title: STT2679-LMS-HG-UT-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52677.gif

value: time(change) 48 years

value: No

value: UT


title: STT4417-LMS-f-pleomorphic-HG-ST-P-tRNA

status: Public on Nov 12 2009

type: RNA

city: Stanford

first: Andrew

last: Beck

state: CA

address: Stanford

country: USA

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/55943.gif

hyb_protocol: not provided

scan_protocol: Agilent G2505B scanner

data_processing: VALUE is Log ratio Cy5/Cy3

molecule: total RNA

organism: Homo sapiens

source_name: Universal human reference

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Universal human reference

tag: simple annotation

value: Primary tumor, tumor tissue

tag: phenotype

value: Pleomorphic

tag: measurement

value: time(change) 72 years

tag: individual

tag: compound based treatment

tag: organism part

value: ST - right upper leg

tag: disease state

value: P

tag: sex/mating type

value: F

tag: experiment type

value: Expression


title: STT4445-LMS-f-HG-ST-M-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53440.gif

value: time(change) 52* years

value: ST - left thigh

value: M


title: STT4407-LMS-m-pleomorphic-HG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52134.gif

value: time(change) 52 years

value: ST - right lower arm


title: Human_line1_1

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description: SY5Y cells overexpressing FOXP2 human

hyb_protocol: Manufacturer's instructions

scan_protocol: Manufacturer's instructions

data_processing: Quantile normalization; please see associated published manuscript

label: biotin

source_name: SY5Y cells, line 1, FOXP2 human 1

label_protocol: Manufacturer's instructions

extract_protocol: Qiagen RNeasy kit

tag: cell line


title: STT4415-LMS-m-IG-Epididymis-M-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54532.gif

value: Conventional

value: time(change) 57 years

value: ST - Epididymis


title: STT4411-LMS-f-IG-ST-P(same pt as 4412)-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54474.gif

value: time(change) 48 years

value: No

value: ST - retroperitoneum


title: STT4409-LMS-f-HG-ST-R1(same pt as 4408)-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53443.gif

value: Universal human reference

value: Primary tumor, tumor tissue

value: Pleomorphic

value: time(change) 55 years

value: ST - Retrocoecal tumor


title: Control_line7_4

description: SY5Y cells overexpressing empty vector

source_name: SY5Y cells, line 7, control 4


title: STT4427-LMS-m-myxoid-HG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56489.gif

value: Pleomorphic/Conventional

value: ST - chest wall

value: P

value: Expression


title: Human_line6_1

description: SY5Y cells overexpressing FOXP2 human

source_name: SY5Y cells, line 6, FOXP2 human 1


title: STT4398-LMS-m-IG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56485.gif

value: time(change) 45 years

value: ST - right upper leg

value: M


title: Control_line7_1

description: SY5Y cells overexpressing empty vector

source_name: SY5Y cells, line 7, control 1


title: Control_line7_2

description: SY5Y cells overexpressing empty vector

source_name: SY5Y cells, line 7, control 2


title: Control_line6_2

description: SY5Y cells overexpressing empty vector

source_name: SY5Y cells, line 6, control 2


title: Control_line6_4

description: SY5Y cells overexpressing empty vector

source_name: SY5Y cells, line 6, control 4


title: Control_line7_3

description: SY5Y cells overexpressing empty vector

source_name: SY5Y cells, line 7, control 3


title: Heart(non risk area)_myocardial infarction_24hour_rep1

city: Kanazawa

first: Hiroshi

last: Ootsuji

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Disease Control and Homeostasis

country: Japan

institute: Kanazawa University Graduate School of Medical Science

description: Liver or heart samples were amplified individually without mixing. As a reference for hybridization, we used mixed RNA samples from the sham group at various time-points. Test and reference samples were labeled with fluorescent Cy5 and Cy3, respectively, mixed, and hybridized on a microarray. Supplementary txt file: our nomalized values are in column AI. But, if signal intensity of Cy3 or Cy5 is less than 100, the column AI is blank. In this situation, normalized values is in column AL or AO.

hyb_protocol: Incubate at 50°C for 20 hour in a humid chamber.

scan_protocol: The microarrays were then scanned using ScanArray GX (PerkinElmer, Wellesley, MA) and signal values were calculated using GenePix Pro 4.0 software (Axon Instruments, Union City, CA). Image output files were examined visually for major defects and hybridization artifacts.

data_processing: The signal intensity of each spot was corrected by subtracting adjacent background signals. To normalize the data, we averaged the intensities of all spots obtained with Cy3 and Cy5 in each of the 48 rectangles, and adjusted the intensity of each corrected DNA spot by the average intensity ratio of Cy5:Cy3 (equal to 1.0). This global normalization of intensity provided a smaller variance of the Cy5:Cy3 ratio and results similar to those obtained via normalization using housekeeping genes.

organism: Mus musculus

source_name: Heart(non risk area),myocardial infarction,24hour

label_protocol: Dissolve aRNA sample in 5μl of 0.2M Sodium bicarbonate buffer(pH9.0). Add 5μl of CyDye (dissolved in 45μl of DMSO/vial ;Amersham Bioscience) to sample. Mix well  by vortex. Incubate for 1hour at 40°C keep in dark.

extract_protocol: Total RNA was extracted individually using the RNeasy Mini Kit for liver tissue and RNeasy Fibrous Tissue Mini Kit for myocardium (QIAGEN, Chatsworth, CA), according to the manufacturer’s protocol. RNA was analyzed to determine if it met the minimum purity and integrity standards for total RNA quality (i.e., OD 260/280>1.8, OD 260/230>2.0, and minimal degradation as determined using a NanoDrop 1000A spectrophotometer; NanoDrop Technologies, Wilmington, DE). The quality and degradation of the isolated RNA were estimated after electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Heart or liver samples were pooled in each group at the indicated time-points and amplified using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, Austin, TX), as recommended by the manufacturer.

tag: strain

tag: gender

value: male

tag: age

tag: tissue

value: heart

source_name: Heart,sham operation,24hour


title: Heart(non risk area)_myocardial ischemia-reperfusion_24hour_rep1

source_name: Heart(non risk area),myocardial ischemia-reperfusion,24hour


title: Heart(risk area)_myocardial infarction_24hour_rep1


title: Heart(risk area)_myocardial ischemia-reperfusion_24hour_rep1


title: Heart(risk area)_myocardial ischemia-reperfusion_6hour_rep1

source_name: Heart,sham operation,6hour


title: STT4431-LMS-f-IG-ST-R1(same pt as 4430)-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57175.gif

value: Conventional

value: time(change) 58 years

value: CT+RT

value: ST - right upper arm

value: F


title: Liver_hepatic ischemia-reperfusion_24hour_rep3

value: Liver

source_name: Liver,sham operation,24hour


title: Heart(risk area)_myocardial infarction_6hour_rep1


title: Control_line1_2

description: SY5Y cells overexpressing empty vector

source_name: SY5Y cells, line 1, control 2


title: Control_line6_1

description: SY5Y cells overexpressing empty vector

source_name: SY5Y cells, line 6, control 1


title: Liver_hepatic ischemia-reperfusion_24hour_rep4


title: Chimp_line7_3

description: SY5Y cells overexpressing FOXP2 chimp

source_name: SY5Y cells, line 7, FOXP2 chimp 3


title: Liver_hepatic ischemia-reperfusion_24hour_rep1


title: Control_line1_1

description: SY5Y cells overexpressing empty vector

source_name: SY5Y cells, line 1, control 1


title: Control_line1_4

description: SY5Y cells overexpressing empty vector

source_name: SY5Y cells, line 1, control 4


title: Heart(non risk area)_myocardial ischemia-reperfusion_6hour_rep1

source_name: Heart(non risk area),myocardial ischemia-reperfusion,6hour


title: Liver_hepatic ischemia-reperfusion_24hour_rep5


title: Heart(non risk area)_myocardial infarction_6hour_rep1

source_name: Heart(non risk area),myocardial infarction,6hour


title: Chimp_line6_3

description: SY5Y cells overexpressing FOXP2 chimp

source_name: SY5Y cells, line 6, FOXP2 chimp 3


title: Liver_hepatic ischemia-reperfusion_24hour_rep2


title: Control_line1_3

description: SY5Y cells overexpressing empty vector

source_name: SY5Y cells, line 1, control 3


title: Chimp_line7_2

description: SY5Y cells overexpressing FOXP2 chimp

source_name: SY5Y cells, line 7, FOXP2 chimp 2


title: Chimp_line7_4

description: SY5Y cells overexpressing FOXP2 chimp

source_name: SY5Y cells, line 7, FOXP2 chimp 4


title: Liver_hepatic ischemia-reperfusion_6hour_rep5

source_name: Liver,sham operation,6hour


title: Liver_hepatic ischemia-reperfusion_6hour_rep2


title: Chimp_line6_2

description: SY5Y cells overexpressing FOXP2 chimp

source_name: SY5Y cells, line 6, FOXP2 chimp 2


title: Liver_hepatic ischemia-reperfusion_6hour_rep4


title: Chimp_line6_1

description: SY5Y cells overexpressing FOXP2 chimp

source_name: SY5Y cells, line 6, FOXP2 chimp 1


title: Liver_hepatic ischemia-reperfusion_6hour_rep3


title: Chimp_line6_4

description: SY5Y cells overexpressing FOXP2 chimp

source_name: SY5Y cells, line 6, FOXP2 chimp 4


title: Chimp_line7_1

description: SY5Y cells overexpressing FOXP2 chimp

source_name: SY5Y cells, line 7, FOXP2 chimp 1


title: Liver_hepatic ischemia-reperfusion_6hour_rep1


title: Liver_sham operation treated with hydralazine_24hour_rep4

source_name: Liver,sham operation treated with hydralazine,24hour


title: Liver_sham operation treated with hydralazine_24hour_rep5


title: Chimp_line1_3

description: SY5Y cells overexpressing FOXP2 chimp

source_name: SY5Y cells, line 1, FOXP2 chimp 3


title: Liver_sham operation treated with hydralazine_24hour_rep1


title: Chimp_line1_1

description: SY5Y cells overexpressing FOXP2 chimp

source_name: SY5Y cells, line 1, FOXP2 chimp 1


title: Chimp_line1_2

description: SY5Y cells overexpressing FOXP2 chimp

source_name: SY5Y cells, line 1, FOXP2 chimp 2


title: Liver_sham operation treated with hydralazine_24hour_rep2


title: Liver_sham operation_24hour_rep6

source_name: Liver,sham operation,24hour


title: Liver_sham operation treated with hydralazine_24hour_rep3


title: Chimp_line1_4

description: SY5Y cells overexpressing FOXP2 chimp

source_name: SY5Y cells, line 1, FOXP2 chimp 4


title: Liver_sham operation_24hour_rep4


title: Liver_sham operation_24hour_rep5


title: Liver_sham operation_24hour_rep3


title: Liver_sham operation_24hour_rep2


title: STT4447-LMS-f-HG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54473.gif

source_name: Universal human reference

value: Universal human reference

value: Primary tumor, tumor tissue

value: Pleomorphic

value: time(change) 65 years

value: No

value: ST - right buttock


title: STT4458-LMS-m-IG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/55937.gif

value: time(change) 56 years

value: ST - left leg

value: P

value: Expression


title: Liver_sham operation_6hour_rep5

value: male


title: Liver_sham operation_6hour_rep2


title: STT4424-LMS-f-HG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55556.gif

value: Conventional

value: time(change) 76 years

value: ST -  right inguinal


title: STT4451-LMS-f-HG-ST-M-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55552.gif

value: time(change) 58* years

value: ST - right shoulder

value: M


title: Liver_sham operation_6hour_rep4

value: Liver


title: Liver_myocardial infarction_24hour_rep4

source_name: Liver,myocardial infarction,24hour


title: Liver_myocardial infarction_24hour_rep3


title: Liver_sham operation_6hour_rep1


title: Liver_myocardial infarction_24hour_rep2


title: STT4426-LMS-m-LG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55558.gif

value: Universal human reference

value: Primary tumor, tumor tissue

value: time(change) 21 years

value: ST - retroperitoneum


title: Liver_sham operation_6hour_rep3


title: Liver_myocardial infarction_24hour_rep5


title: Liver_sham operation_24hour_rep1


title: Liver_myocardial infarction_24hour_rep1


title: primary hepatocyte_Osteopontin treatment_8hours_rep2

description: to measure gene expression levels in primary hepatocytes at 8 hours after osteopontin stimulation (mock: n=3 and osteopontin: n=3)

hyb_protocol: Biotin-labeled cRNA samples were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 μl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to arrays for 16 h at 45°C.

