Challenge Time Point 2 (75 min)

scan_protocol: A Genepix 4200A personal scanner was utilized to scanning the arrays following 18 hours of hybridization. Resolution: 5 um. The ID of the block in the supplementary GPR file is Block 7.

value: 75 min


title: A4162010 FA Array Time Point 2 (135 min)

source_name: Lactobacillus Ferulic Acid Challenged Sample (FA 24 mM, 135 min)

treatment_protocol: Induced with 24 mM Ferulic acid; sample harvested at 135 min following induction.


title: A492010 FA Array Time Point 1 (15 min)

source_name: Lactobacillus Ferulic Acid Challenged Sample (FA 24 mM)

treatment_protocol: Induced with 24 mM Ferulic acid; sample harvested at 15 min.


title: A4232010 FA Array Time Point 2 (135 min) (Dye Swap)


title: A4162010 FA Array Time Point 1 (15 min)


title: Gcn4Leu3 60min_3AT_2


title: Gcn4Leu3 45min_3AT_3


title: Gcn4Leu3 60min_3AT_1


title: 14189484_Srrb-_240m_Cy3_M_240m_Cy5_MDS.mev.refIsIB.out

growth_protocol: Cells were grown in TSA media overnight.  Overnight cultures were diluted to an OD600 of 0.1.  Cells were grown to late stationary phase (240 min).

value: late stationary phase.

value: Staphylococcus aureus subsp.aureus strain Newman


title: Gcn4Leu3 45min_3AT_2


title: A492010 FA Array Time Point 2 (135 min)

treatment_protocol: Induced with 24 mM Ferulic acid; sample harvested at 135 min.

value: 100 rpm


title: 14189489_Srrb-_90m_Cy3_M_90m_Cy5_MDS.mev.refIsIB.out

growth_protocol: Cells were grown in TSA media overnight.  Overnight cultures were diluted to an OD600 of 0.1.  Cells were grown to late log(90min).

value: late log.


title: 14190262_Srrb-_60m_Cy5_M_60m_Cy3_MDS.mev.refIsIA.out

value: staphylococcus aureus subsp. aureus strain newman

value: mid log (60 min).

value: Staphylococcus aureus subsp.aureus strain Newman srrb knockout


title: Gat1Leu3 0min_3AT_2

value: GAT1LEU3 double deletion

value: baseline


title: 9QSA_anaerobic_WT_log_cy3_yhcR_cy5_486_MDS.mev.refIsIA.out

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

source_name: Newman (reference) total RNA extracted at log phase under anaerobic growth condition

value: Newman

value: log

value: anaerobic

source_name: Newman yhcR knockout(query) total RNA extracted at log phase under anaerobic growth condition

value: Newman yhcR knockout


title: 14190399_Srrb-_30m_Cy5_M_30m_Cy3_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus subsp.aureus strain Newman

growth_protocol: Cells were grown in TSA media overnight.  Overnight cultures were diluted to an OD600 of 0.1.  Cells were grown to early log(30min).

value: Staphylococcus aureus subsp. aureus strain Newman

value: early log.


title: Gcn4Leu3 45min_3AT_1

value: GCN4LEU3 double deletion


title: 14189508_Srrb-_120m_Cy3_M_120m_Cy5_MDS.mev.refIsIB.out

growth_protocol: Cells were grown in TSA media overnight.  Overnight cultures were diluted to an OD600 of 0.1.  Cells were grown to early stationary(120 min).

value: Staphylococcus aureus subsp. aureus strain Newman srrb knockout

value: early stationary.

tag: staphylococcus aureus subsp.aureus strain newman


title: Gcn4Leu3 20min_3AT_3


title: 9QSA_anaerobic_WT_log_cy3_yhcR_cy5_485_MDS.mev.refIsIA.out


title: UNC971091A

city: Chapel Hill

last: Troester

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

description: Agilent Custom array of UNC971091A

hyb_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized using the University of North Carolina (UNC) microarray database, and then the log(2) ratio (test/reference) was taken.

source_name: Human Reference B

extract_protocol: Total RNA isolated by Stratagene.

value: reference

tag: composition

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

source_name: Normal Tissue Adjacent to Breast Tumor

extract_protocol: Qiagen RNeasy Mini Kit.

tag: tissue

value: normal tissue adjacent to breast tumor

tag: patient id

tag: active or "inactive"

value: positive

tag: age at diagnosis (year)

tag: menopause status

value: unknown

tag: histopathology

value: Invasive

tag: breast cancer subtype (pam50)

tag: er status

tag: hormone treated

value: no

tag: her2 status

tag: tumor grade

tag: tumor size (cm)

tag: overall survival event (dead=1, alive=0)

tag: overall survival (month)


title: UNC971083A

description: Agilent Custom array of UNC971083A

label_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

tag: sample type

value: negative

value: Pre


title: Gcn4Leu3 30min_3AT_2

tag: genotype

tag: collection time after 3at treatment

tag: genetic background

tag: treatment


title: Gcn4Leu3 30min_3AT_1