title: Sorbitol sample 52

city: Wageningen

first: Leo

middle: H

last: De Graaff

address: Dreijenplein 10

department: Microbiology

country: Netherlands

institute: Wageningen University and Research Centre

hyb_protocol: Washing, staining, and hybridization was done according to the Hybridization, Wash, and Stain kit (Affymetrix) according to the manufacturers' recommendations

scan_protocol: Arrays were scanned on an Agilent G2500A Gene Array scanner. Pixel value was 3 um, wavelength 570 nm.

data_processing: RMA values were determined by Agilent's GeneSpring GX software (version 7.3.1) using the RMA preprocessor.

organism: Aspergillus niger

source_name: induced 0.1 mM sorbitol

label_protocol: Extracted totalRNA was processed following the Affymetrix user manual (Eukaryotic Target) using the One-cycle target labeling and control reagents kit (Affymetrix). 15 ug of cRNA was used for labeling.

growth_protocol: Fermentor vessels containing 2.2 liters of minimal medium, supplements, and 100 mM sorbitol were inoculated with 1.1e6 spores per mL and maintained at 30 C. Aeration was done over headspace (50 L/h) while stirring at 300 rpm until dissolved oxygen concentration dropped below 60%. Then, stirrer speed was adjusted to 750 rpm and aeration switched to sparger inlet. The culture was allowed to grow for 14 hours.

extract_protocol: Frozen mycelium was ground using a dismembrator, followed by a trizol-chloroform extraction using the Qiagen Rneasy mini columns according to the “yeast protocol”.

treatment_protocol: 14 hours after the aeration switch to sparger, 50 mL sample was removed from the fermentor. Either D-xylose or sorbitol dissolved in MM (final concentration in fermentor 0.1 mM) was added. One hour after induction, a second sample was removed from the fermentor and the mycelium was snap-frozen in liquid N2 until further use.

tag: Strain 872.11


title: Pool 5_Lung_24H_FORW

status: Public on Dec 31 2008

type: genomic

city: Seattle

first: Allison

last: Mitchell

state: WA

address: 1100 Fairview Ave N

department: Human Biology

country: USA

institute: Fred Hutchinson CRC

description: Forward PCR amplification of the transposon

hyb_protocol: Arrays were hybridized overnight at 65C.  Wash 1: 42C for 5 minutes in 2X SSC + 0.2%SDS, Wash 2: 1 minute in 0.2X SSC +  0.1% SDS, Wash 3: 1 minute in 0.2X SSC, Wash 4 and 5: 0.05X SSC for 1 minute each; all washes were done on shaker at a moderate speed.  Spin at 1,000rpm for 5 minutes.

scan_protocol: Arrays were scanned using Axon Genepix 4000B scanner with Axon Genpix Pro 6.0 software.

data_processing: Data were extracted from Longhorn Array database where duplicate spots per gene were averaged and flagged spots were not included.  Note: Sample data table contains unfiltered data and thus different from the data used for the analysis of the study described in the paper.  Series supplementary file contains filtered data that shows on a per organ/timepoint basis with the ORF comparable across rows.

molecule: genomic DNA

organism: Francisella tularensis subsp. novicida

source_name: Deposition 288-5

label_protocol: The second, nested PCR was done to incorporate aminoallyl-dUTP and the PCR product was cleaned and labeled (deposition-Cy3, output pool-Cy5).

extract_protocol: Bacterial gDNA were extracted using Wizard genomic DNA preparation kit (Promega) then sequences flanking one side of the transposons in each pool were amplified in a two-step PCR.

tag: Bacterial DNA from lung tissue in C57/BL6 mice


title: Sorbitol sample 96

type: RNA

label: biotin

molecule: total RNA


title: Pool 4_Lung_48H_FORW

source_name: Deposition 288-4


title: Pool 4_Lung_72H_FORW


title: D-xylose sample 86 replicate2

source_name: induced 0.1 mM xylose


title: D-xylose sample 76


title: D-xylose sample 86 replicate1


title: Pool 3_Lung_72H_FORW

source_name: Deposition 288-3


title: D-xylose sample 44


title: Pool 2_Lung_24H_FORW

source_name: Deposition 288-2


title: Pool 3_Lung_48H_FORW


title: Pool 3_Lung_24H_FORW


title: Pool 1_Lung_24H_FORW

source_name: Deposition 288-1


title: Pool 1_Lung_72H_FORW


title: Pool 1_Lung_48H_FORW


title: Pool 11_Spleen_72H_REV

description: Reverse PCR amplification of the transposon

source_name: Deposition 288-11

tag: Bacterial DNA from spleen tissue in C57/BL6 mice


title: Pool 11_Spleen_48H_REV


title: D-xylose sample 29


title: Pool 2_Lung_72H_FORW


title: Pool 10_Spleen_72H_REV

source_name: Deposition 288-10


title: Pool 8_Spleen_72H_REV

source_name: Deposition 288-8

source_name: 72h spleen 288-8


title: Pool 10_Spleen_24H_REV


title: Pool 10_Spleen_48H_REV


title: Pool 9_Spleen_72H_REV

source_name: Deposition 288-9

source_name: 72h spleen 288-9


title: Pool 9_Spleen_48H_REV

source_name: 48h spleen 288-9


title: Pool 8_Spleen_48H_REV

source_name: 48h spleen 288-8


title: Pool 6_Spleen_72H_REV

source_name: Deposition 288-6

source_name: 72h spleen 288-6


title: Pool 7_Spleen_72H_REV

source_name: Deposition 288-7

source_name: 72h spleen 288-7


title: Pool 6_Spleen_48H_REV

source_name: 48h spleen 288-6


title: Pool 5_Spleen_24H_REV

source_name: Deposition 288-5

source_name: 24h spleen 288-5


title: Pool 5_Spleen_72H_REV

source_name: 72h spleen 288-5


title: Pool 5_Spleen_48H_REV

source_name: 48h spleen 288-5


title: Pool 3_Spleen_72H_REV

source_name: Deposition 288-3

source_name: 72h spleen 288-3


title: Pool 4_Spleen_48H_REV

source_name: Deposition 288-4

source_name: 48h spleen 288-4


title: Pool 3_Spleen_48H_REV

source_name: 48h spleen 288-3


title: Pool 3_Spleen_24H_REV

source_name: 24h spleen 288-3


title: Pool 4_Spleen_72H_REV

source_name: 72h spleen 288-4


title: Pool 2_Lung_48H_FORW

source_name: Deposition 288-2


title: Pool 4_Spleen_24H_REV

source_name: 24h spleen 288-4


title: Pool 7_Spleen_48H_REV

source_name: 48h spleen 288-7


title: Pool 6_Spleen_24H_REV

source_name: Deposition 288-6

source_name: 24h spleen 288-6


title: Pool 2_Spleen_24H_REV

source_name: 24h spleen 288-2


title: Pool 1_Spleen_72H_REV

source_name: Deposition 288-1

source_name: 72h spleen 288-1


title: Pool 1_Spleen_48H_REV

source_name: 48h spleen 288-1


title: Pool 11_Liver_48H_REV

source_name: Deposition 288-11

tag: Bacterial DNA from liver tissue in C57/BL6 mice


title: Pool 2_Spleen_72H_REV

source_name: 72h spleen 288-2


title: Pool 11_Liver_24H_REV


title: Pool 11_Liver_72H_REV


title: Pool 10_Liver_72H_REV

source_name: Deposition 288-10


title: Pool 1_Spleen_24H_REV

source_name: 24h spleen 288-1


title: Pool 10_Liver_24H_REV


title: Pool 2_Spleen_48H_REV

source_name: 48h spleen 288-2


title: Pool 9_Liver_48H_REV

source_name: Deposition 288-9


title: Pool 9_Liver_72H_REV


title: Pool 9_Liver_24H_REV


title: Pool 8_Liver_72H_REV

source_name: Deposition 288-8


title: Pool 10_Liver_48H_REV


title: Pool 7_Liver_24H_REV

source_name: Deposition 288-7


title: Pool 6_Liver_48H_REV


title: Pool 7_Liver_48H_REV


title: Pool 5_Liver_48H_REV

source_name: Deposition 288-5


title: Pool 8_Liver_24H_REV


title: Pool 7_Liver_72H_REV


title: Pool 6_Liver_24H_REV


title: Pool 5_Liver_72H_REV


title: Pool 4_Lung_24H_FORW

source_name: Deposition 288-4


title: Pool 6_Liver_72H_REV


title: Pool 5_Liver_24H_REV


title: Pool 4_Liver_48H_REV


title: Pool 4_Liver_72H_REV


title: Pool 8_Liver_48H_REV


title: Pool 4_Liver_24H_REV


title: Pool 3_Liver_72H_REV

source_name: Deposition 288-3


title: Pool 3_Liver_24H_REV


title: Pool 2_Liver_72H_REV

source_name: Deposition 288-2


title: Pool 3_Liver_48H_REV


title: Pool 1_Liver_48H_REV


title: Pool 2_Liver_48H_REV


title: Pool 1_Liver_72H_REV


title: Pool 1_Liver_24H_REV


title: Pool 11_Lung_72H_REV


title: Pool 11_Lung_48H_REV


title: Pool 10_Lung_24H_REV


title: Pool 10_Lung_72H_REV


title: Pool 9_Lung_72H_REV


title: Pool 9_Lung_24H_REV


title: Pool 9_Lung_48H_REV


title: Pool 10_Lung_48H_REV


title: Pool 7_Lung_72H_REV


title: Pool 6_Lung_72H_REV

source_name: Deposition 288-6


title: Pool 8_Lung_24H_REV


title: Pool 2_Liver_24H_REV


title: Pool 7_Lung_24H_REV


title: Pool 8_Lung_48H_REV


title: Pool 7_Lung_48H_REV


title: Pool 8_Lung_72H_REV


title: Pool 6_Lung_24H_REV


title: Pool 6_Lung_48H_REV


title: Pool 11_Lung_24H_REV


title: Pool 5_Lung_72H_REV


title: Pool 4_Lung_24H_REV


title: Pool 4_Lung_48H_REV


title: Pool 3_Lung_72H_REV


title: Pool 5_Lung_48H_REV


title: Pool 3_Lung_48H_REV


title: Pool 2_Lung_72H_REV


title: Pool 3_Lung_24H_REV


title: Pool 5_Lung_24H_REV


title: Pool 1_Lung_72H_REV


title: Pool 1_Lung_48H_REV


title: Pool 1_Lung_24H_REV


title: Pool 4_Lung_72H_REV


title: Pool 2_Lung_48H_REV


title: Taihu Pig_longissimus dorsi muscle_ Month 5 vs 4

status: Public on Dec 16 2008

city: Ya'an

first: Mingzhou

last: Li

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

description: Breed:Taihu Pig Tissue:longissimus dorsi muscle Comparison:Month 5 vs 4

hyb_protocol: The hybridization ,blocking and washing were performed by using Pronto!™ Hybridization Kit (Corning,Product #40026) and Pronto!™ cDNA/Long Oligo Hybridization Solution (Corning,Product #40090).

scan_protocol: Imaging screen was scaned at 10μm resolution and stored as 16-bit tiff format file by using ScanArray Express(PerkinElmer Life Sciences).

data_processing: log2-transformed normalized expression ratio (Cy3/Cy5). Backgorund and negative control value subtracted each channel median, then composite loess normalized intensity with positive control genes.

organism: Sus scrofa

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_ Taihu Pig _Month 5

label_protocol: The linear amplification procedure and Labeling reaction were performed by using Agilent Low RNA Input Linear Amplification Kit PLUS_two-color ( 5188-5340).

extract_protocol: The porcine longissimus dorsi muscle tissues stored in RNAlater (Qiagen,Cat. No. 76106). The total RNA isolated by using RNeasy Fibrous Tissue Mini Kit (Qiagen, Cat. No. 74704).