scan_protocol: An Affymetrix GeneChip Scanner 3000 (Affymetrix) was used to measure the fluorescent intensity emitted by the labeled target.

data_processing: Raw data processing was performed using the Affymetrix GeneChip Operating Software 1.4.

source_name: primary hepatocyte, Osteopontin treatment, 8hours

label_protocol: We used GeneChipR One-Cycle Target Labeling and Control Reagents: Affymetrix, P/N 900493 according to protocols in the Affymetrix Expression Analysis Technical Manual.

extract_protocol: Total RNA was extracted individually using the RNeasy Mini Kit (QIAGEN, Chatsworth, CA), according to the manufacturer’s protocol. RNA was analyzed to determine if it met the minimum purity and integrity standards for total RNA quality (i.e., OD 260/280>1.8, OD 260/230>2.0, and minimal degradation as determined using a NanoDrop 1000A spectrophotometer; NanoDrop Technologies, Wilmington, DE). The quality and degradation of the isolated RNA were estimated after electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: liver_primary hepatocyte


title: Liver_myocardial ischemia-reperfusion_24hour_rep5


title: STT4412-LMS-f-IG-ST-M-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54475.gif

value: time(change) 48 years

value: RT

value: ST - retroperioneum

value: F


title: primary hepatocyte_Osteopontin treatment_8hours_rep3

value: male


title: STT4404-LMS-m-HG-ST-M-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52685.gif

value: Pleomorphic/Conventional

value: time(change) 70 years

value: CT

value: ST - left upper leg

value: Expression


title: STT4442-LMS-f-HG-ST-M(same pt as 4451)-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53437.gif

value: Pleomorphic

value: time(change) 59* years

value: ST - right shoulder

value: M


title: STT4420-LMS-m-pleomorphic-HG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54534.gif

value: Universal human reference

value: Primary tumor, tumor tissue

value: time(change) 63 years

value: No

value: P


title: STT4406-LMS-f-pleomorphic-HG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52105.gif

value: time(change) 73 years

value: ST - right gluteal region


title: STT4400-LMS-m-IG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55548.gif

value: Conventional

value: time(change) 49 years

value: ST - right upper leg


title: STT4403-LMS-m-LG-ST-R/M-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52684.gif

value: time(change) 69 years

value: RT

value: ST - left scrotum


title: Liver_myocardial ischemia-reperfusion_24hour_rep1

value: male

value: Liver


title: primary hepatocyte_mock_8hours_rep3

source_name: primary hepatocyte, no treatment, 8hours

value: liver_primary hepatocyte


title: Liver_myocardial infarction_6hour_rep3

source_name: Liver,myocardial infarction,6hour


title: Fasted Liver of WT mice_CT44

city: La Jolla

first: Christopher

last: Vollmers

address: 10010 North Torrey Pines Road

department: Regulatory Biology Laboratory

institute: The Salk Institute for Biological Studies

description: Food was made available ad libitum for two weeks. Mice were then released into constant darkness and food was withdrawn on the first day in constant darkness at CT12 and. 24 hours later tissue was collected at the indicated timepoint on the second day of constant darkness

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix scan protocol

data_processing: Data from CEL files were normalized in R using the 'affy' package and the gcRMA algorithm.  Log transformation of values was reversed and all values of a series of arrays were median normalized to 100

label: Biotin

source_name: Fasted Liver of WT mice at circadian time 44

label_protocol: Standard Affymetrix protocol

extract_protocol: Trizol extraction followed by Qiagen RNeasy columns

tag: Strain

value: C57/B6, Gender:male, Age:8-12 weeks, Condition:Fasted


title: Fasted Liver of WT mice_CT42

source_name: Fasted Liver of WT mice at circadian time 42


title: Liver_myocardial ischemia-reperfusion_24hour_rep3


title: Liver_myocardial infarction_6hour_rep2

source_name: Liver,sham operation,6hour


title: primary hepatocyte_Osteopontin treatment_8hours_rep1


title: Fasted Liver of WT mice_CT43

source_name: Fasted Liver of WT mice at circadian time 43


title: Liver_myocardial infarction_6hour_rep5


title: Liver_myocardial ischemia-reperfusion_6hour_rep5


title: Liver_myocardial ischemia-reperfusion_24hour_rep2


title: Liver_myocardial infarction_6hour_rep4


title: Liver_myocardial infarction_6hour_rep1


title: primary hepatocyte_mock_8hours_rep2


title: Liver_myocardial ischemia-reperfusion_6hour_rep3


title: Fasted Liver of WT mice_CT45

source_name: Fasted Liver of WT mice at circadian time 45


title: Fasted Liver of WT mice_CT40

source_name: Fasted Liver of WT mice at circadian time 40


title: Fasted Liver of WT mice_CT38

source_name: Fasted Liver of WT mice at circadian time 38


title: primary hepatocyte_mock_8hours_rep1


title: Refed Liver of WT mice_CT10

description: Food was made available ad libitum for two weeks. Mice were then released into constant darkness and food was withdrawn on the first day in constant darkness at CT4 and. 24 hours later mice were fed again at CT4 on the second day. Tissue was collected at the indicated timepoint after feeding.

source_name: Refed Liver of WT mice at circadian time 10

value: C57/B6, Gender:male, Age:8-12 weeks, Condition::Fed


title: Refed Liver of WT mice_CT8

source_name: Refed Liver of WT mice at circadian time 8


title: Liver_myocardial ischemia-reperfusion_6hour_rep2

description: Liver or heart samples were amplified individually without mixing. As a reference for hybridization, we used mixed RNA samples from the sham group at various time-points. Test and reference samples were labeled with fluorescent Cy5 and Cy3, respectively, mixed, and hybridized on a microarray. Supplementary txt file: our nomalized values are in column AI. But, if signal intensity of Cy3 or Cy5 is less than 100, the column AI is blank. In this situation, normalized values is in column AL or AO.


title: Fast Liver of WT mice_CT10

description: Food was made available ad libitum for two weeks. Mice were then released into constant darkness and food was withdrawn on the first day in constant darkness at CT4. Tissue was collected approximately 24 hours later during the second day of constant darkness.

source_name: Fasted Liver of WT mice at circadian time 10


title: Liver_myocardial ischemia-reperfusion_6hour_rep4


title: Fasted Liver of WT mice_CT36

source_name: Fasted Liver of WT mice at circadian time 36


title: Temporally restricted feeding in Liver of Cry1,Cry2 KO mice_CT42

description: Food was made available to Cry1,Cry2 double KO mice only during 8 hours of the day for two weeks. Mice were then released into constant darkness while food availability was still restricted to between CT25 and CT33 and tissue was collected during the second day of constant darkness

source_name: Cry1,Cry2 KO mouse Liver under restricted feeding at circadian time 42

value: Cry1,Cry2 double KO, Gender:female, Age:8-16 weeks, Condition:temporally restricted food availability CT1(25)-CT9(33)


title: Fast Liver of WT mice_CT4

description: Food was made available ad libitum for two weeks. Mice were then released into constant darkness and food was withdrawn on the first day in constant darkness at CT4. Tissue was collected approximately 24 hours later during the second day of constant darkness

source_name: Fasted Liver of WT mice at circadian time 4


title: Liver_myocardial ischemia-reperfusion_6hour_rep1


title: Fast Liver of WT mice_CT6

source_name: Fasted Liver of WT mice at circadian time 6


title: Temporally restricted feeding in Liver of Cry1,Cry2 KO mice_CT46

source_name: Cry1,Cry2 KO mouse Liver under restricted feeding at circadian time 46


title: Temporally restricted feeding in Liver of Cry1,Cry2 KO mice_CT36

source_name: Cry1,Cry2 KO mouse Liver under restricted feeding at circadian time 36

value: Cry1,Cry2 double KO, Gender:male, Age:8-16 weeks, Condition:temporally restricted food availability CT1(25)-CT9(33)


title: Temporally restricted feeding in Liver of Cry1,Cry2 KO mice_CT32

source_name: Cry1,Cry2 KO mouse Liver under restricted feeding at circadian time 32


title: Temporally restricted feeding in Liver of Cry1,Cry2 KO mice_CT38

source_name: Cry1,Cry2 KO mouse Liver under restricted feeding at circadian time 38


title: Refed Liver of WT mice_CT6

source_name: Refed Liver of WT mice at circadian time 6


title: Temporally restricted feeding in Liver of Cry1,Cry2 KO mice_CT40

source_name: Cry1,Cry2 KO mouse Liver under restricted feeding at circadian time 40


title: Temporally restricted feeding in Liver of Cry1,Cry2 KO mice_CT44

source_name: Cry1,Cry2 KO mouse Liver under restricted feeding at circadian time 44


title: Temporally restricted feeding in Liver of Cry1,Cry2 KO mice_CT26

source_name: Cry1,Cry2 KO mouse Liver under restricted feeding at circadian time 26


title: Temporally restricted feeding in Liver of Cry1,Cry2 KO mice_CT30

source_name: Cry1,Cry2 KO mouse Liver under restricted feeding at circadian time 30


title: Chimp_FP_6

description:
Adult chimpanzee brain
Identifier #Y06-147

organism: Pan troglodytes

source_name: Chimpanzee frontal pole

extract_protocol: Qiagen miRNeasy kit

value: Chimpanzee frontal pole


title: Chimp_hipp_6

description:
Adult chimpanzee brain
Identifier #Y04-04

source_name: Chimpanzee hippocampus

value: Chimpanzee hippocampus


title: Chimp_hipp_5

description:
Adult chimpanzee brain
Identifier #Y07-147


title: Human_hipp_9

description:
Adult human brain
Identifier #4598

source_name: Human hippocampus

value: Human hippocampus


title: Fasted Liver of WT mice_CT46

source_name: Fasted Liver of WT mice at circadian time 46


title: Chimp_hipp_4

description:
Adult chimpanzee brain
Identifier #Y06-108


title: Temporally restricted feeding in Liver of Cry1,Cry2 KO mice_CT34

source_name: Cry1,Cry2 KO mouse Liver under restricted feeding at circadian time 34


title: Human_hipp_7

description:
Adult human brain
Identifier #4640 rerun


title: Fast Liver of WT mice_CT8

source_name: Fasted Liver of WT mice at circadian time 8


title: Chimp_FP_5


title: Human_hipp_8

description:
Adult human brain
Identifier #1818 rerun
Outlier


title: Human_hipp_6

description:
Adult human brain
Identifier #4593


title: Chimp_caudate_4

source_name: Chimpanzee caudate nucleus

value: Chimpanzee caudate nucleus


title: Fast Liver of WT mice_CT2

source_name: Fasted Liver of WT mice at circadian time 2


title: Temporally restricted feeding in Liver of Cry1,Cry2 KO mice_CT28

source_name: Cry1,Cry2 KO mouse Liver under restricted feeding at circadian time 28


title: Temporally restricted feeding in Liver of Cry1,Cry2 KO mice_CT24

source_name: Cry1,Cry2 KO mouse Liver under restricted feeding at circadian time 24

value: Cry1,Cry2 double KO mice, Gender:male, Age:8-16 weeks, Condition:estricted food availability CT1(25)-CT9(33)


title: Human_hipp_5

description:
Adult human brain
Identifier #1818
Outlier


title: Chimp_caudate_5


title: Human_hipp_4

description:
Adult human brain
Identifier #4640
Outlier


title: 15N_stationary_phase

city: Greifswald

first: Jan

last: Pané-Farré

address: F.-L.-Jahn-Str. 15

department: Department of Microbial Physiology

country: Germany

hyb_protocol: Hybridizations were done in a total sample volume of 40 µl for 17 hours at 65°C at 10 rpm in a dedicated hybridization chamber (Agilent) and hybridisation oven (Robbins Scientific, Sunnyvale, CA, USA). After hybridization the slides were washed for one minute at room temperature in wash buffer 1 followed by a one minute washing step at 37°C with wash buffer 2. The slides were dried by submersion in acetonitrile for 30 seconds. Blocking reagents, hybridization buffer (Gene Expression Hybridization Kit) and washing solutions (Gene Expression Wash Buffer Kit) were purchased from Agilent.

scan_protocol: Scanned on an Agilent G2565AA scanner and quantified using Agilent Feature Extraction Software (v. 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1 ) was used for background subtraction and LOWESS normalization.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus pool exponential growth and stationary phase

label_protocol: Synthesis of Cy5-dCTP or Cy3-dCTP (Perkin-Elmer) labelled cDNA was done with 10 µg of total RNA as template by direct reverse-transcription using Superscript II (Invitrogen) and random hexamers (Promega) as primers. After denaturation of the RNA primer mix for 10 minutes at 70°C the cDNA synthesis was performed in a 50 µl reaction volume at 42°C for 60 minutes. The concentrations of enzyme and reagents in the reverse transcription reaction were as follows: Superscript II (400 units), Cy-dye (1.25 nmol), dATP, dGTP, dTTP (5 nmol each), dCTP (2.5 nmol), random hexamers (1.25 µg), DTT (0.01 M) and 1x first strand buffer. The Superscript II was heat inactivated for 10 minutes at 70°C. For the degradation of the RNA after cDNA synthesis the samples were incubated for 30 min at room temperature with E. coli RNase H (2 units) (Invitrogen). Labelled cDNA was then purified with the CyScribe GFX Purification Kit following the instructions of the manufacturer (Amersham Biosciences). The Cy-dye incorporation was analysed with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Rockland, DE). Approximately 300 ng of each labelled cDNA corresponding to 6 pmol of incorporated dye were used in two-colour pool-cDNA (Cy3) versus sample cDNA (Cy5) competitive hybridization experiments.

growth_protocol: S. aureus was grown in BioExpress Cell Culture Media (Cambridge Isotope laboratories, Andover, MA, USA. Cells were harvested at an optical density (OD 600 nm) of 0.5 or five hours after entry into stationary phase.

extract_protocol: Total RNA was isolated from S. aureus COL using the acid-phenol method with modifications described by Fuchs et al. (2007). In addition, to eliminate traces of contaminating DNA, the RNA was DNase treated according to the protocol described in appendix E of the Qiagen RNeasy Mini Handbook (4th edition, April 2006). Cleanup of RNA from DNase digest was performed with the RNA Clean-Up and Concentration Micro Kit according to the manufacturer’s instructions (Norgen, Thorold, ON, Canada). The integrity of the RNA was checked with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and the concentration and purity were assessed with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Rockland, DE, USA).

treatment_protocol: S. aureus COL cells were harvested on ice-cold killing buffer (20 mM NaN3, 5 mM MgCl2, 20 mM Tris, pH 7.5) by centrifugation (9,000 g, 5 min) at 4°C and the cells were stored at -70°C until processing.

value: COL

source_name: Staphylococcus aureus stationary phase


title: 14N_stationary_phase


title: Human_hipp_3

description:
Adult human brain
Identifier #4548


title: STT1220-LMS-pleomorphic-HG-UT?-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43526.gif

source_name: Universal human reference

value: Universal human reference

value: Primary tumor, tumor tissue

value: Pleomorphic

value: time(change) 46 years

value: No

value: UT**

value: P

value: F

value: Expression


title: Human_FP_6

source_name: Human frontal pole

value: Human frontal pole


title: STT516-LMS-f-ST-IG-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43525.gif

value: Conventional

value: time(change) 68 years

value: ST - retroperitoneum


title: Human_FP_3

description:
Adult human brain
Identifier #4548


title: Human_hipp_1

description:
Adult human brain
Identifier #1905

value: Human hippocampus


title: 15N_exponential_growth

source_name: Staphylococcus aureus exponential growth


title: STT3571-LMS-IG-UT?-M-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43527.gif

value: time(change) 53 years

value: M


title: Human_FP_5

description:
Adult human brain
Identifier #1903


title: Human_hipp_2

description:
Adult human brain
Identifier #4924


title: Human_FP_4

description:
Adult human brain
Identifier #1905


title: 14N_exponential_growth

value: COL


title: Post-transplant sample of DCD patient 06

city: Seoul

first: Chang-Hyun

last: Kang

address: Yeongun-dong, Chongro-gu

country: South Korea

institute: Seoul National University Hospital

description:
Gene expression data from DCD donor lungs 2 hours after reperfusion, this is post-transplant data of sample No_6
sample name: No_16

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U-133 plus2. GeneChips were washed and stained in the Affymetrix Fluidics Station 4500.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3700 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: DCD post-transplant sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

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

value: lung

tag: donation source

value: DCD

tag: sampling time

value: post-transplant


title: Post-transplant sample of DCD patient 05

description:
Gene expression data from DCD donor lungs 2 hours after reperfusion, this is post-transplant data of sample No_5
sample name: No_15


title: Human_FP_2

description:
Adult human brain
Identifier #4598


title: Temporally restricted feeding in the liver of WT mice_CT46

description: Food was made available to mice only during 8 hours of the day for two weeks. Mice were then released into constant darkness while food availability was still restricted to between CT25 and CT33 and tissue was collected during the second day of constant darkness

source_name: WT mouse liver under restricted feeding at circadian time 46

value: C57/B6, Gender:male, Age:8-12 weeks

tag: Condition

value: temporally restricted food availability CT1(25)-CT9(33)


title: Temporally restricted feeding in the liver of WT mice_CT47

source_name: WT mouse liver under restricted feeding at circadian time 47


title: Post-transplant sample of DCD patient 04

description:
Gene expression data from DCD donor lungs 2 hours after reperfusion, this is post-transplant data of sample No_4
sample name: No_14


title: Post-transplant sample of DCD patient 02

description:
Gene expression data from DCD donor lungs 2 hours after reperfusion, this is post-transplant data of sample No_2
sample name: No_12


title: B21F83

status: Public on Dec 01 2009

city: Raleigh

first: Youssef

last: Idaghdour

state: NC

address: South Gardner Hall

department: Genetics

institute: NCSU

hyb_protocol: Illumina's BeadArray protocol

scan_protocol: Illumina's BeadArray protocol and BeadStudio (Gene expression Module)

data_processing: Raw data was log2 transformed and median-centered using JMP Genomics (SAS, Cary NC).

source_name: Leukocytes, Boutroch, Rural

label_protocol: cDNA and cRNA labeling and amplification were all performed using a single kit: Ambion's Illumina TotalPrep RNA Amplification kit.

extract_protocol: Total RNA was extrated from leukocyte samples using Ambion's Leukolocks kit. Quality control was performed using Agilent's Bioanalyzer.

tag: geographic location

value: Boutroch

tag: lifestyle

value: rural

value: female

value: peripheral blood

tag: cell type

value: leukocytes


title: Primary_human_keratinocytes_MeDIP_+Ca_2of2

type: genomic

first: Paul

middle: A

last: Khavari

address: 259 Campus Dr

department: Dermatology

description: Human foreskin keratinocytes; Differentiated; methylated DNA immunoprecipitation profiling on promoter tiling arrays.

hyb_protocol: Hybridization was performed by NimbleGen.

scan_protocol: Scanning was performed by NimbleGen.

data_processing: Raw .pair files were loaded into NimbleScan to produce subsequent .GFF ratio and peak files. Default parameters were used.

molecule: genomic DNA

source_name: Primary Human Keratinocytes; Differentiation conditions; MeDIP profiling

label_protocol: Labeling was performed by NimbleGen.

growth_protocol: Keratinocytes were cultured in Gibco SFM until confluent at which point 1.2mM Ca was added for 3 days to induce differentiation.

extract_protocol: Genomic DNA was isolated from cells using the DNeasy kit (Qiagen). The DNA was sonicated to produce fragments from 300 to 1,000 bp and subject to immunoprecipitation using a monoclonal antibody against 5-methylcytidine (Eurogentec) according to published protocols (Weber, M. et al., 2007, Nat. Genet.) DNA enriched for 5-methylcytidine was subject to amplification using the Whole Genome Amplification kit (Sigma) according to manufacturers protocol.

treatment_protocol: Methylated DNA was immunopreciptated from primary human keratinoctyes cultured in high calcium differentiation conditions.

value: primary keratinocytes

value: male

value: foreskin

tag: status

value: differentiated

tag: antibody

source_name: input

growth_protocol: Keratinocytes were cultured in Gibco SFM in subconfluent conditions.

treatment_protocol: Methylated DNA was immunopreciptated from primary human keratinoctyes cultured in low calcium growth conditions.


title: Primary_human_keratinocytes_MeDIP_-Ca_2of2

description: Human foreskin keratinocytes; methylated DNA immunoprecipitation profiling on promoter tiling arrays.

source_name: Primary Human Keratinocytes; Growth conditions; MeDIP profiling

value: undifferentiated


title: Human_FP_1

value: Human frontal pole


title: Human_caudate_7

description:
Adult human brain
Identifier #4598 rerun
Outlier

source_name: Human caudate nucleus

value: Human caudate nucleus


title: Temporally restricted feeding in the liver of WT mice_CT45

source_name: WT mouse liver under restricted feeding at circadian time 45


title: Human_caudate_8

description:
Adult human brain
Identifier #1818


title: Post-transplant sample of DCD patient 01

description:
Gene expression data from DCD donor lungs 2 hours after reperfusion, this is post-transplant data of sample No_1
sample name: No_11

value: lung


title: Human_caudate_6

description:
Adult human brain
Identifier #4593


title: Sarcoma_11

status: Public on Nov 21 2009

city: Durham

first: Jeffrey

last: Mito

institute: Duke University Medical Center

description: Gene expression data from soft tissue sarcomas compared to normal muscle isolated from mice without tumors.