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu pigs（2♂2♀,Month 5）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Taihu Pig_Month 4

extract_protocol: The porcine longissimus dorsi muscle tissues stored in RNAlater (Qiagen,Cat. No. 76106).The total RNA isolated by using RNeasy Fibrous Tissue Mini Kit (Qiagen, Cat. No. 74704).

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu Pig pigs（2♂2♀,Month 4）.


title: Taihu Pig_longissimus dorsi muscle_ Month 4 vs 3

description: Breed:Taihu Pig Tissue:longissimus dorsi muscle Comparison:Month 4 vs 3

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_ Taihu Pig _Month 4

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu pigs（2♂2♀,Month 4）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Taihu Pig_Month 3

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu Pig pigs（2♂2♀,Month 3）.


title: Pool 2_Lung_24H_REV


title: Landrace vs Taihu Pig_longissimus dorsi muscle_ Month 3 vs 3

description: Breed:Landrace vs Taihu Pig Tissue:longissimus dorsi muscle Comparison:Month 3 vs 3

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_Landrace_Month 3

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Landrace pigs（2♂2♀,Month 3）.

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu Pigs（2♂2♀,Month 3）.


title: Taihu Pig_longissimus dorsi muscle_ Month 2 vs 1

description: Breed:Taihu Pig Tissue:longissimus dorsi muscle Comparison:Month 2 vs 1

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_ Taihu Pig _Month 2

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu pigs（2♂2♀,Month 2）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Taihu Pig_Month 1

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu Pig pigs（2♂2♀,Month 1）.


title: Taihu Pig_longissimus dorsi muscle_ Month 3 vs 2

description: Breed:Taihu Pig Tissue:longissimus dorsi muscle Comparison:Month 3 vs 2

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_ Taihu Pig _Month 3

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu pigs（2♂2♀,Month 3）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Taihu Pig_Month 2

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu Pig pigs（2♂2♀,Month 2）.


title: Landrace_longissimus dorsi muscle_ Month 5 vs 4

description: Breed:Landrace Tissue:longissimus dorsi muscle Comparison:Month 5 vs 4

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_Landrace_Month 5

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Landrace pigs（2♂2♀,Month 5）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Landrace_Month 4

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Landrace pigs（2♂2♀,Month 4）.


title: Taihu Pig_longissimus dorsi muscle_ Month 1 vs 0

description:
Breed:Taihu Pig Tissue:longissimus dorsi muscle Comparison:Month 1 vs 0
“Month 0” means the piglet was just born.

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_ Taihu Pig _Month 1

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu pigs（2♂2♀,Month 1）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Taihu Pig_Month 0

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu Pig pigs（2♂2♀,Month 0）.


title: Taihu Pig_longissimus dorsi muscle_ Month 0 vs 5

description:
Breed:Taihu Pig Tissue:longissimus dorsi muscle Comparison:Month 0 vs 5
“Month 0” means the piglet was just born.

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_Taihu Pig_Month 0

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu pigs（2♂2♀,Month 0）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Taihu Pig_Month 5

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu Pig pigs（2♂2♀,Month 5）.


title: Landrace vs Taihu Pig_longissimus dorsi muscle_ Month 5 vs 5

description: Breed:Landrace vs Taihu Pig Tissue:longissimus dorsi muscle Comparison:Month 5 vs 5

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu Pigs（2♂2♀,Month 5）.


title: Landrace vs Taihu Pig_longissimus dorsi muscle_ Month 4 vs 4

description: Breed:Landrace vs Taihu Pig Tissue:longissimus dorsi muscle Comparison:Month 4 vs 4

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_Landrace_Month 4

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu Pigs（2♂2♀,Month 4）.


title: Landrace_longissimus dorsi muscle_ Month 4 vs 3

description: Breed:Landrace Tissue:longissimus dorsi muscle Comparison:Month 4 vs 3

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Landrace_Month 3


title: Yeast_wt+Rapamycin_Cy5 vs wt-Rapamycin_Cy3

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

description: Spots with either a diameter smaller than 120 microm, or fluorescence intensity for Cy3 and Cy5 lower than 150 units, were not considered for further analysis. Intensities for were normalised by the ratio of medians.

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42 oC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 microl of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five microg of salmon sperm DNA was added to the mix before denaturation for 3 min at 95 ºC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42 ºC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 microm. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

data_processing: The GEPAS server (http://gepas.bioinfo.cnio.es) was used to preprocess the data (merging replicates). Spots with either a diameter smaller than 120 microm, or fluorescence intensity Cy3 and Cy5 lower than 150 units, were not considered further analysis. Intensities were normalised by the ratio of medians.

organism: Saccharomyces cerevisiae

source_name: wild type yeast strain in log phase culture, Rapamycin-treated cells

label_protocol: Fluorescent labeled cDNA was prepared from 8 microg of purified total RNA by the indirect dUTP-labeling method, using the CyScribe post-labeling kit (Amersham Biosciences)

growth_protocol: 30 ml of yeast culture was grown at 28 ºC in YPD rich medium, harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 ºC until RNA purification

extract_protocol: Total RNA purification using the Ambion RiboPure™-Yeast Total RNA Isolation Kit.

treatment_protocol: Cell culture at A660=0.5 was treated with 200 ng/ml of Rapamycin for one hour.

tag: Strain BY4741 wt

source_name: wild type yeast strain in log phase culture, Mock-treated cells

treatment_protocol: Mock-treated cells.


title: Yeast_ptc1+Rapamycin_Cy3 vs ptc1-Rapamycin_Cy5

source_name: ptc1 yeast strain in log phase culture, Rapamycin-treated cells

tag: Strain BY4741 ptc1::nat1

source_name: ptc1 yeast strain in log phase culture, Mock-treated cells


title: Landrace_longissimus dorsi muscle_ Month 3 vs 2

description: Breed:Landrace Tissue:longissimus dorsi muscle Comparison:Month 3 vs 2

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_Landrace_Month 3

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Landrace_Month 2

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Landrace pigs（2♂2♀,Month 2）.


title: Yeast_wt+Rapamycin_Cy3 vs wt-Rapamycin_Cy5


title: Landrace vs Taihu Pig_longissimus dorsi muscle_ Month 1 vs 1

description: Breed:Landrace vs Taihu Pig Tissue:longissimus dorsi muscle Comparison:Month 1 vs 1

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_Landrace_Month 1

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Landrace pigs（2♂2♀,Month 1）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Taihu Pig_Month 1

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu Pigs（2♂2♀,Month 1）.


title: Yeast_ptc1+Rapamycin_Cy5 vs ptc1-Rapamycin_Cy3


title: Landrace_longissimus dorsi muscle_ Month 1 vs 0

description:
Breed:Landrace Tissue:longissimus dorsi muscle Comparison:Month 1 vs 0
“Month 0” means the piglet was just born.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Landrace_Month 0

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Landrace pigs（2♂2♀,Month 0）.


title: Landrace vs Taihu Pig_longissimus dorsi muscle_ Month 0 vs 0

description:
Breed:Landrace vs Taihu Pig Tissue:longissimus dorsi muscle Comparison:Month 0 vs 0
“Month 0” means the piglet was just born.

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_Landrace_Month 0

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu Pigs（2♂2♀,Month 0）.


title: Landrace_longissimus dorsi muscle_ Month 0 vs 5

description:
Breed:Landrace   Tissue:longissimus dorsi muscle  Comparison:Month 0 vs 5
“Month 0” means the piglet was just born.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Landrace_Month 5


title: HEPG2-control#2

status: Public on Dec 17 2008

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: Comparison of HepG2 treatment with ethanol (control) or TSA (0.5uM)

label: Biotin

organism: Homo sapiens

source_name: HEPG2 cells treated with ethanol (0.5uM)

label_protocol: Affymetrix 1-cycle IVT

tag: HepG2 cell line


title: Taihu Pig_backfat_ Month 5 vs 4

description: Breed:Taihu Pig Tissue:backfat Comparison:Month 5 vs 4

source_name: Cy3 dye_backfat_total RNA_Taihu Pig_Month 5

extract_protocol: The porcine backfat tissues stored in RNAlater (Qiagen,Cat. No. 76106).The total RNA isolated by using RNeasy Lipid Tissue Mini Kit(Qiagen,Cat. No. 74804).

tag: The total RNA pool of porcine backfat from 4 Taihu pigs（2♂2♀,Month 5）.

source_name: Cy5 dye_backfat_total RNA_Taihu Pig_Month 4

tag: The total RNA pool of porcine backfat from 4 Taihu pigs（2♂2♀,Month 4）.


title: Taihu Pig_backfat_ Month 4 vs 3

description: Breed:Taihu Pig Tissue:backfat Comparison:Month 4 vs 3

source_name: Cy3 dye_backfat_total RNA_Taihu Pig_Month 4

source_name: Cy5 dye_backfat_total RNA_Taihu Pig_Month 3

tag: The total RNA pool of porcine backfat from 4 Taihu pigs（2♂2♀,Month 3）.


title: Taihu Pig_backfat_ Month 1 vs 5

description: Breed:Taihu Pig Tissue:backfat Comparison:Month 1 vs 5

source_name: Cy3 dye_backfat_total RNA_Taihu Pig_Month 1

tag: The total RNA pool of porcine backfat from 4 Taihu pigs（2♂2♀,Month 1）.

source_name: Cy5 dye_backfat_total RNA_Taihu Pig_Month 5


title: Landrace_backfat_ Month 5 vs 4

description: Breed:Landrace Tissue:backfat Comparison:Month 5 vs 4

source_name: Cy3 dye_backfat_total RNA_Landrace_Month 5

tag: The total RNA pool of porcine backfat from 4 Landrace pigs（2♂2♀,Month 5）.

source_name: Cy5 dye_backfat_total RNA_Landrace_Month 4

tag: The total RNA pool of porcine backfat from 4 Landrace pigs（2♂2♀,Month 4）.


title: Taihu Pig_backfat_ Month 3 vs 2

description: Breed:Taihu Pig Tissue:backfat Comparison:Month 3 vs 2

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190579/suppl/GSM190579 False-color Image Cy3.tif.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190579/suppl/GSM190579 False-color Image Cy5.tif.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190579/suppl/GSM190579 Grey-level Image Cy3.tif.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190579/suppl/GSM190579 Grey-level Image Cy5.tif.gz

source_name: Cy3 dye_backfat_total RNA_Taihu Pig_Month 3

source_name: Cy5 dye_backfat_total RNA_Taihu Pig_Month 2

tag: The total RNA pool of porcine backfat from 4 Taihu pigs（2♂2♀,Month 2）.