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hours at 45C on Mouse genome 430A 2.0 arrays and underwent automated washing and staining on the fluidics station.

scan_protocol: Genechips were scanned using the GeneChip Scanner 3000 7g.

data_processing: Data was normalized using the RMA algorithm.

source_name: Soft Tissue Sarcoma

label_protocol: Labeled RNA was prepared from 2 µg total RNA using one-cycle target labeling kit (Affymetrix).

growth_protocol: Tumors were induced via injection of Adeno-Cre ~3 months prior to surgical removal of the tumor.

extract_protocol: Trizol extraction of total RNA was followed by clean up using the RNeasy kit (Qiagen) per manufacturer's protocol.

treatment_protocol: Tumors were isolated from surrounding normal tissue.

value: Soft Tissue Sarcoma

tag: genotype

value: LSL-KrasG12D; Trp53Fl/Fl


title: Pre-transplant sample of DCD patient 07

description:
Gene expression data from DCD donor lungs just after preservation, However this lung was not used for transplantation
sample name: No_7

source_name: DCD pre-transplant sample

value: DCD

value: post-transplant


title: Temporally restricted feeding in the liver of WT mice_CT43

source_name: WT mouse liver under restricted feeding at circadian time 43

value: C57/B6, Gender:male, Age:8-12 weeks

value: temporally restricted food availability CT1(25)-CT9(33)


title: Human_caudate_5

description:
Adult human brain
Identifier #4924


title: Human_caudate_4

description:
Adult human brain
Identifier #4548


title: Pre-transplant sample of DCD patient 06

description:
Gene expression data from DCD donor lungs just after preservation
sample name: No_6

value: pre-transplant


title: Pre-transplant sample of DCD patient 04

description:
Gene expression data from DCD donor lungs just after preservation
sample name: No_4


title: Pre-transplant sample of DCD patient 03

description:
Gene expression data from DCD donor lungs just after preservation
sample name: No_3


title: Temporally restricted feeding in the liver of WT mice_CT44

source_name: WT mouse liver under restricted feeding at circadian time 44


title: Temporally restricted feeding in the liver of WT mice_CT42

source_name: WT mouse liver under restricted feeding at circadian time 42


title: Human_caudate_3

description:
Adult human brain
Identifier #4598
Outlier


title: Temporally restricted feeding in the liver of WT mice_CT40

source_name: WT mouse liver under restricted feeding at circadian time 40


title: Pre-transplant sample of DCD patient 02

description:
Gene expression data from DCD donor lungs just after preservation
sample name: No_2


title: Temporally restricted feeding in the liver of WT mice_CT41

source_name: WT mouse liver under restricted feeding at circadian time 41


title: Pre-transplant sample of DCD patient 01

description:
Gene expression data from DCD donor lungs just after preservation
sample name: No_1


title: Human_caudate_2

description:
Human adult brain
Identifier #4640


title: Temporally restricted feeding in the liver of WT mice_CT39

source_name: WT mouse liver under restricted feeding at circadian time 39


title: Human_caudate_1

description:
Adult human brain
Identifier #1905


title: Temporally restricted feeding in the liver of WT mice_CT38

source_name: WT mouse liver under restricted feeding at circadian time 38


title: Temporally restricted feeding in the liver of WT mice_CT36

source_name: WT mouse liver under restricted feeding at circadian time 36


title: Chimp_hipp_1

description:
Adult chimpanzee brain
Identifier #Y05-12

source_name: Chimpanzee hippocampus

value: Chimpanzee hippocampus


title: Temporally restricted feeding in the liver of WT mice_CT35

source_name: WT mouse liver under restricted feeding at circadian time 35


title: Chimp_caudate_3

description:
Adult chimpanzee brain
Identifier #Y07-25

source_name: Chimpanzee caudate nucleus

value: Chimpanzee caudate nucleus


title: Chimp_hipp_2


title: Chimp_caudate_1

description:
Adult chimpanzee brain
Identifier #Y07-147


title: Temporally restricted feeding in the liver of WT mice_CT34

description: Food was made available to mice only during 8 hours of the day for two weeks. Mice were then released into constant darkness while food availability was still restricted to between CT25 and CT33 and tissue was collected during the second day of constant darkness

source_name: WT mouse liver under restricted feeding at circadian time 34


title: Temporally restricted feeding in the liver of WT mice_CT37

source_name: WT mouse liver under restricted feeding at circadian time 37


title: Temporally restricted feeding in the liver of WT mice_CT29

source_name: WT mouse liver under restricted feeding at circadian time 29

value: C57/B6, Gender:male, Age:8-12 weeks,


title: Chimp_hipp_3

description:
Adult chimpanzee brain
Identifier #Y06-147


title: Chimp_FP_3

source_name: Chimpanzee frontal pole

value: Chimpanzee frontal pole


title: Temporally restricted feeding in the liver of WT mice_CT32

source_name: WT mouse liver under restricted feeding at circadian time 32


title: Chimp_FP_1


title: Temporally restricted feeding in the liver of WT mice_CT30

source_name: WT mouse liver under restricted feeding at circadian time 30


title: Chimp_caudate_2


title: Temporally restricted feeding in the liver of WT mice_CT33

source_name: WT mouse liver under restricted feeding at circadian time 33


title: Temporally restricted feeding in the liver of WT mice_CT28

source_name: WT mouse liver under restricted feeding at circadian time 28


title: Temporally restricted feeding in the liver of WT mice_CT26

source_name: WT mouse liver under restricted feeding at circadian time 26


title: Temporally restricted feeding in the liver of WT mice_CT31

source_name: WT mouse liver under restricted feeding at circadian time 31


title: DeVos_1-6_Treatment_Rep3_ATH1

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: 24 h at 4°C prior to planting Growth chamber Commercial soil 23oC 50% regular 3-week-old Arabidopsis Col-0, grown on soil in 16h-light conditions. Just before bolting.

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system. Significance of gene expression was determined using the LIMMA (Smyth, 2004) program and raw p values of multiple tests were corrected using False Discovery Rate (FDR).

organism: Arabidopsis thaliana

source_name: treatment, rep 3

label_protocol: Labelled using protocol described in Affymetrix manual "3' IVT Express Kit User Manual"

growth_protocol: Seeds of wild-type Arabidopsis (Arabidopsis thaliana) land race Columbia-0 (Col-0) were obtained from the Arabidopsis Biological Resource Center. Seeds were kept in 0.1% Phytagar (Invitrogen, Carlsbad, CA) for 24 h at 4°C prior to planting on Cornell mix (Landry, Chapple & Last, 1995) with Osmocoat fertilizer (Scotts). Plants were grown in Conviron growth chambers in 20- x 40-cm nursery flats at a photosynthetic photon flux density of 200 mmol m-2 s-1 and a 16-h photoperiod. The temperature in the chambers was 23°C and the relative humidity was 50%. Plants were grown for 3 weeks and used in experiments before flowering.

extract_protocol: Qiagen RNAeasy kit protocol

tag: agent

value: Myzus persicae saliva

tag: replicate

tag: developmental stage

tag: stock code


title: DeVos_1-5_Control_Rep3_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)

source_name: control, rep 3

value: control

tag: strain


title: Chimp_FP_2

description:
Adult chimpanzee brain
Identifier #Y03-09


title: Temporally restricted feeding in the liver of WT mice_CT27

source_name: WT mouse liver under restricted feeding at circadian time 27


title: DeVos_1-3_Control_Rep2_ATH1

source_name: control, rep 2

tag: age


title: Temporally restricted feeding in the liver of WT mice_CT25

source_name: WT mouse liver under restricted feeding at circadian time 25


title: DeVos_1-2_Treatment_Rep1_ATH1

source_name: treatment, rep 1


title: Vector only RNA (Cy5) 3

status: Public on Nov 11 2009

city: New Delhi

first: krishan

last: kumar

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: ICGEB

hyb_protocol: The hybridization protocol used was as described by TIGR SOP#8 (http://pfgrc.jcvi.org/index.php/microarray/protocols.html)

scan_protocol: Slides scanned using ScanArray Gx Scanner (PerkinElmer) and image analysis done using ScanArray Express (PerkinElmer)

data_processing: Images were quantified using ScanArray Express (PerkinElmer), using LOWESS algorithm. Mean-background intensity values were transferred to Excel spreadsheets for further analysis. Data was analyzed using Z Score transformation as described previously (Cheadle et al., 2003, published in J. Mol. Diagn.)

organism: Mycobacterium tuberculosis

source_name: Total RNA from Mtb containing pVV16

label_protocol: Equal amount of RNA from each sample (Experimental as well as control- both in triplicates) were labeled with Cy3 and Cy5 dyes using CyScribe First strand cDNA labeling kit (Amersham/GE Healthcare) following manufacturer's protocol.

growth_protocol: Mycobacteria harboring either hcl1pVV16 (EXP) or pVV16 (CTL) were grown till mid-log phase in Middlebrook 7H9 broth supplemented with 10% ADC (Difco) at 37ºC and 200 rpm.

extract_protocol: RNA was extracted using hot phenol method and purified using Rneasy mini kit (Qiagen) followed by on-column DNaseI digestion as instructed by the manufacturer.

treatment_protocol: Mycobacterium tuberculosis H37Rv competent cells were transfromed with either Hcl1pVV16 (Experimental) or pVV16 (Control) plasmids. Three individual colonies from each transformant picked, grown till mid-log phase and total RNA isolated.


title: Vector only RNA (Cy5) 2


title: DeVos_1-1_Control_Rep1_ATH1

source_name: control, rep 1


title: Vector expressing Hcl1 peptide RNA (Cy5) 2

source_name: Total RNA from Mtb containing Hcl1pVV16


title: Medicago truncatula germinated seedlings, 3 days Petri dishes, 180mM NaCl salt stress, 6 hour, rep3

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

institute: Washington University in St. Louis

description: Gene expression data of roots of Medicago truncatula germinated seedlings grown in Petri dishes under salt stress

hyb_protocol: performed at 45℃ with rotation for 16h (Affymetrix GeneChip Hybridization Oven 640)

scan_protocol: using Affymetrix GeneChip Scanner 3000

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4

organism: Medicago truncatula

source_name: Medicago truncatula germinated seedlings, grown 3 days in Petri dishes, 180mM NaCl salt stress, time point 6 hour

label_protocol: using the Custom MessageAmp™ II-Biotin by Ambion according to the manufacturer’s instruction

growth_protocol: grown in Petri dishes for 3 days

extract_protocol: using AutoLab RNA kit (http://www.autolabtech.cn/) performed according to the manufacturer’s instruction

treatment_protocol: 180mM NaCl salt stress

tag: grown in Petri dishes for 3 days

tag: 180mM NaCl salt stress

tag: 2 ug of total RNA was used to synthesize doublestranded cDNA


title: Temporally restricted feeding in the liver of WT mice_CT24

source_name: WT mouse liver under restricted feeding at circadian time 24

tag: Strain


title: Medicago truncatula germinated seedlings, 3 days Petri dishes, 180mM NaCl salt stress, 24 hour, rep2

source_name: Medicago truncatula germinated seedlings, grown 3 days in Petri dishes, 180mM NaCl salt stress, time point 24 hour


title: Medicago truncatula germinated seedlings, 3 days Petri dishes, 180mM NaCl salt stress, 6 hour, rep2


title: Primary_human_keratinocytes_MeDIP_+Ca_1of2

description: Human foreskin keratinocytes; Differentiated; methylated DNA immunoprecipitation profiling on promoter tiling arrays.

source_name: Primary Human Keratinocytes; Differentiation conditions; MeDIP profiling

value: primary keratinocytes

tag: gender

value: male

tag: tissue

value: foreskin

value: differentiated

source_name: input


title: Medicago truncatula germinated seedlings, 3 days Petri dishes, 180mM NaCl salt stress, 48 hour, rep1

source_name: Medicago truncatula germinated seedlings, grown 3 days in Petri dishes, 180mM NaCl salt stress, time point 48 hour


title: Medicago truncatula germinated seedlings, 3 days Petri dishes, 180mM NaCl salt stress, 0 hour, rep2

source_name: Medicago truncatula germinated seedlings, grown 3 days in Petri dishes, 180mM NaCl salt stress, time point 0 hour


title: Medicago truncatula germinated seedlings, 3 days Petri dishes, 180mM NaCl salt stress, 24 hour, rep3


title: DeVos_1-4_Treatment_Rep2_ATH1

source_name: treatment, rep 2


title: Medicago truncatula germinated seedlings, 3 days Petri dishes, 180mM NaCl salt stress, 48 hour, rep3


title: Medicago truncatula germinated seedlings, 3 days Petri dishes, 180mM NaCl salt stress, 0 hour, rep3


title: Medicago truncatula germinated seedlings, 3 days Petri dishes, 180mM NaCl salt stress, 0 hour, rep1


title: Vector expressing Hcl1 peptide RNA (Cy5) 3


title: Medicago truncatula germinated seedlings, 3 days Petri dishes, 180mM NaCl salt stress, 48 hour, rep2


title: Medicago truncatula germinated seedlings, 3 days Petri dishes, 180mM NaCl salt stress, 6 hour, rep1


title: Medicago truncatula germinated seedlings, 3 days Petri dishes, 180mM NaCl salt stress, 24 hour, rep1


title: Vector expressing Hcl1 peptide RNA (Cy3) 2


title: Vector only RNA (Cy5) 1


title: Vector expressing Hcl1 peptide RNA (Cy3) 3


title: Vector only RNA (Cy3) 3


title: Vector only RNA (Cy3) 2


title: Primary_human_keratinocytes_MeDIP_-Ca_1of2

description: Human foreskin keratinocytes; methylated DNA immunoprecipitation profiling on promoter tiling arrays.

source_name: Primary Human Keratinocytes; Growth conditions; MeDIP profiling

value: undifferentiated


title: Vector expressing Hcl1 peptide RNA (Cy5) 1


title: Vector only RNA (Cy3) 1


title: Vector expressing Hcl1 peptide RNA (Cy3) 1


title: N. meningitidis strain with heterologous pfkA - Replicate 3

city: Gent

first: Gino

last: Baart

state: East Flanders

address: Technologiepark 927

department: Plant Systems Biology

country: Belgium

institute: Ghent University

hyb_protocol: hybridization buffer was added, and samples were applied to microarrays enclosed in hybridization chambers. After hybridization, slides were washed and scanned

scan_protocol: The microarrays were scanned with a ScanArray Express microarray scanner (Perkin Elmer, The Netherlands) and median fluorescence intensities were quantified for each spot using ArrayVision software (Imaging Research, The Netherlands) Images were quantified using Arrayvision Software (version 8.0).

data_processing: quantile normalized, background subtracted data obtained from natural log of processed Cy3 signal, using the Cy5 signal as common reference

organism: Neisseria meningitidis

label_protocol: 5 µg of total RNA were primed with 2 µl of random primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of RTase (Promega Chipshot labeling Aminoallyl protocol), RNA was degraded and cDNA labelled with Cy3/Cy5. Purification of samples was done with Promega Chipshot columns, according to manufacturer's instructions

extract_protocol: Total RNA extracted using Promega SV Total RNA isolation system following manufacturer's instructions

tag: mutant state

value: with heterologous pfkA

source_name: Common reference sample (equal mix of 6 RNA samples)


title: N. meningitidis strain with heterologous pfkA - Replicate 2


title: Day 7 heart control

city: Houston

first: Malgorzata

last: Kloc

address: 6565 Fannin Street

department: Surgery

institute: The Methodist Hospital

hyb_protocol: For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC.  Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.

scan_protocol: Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000.  Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.

data_processing: The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).

organism: Rattus norvegicus

source_name: Day 7 heart control

label_protocol: Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences).  After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences).  The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).

growth_protocol: Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.

extract_protocol: Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol.  The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).

value: heart

value: Wistar Furth


title: Day 3 T Cells control

source_name: Day 3 T Cells control

tag: cell type

value: T cell


title: Day 3 heart control

source_name: Day 3 heart control


title: Day 1 T Cells control

source_name: Day 1 T Cells control


title: Day 1 heart control

source_name: Day 1 heart control


title: Day 7 T Cells control

source_name: Day 7 T Cells control


title: N. meningitidis strain with heterologous pfkA - Replicate 1


title: Day 7 heart Cyc + peptide

source_name: Day 7 heart Cyc + peptide


title: Day 3 T Cells Cyc + peptide

source_name: Day 3 T Cells Cyc + peptide


title: Day 1 heart Cyc + peptide

source_name: Day 1 heart Cyc + peptide


title: Day 3 heart Cyc + pepetide

source_name: Day 3 heart Cyc + pepetide


title: Day 1 heart Cyclosporin

source_name: Day 1 heart Cyclosporin


title: Control N. meningitidis strain without pfkA - Replicate 1

value: no heterologous pfkA


title: Day 3 heart Cyclosporin

source_name: Day 3 heart Cyclosporin


title: Day 7 T Cells Cyc + peptide

source_name: Day 7 T Cells Cyc + peptide


title: Day 1 T Cells Cyc + peptide

source_name: Day 1 T Cells Cyc + peptide


title: Day 7 heart Cyclosporin

source_name: Day 7 heart Cyclosporin


title: Day 7 T Cells Cyclosporin

source_name: Day 7 T Cells Cyclosporin


title: Day 3 T Cells Cyclosporin

source_name: Day 3 T Cells Cyclosporin


title: Control N. meningitidis strain without pfkA - Replicate 3

source_name: Common reference sample (equal mix of 6 RNA samples)


title: Day 1 T Cells Cyclosporin

source_name: Day 1 T Cells Cyclosporin


title: Ribosome density experiment: mock 12 hrs. (5-20-08)

status: Public on Nov 10 2009

first: Patrick

middle: O

last: Brown

address: Beckman Center b439

department: Department of biochemistry

institute: Stanford university school of medicine

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80377.gif

scan_protocol: GenePix

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: aRNA generated from pooled mRNA associated with the light fractions of the polysome

source_name: aRNA generated from pooled mRNA associated with the heavy fractions of the polysome


title: 13466806

status: Public on Nov 20 2009

city: Ames

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

description: Maize seedlings were grown under controlled conditions and were harvested at the 14 day old stage. Total RNA was isolated from four replications of RIL@, B73xRIL, and Mo17xRIL for 30 RILs (with 6 individual seedlings pooled for each genotype in each replication) using Trizol reagent. Approximately 500 micrograms of total RNA were used for mRNA isolation with the OligoTex mRNA midi kit (Qiagen, Valencia, CA ) as per manufacturer's protocol with slight modification. Two micrograms of mRNA were labeled according to Nakozono et al. (2003) with slight modifications. Each sample was labeled with Cy dye and hybridized to the GPL3333 platform (4 replications) and GPL3538 platform (2 replications).

hyb_protocol: Fluorescent targets were hybridized as described in the "cDNA microarray protocol" file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/

scan_protocol: Each microarray chip was scanned a minimum of four times with constant PMT and increasing laser power settings.  Slides were scanned with a Pro Scan Array HT (Perkin Elmer, Wellesley, MA).

data_processing: All scans from each slide were quantified using ImaGene (BioDiscovery, El Segundo, CA). For each slide and dye combination, median scan intensities were extrapolated using data from the multiple scans collected using a variation of a previously published linear regression method (DUDLEY et al. 2002).  Non-informative spots were removed prior to analysis.  In total, 14,401 (GPL3333) and 14,260 (GPL3538) informative spots were analyzed. Within-slide correlation coefficient between the Cy3 and Cy5 background-corrected raw signal intensities was used to quantify the quality of each slide in the eQTL experiment.  A correlation coefficient cutoff of 0.90 flagged 4% (N=15) of the SAM1.1 slides for removal prior to analysis.  In many cases, these slides had visually apparent technical artifacts.  Using the same cutoff for SAM3.0 slides, less than 1% (N=1) of the slides were below this cutoff, and none were removed. For the remaining slides, lowess normalization was applied to the natural log (ie, log base e) of the background-corrected raw signal intensities to remove signal-intensity-dependent dye effects on each slide (CUI et al. 2003; DUDOIT et al. 2002).  Normalization was conducted separately for each slide to avoid introducing dependencies among expression values.  After normalization, data for each slide/dye combination were median-centered so expression measures would be comparable across slides.  Post-normalized data was summarized by taking the average of all technical and biological replicates within a genotype.

organism: Zea mays

source_name: Seedling stage above ground tissue

extract_protocol: total RNA extraction with Trizol, mRNA isolation with Oligotex Kit (Qiagen, Valencia, CA) as per manufacturer's instructions

value: Above ground seedling

value: 14 days old

tag: sample name

value: Rep 3 BxRILM0027

label_protocol: Fluorescent cDNA targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/. Labeled targets containing a minimum of 3000 picomoles of cDNA, 50 picomoles of Cy dye, and more than one dye molecule per 50 (100) bases of Cy3 (Cy5) were used for hybridizations.