title: Landrace vs Taihu Pig_backfat_ Month 5 vs 5

description: Breed:Landrace vs Taihu Pig Tissue:backfat Comparison:Month 5 vs 5


title: HepG2-TSA#1

source_name: HEPG2 cells treated with TSA (0.5uM)

tag: HEpg2 cell line


title: Landrace_backfat_ Month 4 vs 3

description: Breed:Landrace Tissue:backfat Comparison:Month 4 vs 3

source_name: Cy3 dye_backfat_total RNA_Landrace_Month 4

source_name: Cy5 dye_backfat_total RNA_Landrace_Month 3

tag: The total RNA pool of porcine backfat from 4 Landrace pigs（2♂2♀,Month 3）.


title: Landrace vs Taihu pig_backfat_ Month 3 vs 3

description: Breed:Landrace vs Taihu pig Tissue:backfat Comparison:Month 3 vs 3

source_name: Cy3 dye_backfat_total RNA_Landrace_Month 3

source_name: Cy5 dye_backfat_total RNA_Taihu pig_Month 3

tag: The total RNA pool of porcine backfat from 4 Taihu  pigs（2♂2♀,Month 3）.


title: Landrace vs Taihu Pig_backfat_ Month 4 vs 4

description: Breed:Landrace vs Taihu pig Tissue:backfat Comparison:Month 4 vs 4


title: Landrace vs Taihu pig_backfat_ Month 2 vs 2

description: Breed:Landrace vs Taihu Pig Tissue:backfat Comparison:Month 2 vs 2

source_name: Cy3 dye_backfat_total RNA_Landrace_Month 2

tag: The total RNA pool of porcine backfat from 4 Landrace pigs（2♂2♀,Month 2).

source_name: Cy5 dye_backfat_total RNA_Taihu pig_Month 2

tag: The total RNA pool of porcine backfat from 4 Taihu pigs（2♂2♀,Month 2).


title: Landrace_backfat_ Month 3 vs 2

description: Breed:Landrace Tissue:backfat Comparison:Month 3 vs 2

source_name: Cy5 dye_backfat_total RNA_Landrace_Month 2

tag: The total RNA pool of porcine backfat from 4 Landrace pigs（2♂2♀,Month 2）.


title: Landrace_backfat_ Month 2 vs 1

description: Breed:Landrace Tissue:backfat Comparison:Month 2 vs 1

source_name: Cy5 dye_backfat_total RNA_Landrace_Month 1

tag: The total RNA pool of porcine backfat from 4 Landrace pigs（2♂2♀,Month 1）.


title: HepG2-control#3

source_name: HepG2 cells treated with ethanol (0.5uM)


title: HepG2-TSA#3

tag: HEPG2 cell line


title: HEPG2-control#1

source_name: HEPG2 cells treated with ethanol (0.5uM)


title: Landrace_backfat_ Month 1 vs 5

description: Breed:Landrace  Tissue:backfat  Comparison:Month 1 vs 5

hyb_protocol: The hybridization ,blocking and washing were performed by using Pronto!™ Hybridization Kit (Corning,Product #40026) and  Pronto!™ cDNA/Long Oligo Hybridization Solution (Corning,Product #40090).

scan_protocol: Imaging screen was scaned at 10μm resolution and stored as 16-bit tiff format file by using  ScanArray Express(PerkinElmer Life Sciences).

source_name: Cy3 dye_backfat_total RNA_Landrace_Month 1

label_protocol: The linear amplification procedure and Labeling  reaction were performed by using  Agilent Low RNA Input Linear Amplification Kit PLUS_two-color ( 5188-5340).

extract_protocol: The porcine backfat tissues  stored in RNAlater (Qiagen,Cat. No. 76106).The total RNA isolated by using RNeasy Lipid Tissue Mini Kit(Qiagen,Cat. No. 74804) .

source_name: Cy5 dye_backfat_total RNA_Landrace_Month 5


title: Landrace vs Taihu pig_backfat_ Month 1 vs 1

description: Breed:Landrace vs Taihu pig Tissue:backfat Comparison:Month 1 vs 1

source_name: Cy5 dye_backfat_total RNA_Taihu pig_Month 1


title: Taihu Pig_backfat_ Month 2 vs 1

description: Breed:Taihu Pig Tissue:backfat Comparison:Month 2 vs 1

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190578/suppl/GSM190578 False-color Image Cy3.tif.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190578/suppl/GSM190578 False-color Image Cy5.tif.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190578/suppl/GSM190578 Grey-level Image Cy3.tif.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190578/suppl/GSM190578 Grey-level Image Cy5.tif.gz

source_name: Cy3 dye_backfat_total RNA_Taihu Pig_Month 2

source_name: Cy5 dye_backfat_total RNA_Taihu Pig_Month 1


title: HEPG2-TSA#2

tag: HEpG2 cell line


title: Patient 2 (2)

status: Public on Dec 08 2008

city: Jinan

first: Xiao-Lin

last: Zhang

state: Shandong Province

address: West Wen Hua Road 107

department: Department of Hematology

institute: Qilu Hospital, Shandong University

description: For individual channel data extract, faint spots were removed for which intensities were below 400 unit after background subtracted in both channels (Cy3 and Cy5).

hyb_protocol: Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min) at room temperature.

scan_protocol: The scanning setting for the Cy3 and Cy5 channels was manually balanced by visual inspection of the external control spots. The data from the obtained images were extracted with SpotData software (CapitalBio Corp.).

data_processing: A spot-exclusion method was adopted to filter faint spots in which genes whose signal intensities were in the lowest 50% were excluded from further analysis.Statistical comparisons were done by using the one class method in significance analysis of microarray (SAM) software.

source_name: Monocyte-derived  DCs

label_protocol: Double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 5μg total RNA using the cDNA synthesis system according to the manufacturer’s protocol (Promega, USA). A T7-oligo(dT) primer (5’-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT- 3’) was used instead of the poly-T primer provided in the kit.After completion of double-stranded cDNA synthesis, cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and eluted with 30 μL elution buffer. The eluted double-stranded cDNA products were vacuum evaporated to 8 μL and subjected to 20μL in vitro transcription reactions at 37℃ for 3 hr using the T7 RiboMAX Express large scale RNA production system (Promega). The amplified RNA was purified using the RNA Clean-up Kit (MN). Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice. 4 μL of first-strand buffer, 2 μL of 0.1M DTT, 1μL 10 mM dNTP, and 1.5 μL M-MLV (Promega) were subsequently added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14μL. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 2.5 μL Klenow buffer, dNTP, and Cy3-dCTP (Amersham Pharmacia Biotech) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1μL Klenow enzyme (TaKaRa) was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy3-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray.

extract_protocol: Total RNA samples were prepared from monocyte-derived DCs from peripheral blood mononuclear cells from patients with ITP using Trizol reagent (Invitrogen) according to the manufacture’s instructions. RNA was further purified with an RNA clean-up kit (Macherey-Nagel, Germany) and quantified by using of spectrophotometer. RNA quality from each sample was assessed by visualization of the 28S/18S ribosomal RNA ratio on 1.2% formamide agarose gel .

tag: Patients with idiopathic thrombocytopenic purpura(ITP).27 yrs. Female

tag: Monocyte-derived DCs were treated with induced-regulatory T cells. Then, induced-regulatory T cells were removed using CD4 magnetic beads (Miltenyi Biotech) before RNA isolation.

source_name: Monocyte-derived DCs

label_protocol: Double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 5μg total RNA using the cDNA synthesis system according to the manufacturer’s protocol (Promega, USA). A T7-oligo(dT) primer (5’-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT- 3’) was used instead of the poly-T primer provided in the kit.After completion of double-stranded cDNA synthesis, cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and eluted with 30 μL elution buffer. The eluted double-stranded cDNA products were vacuum evaporated to 8 μL and subjected to 20μL in vitro transcription reactions at 37℃ for 3 hr using the T7 RiboMAX Express large scale RNA production system (Promega). The amplified RNA was purified using the RNA Clean-up Kit (MN). Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice. 4 μL of first-strand buffer, 2 μL of 0.1M DTT, 1μL 10 mM dNTP, and 1.5 μL M-MLV (Promega) were subsequently added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14μL. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 2.5 μL Klenow buffer, dNTP, and Cy5-dCTP (Amersham Pharmacia Biotech) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1μL Klenow enzyme (TaKaRa) was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray.

extract_protocol: Total RNA samples were prepared from monocyte-derived DCs from peripheral blood mononuclear cells from patients with ITP using Trizol reagent (Invitrogen) according to the manufacture’s instructions. RNA was further purified with an RNA clean-up kit (Macherey-Nagel, Germany) and quantified by using of spectrophotometer. RNA quality from each sample was assessed by visualization of the 28S/18S ribosomal RNA ratio on 1.2% formamide agarose gel.

tag: The same  patients with ITP. 27 yrs.


title: Patient 4 (2)

tag: Patients with idiopathic thrombocytopenic purpura(ITP). 38 yrs. Male. Monocyte-derived  DCs were treated with induced-regulatory T cells. Then, induced-regulatory T cells were removed using CD4 magnetic beads (Miltenyi Biotech) before RNA isolation.

tag: The same patients with idiopathic thrombocytopenic purpura(ITP). 38 yrs.


title: Patient 1 (2)

tag: Patients with idiopathic thrombocytopenic purpura(ITP). 31 yrs. Female

tag: The same patients with idiopathic thrombocytopenic purpura(ITP).


title: Patient 5

data_processing: A spot-exclusion method was adopted to filter faint spots in which genes whose signal intensities were in the lowest 50% were excluded from further analysis.

tag: Patients with idiopathic thrombocytopenic purpura(ITP). 35 yrs. Female

tag: The same female patients with idiopathic thrombocytopenic purpura(ITP). 35 yrs.

tag: Monocyte-derived  DCs were treated with induced-regulatory T cells. Then, induced-regulatory T cells were removed using CD4 magnetic beads (Miltenyi Biotech) before RNA isolation.


title: Patient 3 (2)

tag: Patients with idiopathic thrombocytopenic purpura(ITP). 40 yrs. Female.

tag: The same patients with idiopathic thrombocytopenic purpura(ITP). 40 yrs.


title: Patient 1

source_name: human monocyte-derived  DCs

label_protocol: Double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 5μg total RNA using the cDNA synthesis system according to the manufacturer’s protocol (Promega, USA). A T7-oligo(dT) primer (5’-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT- 3’) was used instead of the poly-T primer provided in the kit.After completion of double-stranded cDNA synthesis, cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and eluted with 30 μL elution buffer. The eluted double-stranded cDNA products were vacuum evaporated to 8 μL and subjected to 20μL in vitro transcription reactions at 37℃ for 3 hr using the T7 RiboMAX Express large scale RNA production system (Promega). The amplified RNA was purified using the RNA Clean-up Kit (MN). Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice.  4 μL of first-strand buffer, 2 μL of 0.1M DTT, 1μL 10 mM dNTP, and 1.5 μL M-MLV (Promega) were subsequently added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14μL. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 2.5 μL Klenow buffer, dNTP, and  Cy3-dCTP (Amersham Pharmacia Biotech) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1μL Klenow enzyme (TaKaRa) was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy3-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray.

tag: Patients with idiopathic thrombocytopenic purpura(ITP). Age:31 yrs.  Female

source_name: human monocyte-derived DCs

label_protocol: Double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 5μg total RNA using the cDNA synthesis system according to the manufacturer’s protocol (Promega, USA). A T7-oligo(dT) primer (5’-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT- 3’) was used instead of the poly-T primer provided in the kit.After completion of double-stranded cDNA synthesis, cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and eluted with 30 μL elution buffer. The eluted double-stranded cDNA products were vacuum evaporated to 8 μL and subjected to 20μL in vitro transcription reactions at 37℃ for 3 hr using the T7 RiboMAX Express large scale RNA production system (Promega). The amplified RNA was purified using the RNA Clean-up Kit (MN). Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice.  4 μL of first-strand buffer, 2 μL of 0.1M DTT, 1μL 10 mM dNTP, and 1.5 μL M-MLV (Promega) were subsequently added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14μL. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 2.5 μL Klenow buffer, dNTP, and  Cy5-dCTP (Amersham Pharmacia Biotech) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1μL Klenow enzyme (TaKaRa) was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray.

tag: The same female patients with idiopathic thrombocytopenic purpura(ITP). Age:31 yrs.


title: Patient 2

tag: Patients with idiopathic thrombocytopenic purpura(ITP). Age:27 yrs. Female

tag: The same female patients with ITP. 27 yrs.


title: ORF J120E#9 hst2D input vs H3 cterm beads

status: Public on Nov 14 2008

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description: Chip on CHIP

hyb_protocol: Robyr et al Methods 31 (2003)

scan_protocol: ChipReader

data_processing: GeneSpring

organism: Schizosaccharomyces pombe

source_name: hst2D input

label_protocol: Robyr et al Methods 31 (2003)

extract_protocol: Robyr et al Methods 31 (2003)

tag: hst2D input

source_name: H3 wt beads

tag: h3 wt beads


title: ORF J120E#10 hst4D input vs H3 cterm beads

description: Chip on CHIP

source_name: hst4D input

tag: hst4D input

source_name: H3 beads wt

tag: H3 beads wt


title: E2+TNFa 2

status: Public on Dec 01 2008

city: Chicago

first: Jonna

last: Frasor

state: IL

address: 835 S. Wolcott MC 901

institute: University of Illinois at Chicago

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data was analyzed in S-Plus 6.2 statistical package with the S+ArrayAnalyzer v2.0.1 from Insightful. Hybridization signal intensities were normalized by quantiles and summarized using the Robust Multi-array  Average (RMA) (Irizarry et al. 2003).

label_protocol: GeneChIP IVT labeling kit

extract_protocol: Trizol followed by RNAeasy

tag: Human breast cancer cell line treated with 10 nM E2 + 10 ng/ml TNFa for 2h


title: Patient 4

tag: Patients with idiopathic thrombocytopenic purpura(ITP). 38 yrs. Male

tag: The same male patients with idiopathic thrombocytopenic purpura(ITP). 38 yrs.


title: TNFa 2

tag: Human breast cancer cell line treated with 10 ng/ml TNFa for 2h


title: IGR J120E#10 hst4D input vs H3 cterm beads

description: Chip on CHIP


title: TNFa 3

source_name: MCF-7 Cells


title: TNFa 1


title: Estradiol 2

tag: Human breast cancer cell line treated with 10 nM estradiol for 2h


title: Patient 3

tag: Patients with idiopathic thrombocytopenic purpura(ITP). 40 yrs. Female

tag: The same female patients with idiopathic thrombocytopenic purpura(ITP). 40 yrs.

tag: Monocyte-derived DCs were treated with induced-regulatory T cells. Then, induced-regulatory T cells were removed using CD4 magnetic beads (Miltenyi Biotech) before RNA isolation.


title: Patient 5 (2)

tag: Patients with idiopathic thrombocytopenic purpura(ITP). 35 yrs. Female

tag: Monocyte-derived  DCs were treated with induced-regulatory T cells. Then, induced-regulatory T cells were removed using CD4 magnetic beads (Miltenyi Biotech) before RNA isolation.

tag: The same patients with idiopathic thrombocytopenic purpura(ITP). 35 yrs.


title: E2+TNFa 3


title: Control 3

source_name: MCF-7 cells

tag: Human breast cancer cell line


title: Estradiol 3


title: Control 2


title: E2+TNFa 1


title: Estradiol 1

tag: Human breast cancer cell line, treated with 10 nM estradiol for 2 hours


title: ORF C270F#7-3 pst3-GFP IP vs beads

description: Chip on CHIP

source_name: pst3-GFP input

tag: pst3-GFP input

source_name: pst3-GFP beads

tag: pst3-GFP beads


title: IGR C270F#7-5 pst3-GFP IP vs beads

description: Chip on CHIP

source_name: Pst3-GFP input


title: IGR J120E#9 hst2D input vs H3 cterm beads

description: Chip on CHIP

tag: hst2D input

source_name: H3 beads

tag: H3 beads


title: ORF C270F#7-5 pst3-GFP IP vs beads

description: Chip on CHIP


title: pst3nmt OFF E020F#16

description: Expression profile of repressed pst3nmt

hyb_protocol: Xue Y. et al Yeast (2004)

scan_protocol: Chip Reader

source_name: pst3nmt Hu1505

label_protocol: Xue Y. et al Yeast (2004)

extract_protocol: Xue Y. et al Yeast (2004)

tag: pst3nmt Hu1505


title: pst3nmtOFF E020F#15

description: Expression profile of repressed pst3nmt

data_processing: Imagene 4.2

tag: pst3nmt sample


title: ORF J120E#1 anti-H3 wt vs WTinput

description: Chip on CHIP

source_name: anti-H3 wt

tag: anti-H3 wt

source_name: wt input

tag: wt input


title: IGR J120E#1 anti-H3 beads vs WT input

description: Chip on CHIP

source_name: anti-H3 beads wt

tag: anti-H3 beads wt


title: Wild type vs htpX mutnat. Heat shock. First experiment

status: Public on Nov 01 2008

city: Boston

first: Kevin

last: Conlon

state: MA

address: 300 Longwood avenue

department: Infectious Disease

institute: Childrens Hospital Boston

description: This experiment examines the differences in global gene expression in a wild type and mutant strain grown under standard shaking conditions to mid log phase (OD600 0.5) followed by heat shock at 50C for 15 minutes.

hyb_protocol: TIGR

scan_protocol: The hybridized slides were scanned using a GenePix 4000B microarray scanner (Axon Instruments, Union City, CA), and spot intensities were defined and quantified using GenePix Pro software (Axon Instruments, Union City, CA).

data_processing: Normalization calculated by working out average intensity per spot and dividing the average intensity in the Cy3 (mutant) labeled sample by the average intensity in the Cy5 (wild type) labeled sample to get figure X. The Cy5 intensities were then corrected for by multiplying by X.

label: Cy3 and Cy5

organism: Mycobacterium tuberculosis

source_name: Mycobacterium Tuberculosis

label_protocol: TIGR

growth_protocol: Grown to OD600 0.5 in 7H9 broth. Shaking

extract_protocol: Trizol

treatment_protocol: Heat shocked at 50C for 15 minutes then placed directly on ice water.

tag: Strain H37Rv


title: IGR C270F#7-3 pst3-GFP IP vs beads

description: Chip on CHIP

source_name: Pst3-GFP beads

tag: Pst3-GFP beads


title: M tuberculosis, wt and htpX mutant strains, standard mid log cultures, replicate 1

description: This study compared global transcription in the wild type strain and a htpX (Rv0563) mutant strain.

hyb_protocol: Protocols provided by TIGR were closely followed

scan_protocol: Scanning was performed with a GenePix 4000B microarray scanner (Axon Instruments, Union City, CA), and spot intensities were defined and quantified using GenePix Pro software (Axon Instruments, Union City, CA).

data_processing: Normalization was achieved by taking the average intensity value in the 532 Cy3 column and dividing it by the average intensity from the 635 Cy5 column. This gave a figure of 0.88. All the values in the 635 Cy5 column were then multiplied by 0.88 to give the Normalization figures.

label: Wild type was labeled with Cy5 and the mutant was labeled with Cy3

source_name: Mycobacterium Tuberculosis. Wild type and htpX mutant strains

growth_protocol: A culture of each strain (wild type and the htpX mutant) were grown in 7H9 broth to  mid log OD600 0.5. 50ml of each culture was harvested.

extract_protocol: Extracted using the Trizol method

tag: Wild type H37Rv and the H37Rv htpX knockout strain


title: Tetrahymena_C2-12

status: Public on Oct 01 2008

city: Rochester

first: Martin

last: Gorovsky

address: Hutchison Hall 432

department: Department of Biology

institute: University of Rochester

description: references: Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.

hyb_protocol: Sample Hybridization protocol provided and performed by NimbleGen.

scan_protocol: Nimblegen. Sample scan protocol provided and performed by NimbleGen.

data_processing: Array normalization was performed using the quantile normalization method of Bolstad et al. (2003). Normalized expression values for the individual probes were used to obtain the expression values for a given open reading frame (ORF) by using the robust multiarray average (RMA) procedure as previously described by Irizarry et al. (2003).

organism: Tetrahymena thermophila

source_name: B2086 mate with CU428 cells at 12 hr postmixing

label_protocol: Sample labeling protocol provided and performed by NimbleGen.

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix;  100X antibiotic- antimycotic mix; starved at 200K cells/ml for 18 hr without shaking. B2086 and CU428 cells were mixed, and samples were collected at 12 hr postmixing.

extract_protocol: Homogenization was done using a Qiashredder spin column and total RNA was extracted using the RNeasy Protect Cell Mini Kit (Qiagen, Valenica, CA) according to manufacturer’s instructions. The concentration of total RNA was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE) and RNA integrity was verified using a Bioanalyzer 1000 (Agilent, Palo Alto, CA).


title: Tetrahymena_C2-18

source_name: B2086 mate with CU428 cells at 18 hr postmixing

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix;  100X antibiotic- antimycotic mix; starved at 200K cells/ml for 18 hr without shaking. B2086 and CU428 cells were mixed, and samples were collected at 18 hr postmixing.


title: Wild type vs htpX mutnat. Heat shock. Third experiment


title: Tetrahymena_C2-16

source_name: B2086 mate with CU428 cells at 16 hr postmixing

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix;  100X antibiotic- antimycotic mix; starved at 200K cells/ml for 18 hr without shaking. B2086 and CU428 cells were mixed, and samples were collected at 16 hr postmixing.


title: Tetrahymena_C2-14

source_name: B2086 mate with CU428 cells at 14 hr postmixing

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix;  100X antibiotic- antimycotic mix; starved at 200K cells/ml for 18 hr without shaking. B2086 and CU428 cells were mixed, and samples were collected at 14 hr postmixing.


title: ORF wt expression 19)806

description: Expression profile of wt

source_name: wt

tag: wt


title: Control 1

source_name: MCF-7 Cells

tag: Breast cancer cell line


title: WT-htpX(2-17). Regular conditions. Second experiment.

data_processing: Normalization was achieved by taking the average intensity value in the 532 Cy3 column and dividing it by the average intensity from the 635 Cy5 column to get figure X. All the values in the 635 Cy5 column were then multiplied by X to give the Normalization figures.