value: Rep 3 RILM0027


title: Ribosome density experiment: mock 12 hrs. (5-12-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80365.gif

extract_protocol: not provided

value: pooled mRNA associated with the light fractions of the polysome

value: pooled mRNA associated with the heavy fractions of the polysome


title: miR-124 12 hrs.IP (5-12-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80423.gif

source_name: total cell lysate aRNA

tag: reference

value: total cell lysate

source_name: immunoprecipitated aRNA

tag: experiment


title: mir-124 12 hrs SS (5-14-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80599.gif
Measurement: concentration(absolute) 60 nM

source_name: universal reference

value: universal reference

tag: cell line


title: Ribosome density experiment: miR-124 12 hrs. (5-20-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80379.gif


title: mock 12 hrs.C-IP (5-12-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80428.gif


title: mock 12 hrs.C-IP (5-14-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80430.gif


title: Ribosome Occupancy experiment: mock 12 hrs. (5-14-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80370.gif

source_name: aRNA generated from pooled mRNA unassociated with ribosomes

value: pooled mRNA unassociated with ribosomes

source_name: aRNA generated from pooled mRNA associated with at least one ribosome


title: mock 12 hrs SS (5-12-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80596.gif

source_name: mock 12 hrs SS (5-12-08) (aRNA)


title: Ribosome Occupancy experiment: mock 12 hrs. (5-20-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80378.gif

value: pooled mRNA associated with at least one ribosome


title: Ribosome density experiment: miR-124 12 hrs. (5-14-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80371.gif


title: miR-124 12 hrs.IP (5-20-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80427.gif


title: mock 12 hrs.IP (5-12-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80422.gif


title: mir-124 12 hrs SS (5-20-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80601.gif
Measurement: concentration(absolute) 60 nM


title: mock 12 hrs SS (5-20-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80600.gif

source_name: mock 12 hrs SS (5-20-08) (aRNA)


title: mir-124 12 hrs SS (5-12-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80597.gif
Measurement: concentration(absolute) 60 nM


title: N. europaea_Fe-replete_pFur::Kan_rep2

city: Corvallis

first: Neeraja

last: Vajrala

state: OR

address: 2082 Cordley Hall

department: Botany & Plant Pathology

institute: Oregon State University

description: This sample is of Nitrosomonas europaea (ATCC 19718) pFur::Kan mutant strain with a kanamycin resistance cassette insertion in the promoter region of the fur (NE0616) gene grown in Fe-replete media. It is the second of three Fe-replete mutant strain biological replicates used in this experiment, each from separate cultures.

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

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

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

organism: Nitrosomonas europaea ATCC 19718

source_name: N. europaea_Fe-replete_pFur::Kan

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

growth_protocol:
Nitrosomonas europaea Fe-replete cells were grown to mid-log phase (O.D.600nm 0.04) aerobically at 30°C in dark in standard Fe-replete media containing 10 µM Fe3+ complexed with EDTA  (Ensign et al., 1993; Stein & Arp, 1998)
Nitrosomonas europaea Fe-limited cells were grown to mid-log phase (O.D.600nm 0.025) aerobically at 30°C in dark in medium made with reagent grade chemicals without any addition of iron salts & was named iron-limited media. This media still contained about 0.2µM iron and has been used in our previous studies relating to N. europaea iron limitation (Wei et al., 2006; Wei et al., 2007)
Nitrosomonas europaea pFur::Kan mutant cells were grown to mid-log phase (O.D.600nm 0.04 & 0.025) aerobically at 30°C in dark in standard Fe-replete  & Fe-limited media as described above.

extract_protocol: Total cellular RNA was extracted using 1 ml of Trizol (Ambion Inc., Austin, TX) following the manufacturer’s instructions. The extracted RNA was purified with an RNeasy Mini kit (Qiagen Inc., Valencia, CA) and treated with RNase-free DNase Ι (Qiagen) to digest residual chromosomal DNA. The concentration of purified RNA was determined by using a Nanodrop spectrophotometer (Nanodrop Technologies, Rockland, DE) and the RNA quality was analyzed by the RNA 6000 Nano LabChip kit on the Agilent Bioanalyzer 2100 (Agilent Technologies Inc., Palo Alto, CA). Intact good quality RNA (A260nm/A280nm 1.9 and RIN score  9.0) was used for the experiments.

tag: genotype

value: Insertion of Kanamycin resistance cassette in promoter region of Fur (NE0616) gene

tag: phenotype

value: Loss of Iron homeostasis control

tag: accession


title: N. europaea_Fe-limited_pFur::Kan_rep3

description: This sample is of Nitrosomonas europaea (ATCC 19718) pFur::Kan mutant strain with a kanamycin resistance cassette insertion in the promoter region of the fur (NE0616) gene grown in Fe-limited media. It is the third of three Fe-limited mutant strain biological replicates used in this experiment, each from separate cultures.

source_name: N. europaea_Fe-limited_pFur::Kan


title: N. europaea_Fe-replete_pFur::Kan_rep1

description: This sample is of Nitrosomonas europaea (ATCC 19718) pFur::Kan mutant strain with a kanamycin resistance cassette insertion in the promoter region of the fur (NE0616) gene grown in Fe-replete media. It is the first of three Fe-replete mutant strain biological replicates used in this experiment, each from separate cultures.


title: N. europaea_Fe-limited_wild-type_rep3

description: This sample is of wild-type Nitrosomonas europaea (ATCC 19718) grown in Fe-limited media. It is the third of three wild-type Fe-limited biological replicates used in this experiment, each from separate cultures.

source_name: N. europaea_Fe-limited_wild-type

value: Wild-type

value: Fe-starved


title: N. europaea_Fe-limited_pFur::Kan_rep1

description: This sample is of Nitrosomonas europaea (ATCC 19718) pFur::Kan mutant strain with a kanamycin resistance cassette insertion in the promoter region of the fur (NE0616) gene grown in Fe-limited media. It is the first of three Fe-limited mutant strain biological replicates used in this experiment, each from separate cultures.


title: N. europaea_Fe-limited_pFur::Kan_rep2

description: This sample is of Nitrosomonas europaea (ATCC 19718) pFur::Kan mutant strain with a kanamycin resistance cassette insertion in the promoter region of the fur (NE0616) gene grown in Fe-limited media. It is the second of three Fe-limited mutant strain biological replicates used in this experiment, each from separate cultures.


title: N. europaea_Fe-replete_pFur::Kan_rep3

description: This sample is of Nitrosomonas europaea (ATCC 19718) pFur::Kan mutant strain with a kanamycin resistance cassette insertion in the promoter region of the fur (NE0616) gene grown in Fe-replete media. It is the third of three Fe-replete mutant strain biological replicates used in this experiment, each from separate cultures.


title: N. europaea_Fe-limited_wild-type_rep2

description: This sample is of wild-type Nitrosomonas europaea (ATCC 19718) grown in Fe-limited media. It is the second of three wild-type Fe-limited biological replicates used in this experiment, each from separate cultures.


title: mock 12 hrs IP #2 (5-20-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80605.gif

hyb_protocol: not provided

label_protocol: not provided


title: mock 12 hrs SS (5-14-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80598.gif

source_name: mock 12 hrs SS (5-14-08) (aRNA)


title: N. europaea_Fe-limited_wild-type_rep1

description: This sample is of wild-type Nitrosomonas europaea (ATCC 19718) grown in Fe-limited media. It is the first of three wild-type Fe-limited biological replicates used in this experiment, each from separate cultures.


title: N. europaea_Fe-replete_wild-type_rep3

description: This sample is of wild-type Nitrosomonas europaea (ATCC 19718) grown in Fe-replete media. It is the third of three wild-type Fe-replete biological replicates used in this experiment, each from separate cultures.

source_name: N. europaea_Fe-replete_wild-type

value: normal


title: miR-124 12 hrs.C-IP (5-20-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80433.gif


title: Ribosome Occupancy experiment: mock 12 hrs. (5-12-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80366.gif


title: N. europaea_Fe-replete_wild-type_rep2

description: This sample is of wild-type Nitrosomonas europaea (ATCC 19718) grown in Fe-replete media. It is the second of three wild-type Fe-replete biological replicates used in this experiment, each from separate cultures.


title: Ribosome Occupancy experiment: mir-124 12 hrs. #2 (5-14-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80453.gif


title: Ribosome Occupancy experiment: miR-124 12 hrs. (5-20-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80380.gif


title: Ribosome density experiment: mock 12 hrs Density #2 (5-14-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80451.gif


title: N. europaea_Fe-replete_wild-type_rep1

description: This sample is of wild-type Nitrosomonas europaea (ATCC 19718) grown in Fe-replete media. It is the first of three wild-type Fe-replete biological replicates used in this experiment, each from separate cultures.


title: miR-124 12 hrs.C-IP (5-12-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80429.gif


title: miR-124 12 hrs.IP (5-14-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80425.gif


title: Strain DMS1753 rep1

city: Dublin

first: Daniel

middle: M

last: Stoebel

address: Moyne Institute, Trinity College

department: Department of Microbiology

country: Ireland

institute: Trinity College, Dublin

hyb_protocol: Perfromed by Roche Nimblegen, www.nimblegen.com

data_processing: Data were extracted and RMA normalized by Roche Nimblegen

organism: Escherichia coli

source_name: DMS1753(evolved rpoS-)

growth_protocol: Grow in MOPS minimal media + 0.2% glucose + 0.3M NaCl, harvested at OD600 of 0.25 to 0.3

extract_protocol: Growth was stopped by the addition of 5 mL ice-cold phenol:ethanol (5:95 by volume), and the cells were left on ice for 20 to 40 minutes. Cells were pelleted by centrifugation and resuspended in Trizol (Sigma-Aldrich). The resuspension was frozen at -80°C for up to one week before RNA was extracted following the manufacturers specification. Any contaminating DNA was removed with RNase-free DNAse I (Ambion Inc). After checking that RNA was not degraded, RNA from both flasks from each of two separate days was pooled. Double-stranded cDNA synthesis followed the instructions of the manufacturer (Invitrogen).

tag: DMS1753(evolved rpoS-)


title: Strain DMS1753 rep2

scan_protocol: Perfromed by Roche Nimblegen, www.nimblegen.com


title: Strain DMS1747 rep1

source_name: DMS1747(evolved rpoS-)

label_protocol: Perfromed by Roche Nimblegen, www.nimblegen.com

tag: DMS1747(evolved rpoS-)


title: Strain DMS1749 rep1

source_name: DMS1749(evolved rpoS-)

tag: DMS1749(evolved rpoS-)


title: Strain DMS1751 rep2

source_name: DMS1751(evolved rpoS-)

tag: DMS1751(evolved rpoS-)


title: Strain DMS1751 rep1


title: Strain DMS1747 rep2


title: 429 A

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: Following fragmentation, cRNA was hybridized on Mouse430 2.0 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10% of intensity values

source_name: 344SQ lung cancer cells with miR-200b-200a-429 over-expression

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

growth_protocol: Cell lines from p53R172H∆g/+ K-rasLA1/+ mice were derived from tumor tissues removed at autopsy from two different mice (#344 and #393). The tissues were minced, placed in culture, and passed serially in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), which yielded mass populations of tumor cells derived from primary lung tumors (344P and 393P), mediastinal lymph nodes (344LN and 393LN), and a subcutaneous site (344SQ).