label_protocol: Protocols provided by TIGR were closely followed

treatment_protocol: Standard treatment

tag: Wild type strain H37Rv hybridised against the htpX knockout strain


title: Tetrahymena_C2-4

source_name: B2086 mate with CU428 cells at 4 hr postmixing

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix;  100X antibiotic- antimycotic mix; starved at 200K cells/ml for 18 hr without shaking. B2086 and CU428 cells were mixed, and samples were collected at 4 hr postmixing.


title: Wild type vs htpX mutnat. Heat shock. Second experiment


title: Tetrahymena_C2-8

source_name: B2086 mate with CU428 cells at 8 hr postmixing

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix;  100X antibiotic- antimycotic mix; starved at 200K cells/ml for 18 hr without shaking. B2086 and CU428 cells were mixed, and samples were collected at 8 hr postmixing.


title: Tetrahymena_C2-6

source_name: B2086 mate with CU428 cells at 6 hr postmixing

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix;  100X antibiotic- antimycotic mix; starved at 200K cells/ml for 18 hr without shaking. B2086 and CU428 cells were mixed, and samples were collected at 6 hr postmixing.


title: WT-htpX(2-09). Regular conditions. Third experiment.


title: Tetrahymena_C2-0

source_name: B2086 mate with CU428 cells at 0 hr postmixing

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix;  100X antibiotic- antimycotic mix; starved at 200K cells/ml for 18 hr without shaking. B2086 and CU428 cells were mixed, and samples were collected at 0 hr postmixing.


title: Tetrahymena_C1-16

tag: B2086 mate with CU428 cells at 16 hr postmixing


title: Tetrahymena_C1-14

tag: B2086 mate with CU428 cells at 14 hr postmixing


title: Tetrahymena_C1-18

tag: B2086 mate with CU428 cells at 18 hr postmixing


title: Tetrahymena_C2-2

source_name: B2086 mate with CU428 cells at 2 hr postmixing

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix;  100X antibiotic- antimycotic mix; starved at 200K cells/ml for 18 hr without shaking. B2086 and CU428 cells were mixed, and samples were collected at 2 hr postmixing.


title: Tetrahymena_C1-12

tag: B2086 mate with CU428 cells at 12 hr postmixing


title: Tetrahymena_C1-8

tag: B2086 mate with CU428 cells at 8 hr postmixing


title: Tetrahymena_C1-6

tag: B2086 mate with CU428 cells at 6 hr postmixing


title: Rehybridization after stripped once, 2mM NaOH treatment

type: mixed

city: Minneapolis

first: Xiaoxiao

address: 312 Church St. SE

institute: University of Minnesota

description: Rehybridization after stripped once

hyb_protocol: A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al), inside a MAUI mixer in a MAUI hybridization system (BioMicro® System, Inc, Salt Lake City, UT, USA).  Thomson, J.M., Parker, J., Perou, C.M., and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.

scan_protocol: Slides were scanned with a ScanArray 5000 machine (Perkin Elmer®, Waltham, MA, USA).

data_processing: BlueFuse (BlueGenome, Cambridge, UK) was used to quantify pixel intensities.  GeneSpring GX 7.3.1 (Agilent Technologies) was used for data normalization.

source_name: Total RNA are from 293T cells, 2mM NaOH treated

label_protocol: Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’.  Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.

growth_protocol: Cells are grown in DMEM

extract_protocol: Trizol® reagent (Invitrogen) was used to extract total RNA from 293T cells

treatment_protocol: Sample 1x-A is from the sample New-A which is rehybridized after once-stripped. Sample 1x-B is from the sample New-B which is rehybridized after once-stripped. Sample 2x-B and 3x-B is from New-B which is rehybridized after twice-, and triple-stripped subsequently.

tag: 293T cells

label: Alexa Fluor® 647

organism: synthetic construct

source_name: reference DNA oligonucleotides

tag: reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs


title: Rehybridization after stripped three times, 1mM NaOH treatment

source_name: Total RNA are from 293T cells, 1mM NaOH treated


title: 293T New B, 2mM NaOH treatment

description: 293T New B


title: Tetrahymena_C1-10

source_name: B2086 mate with CU428 cells at 10 hr postmixing

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix;  100X antibiotic- antimycotic mix; starved at 200K cells/ml for 18 hr without shaking. B2086 and CU428 cells were mixed, and samples were collected at 10 hr postmixing.


title: Rehybridization after stripped once, 1mM NaOH treatment

description: Rehybridization after stripped once


title: Rehybridization after stripped twice, 1mM NaOH treatment

description: Rehybridization after stripped twice


title: 293T New A, 1mM NaOH treatment

description: 293T New A


title: Tetrahymena_C2-10

tag: B2086 mate with CU428 cells at 10 hr postmixing


title: Tetrahymena_S3-9

source_name: CU428 cells starved for 9 hr

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix; starved at 200K cells/ml for 9 hr without shaking.

tag: CU428 cells starved for 9 hr


title: Tetrahymena_S3-24

source_name: CU428 cells starved for 24 hr

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix; starved at 200K cells/ml for 24 hr without shaking.

tag: CU428 cells starved for 24 hr


title: Tetrahymena_C1-2

tag: B2086 mate with CU428 cells at 2 hr postmixing


title: Tetrahymena_S3-6

source_name: CU428 cells starved for 6 hr

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix; starved at 200K cells/ml for 6 hr without shaking.

tag: CU428 cells starved for 6 hr


title: Tetrahymena_C1-0

tag: B2086 mate with CU428 cells at 0 hr postmixing


title: Tetrahymena_S3-12

source_name: CU428 cells starved for 12 hr

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix; starved at 200K cells/ml for 12 hr without shaking.

tag: CU428 cells starved for 12 hr


title: Tetrahymena_S3-3

source_name: CU428 cells starved for 3 hr

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix; starved at 200K cells/ml for 3 hr without shaking.

tag: CU428 cells starved for 3 hr


title: Tetrahymena_C1-4

tag: B2086 mate with CU428 cells at 4 hr postmixing


title: Tetrahymena_S3-15

source_name: CU428 cells starved for 15 hr

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix; starved at 200K cells/ml for 15 hr without shaking.

tag: CU428 cells starved for 15 hr


title: Tetrahymena_S2-24


title: Tetrahymena_S3-0

source_name: CU428 cells starved for 0 hr

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix; starved at 200K cells/ml for 0 hr without shaking.

tag: CU428 cells starved for 0 hr


title: Tetrahymena_S2-15


title: Tetrahymena_S2-9


title: Landrace_longissimus dorsi muscle_ Month 2 vs 1

description: Breed:Landrace Tissue:longissimus dorsi muscle Comparison:Month 2 vs 1

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_Landrace_Month 2

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Landrace pigs（2♂2♀,Month 2）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Landrace_Month 1

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Landrace pigs（2♂2♀,Month 1）.


title: Tetrahymena_S2-6


title: Tetrahymena_S2-3


title: Tetrahymena_S2-12


title: Rat extraocular muscles exp rep3

city: St Louis

first: Bendi

last: Gong

state: MO

address: 1402 S Grand Ave

department: Neurology & Psychiaty

institute: St Louis University

description: Raw data from microarray scans were analyzed with Affymetrix GCOS 2.0.  GCOS evaluates sets of perfect match (PM) and mismatch (MM) probe sequences to obtain both hybridization signal values and present/absent calls for each transcript

hyb_protocol: Fragmented cRNA (15 ug) was used in a 300 ul hybridization cocktail containing herring sperm DNA and BSA as carrier molecules, spiked IVT controls, and buffering agents.  A 200 ul aliquot of this cocktail was used for hybridization to Affymetrix rat REA230 (Santa Clara, CA) microarrays for 16 hrs at 45o C.

scan_protocol: an Affymetrix GeneChip Fluidics Station 400 and a Hewlett Packard Gene Array scanner.

data_processing: Microarrays were scaled to the same target intensity and pairwise comparisons were made between experimental and control samples

label: biotinylated

organism: Rattus norvegicus

source_name: extraocular muscles

label_protocol: Double strand cDNA was synthesized and used in an in vitro transcription (IVT) reaction to generate biotinylated cRNA.

extract_protocol: Total RNA was extracted using TRIzol reagent (GibcoBRL, Rockville, MD).  RNA pellets were cleaned by RNasey kits and resuspended at 1 mg RNA/ml DEPC-treated water

tag: Six to eight week old female Lewis rats weighing 120 -150 g (Harlan, Indianapolis, IN)


title: Tetrahymena_S1-24


title: Tetrahymena_S1-6


title: Tetrahymena_S2-0


title: Tetrahymena_S1-15


title: Rat extraocular muscles exp rep1


title: Rat extraocular muscles ctrl rep3


title: Rat extensor digitorum longus exp rep3

source_name: extensor digitorum longus


title: Rat extraocular muscles ctrl rep1


title: Rat extraocular muscles ctrl rep2


title: Tetrahymena_S1-12


title: Rat extensor digitorum longus  exp rep1


title: Tetrahymena_S1-9


title: Tetrahymena_S1-3


title: Rat extensor digitorum longus  exp rep2


title: Rat diaphragm ctrl rep3

source_name: diaphragm


title: Rat extraocular muscles exp rep2


title: Rat extensor digitorum longus  ctrl rep3


title: Tetrahymena_S1-0


title: Rat extensor digitorum longus  ctrl rep2


title: Tetrahymena_L3-m

source_name: growing CU428 cells at low cell densities (350,000 cells/ml)

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C); 350,000 cells/ml.


title: Tetrahymena_L3-h

source_name: growing CU428 cells at low cell densities (1000,000 cells/ml)

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C); 1000,000 cells/ml.


title: Rat diaphragm exp rep3


title: Rat extensor digitorum longus  ctrl rep1


title: Tetrahymena_L2-h

tag: growing CU428 cells at low cell densities (1000,000 cells/ml)


title: Tetrahymena_L3-l

source_name: growing CU428 cells at low cell densities (100,000 cells/ml)

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C); 100,000 cells/ml.


title: Tetrahymena_L1-m

description:
references:
Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.

extract_protocol: Homogenization was done using a Qiashredder spin column and total RNA was extracted using the RNeasy Protect Cell Mini Kit (Qiagen, Valenica, CA) according to manufacturer’s instructions.  The concentration of total RNA was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE) and RNA integrity was verified using a Bioanalyzer 1000 (Agilent, Palo Alto, CA).

tag: growing CU428 cells at low cell densities (350,000 cells/ml)


title: Rat diaphragm exp rep2


title: Tetrahymena_L1-h


title: white muscle tissue individu 499al

status: Public on Sep 01 2008

city: Québec

first: Nicolas

last: Derome

state: QC

address: Av de la médecine

department: Biologie

country: Canada

institute: Université LAVAL

description: Spot location and quantification was done with the QuantArray© (Perkin Elmer) software, retaining the mean intensity value for each spot.

hyb_protocol: following the procedures at http://web.uvic.ca/cbr/grasp/ (Genisphere Array 50 Protocol).

scan_protocol: The transcript levels inferred from fluorescent labels were quantified by scanning microarrays using a ScanArray Express scanner (Packard Bioscience).

data_processing: Aberrant spot signals were removed before analysis and their values were estimated using the “K-Nearest Neighbors Imputer” function implemented in SAM software (Tusher et al 2001). Genes with intensity less than the mean of the empty spot controls plus 2.5 times their standard deviation were removed from the analysis. According to this criterion, 2,255 among the 16,006 transcripts passed this threshold and were considered for subsequent analyses. After correcting for local background, raw intensity values were both log2 transformed and normalized using the regional LOWESS method implemented in the R/MANOVA software (Kerr et al. 2000), available at: http://www.jax.org/staff/churchill/labsite/software/Rmaanova.

label: Alexa 647

organism: Coregonus clupeaformis

source_name: white muscle tissue

label_protocol: Reverse transcriptase PCR was performed using 15 μg of total RNA per sample following the SuperScriptä II Reverse Transcriptase protocol (Invitrogen life technologies). Indirect labeling was performed on individual cDNA following the Array 50 kit protocol (Genisphere).

extract_protocol: Dissected white muscle tissue (250-350 mg) was sampled for 65 individuals from the hybrid x dwarf backcross mapping family, and stored at - 80°C until RNA extraction. RNA was extracted according to the Trizol Reagent protocol (Gibco BRL) and quantified with a GeneQuant spectrometer (Pharmacia), and RNA integrity was verified with a 2100 Bioanalyzer (Agilent).

tag: hybrid 499

tag: female


title: white muscle tissue individu 499cy


title: Tetrahymena_L2-m


title: white muscle tissue individu 496cy

tag: hybrid 496


title: Rat diaphragm ctrl rep2


title: white muscle tissue individu 496al


title: Tetrahymena_L1-l

source_name: growing CU428 cells at low cell densities (~100,000 cells/ml)

tag: growing CU428 cells at low cell densities (100,000 cells/ml)


title: white muscle tissue individu 333cy

tag: hybrid 333


title: white muscle tissue individu 333al


title: Rat diaphragm  ctrl rep1

source_name: diaphragm muscle


title: Tetrahymena_L2-l


title: Rat diaphragm exp rep1


title: white muscle tissue individu 496_2al


title: white muscle tissue individu 496_2cy


title: white muscle tissue individu 494cy

tag: hybrid 494


title: white muscle tissue individu 487cy

tag: hybrid 487

tag: male


title: white muscle tissue individu 494al


title: white muscle tissue individu 493cy

tag: hybrid 493


title: white muscle tissue individu 492al

tag: hybrid 492


title: white muscle tissue individu 493al


title: white muscle tissue individu 492cy


title: white muscle tissue individu 482cy

tag: hybrid 482


title: white muscle tissue individu 480cy

tag: hybrid 480


title: white muscle tissue individu 482al


title: white muscle tissue individu 479cy

tag: hybrid 479


title: white muscle tissue individu 480al


title: white muscle tissue individu 487al


title: white muscle tissue individu 485cy

tag: hybrid 485


title: white muscle tissue individu 485al


title: white muscle tissue individu 478al

tag: hybrid 478


title: white muscle tissue individu 478cy


title: white muscle tissue individu 479al


title: white muscle tissue individu 477cy

tag: hybrid 477


title: white muscle tissue individu 473al

tag: hybrid 473


title: white muscle tissue individu 477al


title: white muscle tissue individu 472cy

tag: hybrid 472


title: white muscle tissue individu 472al

tag: female


title: white muscle tissue individu 471cy

tag: hybrid 471


title: white muscle tissue individu 473cy


title: white muscle tissue individu 471al


title: white muscle tissue individu 470cy

tag: hybrid 470


title: white muscle tissue individu 470al


title: white muscle tissue individu 468al

tag: hybrid 468


title: white muscle tissue individu 466al

tag: hybrid 466


title: white muscle tissue individu 468cy


title: white muscle tissue individu 466cy


title: white muscle tissue individu 462cy

tag: hybrid 462


title: white muscle tissue individu 462al


title: white muscle tissue individu 460cy

tag: hybrid 460


title: white muscle tissue individu 460al


title: white muscle tissue individu 459cy

tag: hybrid 459


title: white muscle tissue individu 459al


title: white muscle tissue individu 449cy

tag: hybrid 449

tag: male


title: white muscle tissue individu 446al

tag: hybrid 446


title: white muscle tissue individu 446cy


title: white muscle tissue individu 449al


title: white muscle tissue individu 444al

tag: hybrid 444


title: white muscle tissue individu 445al

tag: hybrid 445


title: white muscle tissue individu 444cy


title: white muscle tissue individu 434cy

tag: hybrid 434


title: white muscle tissue individu 443cy

tag: hybrid 443


title: white muscle tissue individu 439al

tag: hybrid 439


title: white muscle tissue individu 445cy


title: white muscle tissue individu 439cy


title: white muscle tissue individu 443al


title: white muscle tissue individu 436al

tag: hybrid 436


title: white muscle tissue individu 437al

tag: hyrid 437

tag: female


title: white muscle tissue individu 436cy


title: white muscle tissue individu 435cy


title: white muscle tissue individu 433cy

tag: hybrid 433


title: white muscle tissue individu 434al


title: white muscle tissue individu 435al

tag: hybrid 435


title: white muscle tissue individu 438cy

tag: hybrid 438


title: white muscle tissue individu 437cy

tag: hybrid 437


title: white muscle tissue individu 438al


title: white muscle tissue individu 433al


title: white muscle tissue individu 428cy

tag: hybrid 428


title: white muscle tissue individu 428al


title: white muscle tissue individu 429al

tag: hybrid 429


title: white muscle tissue individu 425al

tag: hybrid 425


title: white muscle tissue individu 429cy

tag: male


title: white muscle tissue individu 422cy

tag: hybrid 422


title: white muscle tissue individu 419cy

tag: hybrid 419


title: white muscle tissue individu 422al


title: white muscle tissue individu 425cy


title: white muscle tissue individu 419al


title: white muscle tissue individu 415al

tag: hybrid 415


title: white muscle tissue individu 415cy


title: white muscle tissue individu 413al

tag: hybrid 413


title: white muscle tissue individu 413cy


title: white muscle tissue individu 407cy

tag: hybrid 407


title: white muscle tissue individu 411al

tag: hybrid 411


title: white muscle tissue individu 408al

tag: hybrid 408


title: white muscle tissue individu 397cy

tag: hybrid 397


title: white muscle tissue individu 407al

tag: female


title: white muscle tissue individu 411cy


title: white muscle tissue individu 397al


title: white muscle tissue individu 387cy

tag: hybrid 387


title: white muscle tissue individu 418cy

tag: hybrid 418


title: white muscle tissue individu 418al


title: white muscle tissue individu 408cy


title: white muscle tissue individu 387al


title: white muscle tissue individu 417cy

tag: hybrid 417


title: white muscle tissue individu 391cy

tag: hybrid 391


title: white muscle tissue individu 391al


title: white muscle tissue individu 392cy

tag: hybrid 392


title: white muscle tissue individu 392al


title: white muscle tissue individu 396cy

tag: hybrid 396


title: white muscle tissue individu 396al


title: white muscle tissue individu 385cy

tag: hybrid 385


title: white muscle tissue individu 417al

tag: male


title: white muscle tissue individu 380al

tag: hybrid 380


title: white muscle tissue individu 381cy

tag: hybrid 381


title: white muscle tissue individu 381al


title: white muscle tissue individu 380cy


title: white muscle tissue individu 367cy

tag: hybrid 367


title: white muscle tissue individu 379cy

tag: hybrid 379


title: white muscle tissue individu 377al

tag: hybrid 377


title: white muscle tissue individu 385al


title: white muscle tissue individu 377cy


title: white muscle tissue individu 350cy

tag: hybrid 350


title: white muscle tissue individu 367al


title: white muscle tissue individu 352al

tag: hybrid 352


title: white muscle tissue individu 350al


title: white muscle tissue individu 382al

tag: hybrid 382


title: white muscle tissue individu 343al

tag: hybrid 343

tag: female


title: white muscle tissue individu 341al

tag: hybrid 341


title: white muscle tissue individu 343cy


title: white muscle tissue individu 379al


title: white muscle tissue individu 382cy


title: white muscle tissue individu 341cy


title: white muscle tissue individu 352cy


title: white muscle tissue individu 319al

tag: hybrid 319


title: white muscle tissue individu 319cy


title: white muscle tissue individu 324al

tag: hybrid 324


title: white muscle tissue individu 324cy


title: white muscle tissue individu 328al

tag: hybrid 328


title: white muscle tissue individu 328cy

tag: hybrid 328cy


title: white muscle tissue individu 314al

tag: hybrid 314


title: white muscle tissue individu 314cy

tag: male


title: white muscle tissue individu 303cy

tag: hybrid 303


title: white muscle tissue individu 303al


title: white muscle tissue individu 293al

tag: hybrid 293

tag: Female


title: white muscle tissue individu 293cy


title: white muscle tissue individu 266cy

tag: hybrid 266


title: white muscle tissue individu 266al


title: white muscle tissue individu 268cy

tag: hybrid 268


title: white muscle tissue individu 313 al

tag: Hybrid 313


title: white muscle tissue individu 257al

tag: hybrid 257


title: white muscle tissue individu 268al


title: white muscle tissue individu 288cy

tag: hybrid 288


title: white muscle tissue individu 313 cy

tag: hybrid 313


title: white muscle tissue hybrid 253

tag: hybrid 253

tag: female


title: white muscle tissue individu 253cy


title: white muscle tissue hybrid 251cy

tag: hybrid 251


title: white muscle tissue hybrid 251

tag: Hybrid  251


title: white muscle tissue individu 254al

tag: Hybrid 254


title: white muscle tissue individu 257cy


title: white muscle tissue individu 254cy

tag: hybrid 254


title: white muscle tissue individu 288al


title: 176632 - L. lactis ΔlmrCD and cholate-adapted L. lactis ΔlmrCDR

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

hyb_protocol: Hybridization (16 h at 45 °C) of labeled cDNA was performed in Ambion Slidehyb #1 hybridization buffer (Ambion Europe) on superamine glass slides (Array-It; SMMBC), containing technical replicates.

scan_protocol: Slides were scanned using the Genepix 4200AL DNA micro array slide scanner. Quantification of the signal of the spots on slides was done with ArrayPro 4.5.

data_processing: Slide data were processed and normalized using MicroPreP, and CyberT implementation of the Student's t test (PMID: 15130795).

organism: Lactococcus lactis

source_name: WT4 L. lactis ΔlmrCD (labeled with Cy3)

label_protocol: Synthesis of cDNA and indirect Cy-3/Cy-5-dCTPs labeling of 15–20 µg of total RNA was performed with the CyScribe Post labeling kit (Amersham Biosciences) according to the supplier's instructions.

extract_protocol: RNA was isolated from two replicate cultures of both L. lactis ΔlmrCD and cholate-adapted L. lactis ΔlmrCDR. Cultures were grown at 30 ºC in GM17 medium and cells were harvested at the OD660 of ~ 1.RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (PMID: 17085554). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). Synthesis, subsequent labeling of cDNA, and microarray hybridization was performed as described (PMID: 17085554 and 15907200). In all cases, dye-swapping was performed.