extract_protocol: Total RNA was isolated by the Ambion kit. RNA quality and quantity were evaluated on a NanoDrop spectrophotometer and the Agilent 2100 Bioanalyzer.

treatment_protocol: Stable 344SQ cell lines expressing the miR-200b-200a-429 cluster or control vector were generated by transduction with the previously described lentivirus vectors (Gregory et al., 2008), generated in the Trans-Lentiviral pLEX packaging system with TLA-HEK293T cells (Open Biosystems). GFP positive transfectant pools were selected by growth in RPMI 1640 with 10% FBS and puromycin.

value: 344SQ cells

tag: genetic modification

value: miR-200b-200a-429 over-expression


title: Strain DMS1745 rep2

source_name: DMS1745(evolved rpoS-)

tag: DMS1745(evolved rpoS-)


title: Adult mesothelial cells_Mesothelin-sorted_rep1

city: Bunkyo-ku

first: Minoru

last: Tanaka

state: Tokyo

address: 1-1-1 Yoyoi

department: IMCB

institute: University of Tokyo

description: Gene expression data from Mesothelin+ mesothelial cells of adult mouse livers

hyb_protocol: Following fragmentation, 15ug of cRNA were hybridized for 16 hr  on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 after Phycoerythrin staining.

data_processing: The data were analyzed with AGCC (Affymetrix® GeneChip® Command Console® Software) and Affymetrix® Expression Console

source_name: Adult mouse liver mesothelial cells

label_protocol: Each cDNA was synthesized from 10 ng total RNA. First cycle cRNA was synthesized from cDNA. All 1st cycle cRNA was used for 2nd cycle cDNA  synthesis. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2nd cycle cRNA.

extract_protocol: High pure RNA extraction of total RNA was performed according to the manufacturer's instructions (Roche).

treatment_protocol: E12.5 or adult livers were digested with collagenase. Mesothelial cells were isolated by a cell sorter using anti-PCLP1 or anti-Mesothelin antibodies. The isolated cells were rinsed with PBS  and their RNA was extracted by High Pure RNA kit (Roche).

value: Liver

tag: strain

tag: developmental stage

value: 8 weeks


title: Control C

source_name: 344SQ lung cancer cells with control vector

value: control vector


title: 429 B


title: Strain DMS1745 rep1


title: Control B


title: 429 C


title: Strain DMS1749 rep2


title: 393P, sample a1249

description: 393P (non-metastatic), sample a1249

tag: 393P (non-metastatic)


title: miR-124 12 hrs.C-IP (5-14-08)

city: Stanford

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80431.gif

source_name: total cell lysate aRNA

source_name: immunoprecipitated aRNA


title: mock 12 hrs IP #2 (5-12-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80604.gif


title: Control A


title: mock 12 hrs.IP (5-20-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80426.gif


title: mock 12 hrs.IP (5-14-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80424.gif


title: E12.5 mesothelial cells_PCLP1-sorted_rep1

description: Gene expression data from PCLP1+ mesothelial cells of E12.5 mouse livers

source_name: E12.5 mouse liver mesothelial cells

tag: tissue

value: Embryonic day 12.5


title: mir-124 12 hrs IP #2 (5-20-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80606.gif


title: Strain DMS1743 rep2

source_name: DMS1743 (evolved rpoS+)

tag: DMS1743 (evolved rpoS+)


title: mock 12 hrs.C-IP (5-20-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80432.gif

tag: reference


title: Control N. meningitidis strain without pfkA - Replicate 2

tag: mutant state

value: no heterologous pfkA

source_name: Common reference sample (equal mix of 6 RNA samples)


title: 393LN, sample a0859

description: 393LN (intermediately metastatic), sample a0859

tag: 393LN (intermediately metastatic)


title: 393P, sample a1195

description: 393P (non-metastatic), sample a1195


title: Strain DMS1743 rep1


title: 393P, sample a1173

description: 393P (non-metastatic), sample a1173


title: Strain DMS1741 rep2

source_name: DMS1741 (evolved rpoS+)

tag: DMS1741 (evolved rpoS+)


title: Strain DMS1741 rep1


title: 393P, sample a1158

description: 393P (non-metastatic), sample a1158


title: 393LN, sample a0808

description: 393LN (intermediately metastatic), sample a0808


title: Strain DMS1688 rep2

source_name: DMS1688 (rpoS-)

tag: DMS1688 (rpoS-)


title: Strain DMS1739 rep2

source_name: DMS1739 (evolved rpoS+)

tag: DMS1739 (evolved rpoS+)


title: Strain DMS1739 rep1


title: Strain DMS1737 rep1

source_name: DMS1737 (evolved rpoS+)

tag: DMS1737 (evolved rpoS+)


title: 393LN, sample a0858

description: 393LN (intermediately metastatic), sample a0858


title: 344SQ, sample a1202

description: 344SQ (highly metastatic), sample a1202

tag: 344SQ (highly metastatic)


title: Strain DMS1737 rep2


title: Strain DMS1735 rep1

source_name: DMS1735 (evolved rpoS+)

tag: DMS1735 (evolved rpoS+)


title: Strain DMS1735 rep2


title: 393LN, sample a0930

description: 393LN (intermediately metastatic), sample a0930


title: 344SQ, sample a1194

description: 344SQ (highly metastatic), sample a1194


title: 344SQ, sample a1192

description: 344SQ (highly metastatic), sample a1192


title: Strain DMS1688 rep1


title: Strain DMS1684 rep2

source_name: Strain DMS1684 (wildtype)

tag: Strain DMS1684 (wildtype)


title: 344SQ, sample a1193

description: 344SQ (highly metastatic), sample a1193


title: Polysome, Perk knockout liver, +tBuHQ, biological rep1

city: Hershey

first: An

last: Dang Do

state: PA

address: 500 University Drive

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

description: Polysome sample

hyb_protocol: 15 ug of fragmented cRNA was used to prepare 300 ul of hybridization cocktail as per the manufacturer's instructions.  200 ul of that hybridization cocktail was hybridized to Mouse Genome 430_2.0 Arrays for 16 hours at 45C.  Arrays were washed and stained using a GeneChip Fluidics Station 400 as per the manufacturer's instructions.

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

data_processing: Affymetrix CHP files containing qualitative and quantitative values of each probe set on the arrays were imported into GeneSpring (Agilent Technologies, Inc., Palo Alto, CA) and sorted for raw expression values > 80 in at least 1 of 16 conditions as an initial filter to eliminate background noise.  The resulting lists were imported into Excel and analyzed using the Z-ratio method (Cheadle et al., J Mol Diagn 5:73-81; Mazan-Mamczarz et al., Biotechniques 39:61-7).  First, the data were transformed using log10.  The transformed values were used in the following calculations:  Zscore = (intensityG – mean intensityG1…Gn)/SDG1…Gn, where G = any gene on hybridization array, G1…Gn = aggregate measure of all genes.  Zratios = [(ZscoreG1ave)Exp – (ZscoreG1ave)Con]/SD of Zscore differencesG1…Gn, where G1 = average Z score for any particular gene being tested under multiple experimental conditions (experimental vs. control), G1…Gn = aggregate measure of all of the genes. Z ratio data is provided as a supplementary file on the Series record.

source_name: liver, Perk-/-, +tBuHQ, polysome

label_protocol: RNA from two perfused liver samples per condition (8 conditions:  unfractionated and polysomal fractions of treated or control wild-type or knockout) were pooled to minimize biological variations.  Twelve μg of total RNA were used in the initial cDNA conversion step.  All steps including double-strand cDNA synthesis, in vitro labeling and cRNA fragmentation were done using the Affymetrix One-Cycle Target Labeling and Control Reagents kit and protocol.

growth_protocol: All animals received water and food (Harkland, TX) ad libitum and were maintained according to the Institutional Animal Care and Use Committee-approved protocol at The Pennsylvania State University College of Medicine.  Alb/Cre Perk-/- and wild-type littermate mice, 3-6 months old, were generated as previously described (Zhang et al., Mol Cell Biol 22:3864-74)

extract_protocol: Total RNA was extracted from one mL of detergent-containing supernatant or from the sucrose density gradient fractions using acid phenol:chloroform (Ambion, Inc., Austin, TX).  Per mL of sample, 40 μL of 0.5 M EDTA, 25 μL of 20% SDS and one volume of acid phenol:chloroform were added.  After a 30 min centrifugation at 3, 000 x g (Beckmann GS-6KR), 4°C, the top clear layer was removed, and RNA extracted a second time with the addition of one volume acid phenol:chloroform.  Precipitation of RNA was done overnight in 2.5 volumes of 100% ethanol and 1/10 volume of 5 M NH4OAc (Ambion).  RNA was pelleted, washed twice with 75% ethanol and resuspended in RNA storage solution plus anti-RNAse (Ambion).  The concentration and purity of RNA samples were measured by the Agilent 2100 Bioanalyzer (Robert Brucklacher, Functional Genomics Core Facility, PSU-COM) prior to hybridization array and QRT-PCR applications.

treatment_protocol: We followed previously published protocols (Feldhoff et al., J Biol Chem 252:3611-6; Tolman et al., J Biol Chem 248:4552-60) for single-pass perfusion.  For perfusion of Perk +/+ and -/- mice, the final CaCl2 concentration was 0.1 mM in perfusion buffer.  2,5-di-tert-butylhydroquinone (tBuHQ; Sigma), a selective inhibitor of ATP-dependent microsomal Ca2+ sequestration, was used to induce ER stress.  Discontinuous, 9-step 20% (10 mM HEPES, pH 7.4; 250 mM KCl; 5 mM MgCl2; 0.5 mM EDTA; 20% w/w sucrose) to 47% (10 mM HEPES, pH 7.4; 250 mM KCl; 5 mM MgCl2; 0.5 mM EDTA; 47% w/w sucrose) sucrose density gradients were used to separate mRNAs based on the number of bound ribosomes.  One mL of detergent-containing supernatant (from perfused liver homogenate) was loaded onto the 20-47% sucrose gradients and centrifuged at 28,000 rpm (Beckmann SW-28), 4°C, for 3 h 38 min for polysome profiles or 22,500 rpm (Beckmann JS-24.38), 4°C, for 19 h 9 min for subunit profiles.  Gradient profiles were visualized using an ISCO UV detection unit with a 254 nm filter and fractionated using an ISCO gradient pump (Teledyne Isco, Inc., Lincoln, NE).