tag: WT4 L. lactis ΔlmrCD (labeled with Cy3)

source_name: M4 L. lactis ΔlmrCD(R) (labeled with Cy5)


title: Abcb4_9weeks_UDCA_4

status: Public on Aug 20 2008

city: Oslo

first: Esten

last: Nakken

address: Kirkeveien 166

department: Ulleval university Hospital

country: Norway

institute: Institute for Experimental Medical Research

description: For feature finding, identification and quality control the Feature Extraction Software (Version 9.5.3) from Agilent was used.

hyb_protocol: All samples were hybridized according to the Agilent’s protocol. Agilent’s Whole Mouse Genome Microarray Kit, 4 x 44K (G4122F)

scan_protocol: Scanning was performed on a GenePix 4000B microarray scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: As measures of spot intensities we used the median of the foreground pixel intensities. To retain spots with more than half of the pixels in saturation, additional lower scans were made and saturated intensities modified. Differential transcription, measured as ratio in transcription between knockout and control, was estimated for each gene fitting a log-linear mixed effect model according to Kerr [10], including parameters for dye, array and gene, together with the gene-specific effects on dye, array and mouse type (knockout/control). The latter effect is the parameter of main concern as it represents the knockout effect on gene transcription for each gene (measured in log2 scale). Parameter estimates were obtained using the MicroArray ANOVA (MAANOVA) package by Wu et al. for the statistical language R. A threshold of significance of at least two-fold change together with a p<0.01 was chosen.

organism: Mus musculus

source_name: Abcb4 (-/-) UDCA 9 weeks

extract_protocol: After sacrifice, livers were excised and divided in two parts; one part snap-frozen in liquid nitrogen for RNA isolation and one part in formalin for histology. RNA was isolated using the RNeasy mini Kit (Qiagen, Valencia, Ca, USA). The quantity of RNA was measured on a nano-drop spectrophotometer and the quality checked on an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, Ca, USA).

tag: FVB.129P2-Abcb4tm1Bor/J. Abcb4 (-/-) mouse liver UDCA feeding 9 weeks

source_name: Abcb4 (+/+) liver

tag: FVB/NJ mouse liver 9 weeks (wild type)


title: 176631 - L. lactis ΔlmrCD and cholate-adapted L. lactis ΔlmrCDR

source_name: WT1 L. lactis ΔlmrCD (labeled with Cy3)

tag: WT1 L. lactis ΔlmrCD (labeled with Cy3)

source_name: M1 L. lactis ΔlmrCD(R) (labeled with Cy5)


title: 176633 - L. lactis ΔlmrCD and cholate-adapted L. lactis ΔlmrCDR

source_name: WT2 L. lactis ΔlmrCD (labeled with Cy5)

tag: WT2 L. lactis ΔlmrCD (labeled with Cy5)

source_name: M5 L. lactis ΔlmrCD(R) (labeled with Cy3)


title: Abcb4_9weeks_UDCA_5

label_protocol: All samples were hybridized according to the Agilent’s protocol. Agilent’s Whole Mouse Genome Microarray Kit, 4 x 44K (G4122F)


title: 176634 - L. lactis ΔlmrCD and cholate-adapted L. lactis ΔlmrCDR

source_name: WT5 L. lactis ΔlmrCD (labeled with Cy5)

tag: WT5 L. lactis ΔlmrCD (labeled with Cy5)

source_name: M2 L. lactis ΔlmrCD(R)(labeled with Cy3)


title: Abcb4_9weeks_CA_6

source_name: Abcb4 (-/-) CA 9 weeks

tag: FVB.129P2-Abcb4tm1Bor/J. Abcb4 (-/-) mouse liver CA feeding 9 weeks


title: Abcb4_9weeks_CA_2


title: Abcb4_9weeks_CA_3


title: Abcb4_9weeks_UDCA_3


title: Abcb4_9weeks_UDCA_1


title: Abcb4_9weeks_CA_5


title: Abcb4_9weeks_UDCA_6


title: Abcb4_9weeks_CA_4


title: Abcb4_9weeks_CA_1

treatment_protocol: Cholic acid feeding


title: C-lim anaerobic 500 mM lactic acid (pH 3) #3

status: Public on Jul 30 2008

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

hyb_protocol: According to manufacturer's procedures

scan_protocol: Data acquisition was performed using the Affymetrix scanner 3000, quantification of array images and data filtering were performed with the Affymetrix software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0.

data_processing: Chip file GCOS (Affymetrix - version 1.2.0.037)

label: SAPE

source_name: Chemostat sample

label_protocol:
Sampling of chemostat cultures, probe preparation and hybridization to Affymetrix GeneChip microarrays was performed as described previously (Piper et al., 2002), but with the following modifications.  Double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix).  The double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix).  Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA.
Piper MDW, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J & Pronk JT (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277: 37001-37008.

growth_protocol:
The laboratory reference strain CEN.PK 113-7D (MATa) was grown at 30 °C in 1.5-L chemostat fermentors (Applikon, Schiedam, The Netherlands) with a working volume of 1-L using an electronic level sensor to maintain a constant volume.  All cultures, including the reference, were fed with minimal medium as described by Verduyn et al. (1992) with 25 g L-1 glucose as the limiting nutrient and 0.15 ml L-1 silicone antifoam (BDH, Poole, England) to prevent excessive foaming.  The dilution rate was set to 0.10 h-1 and the pH was controlled at 3.0 with the automatic addition (ADI 1031 bio controller, Applikon) of 2 M KOH.  The stirrer speed was set at 800 RPM and anaerobicity was maintained by sparging the fermentor with N2 gas at 500 ml min-1.  To prevent diffusion of oxygen, the fermentor was equipped with Norprene tubing and Viton O-rings and the medium vessel was also flushed with N2 gas.
Verduyn C, Postma E, Scheffers WA & van Dijken JP (1992) Effect of benzoic acid on metabolic fluxes in yeast: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-517.

extract_protocol:
Sampling of chemostat cultures and probe preparation was performed as described previously (Piper et al., 2002), but quenching was performed in ice-cold TRIS-EDTA rather than liquid nitrogen. Cultures were quenched in ice-cold TRIS-EDTA (TE) buffer at pH 8 (5 times the volume of sample (5x volume)), then washed in ice-cold TE buffer (2x volume) followed by ice-cold demi-water (2x volume).
Piper MDW, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J & Pronk JT (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277: 37001-37008.

treatment_protocol: Quenching in ice-cold TRIS-EDTA (pH 8)

tag: Saccharomyces cerevisiae CEN.PK 113-7D (MATa)


title: C-lim anaerobic 900 mM lactic acid (pH 5) #2

extract_protocol:
Sampling of chemostat cultures and probe preparation was performed as described previously (Piper et al., 2002).
Piper MDW, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J & Pronk JT (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277: 37001-37008.

treatment_protocol: Quenching in liquid nitrogen


title: C-lim anaerobic 500 mM lactic acid (pH 3) #2


title: C-lim anaerobic reference (pH 3) #2

description: C-lim anaerobic reference (pH 3) #2


title: C-lim anaerobic 900 mM lactic acid (pH 5) #3


title: Abcb4_9weeks_UDCA_2


title: C-lim anaerobic 500 mM lactic acid (pH 3) #1


title: C-lim anaerobic reference (pH 3) #3

description: C-lim anaerobic reference (pH 3) #3


title: C-lim anaerobic reference (pH 3) #1

description: C-lim anaerobic reference (pH 3) #1


title: C-lim anaerobic 900 mM lactic acid (pH 5) #1


title: TotalRNA_60min_U0126_B

status: Public on Jul 01 2008

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

description: RNA mapping with total RNA, FGF 60 min + U0126, Affymetrix Mouse Tiling 2.0R B array

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Bar files were created using Affymetrix Tiling SDK release2 (BPMAP = NCBIv35, Quantile normalization, Bandwidth = 250, Signal scale = log2).

source_name: FGF 60 min + U0126

label_protocol: Standard Affymetrix protocol (WT double stranded DNA terminal labeling)

growth_protocol: NIH3T3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% calf serum.

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit according to the manufacturer’s protocol. The rest of the protocols were adopted from Affymetrix WT double-stranded target assay manual (SuperScript III RT at 50 °C instead of SuperScript II RT at 42°C).

treatment_protocol: Serum starvation 36 h, 50 ng/ml FGF 60 min + 20 mM U0126

tag: NIH3T3 cell


title: TotalRNA_0min_DMSO_B

description: RNA mapping with total RNA, 0 min + DMSO, Affymetrix Mouse Tiling 2.0R B array

source_name: 0 min + DMSO

treatment_protocol: Serum starvation 36 h, 0 min + control DMSO


title: TotalRNA_60min_DMSO_B

description: RNA mapping with total RNA, FGF 60 min + DMSO, Affymetrix Mouse Tiling 2.0R B array

source_name: FGF 60 min + DMSO

treatment_protocol: Serum starvation 36 h, 50 ng/ml FGF 60 min + control DMSO


title: Exercised rat 10

status: Public on Jul 15 2008

city: Florence

first: Betti

last: Giusti

address: viale Morgagni, 85

department: Dpt. of Medical and Surgical Critical Care

country: Italy

institute: University of Florence

description: Gene expression data from left ventricle of exercise-trained rat

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Bioconductor Packages.

source_name: Left ventricle of exercise-trained rat

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

growth_protocol: We used 20 male Sprague–Dawley-CD rats (8 weeks old, 360±15 g body weight at the beginning of the study), randomly divided into two groups: sedentary- controls and exercise-trained animals. During the experimental period, all animals had free access to water and conventional laboratory diet (Standard diet n.48, Laboratorio Dottori Piccioni,Gessate, Milan, Italy) until sacrifice. Room temperature was kept at 21 ± 2°C and 12 h of light were automatically alternated to 12 h of dark.

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

tag: Sprague-Dawley-CD rat (8 weeks old, 360±15 g body weight at the beginning of the study)


title: NuclearRNA_60min_B

description: RNA mapping with nuclear RNA, FGF 60 min, Affymetrix Mouse Tiling 2.0R B array

molecule: nuclear RNA

source_name: FGF 60 min

extract_protocol: Nuclear RNA was isolated from buffer RLN-lysed pellet using a Qiagen RNeasy kit (see Qiagen's supplementary protocol). On-column DNase digestion. The rest of the protocols were adopted from Affymetrix WT double-stranded target assay manual (SuperScript III RT at 50 °C instead of SuperScript II RT at 42°C).

treatment_protocol: Serum starvation 36 h, 50 ng/ml FGF 60 min


title: Exercised rat 9


title: NuclearRNA_20min_B

description: RNA mapping with nuclear RNA, FGF 20 min, Affymetrix Mouse Tiling 2.0R B array

source_name: FGF 20 min

treatment_protocol: Serum starvation 36 h, 50 ng/ml FGF 20 min


title: Exercised rat 1


title: Exercised rat 4


title: Exercised rat 5


title: Sedentary rat 7

description: Gene expression data from left ventricle of sedentary rat

source_name: Left ventricle of sedentary rat


title: Exercised rat 6


title: Sedentary rat 6


title: Exercised rat 8


title: Exercised rat 2


title: Sedentary rat 8


title: Exercised rat 3


title: Sedentary rat 9


title: Sedentary rat 1


title: Exercised rat 7


title: Sedentary rat 10


title: NuclearRNA_0min_B

description: RNA mapping with nuclear RNA, 0 min, Affymetrix Mouse Tiling 2.0R B array

source_name: 0 min

treatment_protocol: Serum starvation 36 h, 0 min


title: TotalRNA_60min_U0126_G

description: RNA mapping with total RNA, FGF 60 min + U0126, Affymetrix Mouse Tiling 2.0R G array


title: Sedentary rat 3


title: Sedentary rat 5


title: SRFChIP_IP

description: ChIP-chip with anti-SRF antibody, IP'd sample, Affymetrix Mouse Promoter 1.0R array

source_name: IP'd sample

extract_protocol: Chromatin immunoprecipitation was performed using an anti-SRF antibody (Santa cruz G-20) and a ChIP-IT Express Enzymatic kit (Active motif) according to the manufacture’s protocol. The immunoprecipitated DNA was amplified by in vitro transcription.

treatment_protocol: Random culture


title: TotalRNA_60min_DMSO_G

description: RNA mapping with total RNA, FGF 60 min + DMSO, Affymetrix Mouse Tiling 2.0R G array


title: NuclearRNA_60min_G

description: RNA mapping with nuclear RNA, FGF 60 min, Affymetrix Mouse Tiling 2.0R G array


title: TotalRNA_0min_DMSO_G

description: RNA mapping with total RNA, 0 min + DMSO, Affymetrix Mouse Tiling 2.0R G array


title: SRFChIP_Input

description: ChIP-chip with anti-SRF antibody, Input sample, Affymetrix Mouse Promoter 1.0R array

source_name: Input sample

extract_protocol: Chromatin immunoprecipitation was performed using a ChIP-IT Express Enzymatic kit (Active motif) according to the manufacture’s protocol. The input DNA was amplified by in vitro transcription.


title: NuclearRNA_20min_G

description: RNA mapping with nuclear RNA, FGF 20 min, Affymetrix Mouse Tiling 2.0R G array


title: NuclearRNA_0min_G

description: RNA mapping with nuclear RNA, 0 min, Affymetrix Mouse Tiling 2.0R G array


title: TotalRNA_60min_U0126_F

description: RNA mapping with total RNA, FGF 60 min + U0126, Affymetrix Mouse Tiling 2.0R F array


title: TotalRNA_0min_DMSO_F

description: RNA mapping with total RNA, 0 min + DMSO, Affymetrix Mouse Tiling 2.0R F array


title: Sedentary rat 2


title: TotalRNA_60min_U0126_A

description: RNA mapping with total RNA, FGF 60 min + U0126, Affymetrix Mouse Tiling 2.0R A array


title: TotalRNA_60min_DMSO_F

description: RNA mapping with total RNA, FGF 60 min + DMSO, Affymetrix Mouse Tiling 2.0R F array


title: TotalRNA_60min_DMSO_A

description: RNA mapping with total RNA, FGF 60 min + DMSO, Affymetrix Mouse Tiling 2.0R A array


title: NuclearRNA_60min_A

description: RNA mapping with nuclear RNA, FGF 60 min, Affymetrix Mouse Tiling 2.0R A array


title: NuclearRNA_20min_F

description: RNA mapping with nuclear RNA, FGF 20 min, Affymetrix Mouse Tiling 2.0R F array


title: TotalRNA_0min_DMSO_A

description: RNA mapping with total RNA, 0 min + DMSO, Affymetrix Mouse Tiling 2.0R A array


title: NuclearRNA_0min_A

description: RNA mapping with nuclear RNA, 0 min, Affymetrix Mouse Tiling 2.0R A array


title: rge1-1 vs Col-0, rep2

city: Yokohama

first: Minami

last: Matsui

address: Suyehirocho 1-7-22 , Tsurumiku

department: Plant Science Center

institute: RIKEN

description: Comparison of gene expression between retarded growth of embryo mutant (rge1-1) and wild-type plants (Col-0).

hyb_protocol: Agilent Arabidopsis2 oligo microarray hybridization protocol

scan_protocol: Dual-laser Microarray scanner Agilent Technologies, 5µm resolution, 50% PMT

data_processing: Spot intensities on the DNA microarray were quantified by Feature Extraction Software ver.7.1.1 (Agilent Technologies) with default parameters.

organism: Arabidopsis thaliana

source_name: rge1-1 silique

label_protocol: One micro-gram of total RNA was fluorescently labeled using a Low Input RNA Fluorescent Linear Amplification Kit (Agilent Technologies).

growth_protocol: Plants were grown at 22°C in a cultivation container system (ARACON) in long-day conditions (16 hr light and 8 hr dark) under white fluorescent tubes (FL40SW, Sanyo, Osaka, Japan).

extract_protocol: RNAqueous Kit (Ambion, Inc, USA)

treatment_protocol: No treatment

tag: Siliques at 12 days after flowering (DAF)

source_name: Col-0 silique


title: NuclearRNA_20min_A

description: RNA mapping with nuclear RNA, FGF 20 min, Affymetrix Mouse Tiling 2.0R A array


title: NuclearRNA_0min_F

description: RNA mapping with nuclear RNA, 0 min, Affymetrix Mouse Tiling 2.0R F array


title: TotalRNA_60min_U0126_E

description: RNA mapping with total RNA, FGF 60 min + U0126, Affymetrix Mouse Tiling 2.0R E array


title: TotalRNA_240min_E

description: RNA mapping with total RNA, FGF 240 min, Affymetrix Mouse Tiling 2.0R E array

source_name: FGF 240 min

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit according to the manufacturer’s protocol. On-column DNase digestion. The rest of the protocols were adopted from Affymetrix WT double-stranded target assay manual (SuperScript III RT at 50 °C instead of SuperScript II RT at 42°C).

treatment_protocol: Serum starvation 36 h, 50 ng/ml FGF 240 min


title: TotalRNA_0min_DMSO_E

description: RNA mapping with total RNA, 0 min + DMSO, Affymetrix Mouse Tiling 2.0R E array


title: TotalRNA_60min_DMSO_E

description: RNA mapping with total RNA, FGF 60 min + DMSO, Affymetrix Mouse Tiling 2.0R E array


title: TotalRNA_20min_E

description: RNA mapping with total RNA, FGF 20 min, Affymetrix Mouse Tiling 2.0R E array


title: TotalRNA_120min_E

description: RNA mapping with total RNA, FGF 120 min, Affymetrix Mouse Tiling 2.0R E array

source_name: FGF 120 min

treatment_protocol: Serum starvation 36 h, 50 ng/ml FGF 120 min


title: H3AcChIP_60min_C

description: ChIP-chip with anti-acetylated histone H3 antibody, FGF 60min, Affymetrix Mouse Tiling 2.0R C array

extract_protocol: Chromatin immunoprecipitation was performed using anti-acetylated histone H3 antibody (Upstate 06-599). The immunoprecipitated DNA was amplified by in vitro transcription.


title: TotalRNA_60min_E

description: RNA mapping with total RNA, FGF 60 min, Affymetrix Mouse Tiling 2.0R E array


title: H3AcChIP_10min_C

description: ChIP-chip with anti-acetylated histone H3 antibody, FGF 10min, Affymetrix Mouse Tiling 2.0R C array

source_name: FGF 10 min

treatment_protocol: Serum starvation 36 h, 50 ng/ml FGF 10 min


title: rge1-1 vs Col-0, rep1


title: TotalRNA_0min_E

description: RNA mapping with total RNA, 0 min, Affymetrix Mouse Tiling 2.0R E array


title: H3AcChIP_0min_C

description: ChIP-chip with anti-acetylated histone H3 antibody, 0min, Affymetrix Mouse Tiling 2.0R C array


title: TotalRNA_0min_DMSO_C

description: RNA mapping with total RNA, 0 min + DMSO, Affymetrix Mouse Tiling 2.0R C array


title: TotalRNA_10min_E

description: RNA mapping with total RNA, FGF 10 min, Affymetrix Mouse Tiling 2.0R E array


title: TotalRNA_60min_U0126_C

description: RNA mapping with total RNA, FGF 60 min + U0126, Affymetrix Mouse Tiling 2.0R C array


title: NuclearRNA_60min_E

description: RNA mapping with nuclear RNA, FGF 60 min, Affymetrix Mouse Tiling 2.0R E array


title: TotalRNA_60min_DMSO_C

description: RNA mapping with total RNA, FGF 60 min + DMSO, Affymetrix Mouse Tiling 2.0R C array


title: NuclearRNA_20min_E

description: RNA mapping with nuclear RNA, FGF 20 min, Affymetrix Mouse Tiling 2.0R E array


title: TotalRNA_60min_U0126_D

description: RNA mapping with total RNA, FGF 60 min + U0126, Affymetrix Mouse Tiling 2.0R D array


title: NuclearRNA_60min_F

description: RNA mapping with nuclear RNA, FGF 60 min, Affymetrix Mouse Tiling 2.0R F array


title: NuclearRNA_0min_E

description: RNA mapping with nuclear RNA, 0 min, Affymetrix Mouse Tiling 2.0R E array


title: TotalRNA_120min_C

description: RNA mapping with total RNA, FGF 120 min, Affymetrix Mouse Tiling 2.0R C array


title: TotalRNA_240min_C

description: RNA mapping with total RNA, FGF 240 min, Affymetrix Mouse Tiling 2.0R C array


title: TotalRNA_60min_C

description: RNA mapping with total RNA, FGF 60 min, Affymetrix Mouse Tiling 2.0R C array


title: TotalRNA_60min_DMSO_D

description: RNA mapping with total RNA, FGF 60 min + DMSO, Affymetrix Mouse Tiling 2.0R D array


title: TotalRNA_0min_DMSO_D

description: RNA mapping with total RNA, 0 min + DMSO, Affymetrix Mouse Tiling 2.0R D array


title: TotalRNA_10min_C

description: RNA mapping with total RNA, FGF 10 min, Affymetrix Mouse Tiling 2.0R C array


title: NuclearRNA_60min_D

description: RNA mapping with nuclear RNA, FGF 60 min, Affymetrix Mouse Tiling 2.0R D array


title: NuclearRNA_20min_D

description: RNA mapping with nuclear RNA, FGF 20 min, Affymetrix Mouse Tiling 2.0R D array


title: TotalRNA_0min_C

description: RNA mapping with total RNA, 0 min, Affymetrix Mouse Tiling 2.0R C array


title: NuclearRNA_60min_C

description: RNA mapping with nuclear RNA, FGF 60 min, Affymetrix Mouse Tiling 2.0R C array


title: NuclearRNA_0min_C

description: RNA mapping with nuclear RNA, 0 min, Affymetrix Mouse Tiling 2.0R C array


title: TotalRNA_20min_C

description: RNA mapping with total RNA, FGF 20 min, Affymetrix Mouse Tiling 2.0R C array


title: NuclearRNA_0min_D

description: RNA mapping with nuclear RNA, 0 min, Affymetrix Mouse Tiling 2.0R D array


title: NuclearRNA_20min_C

description: RNA mapping with nuclear RNA, FGF 20 min, Affymetrix Mouse Tiling 2.0R C array