tag: Genotype

value: Perk knockout

tag: Age

value: 3-6 months


title: Polysome, Perk knockout liver, +tBuHQ, biological rep2

description: Polysome sample


title: Strain DMS1684 rep1


title: Polysome, Perk wild-type liver, +tBuHQ, biological rep2

description: Polysome sample

source_name: liver, Perk+/+, +tBuHQ, polysome

value: Perk wild-type


title: Polysome, Perk knockout liver, -tBuHQ, biological rep2

description: Polysome sample

source_name: liver, Perk-/-, -tBuHQ, polysome


title: Polysome, Perk wild-type liver, -tBuHQ, biological rep1

description: Polysome sample

source_name: liver, Perk+/+, -tBuHQ, polysome


title: Unfractionated, Perk knockout liver, +tBuHQ, biological rep2

description: Unfractionated sample

source_name: liver, Perk-/-, +tBuHQ, unfractionated


title: IgG_Control_rep1

first: David

last: MacAlpine

address: Box 3813 DUMC

department: Pharmacology and Cancer Biology

description: chromatin IP

hyb_protocol: Per Agilent protocols

scan_protocol: Per Agilent protocols

data_processing: Processed with MA2C

organism: Drosophila melanogaster

source_name: ChIP enriched DNA

label_protocol: Sequenase labeling protocol; 1.Thaw DNA samples on ice 2.Transfer to 0.2ml pcr tubes. Open tubes and place inside a 1.5ml tube 3.Speed vac samples on medium heat for approx. 15-18 minutes 4.Resusp DNA in sequenase primer mix: 5X sequenase buffer 2ul (US Biochemicals) random nonamer 5ul (NNNNNNNNN; hand mixed 25,25,25,25) Ambion dH2O 1ul 5.Thaw Cy dyes (Cy 3 dUTP and Cy 5 dUTP; Perkin Elmer) on ice and in the dark 6.Add 2ul of cy dye to DNA sample 7.Start pcr program: 95C 3' 4C 2' 37C 30' ramp 95C 2' 4C 2' 37C 30' ramp 4C hold 8.At the first 4C step in program, add the following: 5X sequenase buffer 1ul Low T 1.5ul (5ul dATP, 5ul dCTP, 5ul dGTP, 2ul dTTP, 83ul ambion dH2O) 100 mM BSA 1ul 100mM DTT 0.75ul sequenase 1ul 9.At the second 4C step, add additional sequenase and finish program sequenase buffer DLT 0.7ul sequenase 0.3ul 10.Clean samples on YM-30 microcon column (Millipore) according to directions 11.Spec samples

extract_protocol: ChIP crosslinking and isolation protocol; 1. Cross-link cells at room temperature with 1% formaldehyde (Ted Pella #18505) for 10 min. 2. Quench reaction with 125mM glycine for 5 min. at room temp. 3. Centrifuge cross-linked cells, 1,000 rpm, 10 min. 4. Wash cells with 2X cold 1X PBS. 5. Freeze pellet with liquid nitrogen and store at -80C for at least two hours 6. Thaw pellet on ice and prepare lysis buffers: Lysis Buffer 1: 50mM Hepes-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1/2 mini protease tablet (Roche) per 5ml of buffer Lysis Buffer 2: 10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5 EGTA, 1/2 protease tablet per 5ml of buffer Lysis Buffer 3: 10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1/2 mini protease tablet per 5ml buffer 7. Keep lysis buffers on ice 8. Resuspend pellet in 5ml lysis buffer 1 and incubate with rotation at 4C for 10min. 9. Centrifuge, 4C, 1350xg, 5 min 10.Resuspend pellet in 5ml lysis buffer 2 and incubate with rotation at room temperature for 10 min. 11. Follow step 9 12. Resuspend in 3ml lysis buffer 3 13. sonicate extract to an average size of 1Kb. 14. Add Triton X-100 to 1%. vortex gently 15. Centrifuge at 4C, 20,000xg, 10min. 16. Aliquot extracts into ~500ul samples.ChIP protocol; The chromatin was immunoprecipitated with  IgG.

tag: cell line

tag: affinity tag

tag: antibody

value: IgG

source_name: Input DNA


title: Polysome, Perk wild-type liver, -tBuHQ, biological rep2

description: Polysome sample


title: TAP_ORC2_rep2

description: chromatin IP

value: TAP


title: Unfractionated, Perk knockout liver, -tBuHQ, biological rep2

description: Unfractionated sample

source_name: liver, Perk-/-, -tBuHQ, unfractionated


title: Polysome, Gcn2 knockout liver, -Met, biological rep2

description: Polysome sample

data_processing: Affymetrix CHP files containing qualitative and quantitative values of each probe set on the arrays were imported into GeneSpring (Agilent Technologies, Inc., Palo Alto, CA) and sorted for raw expression values > 80 in at least 1 of 16 conditions as an initial filter to eliminate background noise.  The resulting lists were imported into Excel and analyzed using the Z-ratio method (Cheadle et al., J Mol Diagn 5:73-81; Mazan-Mamczarz et al., Biotechniques 39:61-7).  First, the data were transformed using log10.  The transformed values were used in the following calculations:  Zscore = (intensityG – mean intensityG1…Gn)/SDG1…Gn, where G = any gene on hybridization array, G1…Gn = aggregate measure of all genes.  Zratios = [(ZscoreG1ave)Exp – (ZscoreG1ave)Con]/SD of Zscore differencesG1…Gn, where G1 = average Z score for any particular gene being tested under multiple experimental conditions (experimental vs. control), G1…Gn = aggregate measure of all of the genes. Z ratio data provided as a supplementary file on the Series record.

source_name: liver, Gcn2-/-, -Met, polysome

growth_protocol: All animals received water and food (Harkland, TX) ad libitum and were maintained according to the Institutional Animal Care and Use Committee-approved protocol at The Pennsylvania State University College of Medicine.  Global Gcn2-/- and wild-type littermate mice, 3-6 months old, were generated according to a previously published protocol (Zhang et al., Mol Cell Biol 22:6681-8).

treatment_protocol: We followed previously published protocols (Feldhoff et al., J Biol Chem 252:3611-6; Tolman et al., J Biol Chem 248:4552-60) for single-pass perfusion.  For perfusion of Gcn2 +/+ and -/- mice, methionine was omitted from the perfusate for the treated condition.  Discontinuous, 9-step 20% (10 mM HEPES, pH 7.4; 250 mM KCl; 5 mM MgCl2; 0.5 mM EDTA; 20% w/w sucrose) to 47% (10 mM HEPES, pH 7.4; 250 mM KCl; 5 mM MgCl2; 0.5 mM EDTA; 47% w/w sucrose) sucrose density gradients were used to separate mRNAs based on the number of bound ribosomes.  One mL of detergent-containing supernatant (from perfused liver homogenate) was loaded onto the 20-47% sucrose gradients and centrifuged at 28,000 rpm (Beckmann SW-28), 4°C, for 3 h 38 min for polysome profiles or 22,500 rpm (Beckmann JS-24.38), 4°C, for 19 h 9 min for subunit profiles.  Gradient profiles were visualized using an ISCO UV detection unit with a 254 nm filter and fractionated using an ISCO gradient pump (Teledyne Isco, Inc., Lincoln, NE).

value: Gcn2 knockout


title: Unfractionated, Perk wild-type liver, -tBuHQ, biological rep2

description: Unfractionated sample

source_name: liver, Perk+/+, -tBuHQ, unfractionated


title: Polysome, Perk knockout liver, -tBuHQ, biological rep1

description: Polysome sample


title: Polysome, Perk wild-type liver, +tBuHQ, biological rep1

description: Polysome sample


title: Unfractionated, Perk wild-type liver, +tBuHQ, biological rep1

description: Unfractionated sample

source_name: liver, Perk+/+, +tBuHQ, unfractionated


title: Unfractionated, Perk knockout liver, -tBuHQ, biological rep1

description: Unfractionated sample


title: Unfractionated, Perk knockout liver, +tBuHQ, biological rep1

description: Unfractionated sample


title: Unfractionated, Perk wild-type liver, +tBuHQ, biological rep2

description: Unfractionated sample


title: TAP_ORC2_rep1

description: chromatin IP


title: Polysome, Gcn2 knockout liver, -Met, biological rep1

description: Polysome sample


title: Polysome, Gcn2 wild-type liver, -Met, biological rep2

description: Polysome sample

source_name: liver, Gcn2+/+, -Met, polysome

value: Gcn2 wild-type


title: Polysome, Gcn2 knockout liver, +Met, biological rep1

description: Polysome sample

source_name: liver, Gcn2-/-, +Met, polysome


title: miR-124 12 hrs 10_09 (1) NO AMP

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85424.gif

source_name: universal reference AMPLIFIED

value: universal reference AMPLIFIED

source_name: mir124 12 hrs no amp

tag: experiment

value: mir124 12 hrs no amp


title: Polysome, Gcn2 wild-type liver, +Met, biological rep2

description: Polysome sample

source_name: liver, Gcn2+/+, +Met, polysome


title: Polysome, Gcn2 wild-type liver, -Met, biological rep1

description: Polysome sample


title: mock 12 hrs 10_09 (2) NO AMP

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85422.gif

source_name: mock 12 hrs no amp

value: mock 12 hrs no amp


title: mock 12 hrs 10_09 (4) NO AMP

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85429.gif

source_name: mock 12 hrs NO AMP

value: mock 12 hrs NO AMP


title: Polysome, Gcn2 wild-type liver, +Met, biological rep1

description: Polysome sample


title: miR-124 12 hrs 10_09 (3) NO AMP

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85426.gif


title: mgrR knockout mutation containing pBR Plac mgrR plasmid, 2

city: BETHESDA

first: Deborah

last: Hinton

state: MD

address: 8 center Dr., Building 8, Rm 2A21

institute: NIH

description: Gene expression from mgrR mutant derived from  E. coli K12 MG1655 containing vector control pBR Plac-mgrR

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

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

organism: Escherichia coli K-12

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: A fresh colony of each strain was innoculated in LB (with ampicilline if strains contain plasmids) and was grown at 37C with agitation. The cells were grown to OD600=0.5.

extract_protocol: Hot phenol extraction method was used for RNA purification according to the manufacturer's instructions.

treatment_protocol: To induce MgrR, IPTG was added into culture at a final concentration of 100uM for 15min.

tag: genotype/variation


title: mgrR knockout mutation containing pBR Plac mgrR plasmid, 1


title: Unfractionated, Gcn2 knockout liver, -Met, biological rep2

description: Unfractionated sample

source_name: liver, Gcn2-/-, -Met, unfractionated


title: miR-124 12 hrs 10_09 (2) NO AMP

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85425.gif

tag: reference


title: Unfractionated, Perk wild-type liver, -tBuHQ, biological rep1

description: Unfractionated sample


title: mgrR knockout mutation containing pBR Plac plasmid, 2

description: Gene expression from mgrR mutant derived from  E. coli K12 MG1655 containing vector control pBR Plac


title: Unfractionated, Gcn2 knockout liver, -Met, biological rep1

description: Unfractionated sample


title: Unfractionated, Gcn2 knockout liver, +Met, biological rep2

description: Unfractionated sample

source_name: liver, Gcn2-/-, +Met, unfractionated


title: mgrR knockout mutation containing pBR Plac plasmid, 1


title: miR-124 12 hrs 10_09 (6) NO AMP

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85433.gif

source_name: miR-124 12 hrs NO AMP

value: miR-124 12 hrs NO AMP